WO2022076353A1 - Compositions and methods for treating mage-a1-expressing disease - Google Patents
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Definitions
- TCR affinity is an important determinant of CTL avidity (Zoete et al., Frontiers Immunol.4:268, 2013)
- strategies have been developed to redirect the antigen specificity of donor or patient T cells using high affinity TCR ⁇ / ⁇ genes isolated from a well-characterized T cell clone specific for a tumor-specific antigen (Stromnes et al., Immunol. Rev.257:145, 2014; Robbins et al., J. Clin. Oncol.29:917, 2011).
- T cells that express self/tumor- reactive TCRs are subject to central and peripheral tolerance (Stone and Kranz, Frontiers Immunol.4:244, 2013), with relative TCR affinities varying widely between donors. Therefore, many matched donors must be screened to identify a sufficiently high-affinity tumor-specific T cell clone from which a TCR ⁇ / ⁇ gene therapy construct can be generated.
- WT1 Tumor antigen 1
- WT1-specific TCR Tumor antigen 1
- FIGS 1A and 1B show representative data illustrating that high- affinity T cells for viral antigens are found at higher frequencies (A) than high-affinity T cells for self-antigens, which are found at very low frequencies (B).
- Figures 2A and 2B show, respectively, (A) a schematic of a T cell enrichment assay, (B) flow cytometry data from a series of sorting experiments used to enrich for antigen-specific CD8 + T cells.
- Figure 3 shows representative data from a TCR ⁇ CDR3 enrichment scheme of the present disclosure using MAGE-A1:HLA tetramers.
- Figures 4A and 4B show, respectively, (A) specific binding of MAGE- A1:HLA tetramers by TCRs identified using methods of the present disclosure and (B) enrichment of MAGE-A1-specific TCRs.
- Figures 5A-5C provide, respectively, (A) flow cytometry data showing MAGE- A1-specific CD8 + T cells of the present disclosure binding MAGE-A1:HLA tetramers, (B) cytokine production by MAGE-A1-specific CD8 + T cells in the absence (left) or presence (right) of antigen-expressing U266 myeloma cells, and (C) specific lysis data showing that high-affinity MAGE-A1 TCR-transduced CD8 + T cells of this disclosure bind antigen:MHC tetramers and kill cells presenting MAGE-A1: MHC (A*0201).
- FIG. 6A illustrates an immunotherapy approach according to the present disclosure in which CD4 + T cells are transduced to express a TCR cloned from a CD8 + T cell that is specific for a peptide antigen, and a CD8 co-receptor. Activation of the transduced CD4 + T cell can augment or improve the antigenic response of CD8 + T cells, such as infused CTLs in an immunotherapy setting.
- Figure 6B shows the design of an experiment ("Test #1") in which a CD4 + T cell was transduced to express a CD8- independent MHC Class I-restricted TCR, but not a CD8 co-receptor.
- Figure 7A shows flow cytometry data from an experiment in which T cells (CD8 + and CD4 + ) expressing high-affinity (CD8+ T cell-derived) anti-MAGE-A1 TCR were assayed for binding to MAGE-A1:MHC tetramers.
- Figure 7B shows specific binding by the MAGE-A1-specific T cells to MAGE-A1:MHC tetramers.
- Figure 7C shows target cell lysis (Cr 51 release) by CD8 + T cells expressing MAGE-A1-specific TCR of this disclosure and the lack of killing by comparable CD4 + T cells.
- Figure 8A shows a schematic illustrating an experiment in which CD4 + T cells were transduced to express a high-affinity MAGE A1 Class I TCR plus a CD8 ⁇ co-receptor and examined for functionality in the presence of cells expressing peptide:MHC.
- Figure 8B shows that a higher proportion of the CD4 + T cells transduced with both MAGE-A1 TCR and CD8 co-receptor produced cytokines as compared to CD4 + T cells expressing the MAGE-A1 TCR alone.
- Figure 8C shows specific lysis of antigen-presenting MEL526 melanoma target cells by the indicated T cells.
- Figure 8D shows expansion of the two groups of transduced CD4 + T cells following stimulation with antigen.
- Figures 9A and 9B show that exemplary cells of the present disclosure (MagIC TCR-T; see Example 5) specifically kill HLA-A2-positive / MAGE-A1- positive tumor cell lines.
- FIG. 10A IgE levels over time in the serum (ng/ml) of U266 (i.v.-injected) tumor-bearing NSG mice with or without MagIC TCR-T cell transfer.
- MagIC TCR-T cells used were CD8+ T cells ("CD8 TCR-T"), CD4+ T cells (“CD4 TCR-T”), or a combination of CD8+ T cells and CD4+ T cells (“CD8 + CD4 TCR-T").
- Figures 11A and 11B show that MagIC TCR-T cells do not recognize self-peptides presented by HLA-A2*01 on healthy human cell lines.
- Figure 11A IFN- ⁇ production by MagIC TCR-T after co-culture of HLA-A:02*01 iPS-derived human cell lines or harvested normal human cell lines (determined by ICS or ELISA). Independent experiments performed from 3-5 healthy human donors. Cytokine production normalized to amount/percentage produced after co-culture with MAGE-A1 peptide-loaded cells.
- Figures 12A and 12B show that MagIC TCR-T cells recognize HLA- B:49*01.
- Figure 13 shows a phase-I trial study design investigating MagIC TCR-T cells in accordance with presently disclosed compositions and methods.
- the present disclosure provides methods and compositions for treating a cancer or other disease or disorder that is associated with expression of MAGE-A1 (e.g., expression of a MAGE-A1 antigen such as SEQ ID NO.:123, e.g., in complex with an HLA molecule such as HLA-A*02:01), such as, for example, triple negative breast cancer, non-small cell lung cancer, or urothelial cancer.
- MAGE-A1 e.g., expression of a MAGE-A1 antigen such as SEQ ID NO.:123, e.g., in complex with an HLA molecule such as HLA-A*02:01
- HLA-A*02:01 e.g., triple negative breast cancer, non-small cell lung cancer, or urothelial cancer.
- the present disclosure provides methods for treating a cancer or disease or disorder that is associated with MAGE-A1 expression in a subject, wherein the methods comprise administering to the subject a population of modified T cells comprising a binding protein (e.g., a T cell receptor (TCR) or a single-chain T cell receptor) capable of specifically binding to a MAGE-A1 peptide antigen (e.g. a MAGE- A1 peptide antigen:HLA complex), wherein the subject is negative for or has been identified as negative for expression of HLA B*49:01, and wherein the binding protein is optionally encoded by a heterologous polynucleotide comprised in the modified T cells.
- a binding protein e.g., a T cell receptor (TCR) or a single-chain T cell receptor
- MAGE-A1 peptide antigen e.g. a MAGE- A1 peptide antigen:HLA complex
- the MAGE-A1 peptide antigen is capable of binding to or being presented by a human HLA-A*02:01. In certain embodiments, the MAGE-A1 peptide antigen comprises or consists of the amino acid sequence set forth in SEQ ID NO.:123.
- the present disclosure provides methods for treating a cancer or disease or disorder that is associated with MAGE-A1 expression in a subject, the method comprising administering to the subject a population of modified immune cells comprising a binding protein, the binding protein comprising: (a) a TCR ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and a TCR ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively; (b) a T cell receptor (TCR) ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 30- 32, respectively, and a TCR ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 27-29, respectively; (c) T cell receptor
- the present disclosure provides methods for treating a cancer, comprising administering to a subject in need thereof a population of modified cells comprising a binding protein, the binding protein comprising: (a) a T cell receptor (TCR) ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and a TCR ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively; (b) a T cell receptor (TCR) ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 30- 32, respectively, and a TCR ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 27-29, respectively; (c) a T cell receptor (TCR) ⁇ chain variable (V ⁇ ) domain having CDR1,
- the present disclosure provides an isolated polynucleotide that encodes (i) one or more CD8 co-receptor polypeptide or a portion thereof, and/or (ii) one or more MAGE-A1-specific TCR chain or a portion thereof. Also provided are vectors that comprise the polynucleotide, host cells that comprise the polynucleotide and/or vector, and host cell compositions.
- TAAs tumor-associated antigens
- T cells are sorted by their relative ability to bind to antigens in order to prepare the immune system to respond against a foreign invader (i.e., recognition of non-self-antigen) while at the same time preventing an autoimmune response (i.e., recognition of self-antigen).
- This tolerance mechanism limits naturally occurring T cells that can recognize tumor (self) antigens with high affinity and, therefore, eliminates the T cells that would effectively eliminate tumor cells.
- the instant disclosure provides TCRs specific for MAGE-A1 (also called MAGE-1, MAGE family member A1, CT 1.1, and Melanoma-Antigen Gene 1) peptides, such as high affinity TCRs specific for MAGE- A1 peptides, wherein a cell expressing such a TCR is capable of binding to a MAGE- A1:HLA complex independent of CD8.
- TCRs may optionally be capable of more efficiently associating with a CD3 protein as compared to endogenous TCRs.
- a method was developed to quickly and simultaneously screen and rank T cell clonotypes (based on affinity) from a large cohort of HLA-matched donors in a short time (about 6-8 weeks).
- the instant disclosure provides methods for enriching for cells with high-affinity TCRs by using limiting concentrations of antigen-specific pMHC multimers in the presence of a subject’s immune cells (e.g., PBMCs).
- PBMCs immune cells
- An advantage of these methods is that they allow for a quick comparison of the TCR affinity of thousands of clones from multiple donors as opposed to cloning individual TCRs.
- compositions and methods described herein will in certain embodiments have therapeutic utility for the treatment of diseases and conditions associated with MAGE-A1 expression.
- diseases include various forms of hyperproliferative disorders, such as hematological malignancies and solid cancers.
- Non-limiting examples of these and related uses are described herein and include in vitro, ex vivo and in vivo stimulation of MAGE-A1 antigen-specific T cell responses, such as by the use of recombinant T cells expressing an enhanced or high affinity TCR specific for a MAGE-A1 peptide.
- any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated.
- any number range recited herein relating to any physical feature, such as polymer subunits, size or thickness are to be understood to include any integer within the recited range, unless otherwise indicated.
- the term “about” means ⁇ 20% of the indicated range, value, or structure, unless otherwise indicated. It should be understood that the terms “a” and “an” as used herein refer to “one or more” of the enumerated components.
- a protein domain, region, or module e.g., a binding domain, hinge region, linker module
- a protein which may have one or more domains, regions, or modules
- an “immune system cell” means any cell of the immune system that originates from a hematopoietic stem cell in the bone marrow, which gives rise to two major lineages, a myeloid progenitor cell (which give rise to myeloid cells such as monocytes, macrophages, dendritic cells, megakaryocytes and granulocytes) and a lymphoid progenitor cell (which give rise to lymphoid cells such as T cells, B cells and natural killer (NK) cells).
- myeloid progenitor cell which give rise to myeloid cells such as monocytes, macrophages, dendritic cells, megakaryocytes and granulocytes
- lymphoid progenitor cell which give rise to lymphoid cells such as T cells, B cells and natural killer (NK) cells.
- Exemplary immune system cells include a CD4+ T cell, a CD8+ T cell, a CD4- CD8- double negative T cell, a ⁇ T cell, a regulatory T cell, a natural killer cell, and a dendritic cell.
- Macrophages and dendritic cells may be referred to as “antigen presenting cells” or “APCs,” which are specialized cells that can activate T cells when a major histocompatibility complex (MHC) receptor on the surface of the APC complexed with a peptide interacts with a TCR on the surface of a T cell.
- MHC major histocompatibility complex
- MHC Major histocompatibility complex
- MHC class I molecules are heterodimers having a membrane spanning ⁇ chain (with three ⁇ domains) and a non-covalently associated ⁇ 2 microglobulin.
- MHC class II molecules are composed of two transmembrane glycoproteins, ⁇ and ⁇ , both of which span the membrane. Each chain has two domains.
- MHC class I molecules deliver peptides originating in the cytosol to the cell surface, where a peptide:MHC complex is recognized by CD8 + T cells.
- MHC class II molecules deliver peptides originating in the vesicular system to the cell surface, where they are recognized by CD4 + T cells.
- Human MHC is referred to as human leukocyte antigen (HLA).
- T cell is an immune system cell that matures in the thymus and produces T cell receptors (TCRs).
- T cells can be na ⁇ ve (not exposed to antigen; increased expression of CD62L, CCR7, CD28, CD3, CD127, and CD45RA, and decreased expression of CD45RO as compared to TCM), memory T cells (TM) (antigen- experienced and long-lived), and effector cells (antigen-experienced, cytotoxic).
- TM can be further divided into subsets of central memory T cells (T CM , increased expression of CD62L, CCR7, CD28, CD127, CD45RO, and CD95, and decreased expression of CD54RA as compared to na ⁇ ve T cells) and effector memory T cells (TEM, decreased expression of CD62L, CCR7, CD28, CD45RA, and increased expression of CD127 as compared to na ⁇ ve T cells or T CM ).
- Effector T cells (T E ) refers to antigen-experienced CD8+ cytotoxic T lymphocytes that have decreased expression of CD62L, CCR7, CD28, and are positive for granzyme and perforin as compared to TCM.
- T cell receptor refers to an immunoglobulin superfamily member comprising comprising a variable binding domain, a constant domain, a transmembrane region, and a short cytoplasmic tail; see, e.g., Janeway et al., Immunobiology: The Immune System in Health and Disease, 3 rd Ed., Current Biology Publications, p.4:33, 1997) and capable of specifically binding to an antigen peptide bound to an MHC receptor.
- a TCR can be found on the surface of a cell or in soluble form and generally is comprised of a heterodimer having ⁇ and ⁇ chains (also known as TCR ⁇ and TCR ⁇ , respectively), or ⁇ and ⁇ chains (also known as TCR ⁇ and TCR ⁇ , respectively).
- the extracellular portion of a TCR chain e.g., ⁇ -chain, ⁇ -chain
- a variable domain e.g., ⁇ -chain variable domain or V ⁇ , ⁇ -chain variable domain or V ⁇ ; typically amino acids 1 to 116 based on Kabat numbering Kabat et al., “Sequences of Proteins of Immunological Interest, US Dept.
- variable domains contain complementary determining regions (CDRs) separated by framework regions (FRs) (see, e.g., Jores et al., Proc. Nat’l Acad. Sci.
- V ⁇ and V ⁇ of a native TCR generally have similar structures, with each variable domain comprising four conserved FRs and three CDRs.
- the V ⁇ domain is encoded by two separate DNA segments, the variable gene segment and the joining gene segment (V-J); the V ⁇ domain is encoded by three separate DNA segments, the variable gene segment, the diversity gene segment, and the joining gene segment (V-D-J).
- V-J variable gene segment and the joining gene segment
- V-D-J the joining gene segment
- a single V ⁇ or V ⁇ domain may be sufficient to confer antigen-binding specificity.
- TCRs that bind a particular antigen may be isolated using a V ⁇ or V ⁇ domain from a TCR that binds the antigen to screen a library of complementary V ⁇ or V ⁇ domains, respectively.
- a TCR is found on the surface of T cells (or T lymphocytes) and associates with the CD3 complex.
- the source of a TCR as used in the present disclosure may be from various animal species, such as a human, mouse, rat, rabbit or other mammal.
- the term “CD8 co-receptor” or “CD8” means the cell surface glycoprotein CD8, either as an alpha-alpha homodimer or an alpha-beta heterodimer.
- the CD8 co-receptor assists in the function of cytotoxic T cells (CD8 + ) and functions through signaling via its cytoplasmic tyrosine phosphorylation pathway (Gao and Jakobsen, Immunol. Today 21:630-636, 2000; Cole and Gao, Cell. Mol. Immunol.1:81- 88, 2004).
- CD8 beta chains see UniProtKB identifier P10966
- CD8 alpha chain see UniProtKB identifier P01732
- CD8 generally binds pMHC Class I complexes.
- CD4 co-receptor refers to an immunoglobulin co-receptor glycoprotein that assists the TCR in communicating with antigen-presenting cells (see, Campbell & Reece, Biology 909 (Benjamin Cummings, Sixth Ed., 2002)). CD4 is found on the surface of immune cells such as T helper cells, monocytes, macrophages, and dendritic cells, and includes four immunoglobulin domains (D1 to D4) that are expressed at the cell surface.
- CD4 During antigen presentation, CD4 is recruited, along with the TCR complex, to bind to different regions of the MHCII molecule (CD4 binds MHCII ⁇ 2, while the TCR complex binds MHCII ⁇ 1/ ⁇ 1).
- CD4 binds MHCII ⁇ 2
- TCR complex binds MHCII ⁇ 1/ ⁇ 1.
- ITAMs immunoreceptor tyrosine activation motifs
- CD3 is a multi-protein complex of six chains (see, Abbas and Lichtman, 2003; Janeway et al., p172 and 178, 1999). In mammals, the complex comprises a CD3 ⁇ chain, a CD3 ⁇ chain, two CD3 ⁇ chains, and a homodimer of CD3 ⁇ chains.
- the CD3 ⁇ , CD3 ⁇ , and CD3 ⁇ chains are highly related cell surface proteins of the immunoglobulin superfamily containing a single immunoglobulin domain.
- the transmembrane regions of the CD3 ⁇ , CD3 ⁇ , and CD3 ⁇ chains are negatively charged, which is a characteristic that allows these chains to associate with positively charged regions of T cell receptor chains.
- CD3 ⁇ , CD3 ⁇ , and CD3 ⁇ chains each contain a single conserved motif known as an immunoreceptor tyrosine- based activation motif or ITAM, whereas each CD3 ⁇ chain has three.
- ITAMs are important for the signaling capacity of a TCR complex.
- CD3 as used in the present disclosure may be from various animal species, including human, mouse, rat, or other mammals.
- TCR complex refers to a complex formed by the association of CD3 with TCR.
- a TCR complex can be composed of a CD3 ⁇ chain, a CD3 ⁇ chain, two CD3 ⁇ chains, a homodimer of CD3 ⁇ chains, a TCR ⁇ chain, and a TCR ⁇ chain.
- a TCR complex can be composed of a CD3 ⁇ chain, a CD3 ⁇ chain, two CD3 ⁇ chains, a homodimer of CD3 ⁇ chains, a TCR ⁇ chain, and a TCR ⁇ chain.
- a “component of a TCR complex,” as used herein, refers to a TCR chain (i.e., TCR ⁇ , TCR ⁇ , TCR ⁇ or TCR ⁇ ), a CD3 chain (i.e., CD3 ⁇ , CD3 ⁇ , CD3 ⁇ or CD3 ⁇ ), or a complex formed by two or more TCR chains or CD3 chains (e.g., a complex of TCR ⁇ and TCR ⁇ , a complex of TCR ⁇ and TCR ⁇ , a complex of CD3 ⁇ and CD3 ⁇ , a complex of CD3 ⁇ and CD3 ⁇ , or a sub-TCR complex of TCR ⁇ , TCR ⁇ , CD3 ⁇ , CD3 ⁇ , and two CD3 ⁇ chains).
- TCR chain i.e., TCR ⁇ , TCR ⁇ , TCR ⁇ or TCR ⁇
- a CD3 chain i.e., CD3 ⁇ , CD3 ⁇ , CD3 ⁇ or CD3 ⁇
- a complex formed by two or more TCR chains or CD3 chains e.g., a
- a “binding domain” refers to a molecule or portion thereof (e.g., peptide, oligopeptide, polypeptide, protein) that possesses the ability to specifically and non- covalently associate, unite, or combine with a target (e.g., MAGE-A1, MAGE-A1 peptide:MHC complex).
- a binding domain includes any naturally occurring, synthetic, semi-synthetic, or recombinantly produced binding partner for a biological molecule, a molecular complex (i.e., complex comprising two or more biological molecules), or other target of interest.
- binding domains include single chain immunoglobulin variable regions (e.g., scTCR, scTv, scFv), receptor ectodomains, ligands (e.g., cytokines, chemokines), or synthetic polypeptides selected for their specific ability to bind to a biological molecule, a molecular complex or other target of interest.
- immunoglobulin variable regions e.g., scTCR, scTv, scFv
- receptor ectodomains e.g., cytokines, chemokines
- synthetic polypeptides selected for their specific ability to bind to a biological molecule, a molecular complex or other target of interest.
- binding protein e.g., TCR receptor
- binding domain or fusion protein thereof
- K a an affinity or K a (i.e., an equilibrium association constant of a particular binding interaction with units of 1/M) equal to or greater than 10 5 M -1 (which equals the ratio of the on-rate [kon] to the off-rate [koff] for this association reaction), while not significantly associating or uniting with any other molecules or components in a sample.
- Binding proteins or binding domains may be classified as “high affinity” binding proteins or binding domains (or fusion proteins thereof) or as “low affinity” binding proteins or binding domains (or fusion proteins thereof). “High affinity” binding proteins or binding domains refer to those binding proteins or binding domains having a Ka of at least 10 7 M -1 , at least 10 8 M -1 , at least 10 9 M -1 , at least 10 10 M -1 , at least 10 11 M -1 , at least 10 12 M- 1 , or at least 10 13 M -1 .
- “Low affinity” binding proteins or binding domains refer to those binding proteins or binding domains having a Ka of up to 10 7 M -1 , up to 10 6 M -1 , up to 10 5 M -1 .
- affinity may be defined as an equilibrium dissociation constant (Kd) of a particular binding interaction with units of M (e.g., 10 -5 M to 10 -13 M).
- Kd equilibrium dissociation constant
- a receptor or binding domain may have “enhanced affinity,” which refers to selected or engineered receptors or binding domains with stronger binding to a target antigen than a wild type (or parent) binding domain.
- enhanced affinity may be due to a Ka (equilibrium association constant) for the target antigen that is higher than the wild type binding domain, due to a K d (dissociation constant) for the target antigen that is less than that of the wild type binding domain, due to an off-rate (koff) for the target antigen that is less than that of the wild type binding domain, or a combination thereof.
- polynucleotides encoding binding protein e.g., TCRs, such as enhanced affinity TCRs
- TCRs such as enhanced affinity TCRs
- TCRs may be codon optimized to enhance expression in a particular host cell, such as T cells (e.g., Scholten et al., Clin. Immunol.119:135, 2006).
- binding domains of the present disclosure that specifically bind a particular target, as well as determining binding domain or fusion protein affinities, such as such as multimer/tetramer staining (e.g., peptide:MHC tetramer), Western blot, ELISA, analytical ultracentrifugation, spectroscopy and surface plasmon resonance (Biacore®) analysis (see, e.g., Scatchard et al., Ann. N.Y. Acad. Sci.51:660, 1949; Wilson, Science 295:2103, 2002; Wolff et al., Cancer Res.53:2560, 1993; and U.S.
- multimer/tetramer staining e.g., peptide:MHC tetramer
- Western blot e.g., ELISA, analytical ultracentrifugation, spectroscopy and surface plasmon resonance (Biacore®) analysis
- Biacore® surface plasmon resonance
- MAGE-A1-specific binding protein refers to a protein or polypeptide that specifically binds to MAGE-A1 or a peptide or fragment thereof.
- a MAGE-A1-specific binding protein or polypeptide binds to MAGE-A1 or a peptide thereof, such as a MAGE-A1 peptide complexed with an MHC or HLA molecule, e.g., on a cell surface, with at least, or at least about, a particular affinity.
- a MAGE-A1-specific binding protein binds a MAGE- A1-derived peptide:HLA complex (or MAGE-A1-derived peptide:MHC complex) with a Kd of less than about 10 -8 M, less than about 10 -9 M, less than about 10 -10 M, less than about 10 -11 M, less than about 10 -12 M, or less than about 10 -13 M, or with an affinity that is about the same as, at least about the same as, or is greater than at or about the affinity exhibited by an exemplary MAGE-A1 specific binding protein provided herein, such as any of the MAGE-A1-specific TCRs provided herein, for example, as measured by the same assay.
- a MAGE-A1-specific binding protein comprises a MAGE-A1-specific immunoglobulin superfamily binding protein or binding portion thereof.
- Assays for assessing affinity or apparent affinity or relative affinity include, for example, measuring apparent affinity for a TCR (or for a binding protein comprising a binding domain derived from a TCR) by assessing binding to various concentrations of tetramers, for example, by flow cytometry using labeled tetramers.
- apparent K D of a TCR is measured using 2-fold dilutions of labeled tetramers at a range of concentrations, followed by determination of binding curves by non-linear regression, apparent K D being determined as the concentration of ligand that yielded half-maximal binding.
- MAGE-A1 binding domain or “MAGE-A1 binding fragment” refer to a domain, or portion of a MAGE-A1-specific binding protein, responsible for the specific MAGE-A1 binding.
- a MAGE-A1-specific binding domain alone (i.e., without any other portion of a MAGE-A1-specific binding protein) can be soluble and can bind to MAGE-A1 with a Kd of less than about 10 -8 M, less than about 10 -9 M, less than about 10 -10 M, less than about 10 -11 M, less than about 10 -12 M, or less than about 10 -13 M.
- MAGE-A1-specific binding domains include, for example, MAGE- A1-specific TCR, scTCR (e.g., single chain ⁇ ⁇ TCR or scTv proteins such as V ⁇ -L-V ⁇ , V ⁇ -L-V ⁇ , V ⁇ -L-V ⁇ -C ⁇ , or V ⁇ -L-V ⁇ -C ⁇ , wherein V ⁇ and V ⁇ are TCR ⁇ and ⁇ variable domains respectively, C ⁇ and C ⁇ are TCR ⁇ and ⁇ constant domains, respectively, and L is a linker) and scFv fragments as described herein, which can be derived from an anti-MAGE-A1 TCR or antibody.
- scTCR e.g., single chain ⁇ ⁇ TCR or scTv proteins such as V ⁇ -L-V ⁇ , V ⁇ -L-V ⁇ , V ⁇ -L-V ⁇ -C ⁇ , or V ⁇ -L-V ⁇ -C ⁇ , wherein V ⁇ and V
- APC antigen presenting cells
- MHC major histocompatibility complex
- processed antigen peptides originating in the cytosol are generally from about 7 amino acids to about 11 amino acids in length and will associate with class I MHC molecules
- peptides processed in the vesicular system e.g., bacterial, viral
- MAGE-A1 antigen or “MAGE-A1 peptide antigen” refer to a naturally or synthetically produced portion of a MAGE-A1 protein ranging in length from about 7 amino acids to about 15 amino acids, which can form a complex with a MHC (e.g., HLA) molecule and such a complex can bind with a TCR specific for a MAGE-A1 peptide:MHC (e.g., HLA) complex.
- a MAGE-A1 peptide antigen comprises or consists of the amino acid sequence set forth in SEQ ID NO.:123.
- a “linker” refers to an amino acid sequence that connects two proteins, polypeptides, peptides, domains, regions, or motifs and may provide a spacer function compatible with interaction of the two sub-binding domains so that the resulting polypeptide retains a specific binding affinity (e.g., scTCR) to a target molecule or retains signaling activity (e.g., TCR complex).
- a linker is comprised of about two to about 35 amino acids, for instance, or about four to about 20 amino acids or about eight to about 15 amino acids or about 15 to about 25 amino acids.
- “Junction amino acids” or “junction amino acid residues” refer to one or more (e.g., about 2-10) amino acid residues between two adjacent motifs, regions, or domains of a polypeptide, such as between a binding domain and an adjacent constant domain or between a TCR chain and an adjacent self-cleaving peptide. Junction amino acids may result from the construct design of a fusion protein (e.g., amino acid residues resulting from the use of a restriction enzyme site during the construction of a nucleic acid molecule encoding a fusion protein).
- an “altered domain” or “altered protein” refers to a motif, region, domain, peptide, polypeptide, or protein with a non-identical sequence identity to a wild type motif, region, domain, peptide, polypeptide, or protein (e.g., a wild type TCR ⁇ chain, TCR ⁇ chain, TCR ⁇ constant domain, TCR ⁇ constant domain) of at least 85% (e.g., 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9%).
- nucleic acid or “nucleic acid molecule” or “polynucleotide” refers to any of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), oligonucleotides, fragments generated, for example, by the polymerase chain reaction (PCR) or by in vitro translation, and fragments generated by any of ligation, scission, endonuclease action, or exonuclease action.
- the nucleic acids of the present disclosure are produced by PCR.
- Nucleic acids may be composed of monomers that are naturally occurring nucleotides (such as deoxyribonucleotides and ribonucleotides), analogs of naturally occurring nucleotides (e.g., ⁇ -enantiomeric forms of naturally-occurring nucleotides), or a combination of both.
- Modified nucleotides can have modifications in or replacement of sugar moieties, or pyrimidine or purine base moieties.
- Nucleic acid monomers can be linked by phosphodiester bonds or analogs of such linkages.
- Analogs of phosphodiester linkages include phosphorothioate, phosphorodithioate, phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate, phosphoranilidate, phosphoramidate, and the like.
- Nucleic acid molecules can be either single stranded or double stranded.
- isolated means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally occurring nucleic acid or polypeptide present in a living animal is not isolated, but the same nucleic acid or polypeptide, separated from some or all of the co-existing materials in the natural system, is isolated.
- nucleic acid could be part of a vector and/or such nucleic acid or polypeptide could be part of a composition (e.g., a cell lysate), and still be isolated in that such vector or composition is not part of the natural environment for the nucleic acid or polypeptide.
- the term “gene” means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region “leader and trailer” as well as intervening sequences (introns) between individual coding segments (exons).
- modified refers to a cell, microorganism, nucleic acid molecule, or vector that has been genetically engineered by human intervention – that is, modified by introduction of an exogenous or heterologous nucleic acid molecule, or refers to a cell or microorganism that has been altered such that expression of an endogenous nucleic acid molecule or gene is controlled, deregulated or constitutive.
- Human-generated genetic alterations may include, for example, modifications that introduce nucleic acid molecules (which may include an expression control element, such as a promoter) that encode one or more proteins or enzymes, or other nucleic acid molecule additions, deletions, substitutions, or other functional disruption of or addition to a cell’s genetic material.
- Exemplary modifications include those in coding regions or functional fragments thereof of heterologous or homologous polypeptides from a reference or parent molecule.
- “mutation” refers to a change in the sequence of a nucleic acid molecule or polypeptide molecule as compared to a reference or wild-type nucleic acid molecule or polypeptide molecule, respectively.
- a mutation can result in several different types of change in sequence, including substitution, insertion or deletion of nucleotide(s) or amino acid(s).
- a mutation is a substitution of one or three codons or amino acids, a deletion of one to about five codons or amino acids, or a combination thereof.
- a “conservative substitution” is recognized in the art as a substitution of one amino acid for another amino acid that has similar properties. Exemplary conservative substitutions are described in, for example: WO 97/09433 at page 10; Lehninger, Biochemistry, 2 nd Edition; Worth Publishers, Inc. NY, NY, pp.71-77, 1975; and Lewin, Genes IV, Oxford University Press, NY and Cell Press, Cambridge, MA, p.
- amino acids may occur naturally or may be introduced when a binding protein or TCR is recombinantly produced.
- Amino acid substitutions, deletions, and additions may be introduced into a protein using mutagenesis methods known in the art (see, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, 3d ed., Cold Spring Harbor Laboratory Press, NY, 2001).
- Oligonucleotide-directed site-specific (or segment specific) mutagenesis procedures may be employed to provide an altered polynucleotide that has particular codons altered according to the substitution, deletion, or insertion desired.
- construct refers to any polynucleotide that contains a recombinant nucleic acid molecule.
- a construct may be present in a vector (e.g., a bacterial vector, a viral vector) or may be integrated into a genome.
- a “vector” is a nucleic acid molecule that is capable of transporting another nucleic acid molecule.
- Vectors may be, for example, plasmids, cosmids, viruses, a RNA vector or a linear or circular DNA or RNA molecule that may include chromosomal, non-chromosomal, semi-synthetic or synthetic nucleic acid molecules.
- Exemplary vectors are those capable of autonomous replication (episomal vector) or expression of nucleic acid molecules to which they are linked (expression vectors).
- operably linked or “operatively-linked” refers to the association of two or more nucleic acid molecules on a single nucleic acid molecule or fragment so that the function of one is affected by the other.
- a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., the coding sequence is under the transcriptional control of the promoter).
- “Unlinked” means that the associated genetic elements are not closely associated with one another and the function of one does not affect the other.
- expression vector refers to a DNA construct containing a nucleic acid molecule that is operably-linked to a suitable control sequence capable of effecting the expression of the nucleic acid molecule in a suitable host.
- control sequences include a promoter to effect transcription, an optional operator sequence to control such transcription, a sequence encoding suitable mRNA ribosome binding sites, and sequences which control termination of transcription and translation.
- the vector may be a plasmid, a phage particle, a virus, or simply a potential genomic insert. Once transformed into a suitable host, the vector may replicate and function independently of the host genome, or may, in some instances, integrate into the genome itself.
- plasmid “expression plasmid,” “virus” and “vector” are often used interchangeably.
- expression refers to the process by which a polypeptide is produced based on the encoding sequence of a nucleic acid molecule, such as a gene. The process may include transcription, post-transcriptional control, post-transcriptional modification, translation, post-translational control, post- translational modification, or any combination thereof.
- the term “introduced” in the context of inserting a nucleic acid molecule into a cell means “transfection”, or ‘transformation” or “transduction” and includes reference to the incorporation of a nucleic acid molecule into a eukaryotic or prokaryotic cell wherein the nucleic acid molecule may be incorporated into the genome of a cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
- a cell e.g., chromosome, plasmid, plastid, or mitochondrial DNA
- transiently expressed e.g., transfected mRNA
- heterologous or exogenous nucleic acid molecule, construct or sequence refers to polynucleotide or portion of a polynucleotide that is not native to a host cell, but may be homologous to a polynucleotide or portion of a polynucleotide from the host cell.
- the source of the heterologous or exogenous polynucleotide, construct or sequence may be from a different genus or species.
- a heterologous or exogenous polynucleotide is added (i.e., not endogenous or native) to a host cell or host genome by, for example, conjugation, transformation, transfection, electroporation, or the like, wherein the added molecule may integrate into the host genome or exist as extra-chromosomal genetic material (e.g., as a plasmid or other form of self-replicating vector) and may be present in multiple copies.
- heterologous refers to a non-native enzyme, protein or other activity encoded by an exogenous polynucleotide introduced into the host cell, even if the host cell encodes a homologous protein or activity.
- the polynucleotide is "heterologous" to progeny of the host cell, whether or not the progeny were themselves manipulated (e.g., transduced) to contain the polynucleotide.
- a host cell may be referred-to as a "modified" host cell, whether the subject host cell was itself modified to comprise the polynucleotide, or whether an ancestor cell of the subject host cell was modified to comprise the polynucleotide.
- more than one heterologous or exogenous nucleic acid molecule can be introduced into a host cell as separate polynucleotides, as a plurality of individually controlled genes, as a polycistronic polynucleotide, as a single nucleic acid molecule encoding a fusion protein, or any combination thereof.
- a host cell can be modified to express two or more heterologous or exogenous polynucleotides encoding a desired binding protein (e.g., encoding a TCR) specific for a MAGE-A1 antigen peptide (e.g., TCR ⁇ and TCR ⁇ ).
- the two or more exogenous nucleic acid molecules can be introduced as a single polynucleotide (e.g., on a single vector), on separate vectors, integrated into the host chromosome at a single site or multiple sites, or any combination thereof.
- the number of referenced heterologous nucleic acid molecules or protein activities refers to the number of encoding nucleic acid molecules or the number of protein activities, not the number of separate polynucleotides introduced into a host cell.
- the term “endogenous” or “native” refers to a gene, protein, or activity that is normally present in a host cell.
- a gene, protein or activity that is mutated, overexpressed, shuffled, duplicated, or otherwise altered as compared to a parent gene, protein or activity is still considered to be endogenous or native to that particular host cell.
- an endogenous control sequence from a first gene e.g., promoter, translational attenuation sequences
- the term “homologous” or “homolog” refers to a molecule or activity found in or derived from a host cell, species or strain.
- a heterologous or exogenous nucleic acid molecule may be homologous to a native host cell gene, and may optionally have an altered expression level, a different sequence, an altered activity, or any combination thereof.
- sequence identity refers to the percentage of amino acid residues in one sequence that are identical with the amino acid residues in another reference polypeptide sequence after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. The percentage sequence identity values can be generated using the NCBI BLAST2.0 software as defined by Altschul et al.
- hematopoietic progenitor cell is a cell that can be derived from hematopoietic stem cells or fetal tissue and is capable of further differentiation into mature cells types (e.g., immune system cells).
- exemplary hematopoietic progenitor cells include those with a CD24 Lo Lin – CD117 + phenotype or those found in the thymus (referred to as progenitor thymocytes).
- the term “host cell” refers to a cell (e.g., T cell) or microorganism targeted for genetic modification with a heterologous or exogenous nucleic acid molecule to produce a polypeptide of interest (e.g., a binding protein such as high-affinity or enhanced- affinity anti- MAGE-A1 TCR).
- a host cell may optionally already possess or be modified to include other genetic modifications that confer desired properties related or unrelated to biosynthesis of the heterologous or exogenous protein (e.g., inclusion of a detectable marker; deleted, altered or truncated endogenous TCR; increased co-stimulatory factor expression).
- a host cell is a human hematopoietic progenitor cell transduced with a heterologous or exogenous nucleic acid molecule encoding a TCR specific for a MAGE-A1 antigen peptide.
- “hyperproliferative disorder” refers to excessive growth or proliferation as compared to a normal or undiseased cell.
- hyperproliferative disorders include tumors, cancers, neoplastic tissue, carcinoma, sarcoma, malignant cells, pre-malignant cells, as well as non-neoplastic or non- malignant hyperproliferative disorders (e.g., adenoma, fibroma, lipoma, leiomyoma, hemangioma, fibrosis, restenosis, as well as autoimmune diseases such as rheumatoid arthritis, osteoarthritis, psoriasis, inflammatory bowel disease, or the like).
- proliferative diseases include certain tumors, cancers, neoplastic tissue, carcinoma, sarcoma, malignant cells, pre-malignant cells, as well as non-neoplastic or non-malignant disorders.
- the present disclosure provides a modified cell comprising a binding protein (e.g, a TCR, a single chain TCR (scTCR), a scTv, or a CAR) that binds (e.g., specific binding) to MAGE-A1 or a MAGE-A1 peptide antigen, such as a MAGE-A1 peptide complexed with an HLA molecule.
- a binding protein e.g, a TCR, a single chain TCR (scTCR), a scTv, or a CAR
- binds e.g., specific binding
- MAGE-A1 or a MAGE-A1 peptide antigen such as a MAGE-A1 peptide complexed with an HLA molecule.
- ideal targets for immunotherapy are immunogenic proteins with high expression in malignant tissues and limited-to-absent expression in normal tissues.
- CTAs cancer/testis antigens
- CTAs are especially expressed in higher-grade lesions and aggressive malignancies, and associated with poorer clinical outcomes (Barrow et al., Clin Cancer Res., 12(3 Pt 1):764-71 (2006); Gure, et al. Clin Cancer Res., 11(22):8055-62 (2005); Velazquez et al., Cancer Immun., 7: 11 (2007)).
- MAGE family proteins are CTAs that are broadly expressed in many tumor types such as melanoma, lung, ovarian, multiple myeloma as well as TNBC. Simpson, A.J., et al., Cancer/testis antigens, gametogenesis and cancer, Nat. Rev. Cancer, 2005.5(8):615-25; Weon, J.L.
- a binding protein of the instant disclosure comprises (a) a T cell receptor (TCR) ⁇ -chain variable (V ⁇ ) domain having a CDR3 amino acid sequence according to any one of SEQ ID NOS.:26, 32, 38, 44, 50, or 51, and a TCR ⁇ -chain variable (V ⁇ ) domain; (b) a V ⁇ domain having a CDR3 amino acid sequence according to any one of SEQ ID NOS.:23, 29, 35, 41, or 47, and a V ⁇ domain; or (c) a V ⁇ domain having a CDR3 amino acid sequence according to any one of SEQ ID NOs:26, 32, 38, 44, 50, or 51, and a V ⁇ domain having a CDR3 amino acid sequence according to any one of SEQ ID NOs:26, 32, 38, 44, 50, or 51, and a V ⁇ domain having a CDR3 amino acid sequence according to any
- binding proteins are described in WO 2018/170338 and US 2020-0017568 A1, both of which are incorporated herein by reference in their entireties, including the binding protein amino acid sequences therein, including the CDR, variable domain, and constant domain amino acid sequences of the binding proteins therein, and including the CD8 co- receptor amino acid sequences therein.
- a CDR3 sequence is according to the IMGT junction definition.
- Peptide-MHC complexes such as MAGE-A1 peptide:MHC complexes, are recognized and bound by the TCR V ⁇ and TCR V ⁇ domains, with at least the specificity for peptide:MHC determined by CDRs.
- V ⁇ exons are assembled from different variable and joining gene segments (V-J), and V ⁇ exons are assembled from different variable, diversity, and joining gene segments (V-D-J).
- the TCR ⁇ chromosomal locus has 70-80 variable gene segments and 61 joining gene segments.
- the TCR ⁇ chromosomal locus has 52 variable gene segments, and two separate clusters of each containing a single diversity gene segment, together with six or seven joining gene segments.
- Functional V ⁇ and V ⁇ gene exons are generated by the recombination of a variable gene segment with a joining gene segment for V ⁇ , and a variable gene segment with a diversity gene segment and a joining gene segment for V ⁇ .
- TCR V ⁇ and V ⁇ domains each comprise three hypervariable loops, also referred to as complementary determining regions (CDRs) that contact the peptide- MHC complex (it may be possible in some cases for one or more CDR to not make contact with the peptide-MHC complex, but at least one CDR will make contact with the peptide-MHC complex).
- CDRs complementary determining regions
- the terms “complementarity determining region,” and “CDR,” are synonymous with “hypervariable region” or “HVR,” and are known in the art to refer to sequences of amino acids within immunoglobulin (e.g., TCR) variable regions, which confer antigen specificity and/or binding affinity and are separated from one another by framework regions.
- CDR3 is generally thought to be the main CDR responsible for recognizing processed antigen.
- CDR1 and CDR2 mainly interact with the MHC.
- CDR1 and CDR2 are encoded within the variable gene segment, whereas CDR3 is encoded by the region spanning the variable and joining segments for V ⁇ , or the region spanning variable, diversity, and joining segments for V ⁇ .
- an encoded binding domain comprises a V ⁇ domain that is derived from a TRBV30 allele, a TRBV29 allele, or a TRBV9 allele.
- an encoded binding domain comprises a V ⁇ domain that is derived from a TRAV38-1 allele, a TRAV34 allele, a TRAV16 allele, or a TRAV5 allele.
- TCR variable domain sequences can be aligned to a numbering scheme (e.g., the international Immunogenetics Information System (IMGT; see e.g.
- a numbering scheme provides a standardized delineation of framework regions and CDRs in the TCR variable domains.
- CDRs are according to IMGT numbering.
- variable domains are according to IMGT.
- constant domains are according to IMGT.
- a binding protein comprises a functional variant amino acid sequence as compared to a reference amino acid sequence disclosed herein, wherein the encoded binding protein retains binding characteristics as compared to a binding protein comprising a reference amino acid sequence.
- an encoded V ⁇ domain comprises an amino acid sequence that is at least about 90% identical (e.g., is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%, or 100% identical) to an amino acid sequence according to any one of SEQ ID NOS.:3, 7, 11, 15, and 19, and an encoded V ⁇ domain comprises an amino acid sequence that is at least about 90% identical to the amino acid sequence according to any one of SEQ ID NOS.:1, 5, 9, 13, 17, provided that (a) at least three or four of the CDRs have no change in sequence,
- a V ⁇ domain comprises (i) a CDR1 amino acid sequence according to any one of SEQ ID NOS:24, 30, 36, 42, and 48, and/or (ii) a CDR2 amino acid sequence according to any one of SEQ ID NOS:25, 31, 37, 43, and 49; and/or (b) an encoded V ⁇ domain comprises (iii) a CDR1 amino acid sequence according to any one of SEQ ID NOS:21, 27, 33, 39, and 45, and/or (iv) a CDR2 amino acid sequence according to any one of SEQ ID NOS:22, 28, 34, 40, and 46.
- an encoded binding protein comprises: (a) V ⁇ CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:24-26, respectively, and V ⁇ CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:21-23, respectively; (b) V ⁇ CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:30-32, respectively, and V ⁇ CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:27-29, respectively; (c) V ⁇ CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:36-38, respectively, and V ⁇ CDR1, CDR2, [0083] and CDR3 amino acid sequences according to SEQ ID NOS:33-35, respectively; (d) V ⁇ CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:42-44, respectively, and V ⁇ CDR1, CDR2, and C
- a polypeptide of this disclosure can comprise a “signal peptide” (also known as a leader sequence, leader peptide, or transit peptide).
- Signal peptides target newly synthesized polypeptides to their appropriate location inside or outside the cell.
- a signal peptide may be removed from the polypeptide during or once localization or secretion is completed.
- Polypeptides that have a signal peptide are referred to herein as a “pre-protein” and polypeptides having their signal peptide removed are referred to herein as “mature” proteins or polypeptides.
- a binding protein or fusion protein comprises, or is, a mature protein, or is or comprises a pre-protein.
- the binding proteins described herein are mature proteins that lack a signal peptide.
- a signal peptide if present, can be deduced with reference to the TCR V alpha or V beta allele (i.e., TRAV or TRBV) used by the subject variable domain, and will be N-terminal to the beginning of the sequence encoded by the subject TCR V alpha or V beta allele.
- a binding protein comprises, in a V ⁇ domain, an amino acid sequence encoded by a TRAV38-1, TRAV34, TRAV16, or TRAV5, and/or comprises , in a V ⁇ domain, an amino acid sequence encoded by TRBV30 (e.g., TRBV30*01), TRBV29 or TRBV9.
- TRBV30 e.g., TRBV30*01
- TRBV29 e.g., TRBV30*01
- SEQ ID NO.:19 amino acids 1-18 constitute the signal peptide.
- SEQ ID NO.:19 with the signal peptide removed refers to the amino acid sequence beginning at amino acid residue 19 of SEQ ID NO.:17; in other words, SEQ ID NO.:19 without the first 18 amino acids.
- an encoded TCR V domain or TCR chain comprises an alternative signal peptide, and the signal peptide is removed prior to localization to the cell surface.
- a V ⁇ domain has at least 95%, 97%, or 99% identity to, or comprises or consists of, the amino acid sequence according to SEQ ID NO.:3, 7, 11, 15, or 19, or according to SEQ ID NO.:3, 7, 11, 15, or 19 with the signal peptide removed. In further embodiments, a V ⁇ domain has at least 95%, 97%, 99% identity to, or comprises or consists of, the amino acid sequence according to SEQ ID NO.:1, 5, 9, 13, or 17, or according to SEQ ID NO.:1, 5, 9, 13, or 17 with the signal peptide removed. [0089] In some embodiments, a binding protein comprises a TCR ⁇ -chain constant domain, a TCR ⁇ -chain constant domain, or both.
- a TCR ⁇ -chain constant (C ⁇ ) domain has at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to, or comprises or consists of, the amino acid sequence of any one of SEQ ID NOs.:4, 8, 12, 16, or 20.
- a TCR ⁇ -chain constant (C ⁇ ) domain has at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to, or comprises or consists of, any one of the amino acid sequences of SEQ ID NOs.:2, 6, 10, 14, 18 or 158.
- a binding of the present disclosure comprises a V ⁇ domain, a V ⁇ domain, a C ⁇ domain, and a C ⁇ domain.
- the V ⁇ domain and the C ⁇ domain together comprise a TCR ⁇ chain, and the V ⁇ domain and the C ⁇ domain together comprise a TCR ⁇ chain.
- the TCR ⁇ chain and the TCR ⁇ chain can associate with one another, forming a TCR (or a TCR portion of a protein comprising a TCR), which can be present at the surface of a host cell.
- a binding protein comprises a V ⁇ domain comprising or consisting of SEQ ID NO.:3 (or SEQ ID NO.:3 with the signal peptide removed), a V ⁇ domain comprising or consisting of SEQ ID NO.:1 (or SEQ ID NO.:1 with the signal peptide removed), a C ⁇ domain comprising or consisting of SEQ ID NO.:4, and a C ⁇ domain comprising or consisting of SEQ ID NO.:2.
- a binding protein comprises a V ⁇ domain comprising or consisting of SEQ ID NO.:7 (or SEQ ID NO.:7 with the signal peptide removed), a V ⁇ domain comprising or consisting of SEQ ID NO.:5 (or SEQ ID NO.:5 with the signal peptide removed), a C ⁇ domain comprising or consisting of SEQ ID NO.:8, and a C ⁇ comprising or consisting of SEQ ID NO.:6.
- a binding protein comprises a V ⁇ domain comprising or consisting of SEQ ID NO.:11 (or SEQ ID NO.:11 with the signal peptide removed), a V ⁇ domain comprising or consisting of SEQ ID NO.:9, a C ⁇ domain comprising or consisting of SEQ ID NO.:12 (or SEQ ID NO.:12 with the signal peptide removed), and a C ⁇ domain comprising or consisting of SEQ ID NO.:10.
- a binding protein comprises a V ⁇ domain comprising or consisting of SEQ ID NO.:15 (or SEQ ID NO.:15 with the signal peptide removed), a V ⁇ domain comprising or consisting of SEQ ID NO.: 13, a C ⁇ comprising or consisting of SEQ ID NO.: 16 (or SEQ ID NO.:16 with the signal peptide removed), and a C ⁇ domain comprising or consisting of SEQ ID NO.:14.
- a binding protein comprises a V ⁇ domain comprising or consisting of SEQ ID NO.: 19 (or SEQ ID NO.:19 with the signal peptide removed), a V ⁇ domain comprising or consisting of SEQ ID NO.:17 (or SEQ ID NO.:17 with the signal peptide removed), a C ⁇ domain comprising or consisting of SEQ ID NO.:20, and a C ⁇ domain comprising or consisting of SEQ ID NO.: 18 or 158.
- a binding protein (e.g., in soluble form or expressed on a cell surface of a modified cell of the present disclosure) is capable of binding to a MAGE-A1:HLA-A*201 complex (e.g., a KVLEYVIKV (SEQ ID NO.:123):HLA-A*201 complex) on a cell surface independent of or in the absence of CD8.
- a MAGE-A1 specific binding proteins is or comprises a T cell receptor (TCR), a chimeric antigen receptor or an antigen-binding fragment of a TCR, any of which can be chimeric, humanized, or human.
- an antigen-binding fragment of the TCR comprises a single chain TCR (scTCR) or a chimeric antigen receptor (CAR).
- a MAGE-A1 specific binding protein is a TCR, optionally a scTCR.
- a MAGE-A1-specific binding domain is a CAR comprising a MAGE-A1-specific TCR binding domain (see, e.g., Walseng et al., Scientific Reports 7:10713 (2017), the TCR CAR constructs of which are hereby incorporated by reference in their entirety).
- Methods for making CARs are also described, for example, in U.S. Patent No.6,410,319; U.S. Patent No.7,446,191; U.S. Patent Publication No.2010/065818; U.S. Patent No.8,822,647; PCT Publication No. WO 2014/031687; U.S.
- Methods useful for isolating and purifying recombinantly produced soluble TCR may include obtaining supernatants from suitable host cell/vector systems that secrete the recombinant soluble TCR into culture media and then concentrating the media using a commercially available filter. Following concentration, the concentrate may be applied to a single suitable purification matrix or to a series of suitable matrices, such as an affinity matrix or an ion exchange resin. One or more reverse phase HPLC steps may be employed to further purify a recombinant polypeptide.
- nucleic acid molecules encoding a binding protein or high affinity TCR specific for MAGE-A1 are used to transfect/transduce a host cell (e.g., T cells) for use in adoptive transfer therapy.
- MAGE-A1-specific binding proteins or domains as described herein may be functionally characterized according to any of a large number of art accepted methodologies for assaying T cell activity, including determination of T cell binding, activation or induction and also including determination of T cell responses that are antigen-specific.
- T cell proliferation examples include determination of T cell proliferation, T cell cytokine release, antigen-specific T cell stimulation, MHC restricted T cell stimulation, CTL activity (e.g., by detecting 51 Cr release from pre-loaded target cells), changes in T cell phenotypic marker expression, and other measures of T-cell functions.
- Procedures for performing these and similar assays are may be found, for example, in Lefkovits (Immunology Methods Manual: The Comprehensive Sourcebook of Techniques, 1998).
- MHC-peptide tetramer staining refers to an assay used to detect antigen-specific T cells, which features a tetramer of MHC molecules, each comprising an identical peptide having an amino acid sequence that is cognate (e.g., identical or related to) at least one antigen (e.g., MAGE-A1), wherein the complex is capable of binding T cell receptors specific for the cognate antigen.
- MHC molecules may be tagged with a biotin molecule.
- Biotinylated MHC/peptides are tetramerized by the addition of streptavidin, which can be fluorescently labeled. The tetramer may be detected by flow cytometry via the fluorescent label.
- an MHC- peptide tetramer assay is used to detect or select enhanced affinity TCRs of the instant disclosure.
- Levels of cytokines may be determined according to methods described herein and practiced in the art, including for example, ELISA, ELISPOT, intracellular cytokine staining, and flow cytometry and combinations thereof (e.g., intracellular cytokine staining and flow cytometry).
- Immune cell proliferation and clonal expansion resulting from an antigen-specific elicitation or stimulation of an immune response may be determined by isolating lymphocytes, such as circulating lymphocytes in samples of peripheral blood cells or cells from lymph nodes, stimulating the cells with antigen, and measuring cytokine production, cell proliferation and/or cell viability, such as by incorporation of tritiated thymidine or non-radioactive assays, such as MTT assays and the like.
- lymphocytes such as circulating lymphocytes in samples of peripheral blood cells or cells from lymph nodes
- stimulating the cells with antigen and measuring cytokine production, cell proliferation and/or cell viability, such as by incorporation of tritiated thymidine or non-radioactive assays, such as MTT assays and the like.
- Th1 cytokines such as IFN- ⁇ , IL-12, IL-2, and TNF- ⁇
- Type 2 cytokines such as IL-4, IL-5, IL-9, IL-10, and IL-13.
- polynucleotides and Vectors [0098]
- a polynucleotide encodes a binding protein of the present disclosure (e.g., immunoglobulin superfamily binding protein, such as a TCR, scTv, scTCR, or CAR) specific for a MAGE-A1 antigen, and wherein the polynucleotide is optionally codon optimized for expression in a host cell (e.g., an immune cell of the present disclosure).
- a binding protein of the present disclosure e.g., immunoglobulin superfamily binding protein, such as a TCR, scTv, scTCR, or CAR
- vectors that comprise a polynucleotide of this disclosure, wherein the polynucleotide is operatively associated or operably linked to an expression control sequence (e.g., a promoter).
- an expression control sequence e.g., a promoter.
- Construction of an expression vector to produce a binding protein specific for a MAGE-A1 peptide of this disclosure can be made using restriction endonuclease digestion, ligation, transformation, plasmid purification, DNA sequencing, or a combination thereof, as described in, for example, Sambrook et al. (1989 and 2001 editions; Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, NY) and Ausubel et al. (Current Protocols in Molecular Biology, 2003).
- a polynucleotide contained in an expression construct includes at least one appropriate expression control sequence (also called a regulatory sequence), such as a leader sequence and particularly a promoter operably (i.e., operatively) linked to the nucleotide sequence encoding the binding protein of this disclosure.
- a nucleic acid may be a single- or a double-stranded DNA, cDNA or RNA in any form, and may include a positive and a negative strand of the nucleic acid which complement each other, including anti-sense DNA, cDNA and RNA. Also included are siRNA, microRNA, RNA—DNA hybrids, ribozymes, and other various naturally occurring or synthetic forms of DNA or RNA.
- Isolated or recombinant nucleic acid molecules encoding a binding protein e.g., immunoglobulin superfamily binding protein
- a binding protein e.g., immunoglobulin superfamily binding protein
- high affinity recombinant TCR specific for MAGE-A1 as described herein may be produced and prepared according to various methods and techniques of the molecular biology or polypeptide purification arts.
- a polynucleotide is provided that least has at least 50%, at least 55%, at least 60%, at least 65%, 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the polynucleotide sequence set forth in any one of SEQ ID NOs.:149-153 and 159.
- an isolated polynucleotide that encodes a binding protein having a TCR V ⁇ domain and a TCR V ⁇ domain, wherein the encoded binding protein is capable of specifically binding to a MAGE-A1 peptide:HLA complex on a cell surface independent of CD8 or in the absence of CD8, the isolated polynucleotide comprising: (a) a V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:97, 103, 109, 115 or 121, and a V ⁇ -encoding polynucleotide; (b) a V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:94, 100, 106, 112, or 118, and a V ⁇ - encoding polynucleotide; or (c) a V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:97, 103, 109, 115 or 121 and
- a V ⁇ -encoding polynucleotide is derived from a TRBV30 allele, a TRBV29 allele, or a TRBV9 allele. [0103] In some embodiments, a V ⁇ -encoding polynucleotide is derived from a TRAV38-1 allele, a TRAV34 allele, a TRAV16 allele, or a TRAV5 allele.
- presently disclosed polynucleotides encoding binding proteins can, in some embodiments, comprise: (a) a V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:97 and a V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:94; (b) a V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:103 and a V ⁇ CDR3- encoding polynucleotide according to SEQ ID NO:100; (c) a V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:109 and a V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:106; (d) a V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:115 and a V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:112; or
- an isolated polynucleotide encoding a binding protein further comprises a V ⁇ CDR1-encoding polynucleotide according to SEQ ID NO:95, 101, 107, 113 or 119; (b) a V ⁇ CDR2-encoding polynucleotide according to SEQ ID NO:96, 102, 108, 114 or 120; (c)a V ⁇ CDR1-encoding polynucleotide according to SEQ ID NO:92, 98, 104, 110 or 116; and/or (d) a V ⁇ CDR2-encoding polynucleotide according to SEQ ID NO:93, 99, 105, 111 or 117.
- an isolated polynucleotide encoding a binding protein of the present disclosure comprises (a) a V ⁇ CDR1-encoding polynucleotide according to SEQ ID NO:95, a V ⁇ CDR2- encoding polynucleotide according to SEQ ID NO:96, a V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:97, a V ⁇ CDR1-encoding polynucleotide according to SEQ ID NO:92, a V ⁇ CDR2-encoding polynucleotide according to SEQ ID NO:93, and V ⁇ CDR3-encoding polynucleotide according to SEQ ID NO:94; (b) a V ⁇ CDR1-encoding polynucleotide according to SEQ ID NO:101, a V ⁇ CDR2- encoding polynucleotide according to SEQ ID NO:102, a V ⁇ CDR3-encoding polynu
- the instant disclosure provides a polynucleotide encoding a binding protein, wherein a V ⁇ -encoding polynucleotide comprises a nucleotide sequence having at least 80% identity (e.g., at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%, or 100% identity) to SEQ ID NO:58, 66, 74, 82, or 90, and a V ⁇ -encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:56, 64, 72, 80, or 88.
- a V ⁇ -encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:58 and a V ⁇ -encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:56;
- a V ⁇ -encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:66 and a V ⁇ -encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:64;
- a V ⁇ -encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:74 and a V ⁇ -encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:72;
- a V ⁇ -encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:58 and a V ⁇ -encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:56;
- a V ⁇ -encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:66 and a V ⁇ -encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:64;
- a V ⁇ -encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:74 and a V ⁇ -encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:72;
- a V ⁇ -encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID
- Binding protein-encoding polynucleotides of the instant disclosure may, in certain embodiments, further comprise a polynucleotide that encodes a TCR ⁇ -chain constant domain, a polynucleotide that encodes a TCR ⁇ -chain constant domain, or both.
- an isolated polynucleotide encoding a binding protein of the present disclosure further comprises: (a) a C ⁇ -domain-encoding polynucleotide having at least 80% identity to SEQ ID NO:59, 67, 75, 83, or 91; and/or (b) a C ⁇ - domain-encoding polynucleotide having at least 80% identity to SEQ ID NO:57, 65, 73, 81, or 89.
- a C ⁇ -domain-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:59, 67, 75, 83, or 91
- a C ⁇ -domain-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:57, 65, 73, 81, or 89.
- an isolated polynucleotide encoding a binding protein of the present disclosure comprises: (a) a V ⁇ -encoding polynucleotide according to SEQ ID NO:58, a V ⁇ -encoding polynucleotide according to SEQ ID NO:56, a C ⁇ - domain-encoding polynucleotide according to SEQ ID NO:59, and a C ⁇ - domain-encoding polynucleotide according to SEQ ID NO:57; (b) a V ⁇ -encoding polynucleotide according to SEQ ID NO:66, a V ⁇ -encoding polynucleotide according to SEQ ID NO:64, a C ⁇ -domain-encoding polynucleotide according to SEQ ID NO:67, and a C ⁇ -domain-encoding polynucleotide according to SEQ ID NO:65; (c) a V ⁇ -encoding poly
- two or more substituent gene products of a binding protein of this disclosure are expressed as a single peptide with the parts separated by a cleavable or removable segment.
- self-cleaving peptides useful for expression of separable polypeptides encoded by a single polynucleotide or vector include, for example, a Porcine teschovirus-12A (P2A) peptide, such as a peptide encoded by a polynucleotide having the nucleotide sequence shown in any one of SEQ ID NOS:128 or 129, a Thoseaasigna virus 2A (T2A) peptide, such as a peptide encoded by a polynucleotide having the nucleotide sequence shown in SEQ ID NO:132, an Equine rhinitis A virus (ERAV) 2A (E2A) peptide, such as a peptide encoded by a poly
- P2A Porcine teschovirus-12A
- an isolated polynucleotide encoding a binding protein of the instant disclosure further comprises a polynucleotide encoding a self-cleaving peptide disposed between a TCR ⁇ -chain-encoding polynucleotide and a TCR ⁇ -chain-encoding polynucleotide, or disposed between a TCR V ⁇ domain- encoding polynucleotide and a TCR V ⁇ -encoding polynucleotide, or disposed between a TCR variable domain-encoding polynucleotide and a TCR constant domain-encoding polynucleotide, or any combination thereof.
- a polynucleotide encoding a self-cleaving peptide comprises or consists of a nucleotide sequence according to any one of SEQ ID NOS.:128-132.
- a polynucleotide encodes a self-cleaving peptide comprising or consisting of an amino acid sequence according to any one of SEQ ID NOS.:124-127.
- vectors containing polynucleotides of the instant disclosure are also provided herein.
- Construction of an expression vector that is used for recombinantly producing a binding protein or high affinity engineered TCR specific for a MAGE-A1 peptide of interest can be accomplished by using any suitable molecular biology engineering techniques, including the use of restriction endonuclease digestion, ligation, transformation, plasmid purification, and DNA sequencing as described in, for example, Sambrook et al. (1989 and 2001 editions; Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, NY) and Ausubel et al. (Current Protocols in Molecular Biology, 2003).
- a polynucleotide in each recombinant expression construct includes at least one appropriate expression control sequence, such as a promoter operably (i.e., operatively) linked to a nucleotide sequence encoding a binding protein.
- a polynucleotide encoding a binding protein of this disclosure may also include a sequence encoding a leader sequence at the amino-terminus of the binding protein (also referred to as a pre-binding protein), which leader sequence may be removed by the cell to produce a mature binding protein.
- An exemplary vector may comprise a nucleic acid molecule capable of transporting another nucleic acid molecule to which it has been linked, or which is capable of replication in a host organism.
- Some examples of vectors include plasmids, viral vectors, cosmids, and others.
- Some vectors may be capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors), whereas other vectors may be integrated into the genome of a host cell or promote integration of the polynucleotide insert upon introduction into the host cell and thereby replicate along with the host genome (e.g., lentiviral vector)).
- vectors are capable of directing the expression of genes to which they are operatively linked (these vectors may be referred to as “expression vectors”).
- expression vectors e.g., polynucleotides encoding binding proteins or high affinity recombinant TCRs specific for MAGE-A1, or variants thereof, as described herein.
- agents e.g., polynucleotides encoding binding proteins or high affinity recombinant TCRs specific for MAGE-A1, or variants thereof, as described herein
- each agent may reside in separate or the same vectors, and multiple vectors (each containing a different agent the same agent) may be introduced to a cell or cell population or administered to a subject.
- a polynucleotide encoding a binding protein or a high affinity recombinant TCR specific for MAGE-A1 may be operatively linked to certain elements of a vector.
- polynucleotide sequences that are needed to affect the expression and processing of coding sequences to which they are ligated may be operatively linked.
- Expression control sequences may include appropriate transcription initiation, termination, promoter, and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequences); sequences that enhance protein stability; and possibly sequences that enhance protein secretion.
- Expression control sequences may be operatively linked if they are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest.
- polynucleotides encoding binding proteins of the instant disclosure are contained in an expression vector that is a viral vector, such as a lentiviral vector or a ⁇ -retroviral vector.
- Viral vectors include retrovirus, adenovirus, parvovirus (e.g., adeno- associated viruses), coronavirus, negative strand RNA viruses such as ortho-myxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g., measles and Sendai), positive strand RNA viruses such as picornavirus and alphavirus, and double-stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, fowlpox and canarypox).
- ortho-myxovirus e.g., influenza virus
- rhabdovirus e.g., rabies and vesicular stomatitis virus
- viruses include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus, for example.
- retroviruses include avian leukosis-sarcoma, mammalian C- type, B-type viruses, D type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).
- Lentiviral vector means HIV-based lentiviral vectors for gene delivery, which can be integrative or non-integrative, have relatively large packaging capacity, and can transduce a range of different cell types. Lentiviral vectors are usually generated following transient transfection of three (packaging, envelope, and transfer) or more plasmids into producer cells. Like HIV, lentiviral vectors enter the target cell through the interaction of viral surface glycoproteins with receptors on the cell surface. On entry, the viral RNA undergoes reverse transcription, which is mediated by the viral reverse transcriptase complex. The product of reverse transcription is a double-stranded linear viral DNA, which is the substrate for viral integration into the DNA of infected cells.
- a recombinant or engineered expression vector is delivered to an appropriate cell (i.e., the vector is capable of delivering a protein-encoding polynucleotide of the present disclosure to a host cell), for example, a T cell or an antigen-presenting cell, i.e., a cell that displays a peptide/MHC complex on its cell surface (e.g., a dendritic cell) and optionally lacks CD8.
- a host cell is a hematopoietic progenitor cell or a human immune system cell.
- an immune system cell can be a CD4+ T cell, a CD8+ T cell, a CD4- CD8- double negative T cell, a ⁇ T cell, a natural killer cell, a dendritic cell, or any combination thereof.
- a T cell is the host, the T cell can be na ⁇ ve, a central memory T cell, an effector memory T cell, or any combination thereof.
- Recombinant expression vectors of the present disclosure may therefore also include, for example, lymphoid tissue-specific transcriptional regulatory elements (TREs), such as a B lymphocyte, T lymphocyte, or dendritic cell specific TREs.
- TREs lymphoid tissue-specific transcriptional regulatory elements
- Lymphoid tissue specific TREs are known in the art (see, e.g., Thompson et al., Mol. Cell. Biol.12:1043, 1992); Todd et al., J. Exp. Med.177:1663, 1993); Penix et al., J. Exp. Med.178:1483, 1993).
- certain embodiments relate to host cells that comprise the vectors that are presently disclosed.
- host cells are described further herein; a host cell may include any individual cell or cell culture which may receive a vector or the incorporation of nucleic acids and/or proteins, as well as any progeny cells.
- Suitable host cells may depend on the vector and may include mammalian cells, animal cells, human cells, simian cells, insect cells, yeast cells, and bacterial cells. These cells may be induced to incorporate the vector or other material by use of a viral vector, transformation via calcium phosphate precipitation, DEAE-dextran, electroporation, microinjection, or other methods. See, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual 2d ed. (Cold Spring Harbor Laboratory, 1989).
- host cells i.e., modified cells
- a host cell comprises a human immune cell such as, for example, a T cell (such as, for example, a na ⁇ ve T cell, a central memory T cell, or a stem cell memory T cell), a NK cell, a NK-T cell, a macrophage, and/or a microglia.
- a host cell comprises a CD4 + T cell, a CD8 + T cell (e.g., which can additionally be CD62L + ), or both.
- a plurality of cells that comprise a binding protein as provided herein may be described as a “population”.
- Cells of a population may have one or more additional shared feature but will comprise a binding protein of the present disclosure.
- a population can be administered to a subject in the form of a cell composition for a therapeutic method as provided herein.
- a population comprises CD8+ T cells, CD4+ T cells, or both.
- a binding protein will preferably localize to the surface of a host cell.
- a modified cell comprises a binding protein, wherein the binding protein comprises: (a) a T cell receptor (TCR) ⁇ -chain variable (V ⁇ ) domain having a CDR3 amino acid sequence according to any one of SEQ ID NOS.:26, 32, 38, 44, 50, or 51, and a TCR ⁇ -chain variable (V ⁇ ) domain; (b) a V ⁇ domain having a CDR3 amino acid sequence according to any one of SEQ ID NOS.:23, 29, 35, 41, or 47, and a V ⁇ domain; or (c) a V ⁇ domain having a CDR3 amino acid sequence according to any one of SEQ ID NOS:26, 32, 38, 44, 50, or 51, and a V ⁇ domain having a CDR3 amino acid sequence according to any one of SEQ ID NOs:23, 29, 35, 41, or 47.
- TCR T cell receptor
- V ⁇ TCR ⁇ -chain variable domain having a CDR3 amino acid sequence according to any one of SEQ ID
- the encoded binding protein is capable of specifically binding to a MAGE-A1 peptide:HLA complex on a cell surface independent of CD8 or in the absence of CD8. In some embodiments, the encoded binding protein is capable of specifically binding to a KVLEYVIKV (SEQ ID NO.:123):human leukocyte antigen (HLA) complex with a Kd less than or equal to about 10 -8 M.
- Any appropriate method can be used to transfect or transduce the cells, for example, the T cells, or to administer the polynucleotides or compositions of the present methods.
- Known methods for delivering polynucleotides to host cells include, for example, use of cationic polymers, lipid-like molecules, and certain commercial products such as, for example, IN-VIVO-JET PEI.
- Other methods include ex vivo transduction, injection, electroporation, DEAE-dextran, sonication loading, liposome- mediated transfection, receptor-mediated transduction, microprojectile bombardment, transposon-mediated transfer, and the like.
- Still further methods of transfecting or transducing host cells employ vectors, described in further detail herein.
- a modified immune cell may modified to reduce or eliminate expression (e.g., by a chromosomal gene knockout as described herein) of one or more endogenous genes that encode a polypeptide involved in immune signaling or other related activities, and/or to comprise a heterologous polynucleotide as provided herein.
- exemplary gene knockouts include those that encode PD-1, LAG-3, CTLA4, TIM3, an HLA molecule, a TCR molecule, or the like.
- certain endogenously expressed immune cell proteins may be recognized as foreign by an allogeneic host receiving the modified immune cells, which may result in elimination of the modified immune cells (e.g., an HLA allele), or may downregulate the immune activity of the modified immune cells (e.g., PD-1, LAG-3, CTLA4), or may interfere with the binding activity of a heterologously expressed binding protein of the present disclosure (e.g., an endogenous TCR of a modified T cell that binds a non-MAGE-A1 antigen and may interfere with the modified immune cell binding a cell that expresses MAGE-A1 antigen), or may compete for expression with a heterologous binding protein.
- a heterologously expressed binding protein of the present disclosure e.g., an endogenous TCR of a modified T cell that binds a non-MAGE-A1 antigen and may interfere with the modified immune cell binding a cell that expresses MAGE-A1 antigen
- a modified immune cell is a donor cell (e.g., allogeneic) or an autologous cell.
- a modified immune cell of this disclosure comprises a chromosomal gene knockout of one or more of a gene that encodes PD-1, LAG-3, CTLA4, TIM3, TIGIT, Fas, an HLA component (e.g., a gene that encodes an ⁇ 1 macroglobulin, an ⁇ 2 macroglobulin, an ⁇ 3 macroglobulin, a ⁇ 1 microglobulin, or a ⁇ 2 microglobulin), or a TCR component (e.g., a gene that encodes a TCR variable region or a TCR constant region) (see, e.g., Torikai et al., Nature Sci.
- HLA component e.g., a gene that encodes an ⁇ 1 macroglobulin, an ⁇ 2 macroglobulin, an ⁇ 3 macroglobulin, a ⁇ 1 microglobulin, or a ⁇ 2 microglobulin
- TCR component e.g., a gene that encodes a TCR variable
- chromosomal gene knockout refers to a genetic alteration or introduced inhibitory agent in a host cell that prevents (e.g., reduces, delays, suppresses, or abrogates) production, by the host cell, of a functionally active endogenous polypeptide product.
- Alterations resulting in a chromosomal gene knockout can include, for example, introduced nonsense mutations (including the formation of premature stop codons), missense mutations, gene deletion, and strand breaks, as well as the heterologous expression of inhibitory nucleic acid molecules that inhibit endogenous gene expression in the host cell.
- a chromosomal gene knock-out or gene knock- in is made by chromosomal editing of a host cell. Chromosomal editing can be performed using, for example, endonucleases.
- endonucleases As used herein “endonuclease” refers to an enzyme capable of catalyzing cleavage of a phosphodiester bond within a polynucleotide chain.
- an endonuclease is capable of cleaving a targeted gene thereby inactivating or “knocking out” the targeted gene.
- An endonuclease may be a naturally occurring, recombinant, genetically modified, or fusion endonuclease.
- the nucleic acid strand breaks caused by the endonuclease are commonly repaired through the distinct mechanisms of homologous recombination or non-homologous end joining (NHEJ).
- NHEJ non-homologous end joining
- a donor nucleic acid molecule may be used for a donor gene “knock-in”, for target gene “knock- out”, and optionally to inactivate a target gene through a donor gene knock in or target gene knock out event.
- NHEJ is an error-prone repair process that often results in changes to the DNA sequence at the site of the cleavage, e.g., a substitution, deletion, or addition of at least one nucleotide. NHEJ may be used to “knock-out” a target gene.
- endonucleases include zinc finger nucleases, TALE-nucleases, CRISPR- Cas nucleases, meganucleases, and megaTALs.
- a “zinc finger nuclease” refers to a fusion protein comprising a zinc finger DNA-binding domain fused to a non-specific DNA cleavage domain, such as a Fokl endonuclease.
- Each zinc finger motif of about 30 amino acids binds to about 3 base pairs of DNA, and amino acids at certain residues can be changed to alter triplet sequence specificity (see, e.g., Desjarlais et al., Proc. Natl. Acad. Sci. 90:2256-2260, 1993; Wolfe et al., J. Mol. Biol.285:1917-1934, 1999).
- ZFNs mediate genome editing by catalyzing the formation of a site-specific DNA double strand break (DSB) in the genome, and targeted integration of a transgene comprising flanking sequences homologous to the genome at the site of DSB is facilitated by homology directed repair.
- DSB site-specific DNA double strand break
- a DSB generated by a ZFN can result in knock out of target gene via repair by non-homologous end joining (NHEJ), which is an error-prone cellular repair pathway that results in the insertion or deletion of nucleotides at the cleavage site.
- NHEJ non-homologous end joining
- a gene knockout comprises an insertion, a deletion, a mutation, or a combination thereof, made using a ZFN molecule.
- TALEN transcription activator-like effector nuclease
- a “TALE DNA binding domain” or “TALE” is composed of one or more TALE repeat domains/units, each generally having a highly conserved 33-35 amino acid sequence with divergent 12th and 13th amino acids. The TALE repeat domains are involved in binding of the TALE to a target DNA sequence.
- the divergent amino acid residues correlate with specific nucleotide recognition.
- the natural (canonical) code for DNA recognition of these TALEs has been determined such that an HD (histine-aspartic acid) sequence at positions 12 and 13 of the TALE leads to the TALE binding to cytosine (C), NG (asparagine-glycine) binds to a T nucleotide, NI (asparagine-isoleucine) to A, NN (asparagine-asparagine) binds to a G or A nucleotide, and NG (asparagine-glycine) binds to a T nucleotide.
- C cytosine
- NG asparagine-glycine
- Non-canonical (atypical) RVDs are also known (see, e.g., U.S. Patent Publication No. US 2011/0301073, which atypical RVDs are incorporated by reference herein in their entirety).
- TALENs can be used to direct site-specific double-strand breaks (DSB) in the genome of T cells.
- Non- homologous end joining (NHEJ) ligates DNA from both sides of a double-strand break in which there is little or no sequence overlap for annealing, thereby introducing errors that knock out gene expression.
- homology directed repair can introduce a transgene at the site of DSB providing homologous flanking sequences are present in the transgene.
- a gene knockout comprises an insertion, a deletion, a mutation or a combination thereof, and made using a TALEN molecule.
- CRISPR/Cas CRISPR RNA
- a “clustered regularly interspaced short palindromic repeats/Cas” (CRISPR/Cas) nuclease system refers to a system that employs a CRISPR RNA (crRNA)-guided Cas nuclease to recognize target sites within a genome (known as protospacers) via base-pairing complementarity and then to cleave the DNA if a short, conserved protospacer associated motif (PAM) immediately follows 3’ of the complementary target sequence.
- crRNA CRISPR RNA
- protospacers conserved protospacer associated motif
- CRISPR/Cas systems are classified into three types (i.e., type I, type II, and type III) based on the sequence and structure of the Cas nucleases.
- the crRNA-guided surveillance complexes in types I and III need multiple Cas subunits.
- Type II system the most studied, comprises at least three components: an RNA-guided Cas9 nuclease, a crRNA, and a trans-acting crRNA (tracrRNA).
- the tracrRNA comprises a duplex forming region.
- a crRNA and a tracrRNA form a duplex that is capable of interacting with a Cas9 nuclease and guiding the Cas9/crRNA:tracrRNA complex to a specific site on the target DNA via Watson-Crick base-pairing between the spacer on the crRNA and the protospacer on the target DNA upstream from a PAM.
- Cas9 nuclease cleaves a double-stranded break within a region defined by the crRNA spacer. Repair by NHEJ results in insertions and/or deletions which disrupt expression of the targeted locus.
- a transgene with homologous flanking sequences can be introduced at the site of DSB via homology directed repair.
- the crRNA and tracrRNA can be engineered into a single guide RNA (sgRNA or gRNA) (see, e.g., Jinek et al., Science 337:816-21, 2012). Further, the region of the guide RNA complementary to the target site can be altered or programed to target a desired sequence (Xie et al., PLOS One 9:e100448, 2014; U.S. Pat. Appl. Pub. No. US 2014/0068797, U.S. Pat. Appl. Pub. No. US 2014/0186843; U.S. Pat. No. 8,697,359, and PCT Publication No. WO 2015/071474; each of which is incorporated by reference).
- sgRNA or gRNA single guide RNA
- a gene knockout comprises an insertion, a deletion, a mutation or a combination thereof, and made using a CRISPR/Cas nuclease system.
- Exemplary gRNA sequences and methods of using the same to knock out endogenous genes that encode immune cell proteins include those described in Ren et al., Clin. Cancer Res.23(9):2255-2266 (2017), the gRNAs, Cas9 DNAs, vectors, and gene knockout techniques of which are hereby incorporated by reference in their entirety.
- Alternative Cas nucleases may be used, including but not limited to, Cas 12, Cas 13, and Cas 14 nucleases, and variants thereof.
- Cas nucleases disclosed in WO 2019/178427 which is hereby incorporated by reference in its entirety (including the Cas nucleases, CRISPR-Cas systems, and related methods disclosed therein), may be utilized.
- LAGLIDADG SEQ ID NO: 155
- GIY-YIG SEQ ID NO:156
- HNH HNH
- His-Cys box PD-(D/E)XK (SEQ ID NO:157).
- Exemplary meganucleases include I-SceI, I- CeuI, PI-PspI, PI-Sce, I-SceIV, I-CsmI, I-PanI, I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI, I-TevII and I-TevIII, whose recognition sequences are known (see, e.g., U.S.
- Patent Nos.5,420,032 and 6,833,252 Belfort et al., Nucleic Acids Res.25:3379-3388, 1997; Dujon et al., Gene 82:115-118, 1989; Perler et al., Nucleic Acids Res.22:1125-1127, 1994; Jasin, Trends Genet.12:224-228, 1996; Gimble et al., J. Mol. Biol.263:163-180, 1996; Argast et al., J. Mol. Biol.280:345-353, 1998).
- naturally occurring meganucleases may be used to promote site-specific genome modification of a target selected from PD-1, LAG3, TIM3, CTLA4, TIGIT, an HLA-encoding gene, or a TCR component-encoding gene.
- a target selected from PD-1, LAG3, TIM3, CTLA4, TIGIT, an HLA-encoding gene, or a TCR component-encoding gene.
- an engineered meganuclease having a novel binding specificity for a target gene is used for site-specific genome modification (see, e.g., Porteus et al., Nat. Biotechnol.23:967-73, 2005; Sussman et al., J. Mol.
- a chromosomal gene knockout is generated using a homing endonuclease that has been modified with modular DNA binding domains of TALENs to make a fusion protein known as a megaTAL.
- MegaTALs can be utilized to not only knock-out one or more target genes, but to also introduce (knock in) heterologous or exogenous polynucleotides when used in combination with an exogenous donor template encoding a polypeptide of interest.
- a chromosomal gene knockout comprises an inhibitory nucleic acid molecule that is introduced into a host cell (e.g., an immune cell) comprising a heterologous polynucleotide encoding an antigen-specific receptor that specifically binds to a tumor associated antigen, wherein the inhibitory nucleic acid molecule encodes a target-specific inhibitor and wherein the encoded target-specific inhibitor inhibits endogenous gene expression (i.e., of PD-1, TIM3, LAG3, CTLA4, TIGIT, an HLA component, or a TCR component, or any combination thereof) in the host immune cell.
- a host cell e.g., an immune cell
- a heterologous polynucleotide encoding an antigen-specific receptor that specifically binds to a tumor associated antigen
- the inhibitory nucleic acid molecule encodes a target-specific inhibitor and wherein the encoded target-specific inhibitor inhibits endogenous gene expression (i.e., of PD-1,
- a chromosomal gene knockout can be confirmed directly by DNA sequencing of the host immune cell following use of the knockout procedure or agent. Chromosomal gene knockouts can also be inferred from the absence of gene expression (e.g., the absence of an mRNA or polypeptide product encoded by the gene) following the knockout. [0138] Any of the foregoing gene-editing techniques can be used to introduce a polynucleotide of the present disclosure (e.g., encoding a binding protein and/or a CD8 co-receptor polypeptide) into a host cell genome.
- a polynucleotide of the present disclosure e.g., encoding a binding protein and/or a CD8 co-receptor polypeptide
- a heterologous polynucleotide is introduced into a locus encoding an endogenous TCR component, HLA component, PD-1, LAG-3, Fas, CTLA4, TIM3, or TIGIT, or a safe harbor locus such as Rosa26, AAVS1, CCR5, or the like.
- a heterologous polynucleotide encoding a binding protein and/or encoding a CD8 co-receptor polypeptide is introduced into a host cell TRAC locus.
- a chromosomal knockout of a host cell TRBC locus is introduced.
- a host cell e.g., modified immune cell
- a host cell comprises, in an endogenous TRAC locus, a heterologous polynucleotide encoding a binding protein of the present disclosure, a heterologous polynucleotide encoding a CD8 co-receptor of the present disclosure, or both.
- the host cell comprises a chromosomal knockout of an endogenous TRBC locus.
- a modified cell is a CD4 + T cell that comprises a heterologous polynucleotide encoding a binding protein of the present disclosure.
- a heterologously encoded TCR of a modified CD4 + T cell is a high- affinity TCR.
- a heterologously encoded TCR of a modified CD4 + T cell is capable of specifically binding to a peptide:antigen HLA complex on a cell surface independent of CD8 or in the absence of CD8.
- a modified CD4 + T and/or modified CD8 + T cell further comprises a heterologous polynucleotide encoding at least an extracellular portion of a CD8 co-receptor.
- co-expression of a MAGE- A1-specific binding protein of the present disclosure and at least an extracellular portion of a CD8 co- receptor by a CD4 + T cell can confer a new or improved functionality (e.g., improved cytokine release, CTL response when bound to a MAGE- A1:HLA-expressing target cell) upon the CD4 + T cell.
- An amino acid sequence of a CD8 co-receptor ⁇ -chain is provided in SEQ ID NO:143.
- Amino acid sequences of five different isoforms of CD8 co-receptor ⁇ -chain are provided in SEQ ID NOS:144-148, respectively.
- a modified CD4 + T and/or modified CD8 + T cell of this disclosure further comprises a heterologous polynucleotide encoding a full-length CD8 co-receptor receptor ⁇ -chain, a heterologous polynucleotide encoding a full-length CD8 co-receptor ⁇ -chain, or both.
- a CD8 co-receptor ⁇ -chain comprises or consists of the amino acid sequence set forth in SEQ ID NO.:143 and a CD8 co-receptor ⁇ -chain comprises or consists of the amino acid sequence set forth in any one of SEQ ID NOs.:144-148, preferably SEQ ID NO.:144.
- a CD8 co-receptor-encoding polynucleotide may, in some embodiments, be codon-optimized for expression in a host cell.
- a polynucleotide is provided that encodes (i) a TCR of the present disclosure and one or both of (ii) a CD8 co-receptor ⁇ -chain and (iii) a CD8 co-receptor ⁇ -chain. It will be appreciated that polynucleotides encoding these encoded polypeptides can be provided in any arrangement or order within a single polynucleotide, or can be present as separate nucleic acid molecules.
- a polynucleotide comprises, in a 5’ to 3’ direction: (i) a polynucleotide encoding a CD8 co-receptor ⁇ -chain; (ii) a polynucleotide encoding a CD8 co-receptor ⁇ -chain; and (iii) a polynucleotide encoding a TCR ⁇ -chain, and (iv) a polynucleotide encoding a TCR ⁇ -chain.
- a polynucleotide encoding a self- cleaving peptide is disposed between the polynucleotide of (i) and the polynucleotide of (ii), between the polynucleotide of (ii) and the polynucleotide of (iii), and/or between the polynucleotide of (iii) and the polynucleotide of (iv).
- a TCR-encoding polynucleotide used to modify a CD4 + T cell comprises a nucleotide sequence according to a naturally occurring CD8 + T cell, or is a codon-optimized or otherwise engineered variant of such a naturally occurring polynucleotide.
- compositions e.g., pharmaceutical compositions
- a modified cell or population thereof as disclosed herein and a pharmaceutically acceptable carrier, diluent, or excipient.
- Suitable excipients include water, saline, dextrose, glycerol, or the like and combinations thereof.
- compositions comprising fusion proteins or host cells as disclosed herein further comprise a suitable infusion media.
- Suitable infusion media can be any isotonic medium formulation, typically normal saline, Normosol R (Abbott) or Plasma-Lyte A (Baxter), 5% dextrose in water, Ringer’s lactate can be utilized.
- An infusion medium can be supplemented with human serum albumin or other human serum components.
- Compositions described herein may be presented in unit-dose or multi-dose containers, such as sealed ampoules or vials. Such containers may be frozen to preserve the stability of the formulation until infusion into the patient.
- An “effective amount” of a composition refers to an amount sufficient, at dosages and for periods of time needed, to achieve the desired clinical results or beneficial treatment, as described herein. An effective amount may be delivered in one or more administrations.
- compositions may be administered in a manner appropriate to the disease or condition to be treated (or prevented) as determined by persons skilled in the medical art.
- an appropriate dose and a suitable duration and frequency of administration of the compositions will be determined by such factors as the health condition of the patient, size of the patient (i.e., weight, mass, or body area), the type and severity of the patient’s condition, the particular form of the active ingredient, and the method of administration.
- an appropriate dose and treatment regimen provide the composition(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit (such as described herein, including an improved clinical outcome, such as more frequent complete or partial remissions, or longer disease-free and/or overall survival, or a lessening of symptom severity).
- a dose should be sufficient to prevent, delay the onset of, or diminish the severity of a disease associated with disease or disorder.
- a therapeutically effective dose is an amount of host cells (expressing a binding protein or high affinity recombinant TCR specific for a human MAGE-A1 antigen peptide) used in adoptive transfer that is capable of producing a clinically desirable result (e.g., a sufficient amount to induce or enhance a specific T cell immune response against cells overexpressing MAGE-A1 (e.g., a cytotoxic T cell response) in a statistically significant manner) in a treated human or non-human mammal.
- a clinically desirable result e.g., a sufficient amount to induce or enhance a specific T cell immune response against cells overexpressing MAGE-A1 (e.g., a cytotoxic T cell response) in a statistically significant manner
- the dosage for any one patient depends upon many factors, including the patient’s size, weight, body surface area, age, the particular therapy to be administered, sex, time and route of administration, general health, and other drugs being administered concurrently. Doses will vary, but a preferred dose for administration of a host cell comprising a binding protein, polynucleotide, or recombinant expression vector as described herein is about 10 7 cells/m 2 , about 5 x 10 7 cells/m 2 , about 10 8 cells/m 2 , about 5 x 10 8 cells/m 2 , about 10 9 cells/m 2 , about 5 x 10 9 cells/m 2 , about 10 10 cells/m 2 , about 5 x 10 10 cells/m 2 , or about 10 11 cells/m 2 .
- a unit dose comprises a modified cell as described herein at a dose of about 10 7 cells/m 2 to about 10 11 cells/m 2 .
- a unit dose comprises (i) a composition comprising at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% engineered CD4 + T cells, combined with (ii) a composition comprising at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% engineered CD8 + T cells, in about a 1:1 ratio.
- a unit dose contains a reduced amount or substantially no na ⁇ ve T cells (i.e., has less than about 50%, less than about 40%, less than about 30%, less than about 20%, less than about 10%, less than about 5%, or less than about 1% the population of na ⁇ ve T cells present in a unit dose as compared to a patient sample having a comparable number of PBMCs).
- a unit dose comprises (i) a composition comprising at least about 50% engineered CD4 + T cells, combined with (ii) a composition comprising at least about 50% engineered CD8 + T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
- a unit dose comprises (i) a composition comprising at least about 60% modified CD4 + T cells, combined with (ii) a composition comprising at least about 60% modified CD8 + T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
- a unit dose comprises (i) a composition comprising at least about 70% modified CD4 + T cells, combined with (ii) a composition comprising at least about 70% modified CD8 + T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
- a unit dose comprises (i) a composition comprising at least about 80% modified CD4 + T cells, combined with (ii) a composition comprising at least about 80% modified CD8 + T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
- a unit dose comprises (i) a composition comprising at least about 85% modified CD4 + T cells, combined with (ii) a composition comprising at least about 85% modified CD8 + T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
- a unit dose comprises (i) a composition comprising at least about 90% modified CD4 + T cells, combined with (ii) a composition comprising at least about 90% modified CD8 + T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
- a unit dose comprises equal, or approximately equal numbers, of modified CD45RA- CD3 + CD8 + and modified CD45RA- CD3 + CD4 + TM cells.
- a population comprises engineered CD4+ T cells in combination with CD8+ T cells.
- the CD8+ T cells comprise CD62L+ T cells.
- the CD4+ T cells and the CD8+ T cells are present in the population at a ratio of about 1:1.
- the population of immune cells comprises NK cells, NK-T cells, macrophages, and/or microglia.
- a population comprises (i) at least about 50% engineered CD4 + T cells, combined with (ii) at least about 50% engineered CD8 + T cells, in about a 1:1 ratio, and optionally comprises a reduced amount or substantially no na ⁇ ve T cells.
- a population comprises (i) at least about 60% modified CD4 + T cells, combined with (ii) at least about 60% modified CD8 + T cells, in about a 1:1 ratio, wherein the population optionally contains a reduced amount or substantially no na ⁇ ve T cells.
- a population comprises (i) at least about 70% modified CD4 + T cells, combined with (ii) at least about 70% modified CD8 + T cells, in about a 1:1 ratio, wherein the population optionally contains a reduced amount or substantially no na ⁇ ve T cells.
- a population comprises (i) at least about 80% modified CD4 + T cells, combined with (ii) at least about 80% modified CD8 + T cells, in about a 1:1 ratio, wherein the population optionally contains a reduced amount or substantially no na ⁇ ve T cells. In some embodiments, a population comprises (i) at least about 85% modified CD4 + T cells, combined with (ii) at least about 85% modified CD8 + T cells, in about a 1:1 ratio, wherein the population optionally contains a reduced amount or substantially no na ⁇ ve T cells.
- a population comprises (i) at least about 90% modified CD4 + T cells, combined with (ii) at least about 90% modified CD8 + T cells, in about a 1:1 ratio, wherein the population optionally contains a reduced amount or substantially no na ⁇ ve T cells.
- Suitable non-toxic parenterally acceptable diluents or solvents include water, Ringer’s solution, isotonic salt solution, 1,3-butanediol, ethanol, propylene glycol or polythethylene glycols in mixtures with water.
- Aqueous solutions or suspensions may further comprise one or more buffering agents, such as sodium acetate, sodium citrate, sodium borate or sodium tartrate.
- buffering agents such as sodium acetate, sodium citrate, sodium borate or sodium tartrate.
- any material used in preparing any dosage unit formulation should be pharmaceutically pure and substantially non-toxic in the amounts employed.
- the active compounds may be incorporated into sustained-release preparation and formulations.
- Dosage unit form refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit may contain a predetermined quantity of modified cells or active compound calculated to produce the desired effect in association with an appropriate pharmaceutical carrier.
- administration of a composition refers to delivering the same to a subject, regardless of the route or mode of delivery. Administration may be continuous or intermittent. Administration may be for treating a subject already confirmed as having a recognized condition, disease or disease state, or for treating a subject susceptible to or at risk of developing such a condition, disease or disease state.
- Co-administration with an adjunctive therapy may include simultaneous and/or sequential delivery of multiple agents in any order and on any dosing schedule (e.g., modified cells with one or more cytokines; immunosuppressive therapy such as calcineurin inhibitors, corticosteroids, microtubule inhibitors, low dose of a mycophenolic acid prodrug, HDAC inhibitors, DNA hypomethylation agents, or any combination thereof).
- a plurality of doses of a modified cell or population or composition described herein is administered to the subject, which may be administered at intervals between administrations of about two to about four weeks.
- the instant disclosure is directed to methods for treating a hyperproliferative disorder or a condition characterized by MAGE-A1 expression (e.g., aberrant MAGE-A1 expression) by administering to human subject in need thereof a modified cell, composition, or unit dose as disclosed herein (or any combination thereof).
- a hyperproliferative disorder or a condition characterized by MAGE-A1 expression e.g., aberrant MAGE-A1 expression
- a condition associated with MAGE-A1 expression includes any disorder or condition in which underactivity, over-activity, or improper activity of a MAGE-A1 cellular or molecular event is present and may be the result of unusually high (with statistical significance) levels of MAGE-A1 expression or inappropriate (i.e., not occurring in healthy cells of the given cell type) expression in afflicted cells (e.g., myeloma cells), relative to normal cells.
- afflicted cells e.g., myeloma cells
- a subject having such a disorder or condition would benefit from treatment with a composition or method of the presently described embodiments.
- Some conditions associated with aberrant MAGE-A1 expression thus may include acute as well as chronic disorders and diseases, such as those pathological conditions that predispose the subject to a particular disorder.
- MAGE-A1 in a disease setting can be assessed by, for example, sequencing a MAGE-A1 gene locus in a diseased cell or cells, by immunohistochemistry (IHC), or using qPCR or RT-PCR.
- diseased cells encode or express a MAGE-A1 comprising the amino acid sequence set forth in SEQ ID NO.:123, optionally comprised in SEQ ID NO.:122.
- conditions associated with MAGE-A1 expression include proliferative disorders or hyperproliferative disorders, which refer to states of activated and/or proliferating cells (which may also be transcriptionally overactive) in a subject including tumors, neoplasms, cancer, malignancy, etc.
- the hyperproliferative disorder may also include an aberration or dysregulation of cell death processes, whether by necrosis or apoptosis. Such aberration of cell death processes may be associated with a variety of conditions, including cancer (including primary, secondary malignancies as well as metastasis), or other conditions.
- the presence of a hyperproliferative disorder or malignant condition in a subject refers to the presence of dysplastic, cancerous and/or transformed cells in the subject, including, for example neoplastic, tumor, non-contact inhibited or oncogenically transformed cells, or the like (e.g., solid cancers; hematologic cancers including lymphomas and leukemias, such as acute myeloid leukemia, chronic myeloid leukemia, etc.), which are known in the art and for which criteria for diagnosis and classification are established (e.g., Hanahan and Weinberg, Cell 144:646, 2011; Hanahan and Weinberg, Cell 100:57, 2000; Cavallo et al., Canc. Immunol. Immunother.
- dysplastic, cancerous and/or transformed cells in the subject including, for example neoplastic, tumor, non-contact inhibited or oncogenically transformed cells, or the like (e.g., solid cancers; hematologic cancers including lymphomas and leukemias
- cancer cells may be cells of acute myeloid leukemia, B-cell lymphoblastic leukemia, T- cell lymphoblastic leukemia, or myeloma, including cancer stem cells that are capable of initiating and serially transplanting any of these types of cancer (see, e.g., Park et al., Molec. Therap.17:219, 2009).
- a hyperproliferative disorder such as a hematological malignancy or a solid cancer
- the method comprises administering to a human subject in need thereof a modified cell, composition, or unit dose of the present disclosure.
- hematological malignancies include acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), chronic myelogenous leukemia (CML), chronic eosinophilic leukemia (CEL), myelodysplastic syndrome (MDS), non-Hodgkin’s lymphoma (NHL), or multiple myeloma (MM).
- a hyperproliferative disorder such as a solid cancer is selected from non-small cell lung cancer (NSCLC), triple negative breast cancer (TNBC), ovarian cancer, malignant melanoma, colon cancer, colorectal adenocarcinoma, colorectal cancer, biliary cancer, bladder cancer, bone and soft tissue carcinoma, brain tumor, breast cancer, cervical cancer, desmoid tumor, embryonal cancer, endometrial cancer, esophageal cancer, gastric cancer, gastric adenocarcinoma, glioblastoma multiforme, gynecological tumor, head and neck squamous cell carcinoma, hepatic cancer, lung cancer, mesothelioma, osteosarcoma, pancreatic cancer, pancreatic ductal adenocarcinoma, primary astrocytic tumor, primary thyroid cancer, prostate cancer, renal cancer, renal cell carcinoma, rhabdomyosar
- treat and “treatment,” refer to medical management of a disease, disorder, or condition of a subject (i.e., patient, host, who may be a human or non-human animal) (see, e.g., Stedman’s Medical Dictionary).
- an appropriate dose and treatment regimen provide one or more of a binding protein or high affinity recombinant TCR specific for human MAGE-A1 or a host cell expressing the same, and optionally an adjunctive or combination therapy (e.g., a cytokine such as IL-2, IL-15, IL-21, or any combination thereof; a PD-1/PD-L1 axis inhibitor), in an amount sufficient to provide therapeutic or prophylactic benefit.
- a cytokine such as IL-2, IL-15, IL-21, or any combination thereof; a PD-1/PD-L1 axis inhibitor
- Therapeutic or prophylactic benefit resulting from therapeutic treatment or prophylactic or preventative methods include, for example an improved clinical outcome, wherein the object is to prevent or retard or otherwise reduce (e.g., decrease in a statistically significant manner relative to an untreated control) an undesired physiological change or disorder, or to prevent, retard or otherwise reduce the expansion or severity of such a disease or disorder.
- Beneficial or desired clinical results from treating a subject include abatement, lessening, or alleviation of symptoms that result from or are associated the disease or disorder to be treated; decreased occurrence of symptoms; improved quality of life; longer disease-free status (i.e., decreasing the likelihood or the propensity that a subject will present symptoms on the basis of which a diagnosis of a disease is made); diminishment of extent of disease; stabilized (i.e., not worsening) state of disease; delay or slowing of disease progression; amelioration or palliation of the disease state; and remission (whether partial or total), whether detectable or undetectable; overall survival; or prolonging survival when compared to expected survival if a subject were not receiving treatment.
- treatment results in a decreased rate of growth and/or decreased spread of and/or decreased rate of spread of cancer cells, a decreased number of cancer cells, a decreased size or density of a tumor, a decreased number of tumors, remission, killing of cancer cells, or any combination thereof.
- treatment results in a partial response (also referred-to as partial remission).
- a partial response comprises a decrease in the size of a tumor, or in the extent of cancer in the body, in response to treatment.
- treatment results in a complete response (also referred-to as complete remission).
- a complete response comprises he disappearance of all signs of cancer in response to treatment.
- treatment results in a period of progression-free survival and/or in results an increased duration of progression-free survival (also referred-to as PFS).
- PFS comprises a length of time during and after the treatment of a disease, such as cancer, that a patient lives with the disease but it does not get worse.
- Subjects in need of the methods and compositions described herein include those who already have the disease or disorder, as well as subjects prone to have or at risk of developing the disease or disorder.
- Subjects in need of prophylactic treatment include subjects in whom the disease, condition, or disorder is to be prevented (i.e., decreasing the likelihood of occurrence or recurrence of the disease or disorder).
- compositions and preparations comprising the compositions and methods described herein can be evaluated by design and execution of in vitro assays, preclinical studies, and clinical studies in subjects to whom administration of the compositions is intended to benefit, as described in the examples.
- a subject receiving therapy according to the present disclosure is negative for or has been identified as negative for expression of HLA B*49:01.
- a subject receiving therapy according to the present disclosure is positive for or has been identified as positive for expression of HLA- A*02:01.
- the methods comprise, prior to administering a population of modified immune cells, identifying the subject as being negative for expression of HLA-B*49:01 and/or as being positive for expression of HLA-A*02:01.
- the present disclosure provides a method of treating a cancer or disease or disorder that is associated with MAGE-A1 expression in a subject, comprising administering to the subject a population of modified immune cells comprising a binding protein described herein wherein the subject is negative for or has been identified as negative for expression of HLA B*49:01.
- HLA typing This genetic determination of the HLA expression is referred to herein as “HLA typing” and can determined though molecular approaches in a clinical laboratory licensed for HLA typing.
- HLA typing is performed using PCR amplification followed by high throughput NGS and subsequent HLA determination.
- the HLA haplotype is determined at the major HLA loci (e.g., HLA-A, HLA-B, HLA-C, etc.).
- HLA typing This genetic determination of the HLA expression is referred to herein as “HLA typing” and can determined though molecular approaches in a clinical laboratory licensed for HLA typing.
- HLA typing is performed using PCR amplification followed by high throughput NGS and subsequent HLA determination.
- the HLA haplotype is determined at the major HLA loci (e.g., HLA-A, HLA-B, HLA-C, etc.).
- HLA typing can be performed using any known method, including, for example, protein or nucleic acid testing.
- nucleic acid testing include sequence-based typing (SBT) and use of sequence-specific oligonucleotide probes (SSOP) or sequence-specific primers (SSP).
- SBT sequence-based typing
- SSP sequence-specific primers
- HLA typing is performed using PCR amplification followed by high throughput Next Generation Sequencing (NGS) and subsequent HLA determination.
- NGS Next Generation Sequencing
- sequence typing is performed using a system available through Scisco Genetics (sciscogenetics.com/pages/technology.html, the contents of which is incorporated herein by reference in its entirety).
- Other methods for HLA typing include, e.g., those disclosed in Mayor et al.
- a subject receiving cell therapy (or a combination therapy comprising cell therapy) according to the present disclosure has metastatic disease, and/or disease that is confirmed by archival, initial, or subsequent biopsy or other pathologic material.
- a subject in certain embodiments, a subject must meet the American Society of Clinical Oncology – College of American Pathologists (ASCO-CAP) definition of negative estrogen, progesterone, and HER2 receptor expression.
- ASCO-CAP American Society of Clinical Oncology – College of American Pathologists
- a subject receiving cell therapy (or a combination therapy comprising cell therapy) according to the present disclosure has measurable disease, for example, defined as at least one target lesion that can be measured in at least one dimension (longest diameter to be recorded) as ⁇ 10 mm, unless lymph node, in which case short axis may be ⁇ 15 mm.
- baseline imaging for example, diagnostic CT chest/abdomen/pelvis and imaging of the affected extremity as appropriate
- brain imaging MRI or CT scan
- MRI can be substituted for CT in subjects unable to have CT contrast.
- a subject receiving cell therapy (or a combination therapy comprising cell therapy) according to the present disclosure has received or is receiving treatment with standard-of-care therapy approved by an appropriate regulatory agency (e.g., FDA, EMA, or the like).
- an appropriate regulatory agency e.g., FDA, EMA, or the like.
- subjects with NSCLC who have actionable somatic mutations or alterations in EGFR, ROS1 and ALK with approved drug therapy options receive cell therapy or combination therapy only after treatment with targeted therapies for those mutations have been offered or received.
- subjects with urothelial carcinoma receive cell therapy or combination therapy according to the present disclosure after prior treatment with enfortumab vedotin-ejfv has been offered or received.
- a subject receiving cell therapy has received or is receiving therapy comprising a CPI (immune checkpoint inhibitor, discussed further herein), a PD-1 inhibitor, a PD-L1 inhibitor, and/or a PD-1/PD-L1 axis inhibitor, as described herein.
- a subject has been offered or been previously treated with at least one dose of a PD-L1 axis inhibitor (e.g., PD-1-inhibiting or PD-L1-inhibiting monoclonal antibody such as pembrolizumab, nivolumab, avelumab, atezolizumab, durvalumab, or any combination thereof).
- a PD-L1 axis inhibitor e.g., PD-1-inhibiting or PD-L1-inhibiting monoclonal antibody such as pembrolizumab, nivolumab, avelumab, atezolizumab, durvalumab, or any combination thereof.
- a subject is receiving or has received CPI, PD-1 inhibitor, PD-L1 inhibitor, and/or a PD-1/PD-L1 axis inhibitor therapy in the neoadjuvant or adjuvant setting.
- a first dose of a CPI is administered after a population of modified immune cells is administered, such as within 24 to 72 hours after the population of modified immune cells is administered.
- the CPI or the PD-1/PD-L1 axis inhibitor is selected from atezolizumab, nivolumab, durvalumab, and pembrolizumab.
- the CPI or the PD-1/PD-L1 axis inhibitor comprises atezolizumab.
- the atezolizumab is administered to the subject every three weeks at 1200 mg per administration.
- the method comprises administering a PD-L1 inhibitor and the PD-L1 inhibitor is avelumab.
- a cancer treatable according to the disclosed methods is or comprises a solid tumor.
- a cancer treatable according to the disclosed methods is or comprises triple negative breast cancer (TNBC), wherein, optionally, the TNBC is metastatic TNBC.
- TNBC triple negative breast cancer
- a cancer treatable according to the disclosed methods is or comprises non-small cell lung cancer (NSCLC), wherein, optionally, the NSCLC is metastatic NSCLC.
- NSCLC non-small cell lung cancer
- a cancer treatable according to the disclosed methods is or comprises urothelial cancer.
- the urothelial cancer is a metastatic urothelial cancer or an advanced urothelial cancer.
- subjects have received 1 or more prior systemic regimens for metastatic TNBC or NSCLC.
- a subject receiving cell therapy has an ECOG (Eastern Cooperative Oncology Group) Performance Status of 0, 1, or 2.
- ECOG Stern Cooperative Oncology Group
- a subject receiving cell therapy has not received systemic therapy (e.g., immunotherapy (for example, T-cell infusions, immunomodulatory agents, interleukins, vaccines), small molecule or chemotherapy cancer treatment, other investigational agents) for three or more weeks prior to the cell therapy or combination therapy.
- systemic therapy e.g., immunotherapy (for example, T-cell infusions, immunomodulatory agents, interleukins, vaccines), small molecule or chemotherapy cancer treatment, other investigational agents
- a subject receiving cell therapy may be receiving or has received biophosphonates but has not received concurrent treatment with a RANK-ligand inhibitor (e.g., denosumab) for eight or more weeks prior to the cell therapy or combination therapy.
- a subject receiving cell therapy (or a combination therapy comprising cell therapy) according to the present disclosure is lymphodepeleted or has undergone or receives a lymphodepletion procedure. Lymphodepletion prior to administration of cell therapy can reduce tumor burden, minimize risk of tumor lysis syndrome, and induce lymphopenia to improve persistence of transferred cells.
- lymphodepleted refers to an, optionally artificially induced, condition or state wherein a subject has a reduced amount of lymphocytes present in blood and/or in bone marrow, as compared to a normal or healthy state of the subject.
- a lymphodepleted subject has lymphopenia (also called lymphocytopenia).
- a lymphodepleted subject has an amount of lymphocytes in blood and/or in bone marrow that is reduced by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, or more, as compared to the subject when in a normal healthy condition, and/or as compared to a reference subject in a normal healthy condition, and/or as compared to the subject prior to receiving lymphodepleting therapy.
- lymphodepleting chemotherapy comprising cyclophosphamide, fludarabine, bendamustine, or any combination thereof; anti- thymocyte globulin; or any combination thereof.
- Lymphodepleting chemotherapy can, in some embodiments, be administered intravenously.
- lymphodepleting chemotherapy comprises cyclophosphamide, fludarabine, or a combination thereof, wherein, optionally, the lymphodepleting chemotherapy comprises 300 mg/m 2 cyclophosphamide and/or 30 mg/m 2 fludarabine.
- a method further comprises providing lymphodepletion to the subject, wherein, optionally, the lymphodepletion is provided prior to administering a population of modified immune cells, wherein, further optionally, the lymphodepletion is provided 4 days, 3 days, 2 days, and/or 1 day prior to administering a population of modified immune cells.
- a modified cell is capable of promoting an antigen-specific T cell response against a MAGE-A1 in a class I HLA-restricted manner.
- a class I HLA-restricted response is transporter-associated with antigen processing (TAP) independent.
- an antigen-specific T cell response promoted by a modified cell administered according to the presently disclosed methods comprises at least one of a CD4+ helper T lymphocyte (Th) response and a CD8+ cytotoxic T lymphocyte (CTL) response.
- a CTL response elicited according to the instantly disclosed methods is directed against a cell having aberrant MAGE-A1 expression (e.g., a MAGE-A1+ tumor cell).
- the level of a CTL immune response may be determined by any one of numerous immunological methods described herein and routinely practiced in the art.
- the level of a CTL immune response may be determined prior to and following administration of any one of the herein described MAGE-A1-specific binding proteins expressed by, for example, a T cell.
- Cytotoxicity assays for determining CTL activity may be performed using any one of several techniques and methods routinely practiced in the art (see, e.g., Henkart et al., “Cytotoxic T-Lymphocytes” in Fundamental Immunology, Paul (ed.) (2003 Lippincott Williams & Wilkins, Philadelphia, PA), pages 1127-50, and references cited therein).
- Antigen-specific T cell responses are typically determined by comparisons of observed T cell responses according to any of the herein described T cell functional parameters (e.g., proliferation, cytokine release, CTL activity, altered cell surface marker phenotype, etc.) that may be made between T cells that are exposed to a cognate antigen in an appropriate context (e.g., the antigen used to prime or activate the T cells, when presented by immunocompatible antigen-presenting cells) and T cells from the same source population that are exposed instead to a structurally distinct or irrelevant control antigen.
- a cognate antigen e.g., the antigen used to prime or activate the T cells, when presented by immunocompatible antigen-presenting cells
- a response to the cognate antigen that is greater, with statistical significance, than the response to the control antigen signifies antigen- specificity.
- a biological sample may be obtained from a subject for determining the presence and level of an immune response to a MAGE-A1-derived antigen peptide as described herein.
- a “biological sample” as used herein may be a blood sample (from which serum or plasma may be prepared), biopsy specimen, body fluids (e.g., lung lavage, ascites, mucosal washings, synovial fluid), bone marrow, lymph nodes, tissue explant, organ culture, or any other tissue or cell preparation from the subject or a biological source.
- Biological samples may also be obtained from the subject prior to receiving any immunogenic composition, which biological sample is useful as a control for establishing baseline (i.e., pre-immunization) data.
- Modified cells of this disclosure are useful, in certain embodiments, in adoptive cell therapies.
- a modified cell is modified (e.g., transduced with a recombinant expression vector or polynucleotide of the present disclosure) ex vivo, and then administered to a subject in need thereof.
- modified cell is an allogeneic cell, a syngeneic cell, or an autologous cell (i.e., relative to the subject administered the modified cell).
- a modified cell comprises a modified human immune cell selected from a CD4+ T cell, a CD8+ T cell, a CD4- CD8- double negative T cell, a ⁇ T cell, a natural killer cell, a dendritic cell, or any combination thereof.
- a modified cell is a T cell, e.g., is a na ⁇ ve T cell, a central memory T cell, an effector memory T cell, or any combination thereof.
- a modified cell used in the presently disclosed methods is a CD4+ T cell.
- a modified CD4+ T cell further comprises a heterologous polynucleotide encoding at least an extracellular portion of a CD8 co-receptor, and optionally encodes a complete CD8 ⁇ -chain, a complete CD8 ⁇ -chain, or both.
- Such methods may, in certain embodiments, further comprise administering to the subject a CD8+ T cell that is capable of specifically binding to a MAGE-A1 peptide:HLA complex on a cell surface, such as a CD8+ modified T cell according to the present disclosure.
- Presently disclosed treatment or prevention methods may include any appropriate method of administering or dosing a modified cell, or a combination therapy.
- a plurality of doses of a modified cell as described herein is administered to the subject, which may be administered at intervals between administrations of about two to about four weeks.
- treatment or prevention methods of this disclosure may be administered to a subject as part of a treatment course or regimen, which may comprise additional treatments prior to, or after, administration of the instantly disclosed unit doses, cells, or compositions.
- a cytokine is administered sequentially, provided that the subject was administered the recombinant host cell at least three or four times before cytokine administration.
- the cytokine is administered subcutaneously (e.g., IL-2, IL-15, IL-21).
- the subject being treated is further receiving immunosuppressive therapy, such as calcineurin inhibitors, corticosteroids, microtubule inhibitors, low dose of a mycophenolic acid prodrug, or any combination thereof.
- immunosuppressive therapy such as calcineurin inhibitors, corticosteroids, microtubule inhibitors, low dose of a mycophenolic acid prodrug, or any combination thereof.
- the subject being treated has received a non-myeloablative or a myeloablative hematopoietic cell transplant, wherein the treatment may be administered at least two to at least three months after the non- myeloablative hematopoietic cell transplant.
- subject has been administered one or more of a DNA hypomethylation agent and a HDAC inhibitor, either or both of which may enhance MAGE-A1 expression (see Weon, J.L. and P.R.
- Methods according to the instant disclosure may, in certain embodiments, further include administering one or more additional agents to treat the disease or disorder in a combination therapy.
- a combination therapy comprises administering a modified cell with (concurrently, simultaneously, or sequentially) an immune checkpoint inhibitor.
- a combination therapy comprises administering a modified cell with an agonist of a stimulatory immune checkpoint agent.
- a combination therapy comprises administering a modified cell with a secondary therapy, such as chemotherapeutic agent, a radiation therapy, a surgery, an antibody, or any combination thereof.
- immune suppression agent refers to one or more cells, proteins, molecules, compounds, or complexes providing inhibitory signals to assist in controlling or suppressing an immune response.
- immune suppression agents include those molecules that partially or totally block immune stimulation; decrease, prevent or delay immune activation; or increase, activate, or up regulate immune suppression.
- immunosuppression agents to target include PD-1, PD-L1, PD- L2, LAG3, CTLA4, B7-H3, B7-H4, CD244/2B4, HVEM, BTLA, CD160, TIM3, GAL9, KIR, PVR1G (CD112R), PVRL2, adenosine, A2aR, immunosuppressive cytokines (e.g., IL-10, IL-4, IL-1RA, IL-35), IDO, arginase, VISTA, TIGIT, LAIR1, CEACAM-1, CEACAM-3, CEACAM-5, Treg cells, or any combination thereof.
- immunosuppression agents to target include PD-1, PD-L1, PD- L2, LAG3, CTLA4, B7-H3, B7-H4, CD244/2B4, HVEM, BTLA, CD160, TIM3, GAL9, KIR, PVR1G (CD112R), PVRL2, adenosine, A2
- An immune suppression agent inhibitor (also referred to as an immune checkpoint inhibitor (“CPI”)) may be a compound, an antibody, an antibody fragment, or fusion polypeptide (e.g., Fc fusion, such as CTLA4-Fc or LAG3-Fc), an antisense molecule, a ribozyme or RNAi molecule, or a low molecular weight organic molecule.
- a method may comprise a modified cell with one or more inhibitor of any one of the following immune suppression components, singly or in any combination.
- a modified cell is used in combination with a PD-1 inhibitor, for example a PD-1-specific antibody or binding fragment thereof, such as pidilizumab, nivolumab, pembrolizumab, MEDI0680 (formerly AMP-514), AMP- 224, tislelizumab, cemiplimab, JTX-1041, spartelizumab, camrelizumab, sintilimab, toripalimab, dostarlimab, INCMGA00012 aka MGA012, AMP-224, AMP-514, BMS- 936558 or any combination thereof.
- a PD-1 inhibitor for example a PD-1-specific antibody or binding fragment thereof, such as pidilizumab, nivolumab, pembrolizumab, MEDI0680 (formerly AMP-514), AMP- 224, tislelizumab, cemiplimab, JTX-1041, sparteli
- a modified cell of the present disclosure is used in combination with a PD-L1 specific antibody or binding fragment thereof or peptide, such as BMS-936559, durvalumab (MEDI4736), atezolizumab (RG7446), avelumab (MSB0010718C), MPDL3280A, KN035, CK-301, AUNP12, CA-170, BMS-986189, or any combination thereof.
- PD-1 inhibitors and PD- L1 inhibitors can be referred-to as PD-1/PD-L1 axis inhibitors.
- a CPI, a PD-1/PD-L1 axis inhibitor, a PD-1 inhibitor, and/or a PD-L1 axis inhibitor is administered as a combination with a cell therapy.
- the CPI, PD-1/PD-L1 axis inhibitor, PD-1 inhibitor, and/or PD-L1 axis inhibitor is administered following administration of at least a first dose or infusion of a cell therapy.
- a subject receiving cell therapy (optionally in combination with CPI, PD-1/PD-L1 axis inhibitor, PD-1 inhibitor, and/or PD-L1 axis inhibitor) of the present disclosure may have previously received or initiated a course of therapy comprising the same or a different CPI, PD-1/PD-L1 axis inhibitor, PD-1 inhibitor, and/or PD-L1 axis inhibitor.
- a first dose of the CPI, PD-1/PD-L1 axis inhibitor, PD-1 inhibitor, and/or PD-L1 axis inhibitor according to a presently disclosed cell therapy or combination method refers to the first dose administered in the context of the combination, e.g., following at least a first dose or infusion of the cell therapy, and does not refer to a dose of the CPI, PD-1/PD-L1 axis inhibitor, PD-1 inhibitor, and/or PD-L1 axis inhibitor in a prior line of therapy (i.e., a line of therapy that preceded or began prior to the cell therapy or combination therapy comprising the cell therapy).
- a prior line of therapy i.e., a line of therapy that preceded or began prior to the cell therapy or combination therapy comprising the cell therapy.
- a modified cell of the present disclosure is used in combination with a LAG3 inhibitor, such as LAG525, IMP321, IMP701, 9H12, BMS- 986016, or any combination thereof.
- a modified cell is used in combination with an inhibitor of CTLA4.
- a modified cell is used in combination with a CTLA4 specific antibody or binding fragment thereof, such as ipilimumab, tremelimumab, CTLA4-Ig fusion proteins (e.g., abatacept, belatacept), or any combination thereof.
- a modified cell is used in combination with a B7-H3 specific antibody or binding fragment thereof, such as enoblituzumab (MGA271), 376.96, or both.
- a B7-H4 antibody binding fragment may be a scFv or fusion protein thereof, as described in, for example, Dangaj et al., Cancer Res.73:4820, 2013, as well as those described in U.S. Patent No.9,574,000 and PCT Patent Publication Nos. WO /201740724A1 and WO 2013/025779A1.
- a modified cell is used in combination with an inhibitor of CD244.
- a modified cell is used in combination with an inhibitor of BLTA, HVEM, CD160, or any combination thereof.
- Anti-CD-160 antibodies are described in, for example, PCT Publication No. WO 2010/084158.
- a modified cell is used in combination with an inhibitor of TIM3.
- a modified cell is used in combination with an inhibitor of Gal9.
- a modified cell is used in combination with an inhibitor of adenosine signaling, such as a decoy adenosine receptor. [0202]
- a modified cell is used in combination with an inhibitor of A2aR.
- a modified cell is used in combination with an inhibitor of KIR, such as lirilumab (BMS-986015).
- a modified cell is used in combination with an inhibitor of an inhibitory cytokine (typically, a cytokine other than TGF ⁇ ) or Treg development or activity.
- a modified cell is used in combination with an IDO inhibitor, such as levo-1-methyl tryptophan, epacadostat (INCB024360; Liu et al., Blood 115:3520-30, 2010), ebselen (Terentis et al., Biochem.49:591-600, 2010), indoximod, NLG919 (Mautino et al., American Association for Cancer Research 104th Annual Meeting 2013; Apr 6-10, 2013), 1-methyl-tryptophan (1-MT)-tira-pazamine, or any combination thereof.
- an IDO inhibitor such as levo-1-methyl tryptophan, epacadostat (INCB024360; Liu et al., Blood 115:3520-30, 2010), ebselen (Terentis et al., Biochem.49:591-600, 2010), indoximod, NLG919 (Mautino et al., American Association for Cancer Research
- a modified cell is used in combination with an arginase inhibitor, such as N(omega)-Nitro-L-arginine methyl ester (L-NAME), N- omega-hydroxy-nor-l-arginine (nor-NOHA), L-NOHA, 2(S)-amino-6- boronohexanoic acid (ABH), S-(2-boronoethyl)-L-cysteine (BEC), or any combination thereof.
- an arginase inhibitor such as N(omega)-Nitro-L-arginine methyl ester (L-NAME), N- omega-hydroxy-nor-l-arginine (nor-NOHA), L-NOHA, 2(S)-amino-6- boronohexanoic acid (ABH), S-(2-boronoethyl)-L-cysteine (BEC), or any combination thereof.
- VISTA such as CA-170 (Curis, Lexington
- a modified cell is used in combination with an inhibitor of TIGIT such as, for example, COM902 (Compugen, Toronto, Ontario Canada), an inhibitor of CD155, such as, for example, COM701 (Compugen), or both.
- a modified cell is used in combination with an inhibitor of PVRIG, PVRL2, or both.
- Anti-PVRIG antibodies are described in, for example, PCT Publication No. WO 2016/134333.
- Anti- PVRL2 antibodies are described in, for example, PCT Publication No. WO 2017/021526.
- a modified cell is used in combination with a LAIR1 inhibitor.
- a modified cell is used in combination with an inhibitor of CEACAM-1, CEACAM-3, CEACAM-5, or any combination thereof. [0203] In certain embodiments, a modified cell is used in combination with an agent that increases the activity (i.e., is an agonist) of a stimulatory immune checkpoint molecule.
- a modified cell can be used in combination with a CD137 (4- 1BB) agonist (such as, for example, urelumab), a CD134 (OX-40) agonist (such as, for example, MEDI6469, MEDI6383, or MEDI0562), lenalidomide, pomalidomide, a CD27 agonist (such as, for example, CDX-1127), a CD28 agonist (such as, for example, TGN1412, CD80, or CD86), a CD40 agonist (such as, for example, CP- 870,893, rhuCD40L, or SGN-40), a CD122 agonist (such as, for example, IL-2) an agonist of GITR (such as, for example, humanized monoclonal antibodies described in PCT Patent Publication No.
- a CD137 (4- 1BB) agonist such as, for example, urelumab
- a CD134 (OX-40) agonist such as, for example, MEDI6469
- a method may comprise administering a modified cell with one or more agonist of a stimulatory immune checkpoint molecule, including any of the foregoing, singly or in any combination.
- a combination therapy comprises a modified cell and a secondary therapy comprising one or more of: an antibody or antigen binding-fragment thereof that is specific for a cancer antigen expressed by the non- inflamed solid tumor, a radiation treatment, a surgery, a chemotherapeutic agent, a cytokine, RNAi, or any combination thereof.
- a combination therapy method comprises administering a modified cell and further administering a radiation treatment or a surgery.
- Radiation therapy is well-known in the art and includes X-ray therapies, such as gamma- irradiation, and radiopharmaceutical therapies.
- a combination therapy method comprises administering a modified cell and further administering a chemotherapeutic agent.
- a chemotherapeutic agent includes, but is not limited to, an inhibitor of chromatin function, a topoisomerase inhibitor, a microtubule inhibiting drug, a DNA damaging agent, an antimetabolite (such as folate antagonists, pyrimidine analogs, purine analogs, and sugar-modified analogs), a DNA synthesis inhibitor, a DNA interactive agent (such as an intercalating agent), and a DNA repair inhibitor.
- Illustrative chemotherapeutic agents include, without limitation, the following groups: anti-metabolites/anti-cancer agents, such as pyrimidine analogs (5-fluorouracil, floxuridine, capecitabine, gemcitabine and cytarabine) and purine analogs, folate antagonists and related inhibitors (mercaptopurine, thioguanine, pentostatin and 2- chlorodeoxyadenosine (cladribine)); antiproliferative/antimitotic agents including natural products such as vinca alkaloids (vinblastine, vincristine, and vinorelbine), microtubule disruptors such as taxane (paclitaxel, docetaxel), vincristin, vinblastin, nocodazole, epothilones and navelbine, epidipodophyllotoxins (etoposide, teniposide), DNA damaging agents (actinomycin, amsacrine, anthracyclines, bleomycin, busul
- Cytokines can be used to manipulate host immune response towards anticancer activity. See, e.g., Floros & Tarhini, Semin. Oncol.42(4):539-548, 2015. Cytokines useful for promoting immune anticancer or antitumor response include, for example, IFN- ⁇ , IL-2, IL-3, IL-4, IL-10, IL-12, IL-13, IL-15, IL-16, IL-17, IL-18, IL- 21, IL-24, and GM-CSF, singly or in any combination with a modified cell of this disclosure. Further Numbered Embodiments [0209] The present disclosure also provides the following exemplary Embodiments. 1.
- a method of treating a cancer or disease or disorder that is associated with MAGE-A1 expression in a subject comprising administering to the subject a population of modified immune cells comprising a binding protein, the binding protein comprising: a) a T cell receptor (TCR) ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and a TCR ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively; b) a T cell receptor (TCR) ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 30-32, respectively, and a TCR ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 27-29, respectively; c) a T cell receptor (TCR)
- Embodiment 1 wherein the method further comprises, prior to administering the population of modified immune cells, identifying the subject as being negative for expression of HLA B*49:01. 3.
- the method of Embodiment 1 or Embodiment 2 wherein the subject is positive for or has been identified as positive for expression of HLA A*02:01. 4.
- the method of any one of Embodiments 1-3 wherein the method further comprises, prior to administering the population of modified immune cells, identifying the subject as positive for expression of HLA A*02:01. 5.
- the method of any one of Embodiments 1-4 wherein the subject is lymphodepleted or has undergone a lymphodepletion procedure. 6.
- the method further comprises providing lymphodepletion to the subject, wherein, optionally, the lymphodepletion is provided prior to administering the population of modified immune cells, wherein, further optionally, the lymphodepletion is provided 4 days, 3 days, 2 days, and/or 1 day prior to administering the population of modified immune cells.
- providing lymphodepletion comprises administering a lymphodepleting chemotherapy to the subject.
- the lymphodepleting chemotherapy comprises cyclophosphamide, fludarabine, or a combination thereof, wherein, optionally, the lymphodepleting chemotherapy comprises 300 mg/m 2 cyclophosphamide and/or 30 mg/m 2 fludarabine.
- the lymphodepleting chemotherapy is administered intravenously to the subject.
- the method comprises administering an immune checkpoint inhibitor (CPI) to the subject, wherein, optionally, a first dose of the CPI is administered after the population of modified immune cells is administered, such as within 24 to 72 hours after the population of modified immune cells is administered.
- CPI immune checkpoint inhibitor
- the method comprises administering a PD-1 inhibitor and/or a PD-L1 inhibitor to the subject.
- the method of Embodiment 13 wherein the method comprises administering a PD-1 inhibitor to the subject. 15.
- Embodiment 14 wherein the CPI or the PD-1/PD-L1 axis inhibitor is selected from atezolizumab, nivolumab, durvalumab, and pembrolizumab. 16.
- the method comprises administering a PD-L1 inhibitor and the PD-L1 inhibitor is avelumab. 19.
- the method of any one of Embodiments 1-18, wherein the cancer is or comprises a solid tumor.
- 20. The method of any one of Embodiments 1-19, wherein the cancer is triple negative breast cancer (TNBC), wherein, optionally, the TNBC is metastatic TNBC.
- 21. The method of any one of Embodiments 1-19, wherein the cancer is non- small cell lung cancer (NSCLC), wherein, optionally, the NSCLC is metastatic NSCLC.
- the method of any one of Embodiment 1-19, wherein the cancer is urothelial cancer.
- 23. The method of Embodiment 22, wherein the urothelial cancer is a metastatic urothelial cancer or an advanced urothelial cancer. 24.
- the population of modified immune cells comprises T cells, wherein, optionally, the T cells comprise CD8+ T cells, wherein, further optionally, the CD8+ T cells comprise CD62L+ T cells.
- the population of modified immune cells comprises a CD4+ T cells, wherein, optionally, the CD4+ T cells are present in the population in combination with CD8+ T cells, wherein, further optionally, the CD4+ T cells and the CD8+ T cells are present in the population at a ratio of about 1:1. 26.
- the method of Embodiment 29, wherein the population of modified immune cells comprises between 5 ⁇ 10 8 and 5 ⁇ 10 9 modified immune cells in each of the one or more administration. 31. The method of Embodiment 29, wherein the population of modified immune cells comprises about 5 ⁇ 10 8 modified immune cells in each of the one or more administration. 32. The method of Embodiment 29, wherein the population of modified immune cells comprises about 5 ⁇ 10 9 modified immune cells in each of the one or more administration. 33.
- Embodiments 1-35 wherein the V ⁇ domain has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and the V ⁇ domain has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively.
- 37. The method of Embodiment 36, wherein the V ⁇ domain has at least 95% identity to SEQ ID NO: 19, or has at least 95% identity to SEQ ID NO: 19 with the signal peptide removed.
- 38. The method of Embodiment 36 or 37, wherein the V ⁇ domain has at least 99% identity to SEQ ID NO: 19, or has at least 99% identity to SEQ ID NO: 19 with the signal peptide removed. 39.
- V ⁇ domain comprises the sequence of SEQ ID NO: 19, or comprises the sequence of SEQ ID NO: 19 with the signal peptide removed.
- V ⁇ domain has at least 95% identity to SEQ ID NO: 17, or has at least 95% identity to SEQ ID NO: 17 with the signal peptide removed.
- 41. The method of any one of Embodiments 36-40, wherein the V ⁇ domain has at least 99% identity to SEQ ID NO: 17, or has at least 99% identity to SEQ ID NO: 17 with the signal peptide removed. 42.
- V ⁇ domain comprises the sequence of SEQ ID NO: 17, or comprises the sequence of SEQ ID NO: 17 with the signal peptide removed.
- binding protein comprises a TCR ⁇ chain constant (C ⁇ ) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 20, and wherein, optionally, the V ⁇ domain and the C ⁇ domain together comprise a TCR ⁇ chain.
- the binding protein comprises a TCR ⁇ chain constant (C ⁇ ) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 18, and wherein, optionally, the V ⁇ domain and the C ⁇ domain together comprise a TCR ⁇ chain.
- the method comprises administering the population of modified immune cells to a plurality of subjects, wherein treating comprises inducing a partial response or a complete response in at least 5%, at least 10%, at least 15%, at least 20%, or at least 25% of the plurality of subjects. 46.
- treating comprises reducing the severity and/or the duration of a sign or a symptom of the cancer or disease or disorder in the subject. 47. The method of any one of Embodiments 1-45, wherein treating comprises increasing a duration of progression-free survival of the subject or subjects. 48. The method of any one of Embodiments 1-46, wherein treating comprises inducing a remission of the cancer in the subject or subjects. 49.
- a method of treating a cancer comprising administering to a subject in need thereof a population of modified cells comprising a binding protein, the binding protein comprising: a) a T cell receptor (TCR) ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and a TCR ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively; b) a T cell receptor (TCR) ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 30-32, respectively, and a TCR ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 27-29, respectively; c) a T cell receptor (TCR) ⁇ chain variable (V ⁇ ) domain having CDR1, CDR2, and
- Embodiment 49 wherein the method further comprises, prior to administering the population of modified immune cells, identifying the subject as being negative for expression of HLA B*49:01. 51.
- the method of Embodiment 49 or Embodiment 50 wherein the subject is positive for or has been identified as positive for expression of HLA A*02:01. 52.
- the method of any one of Embodiments 49-51 wherein the method further comprises, prior to administering the population of modified immune cells, identifying the subject as positive for expression of HLA A*02:01. 53.
- the method of any one of Embodiments 49-52 wherein the subject is lymphodepleted or has undergone a lymphodepletion procedure. 54.
- the method further comprises providing lymphodepletion to the subject, wherein, optionally, the lymphodepletion is provided prior to administering the population of modified immune cells, wherein, further optionally, the lymphodepletion is provided 4 days, 3 days, 2 days, and/or 1 day prior to administering the population of modified immune cells.
- providing lymphodepletion comprises administering a lymphodepleting chemotherapy to the subject.
- the lymphodepleting chemotherapy comprises cyclophosphamide, fludarabine, or a combination thereof, wherein, optionally, the lymphodepleting chemotherapy comprises 300 mg/m 2 cyclophosphamide and/or 30 mg/m 2 fludarabine.
- 57. The method of Embodiment 55 or 56, wherein the lymphodepleting chemotherapy is administered intravenously to the subject.
- 58. The method of any one of Embodiments 49-57, wherein the method comprises administering an immune checkpoint inhibitor (CPI) to the subject, wherein, optionally, a first dose of the CPI is administered after the population of modified immune cells is administered, such as within 24 to 72 hours after the population of modified immune cells is administered.
- CPI immune checkpoint inhibitor
- Embodiments 49-58 comprising administering a PD-1/PD-L1 axis inhibitor to the subject.
- 60. The method of Embodiment 58 or 59, wherein the CPI or the PD-1/PD- L1 axis inhibitor comprises nivolumab, pembrolizumab, durvalumab, atezolizumab, avelumab, or any combination thereof.
- 61. The method of any one of Embodiments 49-60, wherein the method comprises administering a PD-1 inhibitor and/or a PD-L1 inhibitor to the subject.
- 62. The method of Embodiment 61, wherein the method comprises administering a PD-1 inhibitor to the subject.
- Embodiment 62 wherein the CPI or the PD-1/PD-L1 axis inhibitor is selected from atezolizumab, nivolumab, durvalumab, and pembrolizumab.
- the method of Embodiment 63, wherein the CPI or the PD-1/PD-L1 axis inhibitor comprises atezolizumab.
- 65 The method of any one of Embodiments 60-64, wherein the atezolizumab is administered to the subject every three weeks at 1200 mg per administration.
- 66 The method of any one of Embodiments 60-65, wherein the method comprises administering avelumab to the subject. 67.
- the cancer is triple negative breast cancer (TNBC), wherein, optionally, the TNBC is metastatic TNBC.
- TNBC triple negative breast cancer
- NSCLC non-small cell lung cancer
- the NSCLC metastatic NSCLC.
- the method of any one of Embodiments 49-67, wherein the cancer is urothelial cancer.
- the population of modified immune cells comprises T cells, wherein, optionally, the T cells comprise CD8+ T cells, wherein, further optionally, the CD8+ T cells comprise CD62L+ T cells.
- the population of modified immune cells comprises CD4+ T cells, wherein, optionally, the CD4+ T cells are present in the population in combination with CD8+ T cells, wherein, further optionally, the CD4+ T cells and the CD8+ T cells are present in the population at a ratio of about 1:1. 74.
- the method of Embodiment 77, wherein the population of modified immune cells comprises between 5 ⁇ 10 8 and 5 ⁇ 10 9 modified immune cells in each of the one or more administration. 79. The method of Embodiment 77, wherein the population of modified immune cells comprises about 5 ⁇ 10 8 modified immune cells in each of the one or more administration. 80. The method of Embodiment 77, wherein the population of modified immune cells comprises about 5 ⁇ 10 9 modified immune cells in each of the one or more administration. 81.
- any one of Embodiments 49-80 comprising (1) a first administration comprising the population of modified immune cells comprising about 1 x 10 9 modified immune cells, and (2) a second, subsequent administration of a population of the modified immune cells that comprises (i) about 1 x 1 x 10 9 modified immune cells, (ii) about 5 x 10 8 modified immune cells, or (iii) about 5 x 10 9 modified immune cells, wherein, optionally, the second, subsequent administration occurs about 6, about 7, about 8, about 9, about 10, about 11, or about 12 weeks after the first administration. 82.
- Embodiments 49-83 wherein the V ⁇ domain has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and the V ⁇ domain has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively.
- Embodiment 84 or 85 wherein the V ⁇ domain has at least 99% identity to SEQ ID NO: 19, or has at least 99% identity to SEQ ID NO: 19 with the signal peptide removed.
- the method of any one of Embodiments 84-87, wherein the V ⁇ domain has at least 95% identity to SEQ ID NO: 17, or has at least 95% identity to SEQ ID NO: 17 with the signal peptide removed. 89.
- the binding protein comprises a TCR ⁇ chain constant (C ⁇ ) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 20, and wherein, optionally, the V ⁇ domain and the C ⁇ domain together comprise a TCR ⁇ chain.
- the binding protein comprises a TCR ⁇ chain constant (C ⁇ ) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 18, and wherein, optionally, the V ⁇ domain and the C ⁇ domain together comprise a TCR ⁇ chain.
- the method comprises administering the population of modified immune cells to a plurality of subjects, wherein treating comprises inducing a partial response or a complete response in at least 5%, at least 10%, at least 15%, at least 20%, or at least 25% of the plurality of subjects.
- treating comprises reducing the severity and/or the duration of a sign or a symptom of the cancer in the subject.
- treating comprises increasing a duration of progression-free survival of the subject or subjects.
- treating comprises inducing a remission of the cancer in the subject or subjects.
- the binding protein is encoded by a polynucleotide comprised in modified immune cells of the population, wherein the polynucleotide comprises a sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprises or consists of, the polynucleotide sequence set forth in any one of SEQ ID NOs.:151-153. 98.
- the binding protein is encoded by a polynucleotide comprised in modified immune cells of the population, wherein the polynucleotide comprises a sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprises or consists of, the polynucleotide sequence set forth in SEQ ID NO.:159. 99.
- modified immune cells of the population further comprise a polynucleotide encoding a CD8 co- receptor ⁇ chain, a CD8 co-receptor ⁇ chain, or both, wherein, optionally, the polynucleotide encoding a CD8 co-receptor ⁇ chain has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the polynucleotide sequence set forth in SEQ ID NO.:149 and the polynucleotide encoding a CD8 co-receptor ⁇ chain has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at
- An isolated polynucleotide comprising any one or more of: (i) the polynucleotide sequence according to SEQ ID NO.:149; (ii) the polynucleotide sequence according to SEQ ID NO.:150; (iii) the polynucleotide sequence according to SEQ ID NO.:151; (iv) the polynucleotide sequence according to SEQ ID NO.:152; and (v) the polynucleotide sequence according to SEQ ID NO.:153.
- a vector comprising the polynucleotide of Embodiment 100 or 101.
- the vector of Embodiment 102, wherein the vector comprises a viral vector.
- the vector of Embodiment 103, wherein the viral vector is a lentiviral vector or a retroviral vector.
- a host cell comprising the polynucleotide of Embodiment 100 or 101 and/or the vector of any one of Embodiments 102-104.
- the host cell of Embodiment 105, wherein the host cell comprises a human immune system cell.
- the host cell of Embodiment 106, wherein the human immune system cell comprises a T cell, a NK cell, a NK-T cell, a macrophage, and/or a microglia. 108.
- a composition comprising a plurality of host cells according to any one of Embodiments 105-109.
- a method comprising introducing the polynucleotide of Embodiment 100 or 101 or the vector of any one of Embodiments 102-104 to a host cell, wherein, optionally, the introducing comprises DNA electroporation or viral transduction.
- PBMCs peripheral blood mononuclear cells
- IL-2, IL-7, IL-15 and IL-21 peripheral blood mononuclear cells
- the stimulated cell lines from all donors were pooled and sorted several times using limited concentrations MAGE-A1 peptide:MHC multimers, which produced enriched populations of high-affinity T cell clones.
- TCR ⁇ genes from the populations were sequenced to the frequency of TCRs in pooled and individual pMHC sorts.
- Figure 3 shows exemplary data from a series of pMHC sorts that enriched for T cells expressing TCR ⁇ CDR3 specific for the MAGE-A1 antigen.
- a high-affinity MAGE-A1-specific CD8 + T cell clone “MA2” generated using the method of Example 1 ( Figure 5A) was selected for further testing.
- MA2 + CD8 + T cells selectively produced cytokines when co-cultured with MAGE-A1-expressing HAL-A*0201 + U266 multiple myeloma cells (effector to target (E:T) ratio of 10:1, 4 hrs).
- E:T effector to target
- MA2 + T cells were capable of killing target cells in the presence or absence of exogenous IFN- ⁇ and MAGE-A1 peptide (Figure 5C).
- CD8 + TCRs recognize antigens presented by class I HLA molecules, while CD4 + TCRs recognize antigens presented in the context of class II HLA.
- CD4 + T cells were transduced with MA2 TCR (see, e.g., schematic diagrams of Figures 6A and 6B).
- CD4 + T cells transduced with MA2 TCR bound MAGE-A1:HLA tetramers with an affinity that was comparable ( ⁇ 5-fold difference in Bmax) to MA2 CD8+ T cells.
- the transformed CD4 + T cells did not kill target cells in vitro.
- CD4 + T cells were transduced with both a high- affinity Class-I-restricted MAGE-A1-specific TCR ("MA1", having V ⁇ , C ⁇ , V ⁇ , and C ⁇ amino acid sequences according to SEQ ID NOs.:19, 20, 17, and 18, respectively) and a CD8 co-receptor.
- Figure 8B shows that a greater proportion of CD4 + T cells transduced with both exogenous CD8 TCR and CD8 co-receptor produced cytokines in response to antigen, as compared to CD4 + T cells transduced with the exogenous CD8 TCR alone.
- FIG 8C shows that the dually transduced CD4 + T cells surprisingly exhibited cytolytic activity against MEL526 target cells, at rates comparable to CD8 + T cells expressing the same high- affinity TCR.
- the dually transduced CD4 + T cells also proliferated more robustly following stimulation with antigen than MA1 + CD4 + cells without CD8.
- These data show that high-affinity MAGE-A1-specific TCRs of the present disclosure, and CD8 + and CD4 + T cells expressing the same, are useful for targeting and killing MAGE-A1-expressing cancer cells and have use in cellular immunotherapies against MAGE-A1-expressing diseases.
- the MA1 TCR comprises a TCR ⁇ chain comprising SEQ ID NO.:19 and SEQ ID NO.:20, with the signal peptide (amino acids 1-18 of SEQ ID NO.:19) removed prior to expression at a host cell surface, and a TCR ⁇ chain comprising SEQ ID NO.:17 and SEQ ID NO.:18, with the signal peptide (amino acids 1-17 of SEQ ID NO.:17) removed prior to expression at the host cell surface.
- T cells transduced with a lentivirus expressing the MA1 TCR and CD8 co-receptor polypeptides are referred to herein as “MagIC TCR-T”.
- T cell products for murine experiments were generated in accordance with T cell products designed for infusion into human patients. Briefly, PBMC first underwent a positive magnetic bead selection for CD4+. The flow through containing a majority of CD8+ T cells was then positively selected for CD62L+ cells. This assures that CD8+ T cell subsets demonstrating improved in vivo persistence, including na ⁇ ve, central memory and stem cell memory CD8+ cells, are selected for transduction with the MAGE-A1-specific TCR.
- CD4+ and CD4-CD62L+ cells at a ratio of 1:3 obtained from frozen PBMC of three individual healthy donors were then stimulated with IL-2 and TransAct TM ( ⁇ CD3/CD28; Miltenyi) two days prior to transduction with a PRRLSIN lentivirus encoding the MA1 TCR and human CD8 co-receptor polypeptides (SEQ ID NOs.:143 and 144) to produce MagIC TCR-T.
- MagIC TCR-T cell products were harvested on day 14 post-stimulation.
- MagIC TCR-T cells were re-challenged once, at 24 hours.
- MagIC TCR-T cells were re-challenged twice, at 24 and 48 hours.
- mice were engrafted with 2x10 6 U266 myeloma cells (i.v.) 7 days prior to MagIC TCR-T cell transfer.
- the U266 myeloma cell line was selected due to its native HLA- A*02:01expression, MAGE-A1 protein expression, and ability grow specifically and consistently in the bone marrow as a xenograft in NSG mice.
- serial tumor burden assessments in individual mice can be performed by serum quantification of secreted IgE by the U266 cells.
- MagIC-TCR T cells did not express detectable IFN ⁇ or exhibit cytotoxicity against healthy human cell lines expressing self-peptides presented by HLA-A*02:01, as measured by live cell imaging when co-cultured in the presence of all tested cell lines with or without upregulation of HLA molecules and alterations in peptide processing by pretreatment with IFN ⁇ ( Figures 11A-11B).
- HLA alleles are summarized in Table 1. Briefly, this assay assesses for alloreactivity of the MagIC-TCR T cells to other HLA types, since human subjects have 6 HLA I alleles; “alloreactivity” can also be described in this context as “non-specific cross-reactivity”.
- HLA typing of cell lines tested [0225] Reactivity to HLA-B*49:01 was confirmed by positive recognition of the HLA- *02:01-negative, HLA-B*49:01-positive Namalwa cell line ( Figures12B). [0226] Patients expressing HLA-B*49:01 are excluded from clinical trials using MagIC TCR T cells. In other words, patients to receive therapy are selected as negative for expression of HLA-B*49:01 and positive for HLA-A*02:01.
- EXAMPLE 7 DOSING STUDY A phase I, open-label interventional study investigating MagIC TCR-T for treatment of up to 15-18 HLA-A*02:01 positive, HLA-B*49:01 negative patients with metastatic TNBC, urothelial carcinoma, or NSCLC is performed. In the phase 1 portion of the trial, T cells are administered. In the phase 1/2 portion of the trial, following T cell infusion, atezolizumab is administered and provided as standard of care.
- HLA typing is determined though a molecular approach in a clinical laboratory licensed for HLA typing.
- HLA typing is performed using PCR amplification followed by high throughput Next Generation Sequencing (NGS) and subsequent HLA determination using a system available through Scisco Genetics (sciscogenetics.com/pages/technology.html, the contents of which is incorporated herein by reference in its entirety).
- NGS Next Generation Sequencing
- Exclusion Criteria Participants expressing HLA-B*49:01 are excluded due to the risk of alloreactivity.
- leukapheresis Following confirmation of eligibility based on HLA typing and MAGE- A1 expression on the tumor, patients undergo leukapheresis. Leukapheresis collection is performed on each patient to obtain peripheral blood mononuclear cells (PBMCs) for the production of the MagIC TCR-T investigational product.
- PBMCs peripheral blood mononuclear cells
- the cell product includes both CD8+ and CD4+ transgenic T cells. Dose is measured based on quantity of transgenic CD3+ cells binding to HLA-A2-MAGE-A1 tetramer. Purity is required to be at least 10% of cells transgenic for the TCR and is expected to range from 20-80%, more typically from 30-50%. Although a 1:1 ratio of CD8+ and CD4+ transgenic T cells in the final product is targeted, cells are co-cultured and there is inherent variability in infused products. [0233] In both phases of the trial, lymphodepleting chemotherapy is administered to subjects prior to T-cell infusion to reduce tumor burden, minimize the risk of tumor lysis syndrome, and induce lymphopenia to improve T-cell persistence.
- T cells are delivered to the patient as a frozen product, which is thawed immediately prior to infusion. T cells are infused intravenously over approximately 15- 20 minutes via nonfiltered tubing at the specified dose. The infusion bag is gently mixed periodically during the infusion.
- doses are initially 1 billion (1 x 10 9 ) (DL1) and 5 billion (5 x 10 9 ) (DL2) MAGE-A1-specific TCR transgenic CD3+ T cells for full dose infusion. All patients included in this study are adults and are thus expected to have similar body surface areas, permitting use of flat rather than weight-based dosing.
- Patients are provided a second infusion of transgenic T cells at the same dose (DL1) as the first infusion if there are no DLT and no evidence for progression by RECIST criteria. [0239] If all four of these patients complete the first infusion without DLT, the next four patients receive the next dose level of 5 x 10 9 CD3+TCR+ cells (DL2) in their first infusion. Approximately 12 weeks following the first infusion, restaging, and evaluation of peripheral blood persistence of infused transgenic T cells is performed. Patients are provided a second infusion of transgenic T cells at the same dose (DL2) as the first infusion if there are no DLT and no evidence for progression by RECIST criteria.
- DL1 dose
- DL2 CD3+TCR+ cells
- the next four patients receive 5 x 10 8 CD3+TCR+ cells (DL-1), with the first patient receiving cellular therapy only and the next three patients receiving lymphodepletion followed by cellular therapy.
- the targeted recommended Phase 2 dose (RP2D) is 5 x 10 9 CD3+TCR+ cells with lymphodepletion; however, a lower dose may be selected by the DAC for the RP2D based on the totality of toxicity data.
- the Phase 1/2 portion of the trial builds on the RP2D with the addition of PD-1/PD-L1-axis therapy (atezolizumab 1200mg IV q3weeks).
- Atezolizumab is a fully humanized monoclonal antibody which targets human PD-L1 and inhibits its interaction with its receptors. Atezolizumab is administered as standard of care starting 24-72 hours after the T cell infusion. [0242] Of note, patients enrolled to this portion of the trial must have previously been offered or received a PD-1 axis inhibitor. If received, they must have either developed progression or still have detectable disease, and not have developed serious adverse events. If no DLT are observed with the addition of PD-1/PD-L1-axis therapy, up to 6 patients may be treated with the cell product:PD-1/PD-L1 axis combination.
- the DAC reviews the data after every 2 patients in this portion of the study and, if PD- 1/PD-L1-axis attributable toxicity is observed, expansion of the number of patients at RP2D may continue without PD-1/PD-L1-axis therapy.
- a DLT if one patient experiences a DLT, three additional patients may be recruited at that dose level (7 patients total). As long as no additional DLT are observed (i.e., as long as 2 or more patients in the total of 7 patients do not experience a DLT), escalation may proceed to the next dose level.
Abstract
The present disclosure provides compositions and methods for use in treating diseases or disorders associated with MAGE-A1 expression, such as certain cancers, including triple negative breast cancer, non-small cell lung cancer, and urothelial cancer. In some embodiments, methods comprise administering a population of modified immune cells that comprise a binding protein specific for a MAGE-A1 to a subject that is negative for HLA-B*49:01. In some embodiments, methods comprise administering a population of modified immune cells that comprise a binding protein specific for a MAGE-A1 to a subject that is lymphodepleted or has undergone a lymphodepletion procedure, is administered a PD-1 inhibitor, and/or a PD-L1 inhibitor, and/or is negative for HLA-B*49:01.
Description
COMPOSITIONS AND METHODS FOR TREATING MAGE-A1-EXPRESSING DISEASE CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims priority to U.S. Provisional Application No. 63/088,389, filed October 6, 2020, the contents of which are incorporated herein by reference in their entirety. DESCRIPTION OF THE TEXT FILE SUBMITTED ELECTRONICALLY [0002] The sequence listing associated with this application is provided in text format in lieu of paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 360056_492WO_SequenceListing.txt. The text file is 106 KB, was created on October 4, 2021, and is being submitted electronically via EFS-Web. BACKGROUND [0003] Adoptive transfer of tumor-specific T-cells is an appealing strategy to eliminate existing tumors and requires the establishment of a robust population of antigen-specific T cells in vivo to eliminate existing tumor and prevent recurrences (Stromnes et al., Immunol. Rev.257:145, 2014). Although transfer of tumor-specific CD8+ cytotoxic T lymphocytes (CTLs) has been shown to be safe in some instances and can mediate direct anti-tumor activity in select patients (Chapuis et al., Cancer Res. 72:LB-136, 2012; Chapuis et al., Sci. Transl. Med.5:174ra127, 2013; Chapuis et al., Proc. Nat’l. Acad. Sci. U.S.A.109:4592, 2012), the variability in the avidity of the CTLs isolated from each patient or donor limits the anti-tumor efficacy in clinical trials (Chapuis et al., 2013). [0004] Since TCR affinity is an important determinant of CTL avidity (Zoete et al., Frontiers Immunol.4:268, 2013), strategies have been developed to redirect the antigen specificity of donor or patient T cells using high affinity TCRα/β genes isolated from a well-characterized T cell clone specific for a tumor-specific antigen (Stromnes et al., Immunol. Rev.257:145, 2014; Robbins et al., J. Clin. Oncol.29:917, 2011). Such high affinity self/tumor-reactive T cells are rare since T cells that express self/tumor- reactive TCRs are subject to central and peripheral tolerance (Stone and Kranz,
Frontiers Immunol.4:244, 2013), with relative TCR affinities varying widely between donors. Therefore, many matched donors must be screened to identify a sufficiently high-affinity tumor-specific T cell clone from which a TCRα/β gene therapy construct can be generated. For example, isolation of a naturally elicited Wilms’ Tumor antigen 1 (WT1)-specific TCR with high functional avidity for a single HLA-allele required screening of hundreds of WT-specific T cell lines representing thousands of individual T cell clones from the peripheral repertoires of greater than 75 normal donors, a very time and labor intensive process (Chapuis et al., 2013; Schmitt et al., Hum. Gene Ther. 20:1240, 2009; Ho et al., J. Immunol. Methods 310:40, 2006). [0005] There is a need for alternative antigen-specific immunotherapies directed against various cancers, such as leukemia and solid tumors. Moreover, such immunotherapies will preferably have low-to-no risk of reactivity against healthy/non- target cells. Presently disclosed embodiments address these needs and provide other related advantages. BRIEF DESCRIPTION OF THE DRAWINGS [0006] Figures 1A and 1B show representative data illustrating that high- affinity T cells for viral antigens are found at higher frequencies (A) than high-affinity T cells for self-antigens, which are found at very low frequencies (B). [0007] Figures 2A and 2B show, respectively, (A) a schematic of a T cell enrichment assay, (B) flow cytometry data from a series of sorting experiments used to enrich for antigen-specific CD8+ T cells. [0008] Figure 3 shows representative data from a TCRβ CDR3 enrichment scheme of the present disclosure using MAGE-A1:HLA tetramers. [0009] Figures 4A and 4B show, respectively, (A) specific binding of MAGE- A1:HLA tetramers by TCRs identified using methods of the present disclosure and (B) enrichment of MAGE-A1-specific TCRs. [0010] Figures 5A-5C provide, respectively, (A) flow cytometry data showing MAGE- A1-specific CD8+ T cells of the present disclosure binding MAGE-A1:HLA tetramers, (B) cytokine production by MAGE-A1-specific CD8+ T cells in the absence (left) or presence (right) of antigen-expressing U266 myeloma cells, and (C) specific lysis data showing that high-affinity MAGE-A1 TCR-transduced CD8+ T cells of this disclosure bind antigen:MHC tetramers and kill cells presenting MAGE-A1: MHC
(A*0201). Data in (C) was from a standard Cr51-release assay in which the CD8+ T cells were co- cultured with U266 cells alone, with exogenous interferon-gamma (IFNγ) or with exogenous MAGE-A1 peptide. [0011] Figure 6A illustrates an immunotherapy approach according to the present disclosure in which CD4+ T cells are transduced to express a TCR cloned from a CD8+ T cell that is specific for a peptide antigen, and a CD8 co-receptor. Activation of the transduced CD4+ T cell can augment or improve the antigenic response of CD8+ T cells, such as infused CTLs in an immunotherapy setting. Figure 6B shows the design of an experiment ("Test #1") in which a CD4+ T cell was transduced to express a CD8- independent MHC Class I-restricted TCR, but not a CD8 co-receptor. [0012] Figure 7A shows flow cytometry data from an experiment in which T cells (CD8+ and CD4+) expressing high-affinity (CD8+ T cell-derived) anti-MAGE-A1 TCR were assayed for binding to MAGE-A1:MHC tetramers. Figure 7B shows specific binding by the MAGE-A1-specific T cells to MAGE-A1:MHC tetramers. Figure 7C shows target cell lysis (Cr51 release) by CD8+ T cells expressing MAGE-A1-specific TCR of this disclosure and the lack of killing by comparable CD4+ T cells. [0013] Figure 8A shows a schematic illustrating an experiment in which CD4+ T cells were transduced to express a high-affinity MAGE A1 Class I TCR plus a CD8αβ co-receptor and examined for functionality in the presence of cells expressing peptide:MHC. Figure 8B shows that a higher proportion of the CD4+ T cells transduced with both MAGE-A1 TCR and CD8 co-receptor produced cytokines as compared to CD4+ T cells expressing the MAGE-A1 TCR alone. Figure 8C shows specific lysis of antigen-presenting MEL526 melanoma target cells by the indicated T cells. Figure 8D shows expansion of the two groups of transduced CD4+ T cells following stimulation with antigen. [0014] Figures 9A and 9B show that exemplary cells of the present disclosure (MagIC TCR-T; see Example 5) specifically kill HLA-A2-positive / MAGE-A1- positive tumor cell lines. In vitro cytotoxic activity of MagIC TCR-T cells from three healthy donors at decreasing effector:target (E:T) ratios (10:1, 5:1, 2.5:1), as measured by dynamic killing (IncuCyteTM assay) of red-labeled (Figure 9A) HS578T breast cell line with a single re-challenge at 24 hours or (Figure 9B) me275 melanoma cell line re- challenged at 24 and 48 hours.
[0015] Figures 10A and 10B show that MagIC TCR-T controls HLA-A2+ MAGE-A1+ U266 tumor xenograft in vivo. (Figure 10A) IgE levels over time in the serum (ng/ml) of U266 (i.v.-injected) tumor-bearing NSG mice with or without MagIC TCR-T cell transfer. (Figure 10B) Tumor burden in the bone marrow 9 weeks post- U266 engraftment in MagIC TCR-T cell treated mice as compared to non-treated control mice (n=4 mice/group). In these experiments, MagIC TCR-T cells used were CD8+ T cells ("CD8 TCR-T"), CD4+ T cells ("CD4 TCR-T"), or a combination of CD8+ T cells and CD4+ T cells ("CD8 + CD4 TCR-T"). [0016] Figures 11A and 11B show that MagIC TCR-T cells do not recognize self-peptides presented by HLA-A2*01 on healthy human cell lines. (Figure 11A) IFN- γ production by MagIC TCR-T after co-culture of HLA-A:02*01 iPS-derived human cell lines or harvested normal human cell lines (determined by ICS or ELISA). Independent experiments performed from 3-5 healthy human donors. Cytokine production normalized to amount/percentage produced after co-culture with MAGE-A1 peptide-loaded cells. (Figure 11B) No evidence of monolayer destruction or limit to healthy normal cell growth during co-culture with MagIC-TCR T (Red, n=3 donors), as measured by IncuCyte live cell imaging. [0017] Figures 12A and 12B show that MagIC TCR-T cells recognize HLA- B:49*01. (Figure 12A) Cytokine production by MagIC TCR-T after co-culture with a panel of B-LCL cell lines (determined by ICS or ELISA). Independent experiments (n=2). (Figure 12B) IFN-γ production by MagIC TCR-T after co-culture of an HLA- B49+ tumor cell line Namalwa (n=3 donor T cell products). [0018] Figure 13 shows a phase-I trial study design investigating MagIC TCR-T cells in accordance with presently disclosed compositions and methods. DETAILED DESCRIPTION [0019] In certain aspects, the present disclosure provides methods and compositions for treating a cancer or other disease or disorder that is associated with expression of MAGE-A1 (e.g., expression of a MAGE-A1 antigen such as SEQ ID NO.:123, e.g., in complex with an HLA molecule such as HLA-A*02:01), such as, for example, triple negative breast cancer, non-small cell lung cancer, or urothelial cancer. [0020] In some aspects, the present disclosure provides methods for treating a cancer or disease or disorder that is associated with MAGE-A1 expression in a subject,
wherein the methods comprise administering to the subject a population of modified T cells comprising a binding protein (e.g., a T cell receptor (TCR) or a single-chain T cell receptor) capable of specifically binding to a MAGE-A1 peptide antigen (e.g. a MAGE- A1 peptide antigen:HLA complex), wherein the subject is negative for or has been identified as negative for expression of HLA B*49:01, and wherein the binding protein is optionally encoded by a heterologous polynucleotide comprised in the modified T cells. In certain embodiments, the MAGE-A1 peptide antigen is capable of binding to or being presented by a human HLA-A*02:01. In certain embodiments, the MAGE-A1 peptide antigen comprises or consists of the amino acid sequence set forth in SEQ ID NO.:123. [0021] In some aspects, the present disclosure provides methods for treating a cancer or disease or disorder that is associated with MAGE-A1 expression in a subject, the method comprising administering to the subject a population of modified immune cells comprising a binding protein, the binding protein comprising: (a) a TCR α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively; (b) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 30- 32, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 27-29, respectively; (c) T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 36-38, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 33-35, respectively; (d) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 42-44, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 39-41, respectively; or (e) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 24- 26, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 21-23, respectively, wherein
the subject is negative for or has been identified as negative for expression of HLA B*49:01. [0022] In some aspects, the present disclosure provides methods for treating a cancer, comprising administering to a subject in need thereof a population of modified cells comprising a binding protein, the binding protein comprising: (a) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively; (b) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 30- 32, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 27-29, respectively; (c) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 36-38, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 33-35, respectively; (d) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 42-44, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 39-41, respectively; or (e) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 24- 26, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 21-23, respectively, wherein the cancer or a cell thereof expresses MAGE-A1, and wherein: (i) the subject is lymphodepleted or has undergone a lymphodepletion procedure; (ii) the method further comprises administering a PD-1 inhibitor and/or a PD-L1 inhibitor to the subject; and/or (iii) the subject is negative for or has been identified as negative for expression of HLA B*49:01. [0023] In some aspects, the present disclosure provides an isolated polynucleotide that encodes (i) one or more CD8 co-receptor polypeptide or a portion thereof, and/or (ii) one or more MAGE-A1-specific TCR chain or a portion thereof. Also provided are vectors that comprise the polynucleotide, host cells that comprise the polynucleotide and/or vector, and host cell compositions.
[0024] By way of background, most tumor targets for T cell-based immunotherapies are self-antigens since tumors arise from previously normal tissue. For example, such tumor-associated antigens (TAAs) may be expressed at high levels in a cancer cell, but may not be expressed or may be minimally expressed in other cells. During T cell development in the thymus, T cells that bind weakly to self-antigens survive and undergo further development and maturation, while T cells that bind strongly to self-antigens are eliminated by the immune system since such cells would mount an undesirable autoimmune response. Hence, T cells are sorted by their relative ability to bind to antigens in order to prepare the immune system to respond against a foreign invader (i.e., recognition of non-self-antigen) while at the same time preventing an autoimmune response (i.e., recognition of self-antigen). This tolerance mechanism limits naturally occurring T cells that can recognize tumor (self) antigens with high affinity and, therefore, eliminates the T cells that would effectively eliminate tumor cells. Consequently, isolating T cells having high affinity TCRs specific for tumor antigens is difficult because most such cells are essentially eliminated by the immune system. [0025] In certain embodiments, the instant disclosure provides TCRs specific for MAGE-A1 (also called MAGE-1, MAGE family member A1, CT 1.1, and Melanoma-Antigen Gene 1) peptides, such as high affinity TCRs specific for MAGE- A1 peptides, wherein a cell expressing such a TCR is capable of binding to a MAGE- A1:HLA complex independent of CD8. In addition, such TCRs may optionally be capable of more efficiently associating with a CD3 protein as compared to endogenous TCRs. [0026] A method was developed to quickly and simultaneously screen and rank T cell clonotypes (based on affinity) from a large cohort of HLA-matched donors in a short time (about 6-8 weeks). In certain embodiments, the instant disclosure provides methods for enriching for cells with high-affinity TCRs by using limiting concentrations of antigen-specific pMHC multimers in the presence of a subject’s immune cells (e.g., PBMCs). The TCRβ repertoire and frequency analysis, coupled with bioinformatics, was used to accurately identify TCR α-chain and β-chain pairs. An advantage of these methods is that they allow for a quick comparison of the TCR affinity of thousands of clones from multiple donors as opposed to cloning individual TCRs.
[0027] The compositions and methods described herein will in certain embodiments have therapeutic utility for the treatment of diseases and conditions associated with MAGE-A1 expression. Such diseases include various forms of hyperproliferative disorders, such as hematological malignancies and solid cancers. Non-limiting examples of these and related uses are described herein and include in vitro, ex vivo and in vivo stimulation of MAGE-A1 antigen-specific T cell responses, such as by the use of recombinant T cells expressing an enhanced or high affinity TCR specific for a MAGE-A1 peptide. [0028] Prior to setting forth this disclosure in more detail, it may be helpful to an understanding thereof to provide definitions of certain terms to be used herein. Additional definitions are set forth throughout this disclosure. [0029] In the present description, any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated. Also, any number range recited herein relating to any physical feature, such as polymer subunits, size or thickness, are to be understood to include any integer within the recited range, unless otherwise indicated. As used herein, the term “about” means ± 20% of the indicated range, value, or structure, unless otherwise indicated. It should be understood that the terms “a” and “an” as used herein refer to “one or more” of the enumerated components. The use of the alternative (e.g., “or”) should be understood to mean either one, both, or any combination thereof of the alternatives. As used herein, the terms “include,” “have” and “comprise” are used synonymously, which terms and variants thereof are intended to be construed as non-limiting. [0030] In addition, it should be understood that the individual compounds, or groups of compounds, derived from the various combinations of the structures and substituents described herein, are disclosed by the present application to the same extent as if each compound or group of compounds was set forth individually. Thus, selection of particular structures or particular substituents is within the scope of the present disclosure. [0031] The term “consisting essentially of” is not equivalent to “comprising” and refers to the specified materials or steps of a claim, or to those that do not materially affect the basic characteristics of a claimed subject matter. For example, a
protein domain, region, or module (e.g., a binding domain, hinge region, linker module) or a protein (which may have one or more domains, regions, or modules) “consists essentially of” a particular amino acid sequence when the amino acid sequence of a domain, region, module, or protein includes extensions, deletions, mutations, or a combination thereof (e.g., amino acids at the amino- or carboxy-terminus or between domains) that, in combination, contribute to at most 20% (e.g., at most 15%, 10%, 8%, 6%, 5%, 4%, 3%, 2% or 1%) of the length of a domain, region, module, or protein and do not substantially affect (i.e., do not reduce the activity by more than 50%, such as no more than 40%, 30%, 25%, 20%, 15%, 10%, 5%, or 1%) the activity of the domain(s), region(s), module(s), or protein (e.g., the target binding affinity of a binding protein). [0032] As used herein, an “immune system cell” means any cell of the immune system that originates from a hematopoietic stem cell in the bone marrow, which gives rise to two major lineages, a myeloid progenitor cell (which give rise to myeloid cells such as monocytes, macrophages, dendritic cells, megakaryocytes and granulocytes) and a lymphoid progenitor cell (which give rise to lymphoid cells such as T cells, B cells and natural killer (NK) cells). Exemplary immune system cells include a CD4+ T cell, a CD8+ T cell, a CD4- CD8- double negative T cell, a γδ T cell, a regulatory T cell, a natural killer cell, and a dendritic cell. Macrophages and dendritic cells may be referred to as “antigen presenting cells” or “APCs,” which are specialized cells that can activate T cells when a major histocompatibility complex (MHC) receptor on the surface of the APC complexed with a peptide interacts with a TCR on the surface of a T cell. [0033] “Major histocompatibility complex” (MHC) refers to glycoproteins that deliver peptide antigens to a cell surface. MHC class I molecules are heterodimers having a membrane spanning α chain (with three α domains) and a non-covalently associated β2 microglobulin. MHC class II molecules are composed of two transmembrane glycoproteins, α and β, both of which span the membrane. Each chain has two domains. MHC class I molecules deliver peptides originating in the cytosol to the cell surface, where a peptide:MHC complex is recognized by CD8+ T cells. MHC class II molecules deliver peptides originating in the vesicular system to the cell surface, where they are recognized by CD4+ T cells. Human MHC is referred to as human leukocyte antigen (HLA).
[0034] A “T cell” is an immune system cell that matures in the thymus and produces T cell receptors (TCRs). T cells can be naïve (not exposed to antigen; increased expression of CD62L, CCR7, CD28, CD3, CD127, and CD45RA, and decreased expression of CD45RO as compared to TCM), memory T cells (TM) (antigen- experienced and long-lived), and effector cells (antigen-experienced, cytotoxic). TM can be further divided into subsets of central memory T cells (TCM, increased expression of CD62L, CCR7, CD28, CD127, CD45RO, and CD95, and decreased expression of CD54RA as compared to naïve T cells) and effector memory T cells (TEM, decreased expression of CD62L, CCR7, CD28, CD45RA, and increased expression of CD127 as compared to naïve T cells or TCM). Effector T cells (TE) refers to antigen-experienced CD8+ cytotoxic T lymphocytes that have decreased expression of CD62L, CCR7, CD28, and are positive for granzyme and perforin as compared to TCM. Other exemplary T cells include regulatory T cells, such as CD4+ CD25+ (Foxp3+) regulatory T cells and Treg17 cells, as well as Tr1, Th3, CD8+CD28-, and Qa-1 restricted T cells. [0035] “T cell receptor” (TCR) refers to an immunoglobulin superfamily member comprising comprising a variable binding domain, a constant domain, a transmembrane region, and a short cytoplasmic tail; see, e.g., Janeway et al., Immunobiology: The Immune System in Health and Disease, 3rd Ed., Current Biology Publications, p.4:33, 1997) and capable of specifically binding to an antigen peptide bound to an MHC receptor. A TCR can be found on the surface of a cell or in soluble form and generally is comprised of a heterodimer having α and β chains (also known as TCRα and TCRβ, respectively), or γ and δ chains (also known as TCRγ and TCRδ, respectively). The extracellular portion of a TCR chain (e.g., α-chain, β-chain) contains two immunoglobulin domains, a variable domain (e.g., α-chain variable domain or Vα, β-chain variable domain or Vβ; typically amino acids 1 to 116 based on Kabat numbering Kabat et al., “Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, Public Health Service National Institutes of Health, 1991, 5th ed.) at the N-terminus, and one constant domain (e.g., α-chain constant domain or Cα, typically amino acids 117 to 259 based on Kabat, β-chain constant domain or C ^, typically amino acids 117 to 295 based on Kabat) adjacent to the cell membrane. Also like immunoglobulins, the variable domains contain complementary determining
regions (CDRs) separated by framework regions (FRs) (see, e.g., Jores et al., Proc. Nat’l Acad. Sci. U.S.A.87:9138, 1990; Chothia et al., EMBO J.7:3745, 1988; see also Lefranc et al., Dev. Comp. Immunol.27:55, 2003). The Vα and Vβ of a native TCR generally have similar structures, with each variable domain comprising four conserved FRs and three CDRs. The Vα domain is encoded by two separate DNA segments, the variable gene segment and the joining gene segment (V-J); the Vβ domain is encoded by three separate DNA segments, the variable gene segment, the diversity gene segment, and the joining gene segment (V-D-J). A single Vα or V β domain may be sufficient to confer antigen-binding specificity. Furthermore, TCRs that bind a particular antigen may be isolated using a Vα or V β domain from a TCR that binds the antigen to screen a library of complementary Vα or V β domains, respectively. In certain embodiments, a TCR is found on the surface of T cells (or T lymphocytes) and associates with the CD3 complex. The source of a TCR as used in the present disclosure may be from various animal species, such as a human, mouse, rat, rabbit or other mammal. [0036] As used herein, the term “CD8 co-receptor” or “CD8” means the cell surface glycoprotein CD8, either as an alpha-alpha homodimer or an alpha-beta heterodimer. The CD8 co-receptor assists in the function of cytotoxic T cells (CD8+) and functions through signaling via its cytoplasmic tyrosine phosphorylation pathway (Gao and Jakobsen, Immunol. Today 21:630-636, 2000; Cole and Gao, Cell. Mol. Immunol.1:81- 88, 2004). There are five (5) different CD8 beta chains (see UniProtKB identifier P10966) and a single CD8 alpha chain (see UniProtKB identifier P01732). CD8 generally binds pMHC Class I complexes. [0037] “CD4 co-receptor” or “CD4” refers to an immunoglobulin co-receptor glycoprotein that assists the TCR in communicating with antigen-presenting cells (see, Campbell & Reece, Biology 909 (Benjamin Cummings, Sixth Ed., 2002)). CD4 is found on the surface of immune cells such as T helper cells, monocytes, macrophages, and dendritic cells, and includes four immunoglobulin domains (D1 to D4) that are expressed at the cell surface. During antigen presentation, CD4 is recruited, along with the TCR complex, to bind to different regions of the MHCII molecule (CD4 binds MHCII β2, while the TCR complex binds MHCII α1/β1). Without wishing to be bound by theory, it is believed that close proximity to the TCR complex allows CD4- associated kinase molecules to phosphorylate the immunoreceptor tyrosine activation
motifs (ITAMs) present on the cytoplasmic domains of CD3. This activity is thought to amplify the signal generated by the activated TCR in order to produce various types of T helper cells. CD4 generally binds pMHC Class II complexes. [0038] “CD3” is a multi-protein complex of six chains (see, Abbas and Lichtman, 2003; Janeway et al., p172 and 178, 1999). In mammals, the complex comprises a CD3γ chain, a CD3δ chain, two CD3ε chains, and a homodimer of CD3ζ chains. The CD3γ, CD3δ, and CD3ε chains are highly related cell surface proteins of the immunoglobulin superfamily containing a single immunoglobulin domain. The transmembrane regions of the CD3γ, CD3δ, and CD3ε chains are negatively charged, which is a characteristic that allows these chains to associate with positively charged regions of T cell receptor chains. The intracellular tails of the CD3γ, CD3δ, and CD3ε chains each contain a single conserved motif known as an immunoreceptor tyrosine- based activation motif or ITAM, whereas each CD3ζ chain has three. Without wishing to be bound by theory, it is believed that the ITAMs are important for the signaling capacity of a TCR complex. CD3 as used in the present disclosure may be from various animal species, including human, mouse, rat, or other mammals. [0039] As used herein, “TCR complex” refers to a complex formed by the association of CD3 with TCR. For example, a TCR complex can be composed of a CD3γ chain, a CD3δ chain, two CD3ε chains, a homodimer of CD3ζ chains, a TCRα chain, and a TCRβ chain. Alternatively, a TCR complex can be composed of a CD3γ chain, a CD3δ chain, two CD3ε chains, a homodimer of CD3ζ chains, a TCRγ chain, and a TCRδ chain. [0040] A “component of a TCR complex,” as used herein, refers to a TCR chain (i.e., TCRα, TCRβ, TCRγ or TCRδ), a CD3 chain (i.e., CD3γ, CD3δ, CD3ε or CD3ζ), or a complex formed by two or more TCR chains or CD3 chains (e.g., a complex of TCRα and TCRβ, a complex of TCRγ and TCRδ, a complex of CD3ε and CD3δ, a complex of CD3γ and CD3ε, or a sub-TCR complex of TCRα, TCRβ, CD3γ, CD3δ, and two CD3ε chains). [0041] A “binding domain” (also referred to as a “binding region” or “binding moiety”), as used herein, refers to a molecule or portion thereof (e.g., peptide, oligopeptide, polypeptide, protein) that possesses the ability to specifically and non- covalently associate, unite, or combine with a target (e.g., MAGE-A1, MAGE-A1 peptide:MHC complex). A binding domain includes any naturally occurring, synthetic,
semi-synthetic, or recombinantly produced binding partner for a biological molecule, a molecular complex (i.e., complex comprising two or more biological molecules), or other target of interest. Exemplary binding domains include single chain immunoglobulin variable regions (e.g., scTCR, scTv, scFv), receptor ectodomains, ligands (e.g., cytokines, chemokines), or synthetic polypeptides selected for their specific ability to bind to a biological molecule, a molecular complex or other target of interest. [0042] As used herein, “specifically binds” or “specific for” refers to an association or union of a binding protein (e.g., TCR receptor) or a binding domain (or fusion protein thereof) to a target molecule with an affinity or Ka (i.e., an equilibrium association constant of a particular binding interaction with units of 1/M) equal to or greater than 105 M-1 (which equals the ratio of the on-rate [kon] to the off-rate [koff] for this association reaction), while not significantly associating or uniting with any other molecules or components in a sample. Binding proteins or binding domains (or fusion proteins thereof) may be classified as “high affinity” binding proteins or binding domains (or fusion proteins thereof) or as “low affinity” binding proteins or binding domains (or fusion proteins thereof). “High affinity” binding proteins or binding domains refer to those binding proteins or binding domains having a Ka of at least 107 M-1, at least 108 M-1, at least 109 M-1, at least 1010 M-1, at least 1011 M-1, at least 1012 M- 1, or at least 1013 M-1. “Low affinity” binding proteins or binding domains refer to those binding proteins or binding domains having a Ka of up to 107 M-1, up to 106 M-1, up to 105 M-1. Alternatively, affinity may be defined as an equilibrium dissociation constant (Kd) of a particular binding interaction with units of M (e.g., 10-5 M to 10-13 M). [0043] In certain embodiments, a receptor or binding domain may have “enhanced affinity,” which refers to selected or engineered receptors or binding domains with stronger binding to a target antigen than a wild type (or parent) binding domain. For example, enhanced affinity may be due to a Ka (equilibrium association constant) for the target antigen that is higher than the wild type binding domain, due to a Kd (dissociation constant) for the target antigen that is less than that of the wild type binding domain, due to an off-rate (koff) for the target antigen that is less than that of the wild type binding domain, or a combination thereof. [0044] In certain embodiments, polynucleotides encoding binding protein (e.g., TCRs, such as enhanced affinity TCRs), may be codon optimized to enhance expression
in a particular host cell, such as T cells (e.g., Scholten et al., Clin. Immunol.119:135, 2006). [0045] A variety of assays are known for identifying binding domains of the present disclosure that specifically bind a particular target, as well as determining binding domain or fusion protein affinities, such as such as multimer/tetramer staining (e.g., peptide:MHC tetramer), Western blot, ELISA, analytical ultracentrifugation, spectroscopy and surface plasmon resonance (Biacore®) analysis (see, e.g., Scatchard et al., Ann. N.Y. Acad. Sci.51:660, 1949; Wilson, Science 295:2103, 2002; Wolff et al., Cancer Res.53:2560, 1993; and U.S. Patent Nos.5,283,173, 5,468,614, or the equivalent). [0046] The term “MAGE-A1-specific binding protein” refers to a protein or polypeptide that specifically binds to MAGE-A1 or a peptide or fragment thereof. In some embodiments, a MAGE-A1-specific binding protein or polypeptide binds to MAGE-A1 or a peptide thereof, such as a MAGE-A1 peptide complexed with an MHC or HLA molecule, e.g., on a cell surface, with at least, or at least about, a particular affinity. In certain embodiments, a MAGE-A1-specific binding protein binds a MAGE- A1-derived peptide:HLA complex (or MAGE-A1-derived peptide:MHC complex) with a Kd of less than about 10-8 M, less than about 10-9 M, less than about 10-10 M, less than about 10-11 M, less than about 10-12 M, or less than about 10-13 M, or with an affinity that is about the same as, at least about the same as, or is greater than at or about the affinity exhibited by an exemplary MAGE-A1 specific binding protein provided herein, such as any of the MAGE-A1-specific TCRs provided herein, for example, as measured by the same assay. In certain embodiments, a MAGE-A1-specific binding protein comprises a MAGE-A1-specific immunoglobulin superfamily binding protein or binding portion thereof. [0047] Assays for assessing affinity or apparent affinity or relative affinity include, for example, measuring apparent affinity for a TCR (or for a binding protein comprising a binding domain derived from a TCR) by assessing binding to various concentrations of tetramers, for example, by flow cytometry using labeled tetramers. In some examples, apparent KD of a TCR is measured using 2-fold dilutions of labeled tetramers at a range of concentrations, followed by determination of binding curves by non-linear regression, apparent KD being determined as the concentration of ligand that yielded half-maximal binding.
[0048] The term “MAGE-A1 binding domain” or “MAGE-A1 binding fragment” refer to a domain, or portion of a MAGE-A1-specific binding protein, responsible for the specific MAGE-A1 binding. A MAGE-A1-specific binding domain alone (i.e., without any other portion of a MAGE-A1-specific binding protein) can be soluble and can bind to MAGE-A1 with a Kd of less than about 10-8 M, less than about 10-9 M, less than about 10-10 M, less than about 10-11 M, less than about 10-12 M, or less than about 10-13 M. MAGE-A1-specific binding domains include, for example, MAGE- A1-specific TCR, scTCR (e.g., single chain α ^TCR or scTv proteins such as Vα-L-V ^, V ^-L-Vα, Vβ-L-Vα-Cα, or Vα-L-V ^-C ^, wherein Vα and V ^ are TCRα and ^ variable domains respectively, Cα and C ^ are TCRα and ^ constant domains, respectively, and L is a linker) and scFv fragments as described herein, which can be derived from an anti-MAGE-A1 TCR or antibody. [0049] Principles of antigen processing by antigen presenting cells (APC) (such as dendritic cells, macrophages, lymphocytes or other cell types), and of antigen presentation by APC to T cells, including major histocompatibility complex (MHC)- restricted presentation between immunocompatible (e.g., sharing at least one allelic form of an MHC gene that is relevant for antigen presentation) APC and T cells, are well established (see, e.g., Murphy, Janeway’s Immunobiology (8th Ed.) 2011 Garland Science, NY; chapters 6, 9 and 16). For example, processed antigen peptides originating in the cytosol (e.g., tumor antigen, intracellular pathogen) are generally from about 7 amino acids to about 11 amino acids in length and will associate with class I MHC molecules, whereas peptides processed in the vesicular system (e.g., bacterial, viral) will vary in length from about 10 amino acids to about 25 amino acids and associate with class II MHC molecules. [0050] “MAGE-A1 antigen” or “MAGE-A1 peptide antigen” refer to a naturally or synthetically produced portion of a MAGE-A1 protein ranging in length from about 7 amino acids to about 15 amino acids, which can form a complex with a MHC (e.g., HLA) molecule and such a complex can bind with a TCR specific for a MAGE-A1 peptide:MHC (e.g., HLA) complex. In certain embodiments, a MAGE-A1 peptide antigen comprises or consists of the amino acid sequence set forth in SEQ ID NO.:123.
[0051] A “linker” refers to an amino acid sequence that connects two proteins, polypeptides, peptides, domains, regions, or motifs and may provide a spacer function compatible with interaction of the two sub-binding domains so that the resulting polypeptide retains a specific binding affinity (e.g., scTCR) to a target molecule or retains signaling activity (e.g., TCR complex). In certain embodiments, a linker is comprised of about two to about 35 amino acids, for instance, or about four to about 20 amino acids or about eight to about 15 amino acids or about 15 to about 25 amino acids. [0052] “Junction amino acids” or “junction amino acid residues” refer to one or more (e.g., about 2-10) amino acid residues between two adjacent motifs, regions, or domains of a polypeptide, such as between a binding domain and an adjacent constant domain or between a TCR chain and an adjacent self-cleaving peptide. Junction amino acids may result from the construct design of a fusion protein (e.g., amino acid residues resulting from the use of a restriction enzyme site during the construction of a nucleic acid molecule encoding a fusion protein). [0053] An “altered domain” or “altered protein” refers to a motif, region, domain, peptide, polypeptide, or protein with a non-identical sequence identity to a wild type motif, region, domain, peptide, polypeptide, or protein (e.g., a wild type TCRα chain, TCR ^ chain, TCRα constant domain, TCR ^ constant domain) of at least 85% (e.g., 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9%). [0054] As used herein, “nucleic acid” or “nucleic acid molecule” or “polynucleotide” refers to any of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), oligonucleotides, fragments generated, for example, by the polymerase chain reaction (PCR) or by in vitro translation, and fragments generated by any of ligation, scission, endonuclease action, or exonuclease action. In certain embodiments, the nucleic acids of the present disclosure are produced by PCR. Nucleic acids may be composed of monomers that are naturally occurring nucleotides (such as deoxyribonucleotides and ribonucleotides), analogs of naturally occurring nucleotides (e.g., α-enantiomeric forms of naturally-occurring nucleotides), or a combination of both. Modified nucleotides can have modifications in or replacement of sugar moieties, or pyrimidine or purine base moieties. Nucleic acid monomers can be linked by phosphodiester bonds or analogs of such linkages. Analogs of phosphodiester linkages include phosphorothioate, phosphorodithioate, phosphoroselenoate,
phosphorodiselenoate, phosphoroanilothioate, phosphoranilidate, phosphoramidate, and the like. Nucleic acid molecules can be either single stranded or double stranded. [0055] The term “isolated” means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally occurring nucleic acid or polypeptide present in a living animal is not isolated, but the same nucleic acid or polypeptide, separated from some or all of the co-existing materials in the natural system, is isolated. Such nucleic acid could be part of a vector and/or such nucleic acid or polypeptide could be part of a composition (e.g., a cell lysate), and still be isolated in that such vector or composition is not part of the natural environment for the nucleic acid or polypeptide. The term “gene” means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region “leader and trailer” as well as intervening sequences (introns) between individual coding segments (exons). [0056] As used herein, the terms “modified”, “engineered”, or “recombinant” refer to a cell, microorganism, nucleic acid molecule, or vector that has been genetically engineered by human intervention – that is, modified by introduction of an exogenous or heterologous nucleic acid molecule, or refers to a cell or microorganism that has been altered such that expression of an endogenous nucleic acid molecule or gene is controlled, deregulated or constitutive. Human-generated genetic alterations may include, for example, modifications that introduce nucleic acid molecules (which may include an expression control element, such as a promoter) that encode one or more proteins or enzymes, or other nucleic acid molecule additions, deletions, substitutions, or other functional disruption of or addition to a cell’s genetic material. Exemplary modifications include those in coding regions or functional fragments thereof of heterologous or homologous polypeptides from a reference or parent molecule. [0057] As used herein, “mutation” refers to a change in the sequence of a nucleic acid molecule or polypeptide molecule as compared to a reference or wild-type nucleic acid molecule or polypeptide molecule, respectively. A mutation can result in several different types of change in sequence, including substitution, insertion or deletion of nucleotide(s) or amino acid(s). In certain embodiments, a mutation is a substitution of one or three codons or amino acids, a deletion of one to about five codons or amino acids, or a combination thereof.
[0058] A “conservative substitution” is recognized in the art as a substitution of one amino acid for another amino acid that has similar properties. Exemplary conservative substitutions are described in, for example: WO 97/09433 at page 10; Lehninger, Biochemistry, 2nd Edition; Worth Publishers, Inc. NY, NY, pp.71-77, 1975; and Lewin, Genes IV, Oxford University Press, NY and Cell Press, Cambridge, MA, p. 8, 1990. Conservative substitutions of amino acids may occur naturally or may be introduced when a binding protein or TCR is recombinantly produced. Amino acid substitutions, deletions, and additions may be introduced into a protein using mutagenesis methods known in the art (see, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, 3d ed., Cold Spring Harbor Laboratory Press, NY, 2001). Oligonucleotide-directed site-specific (or segment specific) mutagenesis procedures may be employed to provide an altered polynucleotide that has particular codons altered according to the substitution, deletion, or insertion desired. Alternatively, random or saturation mutagenesis techniques, such as alanine scanning mutagenesis, error prone polymerase chain reaction mutagenesis, and oligonucleotide-directed mutagenesis may be used to prepare immunogen polypeptide variants (see, e.g., Sambrook et al., supra). [0059] The term “construct” refers to any polynucleotide that contains a recombinant nucleic acid molecule. A construct may be present in a vector (e.g., a bacterial vector, a viral vector) or may be integrated into a genome. [0060] A “vector” is a nucleic acid molecule that is capable of transporting another nucleic acid molecule. Vectors may be, for example, plasmids, cosmids, viruses, a RNA vector or a linear or circular DNA or RNA molecule that may include chromosomal, non-chromosomal, semi-synthetic or synthetic nucleic acid molecules. Exemplary vectors are those capable of autonomous replication (episomal vector) or expression of nucleic acid molecules to which they are linked (expression vectors). [0061] The term “operably linked” or “operatively-linked” refers to the association of two or more nucleic acid molecules on a single nucleic acid molecule or fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., the coding sequence is under the transcriptional control of the promoter). “Unlinked” means that the associated genetic elements are not closely associated with one another and the function of one does not affect the other.
[0062] As used herein, “expression vector” refers to a DNA construct containing a nucleic acid molecule that is operably-linked to a suitable control sequence capable of effecting the expression of the nucleic acid molecule in a suitable host. Such control sequences include a promoter to effect transcription, an optional operator sequence to control such transcription, a sequence encoding suitable mRNA ribosome binding sites, and sequences which control termination of transcription and translation. The vector may be a plasmid, a phage particle, a virus, or simply a potential genomic insert. Once transformed into a suitable host, the vector may replicate and function independently of the host genome, or may, in some instances, integrate into the genome itself. In the present specification, “plasmid,” “expression plasmid,” “virus” and “vector” are often used interchangeably. [0063] The term “expression”, as used herein, refers to the process by which a polypeptide is produced based on the encoding sequence of a nucleic acid molecule, such as a gene. The process may include transcription, post-transcriptional control, post-transcriptional modification, translation, post-translational control, post- translational modification, or any combination thereof. [0064] The term “introduced” in the context of inserting a nucleic acid molecule into a cell, means “transfection”, or ‘transformation” or “transduction” and includes reference to the incorporation of a nucleic acid molecule into a eukaryotic or prokaryotic cell wherein the nucleic acid molecule may be incorporated into the genome of a cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA). [0065] As used herein, “heterologous” or “exogenous” nucleic acid molecule, construct or sequence refers to polynucleotide or portion of a polynucleotide that is not native to a host cell, but may be homologous to a polynucleotide or portion of a polynucleotide from the host cell. The source of the heterologous or exogenous polynucleotide, construct or sequence may be from a different genus or species. In certain embodiments, a heterologous or exogenous polynucleotide is added (i.e., not endogenous or native) to a host cell or host genome by, for example, conjugation, transformation, transfection, electroporation, or the like, wherein the added molecule may integrate into the host genome or exist as extra-chromosomal genetic material (e.g., as a plasmid or other form of self-replicating vector) and may be present in
multiple copies. In addition, “heterologous” refers to a non-native enzyme, protein or other activity encoded by an exogenous polynucleotide introduced into the host cell, even if the host cell encodes a homologous protein or activity. It will be appreciated that in the case of a host cell that comprises a heterologous polynucleotide, the polynucleotide is "heterologous" to progeny of the host cell, whether or not the progeny were themselves manipulated (e.g., transduced) to contain the polynucleotide. Such a host cell may be referred-to as a "modified" host cell, whether the subject host cell was itself modified to comprise the polynucleotide, or whether an ancestor cell of the subject host cell was modified to comprise the polynucleotide. [0066] As described herein, more than one heterologous or exogenous nucleic acid molecule can be introduced into a host cell as separate polynucleotides, as a plurality of individually controlled genes, as a polycistronic polynucleotide, as a single nucleic acid molecule encoding a fusion protein, or any combination thereof. For example, as disclosed herein, a host cell can be modified to express two or more heterologous or exogenous polynucleotides encoding a desired binding protein (e.g., encoding a TCR) specific for a MAGE-A1 antigen peptide (e.g., TCRα and TCR ^). When two or more exogenous nucleic acid molecules are introduced into a host cell, it is understood that the two or more exogenous nucleic acid molecules can be introduced as a single polynucleotide (e.g., on a single vector), on separate vectors, integrated into the host chromosome at a single site or multiple sites, or any combination thereof. The number of referenced heterologous nucleic acid molecules or protein activities refers to the number of encoding nucleic acid molecules or the number of protein activities, not the number of separate polynucleotides introduced into a host cell. [0067] As used herein, the term “endogenous” or “native” refers to a gene, protein, or activity that is normally present in a host cell. Moreover, a gene, protein or activity that is mutated, overexpressed, shuffled, duplicated, or otherwise altered as compared to a parent gene, protein or activity is still considered to be endogenous or native to that particular host cell. For example, an endogenous control sequence from a first gene (e.g., promoter, translational attenuation sequences) may be used to alter or regulate expression of a second native gene or nucleic acid molecule, wherein the expression or regulation of the second native gene or nucleic acid molecule differs from normal expression or regulation in a parent cell.
[0068] The term “homologous” or “homolog” refers to a molecule or activity found in or derived from a host cell, species or strain. For example, a heterologous or exogenous nucleic acid molecule may be homologous to a native host cell gene, and may optionally have an altered expression level, a different sequence, an altered activity, or any combination thereof. [0069] “Sequence identity,” as used herein, refers to the percentage of amino acid residues in one sequence that are identical with the amino acid residues in another reference polypeptide sequence after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. The percentage sequence identity values can be generated using the NCBI BLAST2.0 software as defined by Altschul et al. (1997) “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”, Nucleic Acids Res.25:3389-3402, with the parameters set to default values. [0070] As used herein, a “hematopoietic progenitor cell” is a cell that can be derived from hematopoietic stem cells or fetal tissue and is capable of further differentiation into mature cells types (e.g., immune system cells). Exemplary hematopoietic progenitor cells include those with a CD24Lo Lin– CD117+ phenotype or those found in the thymus (referred to as progenitor thymocytes). [0071] As used herein, the term “host cell” refers to a cell (e.g., T cell) or microorganism targeted for genetic modification with a heterologous or exogenous nucleic acid molecule to produce a polypeptide of interest (e.g., a binding protein such as high-affinity or enhanced- affinity anti- MAGE-A1 TCR). In certain embodiments, a host cell may optionally already possess or be modified to include other genetic modifications that confer desired properties related or unrelated to biosynthesis of the heterologous or exogenous protein (e.g., inclusion of a detectable marker; deleted, altered or truncated endogenous TCR; increased co-stimulatory factor expression). In certain embodiments, a host cell is a human hematopoietic progenitor cell transduced with a heterologous or exogenous nucleic acid molecule encoding a TCR specific for a MAGE-A1 antigen peptide. [0072] As used herein, “hyperproliferative disorder” refers to excessive growth or proliferation as compared to a normal or undiseased cell. Exemplary
hyperproliferative disorders include tumors, cancers, neoplastic tissue, carcinoma, sarcoma, malignant cells, pre-malignant cells, as well as non-neoplastic or non- malignant hyperproliferative disorders (e.g., adenoma, fibroma, lipoma, leiomyoma, hemangioma, fibrosis, restenosis, as well as autoimmune diseases such as rheumatoid arthritis, osteoarthritis, psoriasis, inflammatory bowel disease, or the like). Certain diseases that involve abnormal or excessive growth that occurs more slowly than in the context of a hyperproliferative disease can be referred to as “proliferative diseases”, and include certain tumors, cancers, neoplastic tissue, carcinoma, sarcoma, malignant cells, pre-malignant cells, as well as non-neoplastic or non-malignant disorders. Binding Proteins Specific for MAGE-A1 Antigen Peptides [0073] In certain aspects, the present disclosure provides a modified cell comprising a binding protein (e.g, a TCR, a single chain TCR (scTCR), a scTv, or a CAR) that binds (e.g., specific binding) to MAGE-A1 or a MAGE-A1 peptide antigen, such as a MAGE-A1 peptide complexed with an HLA molecule. [0074] By way of background, ideal targets for immunotherapy are immunogenic proteins with high expression in malignant tissues and limited-to-absent expression in normal tissues. A unique group of proteins, known as cancer/testis antigens (CTAs), have been identified as promising immunotherapeutic targets due to their expression in various malignant tissues but low-level expression in healthy adult tissue except for germ cells of the testis (Ademuyiwa et al. PLoS One, 7(6):e38783 (2012); Badovinac Crnjevic et al., Med Oncol., 29(3):1586-91 (2012); Curigliano, G. et al., Ann. Oncol., 22(1):98-103 (2011). Moreover, CTAs are especially expressed in higher-grade lesions and aggressive malignancies, and associated with poorer clinical outcomes (Barrow et al., Clin Cancer Res., 12(3 Pt 1):764-71 (2006); Gure, et al. Clin Cancer Res., 11(22):8055-62 (2005); Velazquez et al., Cancer Immun., 7: 11 (2007)). MAGE family proteins are CTAs that are broadly expressed in many tumor types such as melanoma, lung, ovarian, multiple myeloma as well as TNBC. Simpson, A.J., et al., Cancer/testis antigens, gametogenesis and cancer, Nat. Rev. Cancer, 2005.5(8):615-25; Weon, J.L. and P.R. Potts, Curr Opin Cell Biol, 2015.37: 1-8; Park, T.S., et al., J Immunother, 2016.39(1): 1-7; Li, X., S.C. Hughes, and R. Wevrick, Cancer Genet, 2015.208(1-102):25-34; Kerkar, S.P., et al., J Immunother, 2016.39(4):181-7. In particular, MAGE- A1 is expressed in 69.1% of TNBC cases overall (n=81) and in
85.7% of Grade III cases. Mrklic, I., et al., Acta Histochem, 2014.116(5): 740-6. Additionally, evidence from melanoma cell lines suggests that MAGE-A1 directly drives tumorogenesis. Wang, D., et al., Biochem Biophys Res Commun, 2016.473(4): 959-65. [0075] In certain embodiments, a binding protein of the instant disclosure comprises (a) a T cell receptor (TCR) α-chain variable (Vα) domain having a CDR3 amino acid sequence according to any one of SEQ ID NOS.:26, 32, 38, 44, 50, or 51, and a TCR β-chain variable (Vβ) domain; (b) a Vβ domain having a CDR3 amino acid sequence according to any one of SEQ ID NOS.:23, 29, 35, 41, or 47, and a Vα domain; or (c) a Vα domain having a CDR3 amino acid sequence according to any one of SEQ ID NOs:26, 32, 38, 44, 50, or 51, and a Vβ domain having a CDR3 amino acid sequence according to any one of SEQ ID NOs:23, 29, 35, 41, or 47. Such binding proteins are described in WO 2018/170338 and US 2020-0017568 A1, both of which are incorporated herein by reference in their entireties, including the binding protein amino acid sequences therein, including the CDR, variable domain, and constant domain amino acid sequences of the binding proteins therein, and including the CD8 co- receptor amino acid sequences therein. In some embodiments, a CDR3 sequence is according to the IMGT junction definition. [0076] Peptide-MHC complexes, such as MAGE-A1 peptide:MHC complexes, are recognized and bound by the TCR Vα and TCR Vβ domains, with at least the specificity for peptide:MHC determined by CDRs. During lymphocyte development, Vα exons are assembled from different variable and joining gene segments (V-J), and Vβ exons are assembled from different variable, diversity, and joining gene segments (V-D-J). The TCRα chromosomal locus has 70-80 variable gene segments and 61 joining gene segments. The TCRβ chromosomal locus has 52 variable gene segments, and two separate clusters of each containing a single diversity gene segment, together with six or seven joining gene segments. Functional Vα and Vβ gene exons are generated by the recombination of a variable gene segment with a joining gene segment for Vα, and a variable gene segment with a diversity gene segment and a joining gene segment for Vβ. [0077] TCR Vα and Vβ domains each comprise three hypervariable loops, also referred to as complementary determining regions (CDRs) that contact the peptide- MHC complex (it may be possible in some cases for one or more CDR to not make
contact with the peptide-MHC complex, but at least one CDR will make contact with the peptide-MHC complex). The terms “complementarity determining region,” and “CDR,” are synonymous with “hypervariable region” or “HVR,” and are known in the art to refer to sequences of amino acids within immunoglobulin (e.g., TCR) variable regions, which confer antigen specificity and/or binding affinity and are separated from one another by framework regions. In general, there are three CDRs in each TCR α- chain variable region (αCDR1, αCDR2, αCDR3) and three CDRs in each TCR β-chain variable region (βCDR1, βCDR2, βCDR3). In TCRs, CDR3 is generally thought to be the main CDR responsible for recognizing processed antigen. Typically, CDR1 and CDR2 mainly interact with the MHC. [0078] CDR1 and CDR2 are encoded within the variable gene segment, whereas CDR3 is encoded by the region spanning the variable and joining segments for Vα, or the region spanning variable, diversity, and joining segments for Vβ. Thus, if the identity of the variable gene segment of a Vα or Vβ is known (e.g., by known TRAV or TRVB alleles), the sequences of their corresponding CDR1 and CDR2 can be deduced. [0079] Moreover, certain of the presently disclosed TCR variable regions specific for MAGE-A1 are encoded by a select TCRα allele or a TCRβ allele. In certain embodiments, an encoded binding domain comprises a Vβ domain that is derived from a TRBV30 allele, a TRBV29 allele, or a TRBV9 allele. In some embodiments, an encoded binding domain comprises a Vα domain that is derived from a TRAV38-1 allele, a TRAV34 allele, a TRAV16 allele, or a TRAV5 allele. [0080] TCR variable domain sequences can be aligned to a numbering scheme (e.g., the international Immunogenetics Information System (IMGT; see e.g. imgt.org and LeFranc, Front Immunol 5:22 (2014); doi: 10.3389/fimmu.2014.00022) and Aho), allowing equivalent residue positions to be annotated and for different molecules to be compared using Antigen receptor Numbering and Receptor Classification (ANARCI) software tool (2016, Bioinformatics 15:298-300). A numbering scheme provides a standardized delineation of framework regions and CDRs in the TCR variable domains. In certain embodiments, CDRs are according to IMGT numbering. In certain embodiments, variable domains are according to IMGT. In certain embodiments, constant domains are according to IMGT. [0081] In certain embodiments, a binding protein comprises a functional variant amino acid sequence as compared to a reference amino acid sequence disclosed herein,
wherein the encoded binding protein retains binding characteristics as compared to a binding protein comprising a reference amino acid sequence. For example, in some embodiments, an encoded Vα domain comprises an amino acid sequence that is at least about 90% identical (e.g., is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%, or 100% identical) to an amino acid sequence according to any one of SEQ ID NOS.:3, 7, 11, 15, and 19, and an encoded Vβ domain comprises an amino acid sequence that is at least about 90% identical to the amino acid sequence according to any one of SEQ ID NOS.:1, 5, 9, 13, 17, provided that (a) at least three or four of the CDRs have no change in sequence, wherein the CDRs that do have sequence changes have only up to two amino acid substitutions, up to a contiguous five amino acid deletion, or a combination thereof, and (b) the encoded binding protein remains capable of specifically binding to a MAGE-A1 peptide:HLA cell surface complex independent, or in the absence, of CD8. [0082] In particular embodiments, (a) a Vα domain comprises (i) a CDR1 amino acid sequence according to any one of SEQ ID NOS:24, 30, 36, 42, and 48, and/or (ii) a CDR2 amino acid sequence according to any one of SEQ ID NOS:25, 31, 37, 43, and 49; and/or (b) an encoded Vβ domain comprises (iii) a CDR1 amino acid sequence according to any one of SEQ ID NOS:21, 27, 33, 39, and 45, and/or (iv) a CDR2 amino acid sequence according to any one of SEQ ID NOS:22, 28, 34, 40, and 46. In further embodiments, an encoded binding protein comprises: (a) Vα CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:24-26, respectively, and V β CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:21-23, respectively; (b) Vα CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:30-32, respectively, and V β CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:27-29, respectively; (c) Vα CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:36-38, respectively, and V β CDR1, CDR2, [0083] and CDR3 amino acid sequences according to SEQ ID NOS:33-35, respectively; (d) Vα CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:42-44, respectively, and Vβ CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:39-41, respectively; or (e) Vα CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:48-50, respectively, and Vβ CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS:45-47, respectively.
[0084] In any of the embodiments described herein, a polypeptide of this disclosure can comprise a “signal peptide” (also known as a leader sequence, leader peptide, or transit peptide). Signal peptides target newly synthesized polypeptides to their appropriate location inside or outside the cell. A signal peptide may be removed from the polypeptide during or once localization or secretion is completed. Polypeptides that have a signal peptide are referred to herein as a “pre-protein” and polypeptides having their signal peptide removed are referred to herein as “mature” proteins or polypeptides. In any of the herein disclosed embodiments, a binding protein or fusion protein comprises, or is, a mature protein, or is or comprises a pre-protein. In some embodiments, the binding proteins described herein are mature proteins that lack a signal peptide. [0085] In the case of an amino acid sequence comprising a TCR variable domain or TCR chain, a signal peptide, if present, can be deduced with reference to the TCR V alpha or V beta allele (i.e., TRAV or TRBV) used by the subject variable domain, and will be N-terminal to the beginning of the sequence encoded by the subject TCR V alpha or V beta allele. Human TCR V alleles and amino acid sequences encoded thereby are provided at, for example, imgt.org/IMGTrepertoire/Proteins/alleles/list_alleles.php?species=Homo%20sapiens&g roup=TRAV, and imgt.org/IMGTrepertoire/Proteins/alleles/list_alleles.php?species=Homo%20sapiens&g roup=TRBV, the contents of each of which are incorporated herein by reference in their entireties. In some embodiments, a binding protein comprises, in a Vα domain, an amino acid sequence encoded by a TRAV38-1, TRAV34, TRAV16, or TRAV5, and/or comprises , in a Vβ domain, an amino acid sequence encoded by TRBV30 (e.g., TRBV30*01), TRBV29 or TRBV9. [0086] In the case of SEQ ID NO.:17, amino acids 1-17 constitute the signal peptide. Thus, "SEQ ID NO.:17 with the signal peptide removed" refers to the amino acid sequence beginning at amino acid residue 18 of SEQ ID NO.:17; in other words, SEQ ID NO.:17 without the first 17 amino acids. In the case of SEQ ID NO.:19, amino acids 1-18 constitute the signal peptide. Thus, "SEQ ID NO.:19 with the signal peptide removed" refers to the amino acid sequence beginning at amino acid residue 19 of SEQ ID NO.:17; in other words, SEQ ID NO.:19 without the first 18 amino acids.
[0087] Also contemplated are embodiments in which an encoded TCR V domain or TCR chain comprises an alternative signal peptide, and the signal peptide is removed prior to localization to the cell surface. [0088] In certain embodiments, a Vα domain has at least 95%, 97%, or 99% identity to, or comprises or consists of, the amino acid sequence according to SEQ ID NO.:3, 7, 11, 15, or 19, or according to SEQ ID NO.:3, 7, 11, 15, or 19 with the signal peptide removed. In further embodiments, a Vβ domain has at least 95%, 97%, 99% identity to, or comprises or consists of, the amino acid sequence according to SEQ ID NO.:1, 5, 9, 13, or 17, or according to SEQ ID NO.:1, 5, 9, 13, or 17 with the signal peptide removed. [0089] In some embodiments, a binding protein comprises a TCR α-chain constant domain, a TCR β-chain constant domain, or both. In certain embodiments, a TCR α-chain constant (Cα) domain has at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to, or comprises or consists of, the amino acid sequence of any one of SEQ ID NOs.:4, 8, 12, 16, or 20. In further embodiments, a TCR β-chain constant (Cβ) domain has at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to, or comprises or consists of, any one of the amino acid sequences of SEQ ID NOs.:2, 6, 10, 14, 18 or 158. [0090] Accordingly, in some embodiments, a binding of the present disclosure comprises a Vα domain, a Vβ domain, a Cα domain, and a Cβ domain. The Vα domain and the Cα domain together comprise a TCR α chain, and the Vβ domain and the Cβ domain together comprise a TCR β chain. The TCR α chain and the TCR β chain can associate with one another, forming a TCR (or a TCR portion of a protein comprising a TCR), which can be present at the surface of a host cell. In further embodiments, a binding protein comprises a Vα domain comprising or consisting of SEQ ID NO.:3 (or SEQ ID NO.:3 with the signal peptide removed), a Vβ domain comprising or consisting of SEQ ID NO.:1 (or SEQ ID NO.:1 with the signal peptide removed), a Cα domain comprising or consisting of SEQ ID NO.:4, and a Cβ domain comprising or consisting of SEQ ID NO.:2. In other embodiments, a binding protein comprises a Vα domain comprising or consisting of SEQ ID NO.:7 (or SEQ ID NO.:7 with the signal peptide removed), a Vβ domain comprising or consisting of SEQ ID NO.:5 (or SEQ ID NO.:5
with the signal peptide removed), a Cα domain comprising or consisting of SEQ ID NO.:8, and a Cβ comprising or consisting of SEQ ID NO.:6. In still further embodiments, a binding protein comprises a Vα domain comprising or consisting of SEQ ID NO.:11 (or SEQ ID NO.:11 with the signal peptide removed), a Vβ domain comprising or consisting of SEQ ID NO.:9, a Cα domain comprising or consisting of SEQ ID NO.:12 (or SEQ ID NO.:12 with the signal peptide removed), and a Cβ domain comprising or consisting of SEQ ID NO.:10. In other embodiments, a binding protein comprises a Vα domain comprising or consisting of SEQ ID NO.:15 (or SEQ ID NO.:15 with the signal peptide removed), a Vβ domain comprising or consisting of SEQ ID NO.: 13, a Cα comprising or consisting of SEQ ID NO.: 16 (or SEQ ID NO.:16 with the signal peptide removed), and a Cβ domain comprising or consisting of SEQ ID NO.:14. In yet other embodiments, a binding protein comprises a Vα domain comprising or consisting of SEQ ID NO.: 19 (or SEQ ID NO.:19 with the signal peptide removed), a Vβ domain comprising or consisting of SEQ ID NO.:17 (or SEQ ID NO.:17 with the signal peptide removed), a Cα domain comprising or consisting of SEQ ID NO.:20, and a Cβ domain comprising or consisting of SEQ ID NO.: 18 or 158. [0091] In any of the embodiments disclosed herein, a binding protein (e.g., in soluble form or expressed on a cell surface of a modified cell of the present disclosure) is capable of binding to a MAGE-A1:HLA-A*201 complex (e.g., a KVLEYVIKV (SEQ ID NO.:123):HLA-A*201 complex) on a cell surface independent of or in the absence of CD8. [0092] In certain embodiments, any of the aforementioned MAGE-A1 specific binding proteins is or comprises a T cell receptor (TCR), a chimeric antigen receptor or an antigen-binding fragment of a TCR, any of which can be chimeric, humanized, or human. In further embodiments, an antigen-binding fragment of the TCR comprises a single chain TCR (scTCR) or a chimeric antigen receptor (CAR). In certain embodiments, a MAGE-A1 specific binding protein is a TCR, optionally a scTCR. Methods for producing engineered TCRs are described in, for example, Bowerman et al., Mol. Immunol., 46(15):3000 (2009), the techniques of which are herein incorporated by reference. In certain embodiments, a MAGE-A1-specific binding domain is a CAR comprising a MAGE-A1-specific TCR binding domain (see, e.g., Walseng et al., Scientific Reports 7:10713 (2017), the TCR CAR constructs of which are hereby incorporated by reference in their entirety). Methods for making CARs are
also described, for example, in U.S. Patent No.6,410,319; U.S. Patent No.7,446,191; U.S. Patent Publication No.2010/065818; U.S. Patent No.8,822,647; PCT Publication No. WO 2014/031687; U.S. Patent No.7,514,537; and Brentjens et al., 2007, Clin. Cancer Res.13:5426, the techniques of which are herein incorporated by reference. [0093] Methods useful for isolating and purifying recombinantly produced soluble TCR, by way of example, may include obtaining supernatants from suitable host cell/vector systems that secrete the recombinant soluble TCR into culture media and then concentrating the media using a commercially available filter. Following concentration, the concentrate may be applied to a single suitable purification matrix or to a series of suitable matrices, such as an affinity matrix or an ion exchange resin. One or more reverse phase HPLC steps may be employed to further purify a recombinant polypeptide. These purification methods may also be employed when isolating an immunogen from its natural environment. Methods for large scale production of one or more of the isolated/recombinant soluble TCR described herein include batch cell culture, which is monitored and controlled to maintain appropriate culture conditions. Purification of the soluble TCR may be performed according to methods described herein and known in the art and that comport with laws and guidelines of domestic and foreign regulatory agencies. [0094] In certain embodiments, nucleic acid molecules encoding a binding protein or high affinity TCR specific for MAGE-A1 are used to transfect/transduce a host cell (e.g., T cells) for use in adoptive transfer therapy. Advances in TCR sequencing have been described (e.g., Robins et al., Blood 114:4099, 2009; Robins et al., Sci. Translat. Med.2:47ra64, 2010; Robins et al., (Sept.10) J. Imm. Meth. Epub ahead of print, 2011; Warren et al., Genome Res.21:790, 2011) and may be employed in the course of practicing the embodiments according to the present disclosure. Similarly, methods for transfecting/transducing T cells with desired nucleic acids have been described (e.g., U.S. Patent Application Pub. No. US 2004/0087025) as have adoptive transfer procedures using T-cells of desired antigen-specificity (e.g., Schmitt et al., Hum. Gen.20:1240, 2009; Dossett et al., Mol. Ther.17:742, 2009; Till et al., Blood 112:2261, 2008; Wang et al., Hum. Gene Ther.18:712, 2007; Kuball et al., Blood 109:2331, 2007; US 2011/0243972; US 2011/0189141; Leen et al., Ann. Rev. Immunol.25:243, 2007), such that adaptation of these methodologies to the presently disclosed embodiments is contemplated, based on the teachings herein, including those
directed to high affinity TCRs specific for MAGE-A1 peptide antigens complexed with an HLA receptor. [0095] MAGE-A1-specific binding proteins or domains as described herein may be functionally characterized according to any of a large number of art accepted methodologies for assaying T cell activity, including determination of T cell binding, activation or induction and also including determination of T cell responses that are antigen-specific. Examples include determination of T cell proliferation, T cell cytokine release, antigen-specific T cell stimulation, MHC restricted T cell stimulation, CTL activity (e.g., by detecting 51Cr release from pre-loaded target cells), changes in T cell phenotypic marker expression, and other measures of T-cell functions. Procedures for performing these and similar assays are may be found, for example, in Lefkovits (Immunology Methods Manual: The Comprehensive Sourcebook of Techniques, 1998). See, also, Current Protocols in Immunology; Weir, Handbook of Experimental Immunology, Blackwell Scientific, Boston, MA (1986); Mishell and Shigii (eds.) Selected Methods in Cellular Immunology, Freeman Publishing, San Francisco, CA (1979); Green and Reed, Science 281:1309 (1998) and references cited therein. [0096] “MHC-peptide tetramer staining” refers to an assay used to detect antigen-specific T cells, which features a tetramer of MHC molecules, each comprising an identical peptide having an amino acid sequence that is cognate (e.g., identical or related to) at least one antigen (e.g., MAGE-A1), wherein the complex is capable of binding T cell receptors specific for the cognate antigen. Each of the MHC molecules may be tagged with a biotin molecule. Biotinylated MHC/peptides are tetramerized by the addition of streptavidin, which can be fluorescently labeled. The tetramer may be detected by flow cytometry via the fluorescent label. In certain embodiments, an MHC- peptide tetramer assay is used to detect or select enhanced affinity TCRs of the instant disclosure. [0097] Levels of cytokines may be determined according to methods described herein and practiced in the art, including for example, ELISA, ELISPOT, intracellular cytokine staining, and flow cytometry and combinations thereof (e.g., intracellular cytokine staining and flow cytometry). Immune cell proliferation and clonal expansion resulting from an antigen-specific elicitation or stimulation of an immune response may be determined by isolating lymphocytes, such as circulating lymphocytes in samples of peripheral blood cells or cells from lymph nodes, stimulating the cells with antigen, and
measuring cytokine production, cell proliferation and/or cell viability, such as by incorporation of tritiated thymidine or non-radioactive assays, such as MTT assays and the like. The effect of an immunogen described herein on the balance between a Th1 immune response and a Th2 immune response may be examined, for example, by determining levels of Th1 cytokines, such as IFN-γ, IL-12, IL-2, and TNF-β, and Type 2 cytokines, such as IL-4, IL-5, IL-9, IL-10, and IL-13. Polynucleotides and Vectors [0098] In another aspect, isolated or recombinant polynucleotides are provided herein, wherein a polynucleotide encodes a binding protein of the present disclosure (e.g., immunoglobulin superfamily binding protein, such as a TCR, scTv, scTCR, or CAR) specific for a MAGE-A1 antigen, and wherein the polynucleotide is optionally codon optimized for expression in a host cell (e.g., an immune cell of the present disclosure). Also provided are vectors (e.g., expression vectors) that comprise a polynucleotide of this disclosure, wherein the polynucleotide is operatively associated or operably linked to an expression control sequence (e.g., a promoter). Construction of an expression vector to produce a binding protein specific for a MAGE-A1 peptide of this disclosure can be made using restriction endonuclease digestion, ligation, transformation, plasmid purification, DNA sequencing, or a combination thereof, as described in, for example, Sambrook et al. (1989 and 2001 editions; Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, NY) and Ausubel et al. (Current Protocols in Molecular Biology, 2003). For efficient transcription and translation, a polynucleotide contained in an expression construct includes at least one appropriate expression control sequence (also called a regulatory sequence), such as a leader sequence and particularly a promoter operably (i.e., operatively) linked to the nucleotide sequence encoding the binding protein of this disclosure. [0099] A nucleic acid may be a single- or a double-stranded DNA, cDNA or RNA in any form, and may include a positive and a negative strand of the nucleic acid which complement each other, including anti-sense DNA, cDNA and RNA. Also included are siRNA, microRNA, RNA—DNA hybrids, ribozymes, and other various naturally occurring or synthetic forms of DNA or RNA. [0100] Isolated or recombinant nucleic acid molecules encoding a binding protein (e.g., immunoglobulin superfamily binding protein) or high affinity recombinant
TCR specific for MAGE-A1 as described herein may be produced and prepared according to various methods and techniques of the molecular biology or polypeptide purification arts. [0101] In certain embodiments, a polynucleotide is provided that least has at least 50%, at least 55%, at least 60%, at least 65%, 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the polynucleotide sequence set forth in any one of SEQ ID NOs.:149-153 and 159. [0102] In certain embodiments, an isolated polynucleotide is provided that encodes a binding protein having a TCR Vα domain and a TCR Vβ domain, wherein the encoded binding protein is capable of specifically binding to a MAGE-A1 peptide:HLA complex on a cell surface independent of CD8 or in the absence of CD8, the isolated polynucleotide comprising: (a) a Vα CDR3-encoding polynucleotide according to SEQ ID NO:97, 103, 109, 115 or 121, and a Vβ-encoding polynucleotide; (b) a Vβ CDR3-encoding polynucleotide according to SEQ ID NO:94, 100, 106, 112, or 118, and a Vα- encoding polynucleotide; or (c) a Vα CDR3-encoding polynucleotide according to SEQ ID NO:97, 103, 109, 115 or 121 and a Vβ CDR3-encoding polynucleotide according to SEQ ID NO:94, 100, 106, 112, or 118. In further embodiments, a Vβ-encoding polynucleotide is derived from a TRBV30 allele, a TRBV29 allele, or a TRBV9 allele. [0103] In some embodiments, a Vα-encoding polynucleotide is derived from a TRAV38-1 allele, a TRAV34 allele, a TRAV16 allele, or a TRAV5 allele. [0104] Presently disclosed polynucleotides encoding binding proteins can, in some embodiments, comprise: (a) a Vα CDR3-encoding polynucleotide according to SEQ ID NO:97 and a Vβ CDR3-encoding polynucleotide according to SEQ ID NO:94; (b) a Vα CDR3-encoding polynucleotide according to SEQ ID NO:103 and a Vβ CDR3- encoding polynucleotide according to SEQ ID NO:100; (c) a Vα CDR3-encoding polynucleotide according to SEQ ID NO:109 and a Vβ CDR3-encoding polynucleotide according to SEQ ID NO:106; (d) a Vα CDR3-encoding polynucleotide according to SEQ ID NO:115 and a Vβ CDR3-encoding polynucleotide according to SEQ ID NO:112; or (e) a Vα CDR3-encoding polynucleotide according to SEQ ID NO:121 and a Vβ CDR3-encoding polynucleotide according to SEQ ID NO:118. In certain embodiments, an isolated polynucleotide encoding a binding protein further comprises a
Vα CDR1-encoding polynucleotide according to SEQ ID NO:95, 101, 107, 113 or 119; (b) a Vα CDR2-encoding polynucleotide according to SEQ ID NO:96, 102, 108, 114 or 120; (c)a Vβ CDR1-encoding polynucleotide according to SEQ ID NO:92, 98, 104, 110 or 116; and/or (d) a Vβ CDR2-encoding polynucleotide according to SEQ ID NO:93, 99, 105, 111 or 117. [0105] In particular embodiments, an isolated polynucleotide encoding a binding protein of the present disclosure comprises (a) a Vα CDR1-encoding polynucleotide according to SEQ ID NO:95, a Vα CDR2- encoding polynucleotide according to SEQ ID NO:96, a Vα CDR3-encoding polynucleotide according to SEQ ID NO:97, a Vβ CDR1-encoding polynucleotide according to SEQ ID NO:92, a Vβ CDR2-encoding polynucleotide according to SEQ ID NO:93, and Vβ CDR3-encoding polynucleotide according to SEQ ID NO:94; (b) a Vα CDR1-encoding polynucleotide according to SEQ ID NO:101, a Vα CDR2- encoding polynucleotide according to SEQ ID NO:102, a Vα CDR3-encoding polynucleotide according to SEQ ID NO:103, a Vβ CDR1- encoding polynucleotide according to SEQ ID NO:98, a Vβ CDR2-encoding polynucleotide according to SEQ ID NO:99, and Vβ CDR3-encoding polynucleotide according to SEQ ID NO:100; (c) a Vα CDR1-encoding polynucleotide according to SEQ ID NO:107, a Vα CDR2- encoding polynucleotide according to SEQ ID NO:108, a Vα CDR3-encoding polynucleotide according to SEQ ID NO:109, a Vβ CDR1- encoding polynucleotide according to SEQ ID NO:104, a Vβ CDR2-encoding polynucleotide according to SEQ ID NO:105, and Vβ CDR3-encoding polynucleotide according to SEQ ID NO:106; (d) a Vα CDR1-encoding polynucleotide according to SEQ ID NO:113, a Vα CDR2- encoding polynucleotide according to SEQ ID NO:114, a Vα CDR3-encoding polynucleotide according to SEQ ID NO:115, a Vβ CDR1- encoding polynucleotide according to SEQ ID NO:110, a Vβ CDR2-encoding polynucleotide according to SEQ ID NO:111, and Vβ CDR3-encoding polynucleotide according to SEQ ID NO:112.; or (e) a Vα CDR1-encoding polynucleotide according to SEQ ID NO:119, a Vα CDR2- encoding polynucleotide according to SEQ ID NO:120, a Vα CDR3-encoding polynucleotide according to SEQ ID NO:121, a Vβ CDR1- encoding polynucleotide according to SEQ ID NO:116, a Vβ CDR2-encoding polynucleotide according to SEQ ID NO:117, and Vβ CDR3-encoding polynucleotide according to SEQ ID NO:118.
[0106] In some embodiments, the instant disclosure provides a polynucleotide encoding a binding protein, wherein a Vα-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity (e.g., at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%, or 100% identity) to SEQ ID NO:58, 66, 74, 82, or 90, and a Vβ-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:56, 64, 72, 80, or 88. [0107] In further embodiments: (a) a Vα-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:58 and a Vβ-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:56; (b) a Vα-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:66 and a Vβ-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:64; (c) a Vα-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:74 and a Vβ-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:72; (d) a Vα-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:82 and a Vβ-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:80; or (e) a Vα-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:90 and a Vβ-encoding polynucleotide comprises a nucleotide sequence having at least 80% identity to SEQ ID NO:88. [0108] In particular embodiments, (a) a Vα-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:58 and a Vβ-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:56; (b) a Vα-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:66 and a Vβ-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:64; (c) a Vα-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:74 and a Vβ-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:72; (d) a Vα-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:82 and a Vβ-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID
NO:80; or (e) a Vα-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:90 and a Vβ-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:88. [0109] Binding protein-encoding polynucleotides of the instant disclosure may, in certain embodiments, further comprise a polynucleotide that encodes a TCR α-chain constant domain, a polynucleotide that encodes a TCR β-chain constant domain, or both. In some embodiments, an isolated polynucleotide encoding a binding protein of the present disclosure further comprises: (a) a Cα-domain-encoding polynucleotide having at least 80% identity to SEQ ID NO:59, 67, 75, 83, or 91; and/or (b) a Cβ- domain-encoding polynucleotide having at least 80% identity to SEQ ID NO:57, 65, 73, 81, or 89. In further embodiments, a Cα-domain-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:59, 67, 75, 83, or 91, and a Cβ-domain-encoding polynucleotide comprises or consists of a nucleotide sequence according to SEQ ID NO:57, 65, 73, 81, or 89. [0110] In particular embodiments, an isolated polynucleotide encoding a binding protein of the present disclosure comprises: (a) a Vα-encoding polynucleotide according to SEQ ID NO:58, a Vβ-encoding polynucleotide according to SEQ ID NO:56, a Cα- domain-encoding polynucleotide according to SEQ ID NO:59, and a Cβ- domain-encoding polynucleotide according to SEQ ID NO:57; (b) a Vα-encoding polynucleotide according to SEQ ID NO:66, a Vβ-encoding polynucleotide according to SEQ ID NO:64, a Cα-domain-encoding polynucleotide according to SEQ ID NO:67, and a Cβ-domain-encoding polynucleotide according to SEQ ID NO:65; (c) a Vα- encoding polynucleotide according to SEQ ID NO:74, a Vβ-encoding polynucleotide according to SEQ ID NO:72, a Cα-domain-encoding polynucleotide according to SEQ ID NO:75, and a Cβ-domain-encoding polynucleotide according to SEQ ID NO:73; (d) a Vα-encoding polynucleotide according to SEQ ID NO:82, a Vβ-encoding polynucleotide according to SEQ ID NO:80, a Cα-domain-encoding polynucleotide according to SEQ ID NO:83, and a Cβ-domain-encoding polynucleotide according to SEQ ID NO:81; or (e) a Vα-encoding polynucleotide according to SEQ ID NO:90, a Vβ- encoding polynucleotide according to SEQ ID NO:88, a Cα-domain-encoding polynucleotide according to SEQ ID NO:91, and a Cβ-domain-encoding polynucleotide according to SEQ ID NO:89.
[0111] In further embodiments, two or more substituent gene products of a binding protein of this disclosure are expressed as a single peptide with the parts separated by a cleavable or removable segment. For instance, self-cleaving peptides useful for expression of separable polypeptides encoded by a single polynucleotide or vector are known in the art and include, for example, a Porcine teschovirus-12A (P2A) peptide, such as a peptide encoded by a polynucleotide having the nucleotide sequence shown in any one of SEQ ID NOS:128 or 129, a Thoseaasigna virus 2A (T2A) peptide, such as a peptide encoded by a polynucleotide having the nucleotide sequence shown in SEQ ID NO:132, an Equine rhinitis A virus (ERAV) 2A (E2A) peptide, such as a peptide encoded by a polynucleotide having the nucleotide sequence shown in SEQ ID NO:131, and a Foot-and-Mouth disease virus 2A (F2A) peptide, such as a peptide encoded by a polynucleotide having the nucleotide sequence shown in SEQ ID NO:130. Another self-cleaving peptide comprises or consists of the amino acid sequence set forth in SEQ ID NO.:154. [0112] Accordingly, in certain embodiments, an isolated polynucleotide encoding a binding protein of the instant disclosure further comprises a polynucleotide encoding a self-cleaving peptide disposed between a TCR α-chain-encoding polynucleotide and a TCR β-chain-encoding polynucleotide, or disposed between a TCR Vβ domain- encoding polynucleotide and a TCR Vα-encoding polynucleotide, or disposed between a TCR variable domain-encoding polynucleotide and a TCR constant domain-encoding polynucleotide, or any combination thereof. In particular embodiments, a polynucleotide encoding a self-cleaving peptide comprises or consists of a nucleotide sequence according to any one of SEQ ID NOS.:128-132. In further embodiments, a polynucleotide encodes a self-cleaving peptide comprising or consisting of an amino acid sequence according to any one of SEQ ID NOS.:124-127. [0113] Also provided herein are vectors containing polynucleotides of the instant disclosure. Construction of an expression vector that is used for recombinantly producing a binding protein or high affinity engineered TCR specific for a MAGE-A1 peptide of interest can be accomplished by using any suitable molecular biology engineering techniques, including the use of restriction endonuclease digestion, ligation, transformation, plasmid purification, and DNA sequencing as described in, for example, Sambrook et al. (1989 and 2001 editions; Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, NY) and Ausubel et al. (Current Protocols in
Molecular Biology, 2003). To obtain efficient transcription and translation, a polynucleotide in each recombinant expression construct includes at least one appropriate expression control sequence, such as a promoter operably (i.e., operatively) linked to a nucleotide sequence encoding a binding protein. In addition, a polynucleotide encoding a binding protein of this disclosure may also include a sequence encoding a leader sequence at the amino-terminus of the binding protein (also referred to as a pre-binding protein), which leader sequence may be removed by the cell to produce a mature binding protein. [0114] An exemplary vector may comprise a nucleic acid molecule capable of transporting another nucleic acid molecule to which it has been linked, or which is capable of replication in a host organism. Some examples of vectors include plasmids, viral vectors, cosmids, and others. Some vectors may be capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors), whereas other vectors may be integrated into the genome of a host cell or promote integration of the polynucleotide insert upon introduction into the host cell and thereby replicate along with the host genome (e.g., lentiviral vector)). Additionally, some vectors are capable of directing the expression of genes to which they are operatively linked (these vectors may be referred to as “expression vectors”). According to related embodiments, it is further understood that, if one or more agents (e.g., polynucleotides encoding binding proteins or high affinity recombinant TCRs specific for MAGE-A1, or variants thereof, as described herein) is co-administered to a subject, that each agent may reside in separate or the same vectors, and multiple vectors (each containing a different agent the same agent) may be introduced to a cell or cell population or administered to a subject. [0115] In certain embodiments, a polynucleotide encoding a binding protein or a high affinity recombinant TCR specific for MAGE-A1, may be operatively linked to certain elements of a vector. For example, polynucleotide sequences that are needed to affect the expression and processing of coding sequences to which they are ligated may be operatively linked. Expression control sequences may include appropriate transcription initiation, termination, promoter, and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequences); sequences that enhance protein stability; and possibly sequences that enhance protein secretion. Expression control sequences may be operatively linked
if they are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest. In certain embodiments, polynucleotides encoding binding proteins of the instant disclosure are contained in an expression vector that is a viral vector, such as a lentiviral vector or a γ-retroviral vector. [0116] Viral vectors include retrovirus, adenovirus, parvovirus (e.g., adeno- associated viruses), coronavirus, negative strand RNA viruses such as ortho-myxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g., measles and Sendai), positive strand RNA viruses such as picornavirus and alphavirus, and double-stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, fowlpox and canarypox). Other viruses include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus, for example. Examples of retroviruses include avian leukosis-sarcoma, mammalian C- type, B-type viruses, D type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996). [0117] “Lentiviral vector,” as used herein, means HIV-based lentiviral vectors for gene delivery, which can be integrative or non-integrative, have relatively large packaging capacity, and can transduce a range of different cell types. Lentiviral vectors are usually generated following transient transfection of three (packaging, envelope, and transfer) or more plasmids into producer cells. Like HIV, lentiviral vectors enter the target cell through the interaction of viral surface glycoproteins with receptors on the cell surface. On entry, the viral RNA undergoes reverse transcription, which is mediated by the viral reverse transcriptase complex. The product of reverse transcription is a double-stranded linear viral DNA, which is the substrate for viral integration into the DNA of infected cells. [0118] In particular embodiments, a recombinant or engineered expression vector is delivered to an appropriate cell (i.e., the vector is capable of delivering a protein-encoding polynucleotide of the present disclosure to a host cell), for example, a T cell or an antigen-presenting cell, i.e., a cell that displays a peptide/MHC complex on its cell surface (e.g., a dendritic cell) and optionally lacks CD8. In certain embodiments,
a host cell is a hematopoietic progenitor cell or a human immune system cell. For example, an immune system cell can be a CD4+ T cell, a CD8+ T cell, a CD4- CD8- double negative T cell, a γδ T cell, a natural killer cell, a dendritic cell, or any combination thereof. In certain embodiments, wherein a T cell is the host, the T cell can be naïve, a central memory T cell, an effector memory T cell, or any combination thereof. Recombinant expression vectors of the present disclosure may therefore also include, for example, lymphoid tissue-specific transcriptional regulatory elements (TREs), such as a B lymphocyte, T lymphocyte, or dendritic cell specific TREs. Lymphoid tissue specific TREs are known in the art (see, e.g., Thompson et al., Mol. Cell. Biol.12:1043, 1992); Todd et al., J. Exp. Med.177:1663, 1993); Penix et al., J. Exp. Med.178:1483, 1993). [0119] In addition to vectors, certain embodiments relate to host cells that comprise the vectors that are presently disclosed. One of skill in the art readily understands that many suitable host cells are available in the art. Host cells are described further herein; a host cell may include any individual cell or cell culture which may receive a vector or the incorporation of nucleic acids and/or proteins, as well as any progeny cells. The term also encompasses progeny of the host cell, whether genetically or phenotypically the same or different. Suitable host cells may depend on the vector and may include mammalian cells, animal cells, human cells, simian cells, insect cells, yeast cells, and bacterial cells. These cells may be induced to incorporate the vector or other material by use of a viral vector, transformation via calcium phosphate precipitation, DEAE-dextran, electroporation, microinjection, or other methods. See, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual 2d ed. (Cold Spring Harbor Laboratory, 1989). Host Cells [0120] In certain aspects, host cells (i.e., modified cells) are provided that comprise a binding protein of this disclosure. In certain embodiments, a host cell comprises a human immune cell such as, for example, a T cell (such as, for example, a naïve T cell, a central memory T cell, or a stem cell memory T cell), a NK cell, a NK-T cell, a macrophage, and/or a microglia. In some embodiments, a host cell comprises a CD4+T cell, a CD8+ T cell (e.g., which can additionally be CD62L+), or both. Methods for transfecting/transducing T cells with desired nucleic acids have been described (e.g.,
U.S. Patent Application Pub. No. US 2004/0087025) as have adoptive transfer procedures using T cells of desired target-specificity (e.g., Schmitt et al., Hum. Gen. 20:1240, 2009; Dossett et al., Mol. Ther.17:742, 2009; Till et al., Blood 112:2261, 2008; Wang et al., Hum. Gene Ther.18:712, 2007; Kuball et al., Blood 109:2331, 2007; US 2011/0243972; US 2011/0189141; Leen et al., Ann. Rev. Immunol.25:243, 2007), such that adaptation of these methodologies to the presently disclosed embodiments is contemplated, based on the teachings herein. [0121] In the present disclosure, a plurality of cells that comprise a binding protein as provided herein may be described as a “population”. Cells of a population may have one or more additional shared feature but will comprise a binding protein of the present disclosure. A population can be administered to a subject in the form of a cell composition for a therapeutic method as provided herein. In some embodiments, a population comprises CD8+ T cells, CD4+ T cells, or both. [0122] A binding protein will preferably localize to the surface of a host cell. [0123] In certain embodiments, a modified cell comprises a binding protein, wherein the binding protein comprises: (a) a T cell receptor (TCR) α-chain variable (Vα) domain having a CDR3 amino acid sequence according to any one of SEQ ID NOS.:26, 32, 38, 44, 50, or 51, and a TCR β-chain variable (Vβ) domain; (b) a Vβ domain having a CDR3 amino acid sequence according to any one of SEQ ID NOS.:23, 29, 35, 41, or 47, and a Vα domain; or (c) a Vα domain having a CDR3 amino acid sequence according to any one of SEQ ID NOS:26, 32, 38, 44, 50, or 51, and a Vβ domain having a CDR3 amino acid sequence according to any one of SEQ ID NOs:23, 29, 35, 41, or 47. In some embodiments, the encoded binding protein is capable of specifically binding to a MAGE-A1 peptide:HLA complex on a cell surface independent of CD8 or in the absence of CD8. In some embodiments, the encoded binding protein is capable of specifically binding to a KVLEYVIKV (SEQ ID NO.:123):human leukocyte antigen (HLA) complex with a Kd less than or equal to about 10-8 M. [0124] Any appropriate method can be used to transfect or transduce the cells, for example, the T cells, or to administer the polynucleotides or compositions of the present methods. Known methods for delivering polynucleotides to host cells include, for example, use of cationic polymers, lipid-like molecules, and certain commercial products such as, for example, IN-VIVO-JET PEI. Other methods include ex vivo
transduction, injection, electroporation, DEAE-dextran, sonication loading, liposome- mediated transfection, receptor-mediated transduction, microprojectile bombardment, transposon-mediated transfer, and the like. Still further methods of transfecting or transducing host cells employ vectors, described in further detail herein. [0125] In any of the foregoing embodiments, a modified immune cell may modified to reduce or eliminate expression (e.g., by a chromosomal gene knockout as described herein) of one or more endogenous genes that encode a polypeptide involved in immune signaling or other related activities, and/or to comprise a heterologous polynucleotide as provided herein. Exemplary gene knockouts include those that encode PD-1, LAG-3, CTLA4, TIM3, an HLA molecule, a TCR molecule, or the like. Without wishing to be bound by theory, certain endogenously expressed immune cell proteins may be recognized as foreign by an allogeneic host receiving the modified immune cells, which may result in elimination of the modified immune cells (e.g., an HLA allele), or may downregulate the immune activity of the modified immune cells (e.g., PD-1, LAG-3, CTLA4), or may interfere with the binding activity of a heterologously expressed binding protein of the present disclosure (e.g., an endogenous TCR of a modified T cell that binds a non-MAGE-A1 antigen and may interfere with the modified immune cell binding a cell that expresses MAGE-A1 antigen), or may compete for expression with a heterologous binding protein. [0126] Accordingly, decreasing or eliminating expression or activity of such endogenous genes or proteins can improve the activity, tolerance, expression of a binding protein, or persistence of the modified immune cells in an autologous or allogeneic host setting, and may allow for universal administration of the cells (e.g., to any recipient regardless of HLA type). In certain embodiments, a modified immune cell is a donor cell (e.g., allogeneic) or an autologous cell. In certain embodiments, a modified immune cell of this disclosure comprises a chromosomal gene knockout of one or more of a gene that encodes PD-1, LAG-3, CTLA4, TIM3, TIGIT, Fas, an HLA component (e.g., a gene that encodes an α1 macroglobulin, an α2 macroglobulin, an α3 macroglobulin, a β1 microglobulin, or a β2 microglobulin), or a TCR component (e.g., a gene that encodes a TCR variable region or a TCR constant region) (see, e.g., Torikai et al., Nature Sci. Rep.6:21757 (2016); Torikai et al., Blood 119(24):5697 (2012); and Torikai et al., Blood 122(8):1341 (2013), the gene-editing techniques, compositions,
and adoptive cell therapies of which are herein incorporated by reference in their entirety). [0127] As used herein, the term “chromosomal gene knockout” refers to a genetic alteration or introduced inhibitory agent in a host cell that prevents (e.g., reduces, delays, suppresses, or abrogates) production, by the host cell, of a functionally active endogenous polypeptide product. Alterations resulting in a chromosomal gene knockout can include, for example, introduced nonsense mutations (including the formation of premature stop codons), missense mutations, gene deletion, and strand breaks, as well as the heterologous expression of inhibitory nucleic acid molecules that inhibit endogenous gene expression in the host cell. [0128] In certain embodiments, a chromosomal gene knock-out or gene knock- in is made by chromosomal editing of a host cell. Chromosomal editing can be performed using, for example, endonucleases. As used herein “endonuclease” refers to an enzyme capable of catalyzing cleavage of a phosphodiester bond within a polynucleotide chain. In certain embodiments, an endonuclease is capable of cleaving a targeted gene thereby inactivating or “knocking out” the targeted gene. An endonuclease may be a naturally occurring, recombinant, genetically modified, or fusion endonuclease. The nucleic acid strand breaks caused by the endonuclease are commonly repaired through the distinct mechanisms of homologous recombination or non-homologous end joining (NHEJ). During homologous recombination, a donor nucleic acid molecule may be used for a donor gene “knock-in”, for target gene “knock- out”, and optionally to inactivate a target gene through a donor gene knock in or target gene knock out event. NHEJ is an error-prone repair process that often results in changes to the DNA sequence at the site of the cleavage, e.g., a substitution, deletion, or addition of at least one nucleotide. NHEJ may be used to “knock-out” a target gene. Examples of endonucleases include zinc finger nucleases, TALE-nucleases, CRISPR- Cas nucleases, meganucleases, and megaTALs. [0129] As used herein, a “zinc finger nuclease” (ZFN) refers to a fusion protein comprising a zinc finger DNA-binding domain fused to a non-specific DNA cleavage domain, such as a Fokl endonuclease. Each zinc finger motif of about 30 amino acids binds to about 3 base pairs of DNA, and amino acids at certain residues can be changed to alter triplet sequence specificity (see, e.g., Desjarlais et al., Proc. Natl. Acad. Sci. 90:2256-2260, 1993; Wolfe et al., J. Mol. Biol.285:1917-1934, 1999). Multiple zinc
finger motifs can be linked in tandem to create binding specificity to desired DNA sequences, such as regions having a length ranging from about 9 to about 18 base pairs. By way of background, ZFNs mediate genome editing by catalyzing the formation of a site-specific DNA double strand break (DSB) in the genome, and targeted integration of a transgene comprising flanking sequences homologous to the genome at the site of DSB is facilitated by homology directed repair. Alternatively, a DSB generated by a ZFN can result in knock out of target gene via repair by non-homologous end joining (NHEJ), which is an error-prone cellular repair pathway that results in the insertion or deletion of nucleotides at the cleavage site. In certain embodiments, a gene knockout comprises an insertion, a deletion, a mutation, or a combination thereof, made using a ZFN molecule. [0130] As used herein, a “transcription activator-like effector nuclease” (TALEN) refers to a fusion protein comprising a TALE DNA-binding domain and a DNA cleavage domain, such as a FokI endonuclease. A “TALE DNA binding domain” or “TALE” is composed of one or more TALE repeat domains/units, each generally having a highly conserved 33-35 amino acid sequence with divergent 12th and 13th amino acids. The TALE repeat domains are involved in binding of the TALE to a target DNA sequence. The divergent amino acid residues, referred to as the Repeat Variable Diresidue (RVD), correlate with specific nucleotide recognition. The natural (canonical) code for DNA recognition of these TALEs has been determined such that an HD (histine-aspartic acid) sequence at positions 12 and 13 of the TALE leads to the TALE binding to cytosine (C), NG (asparagine-glycine) binds to a T nucleotide, NI (asparagine-isoleucine) to A, NN (asparagine-asparagine) binds to a G or A nucleotide, and NG (asparagine-glycine) binds to a T nucleotide. Non-canonical (atypical) RVDs are also known (see, e.g., U.S. Patent Publication No. US 2011/0301073, which atypical RVDs are incorporated by reference herein in their entirety). TALENs can be used to direct site-specific double-strand breaks (DSB) in the genome of T cells. Non- homologous end joining (NHEJ) ligates DNA from both sides of a double-strand break in which there is little or no sequence overlap for annealing, thereby introducing errors that knock out gene expression. Alternatively, homology directed repair can introduce a transgene at the site of DSB providing homologous flanking sequences are present in the transgene. In certain embodiments, a gene knockout comprises an insertion, a deletion, a mutation or a combination thereof, and made using a TALEN molecule.
[0131] As used herein, a “clustered regularly interspaced short palindromic repeats/Cas” (CRISPR/Cas) nuclease system refers to a system that employs a CRISPR RNA (crRNA)-guided Cas nuclease to recognize target sites within a genome (known as protospacers) via base-pairing complementarity and then to cleave the DNA if a short, conserved protospacer associated motif (PAM) immediately follows 3’ of the complementary target sequence. CRISPR/Cas systems are classified into three types (i.e., type I, type II, and type III) based on the sequence and structure of the Cas nucleases. The crRNA-guided surveillance complexes in types I and III need multiple Cas subunits. Type II system, the most studied, comprises at least three components: an RNA-guided Cas9 nuclease, a crRNA, and a trans-acting crRNA (tracrRNA). The tracrRNA comprises a duplex forming region. A crRNA and a tracrRNA form a duplex that is capable of interacting with a Cas9 nuclease and guiding the Cas9/crRNA:tracrRNA complex to a specific site on the target DNA via Watson-Crick base-pairing between the spacer on the crRNA and the protospacer on the target DNA upstream from a PAM. Cas9 nuclease cleaves a double-stranded break within a region defined by the crRNA spacer. Repair by NHEJ results in insertions and/or deletions which disrupt expression of the targeted locus. Alternatively, a transgene with homologous flanking sequences can be introduced at the site of DSB via homology directed repair. The crRNA and tracrRNA can be engineered into a single guide RNA (sgRNA or gRNA) (see, e.g., Jinek et al., Science 337:816-21, 2012). Further, the region of the guide RNA complementary to the target site can be altered or programed to target a desired sequence (Xie et al., PLOS One 9:e100448, 2014; U.S. Pat. Appl. Pub. No. US 2014/0068797, U.S. Pat. Appl. Pub. No. US 2014/0186843; U.S. Pat. No. 8,697,359, and PCT Publication No. WO 2015/071474; each of which is incorporated by reference). In certain embodiments, a gene knockout comprises an insertion, a deletion, a mutation or a combination thereof, and made using a CRISPR/Cas nuclease system. [0132] Exemplary gRNA sequences and methods of using the same to knock out endogenous genes that encode immune cell proteins include those described in Ren et al., Clin. Cancer Res.23(9):2255-2266 (2017), the gRNAs, Cas9 DNAs, vectors, and gene knockout techniques of which are hereby incorporated by reference in their entirety.
[0133] Alternative Cas nucleases may be used, including but not limited to, Cas 12, Cas 13, and Cas 14 nucleases, and variants thereof. For example, Cas nucleases disclosed in WO 2019/178427, which is hereby incorporated by reference in its entirety (including the Cas nucleases, CRISPR-Cas systems, and related methods disclosed therein), may be utilized. [0134] As used herein, a “meganuclease,” also referred to as a “homing endonuclease,” refers to an endodeoxyribonuclease characterized by a large recognition site (double stranded DNA sequences of about 12 to about 40 base pairs). Meganucleases can be divided into five families based on sequence and structure motifs: LAGLIDADG (SEQ ID NO: 155), GIY-YIG (SEQ ID NO:156), HNH, His-Cys box and PD-(D/E)XK (SEQ ID NO:157). Exemplary meganucleases include I-SceI, I- CeuI, PI-PspI, PI-Sce, I-SceIV, I-CsmI, I-PanI, I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI, I-TevII and I-TevIII, whose recognition sequences are known (see, e.g., U.S. Patent Nos.5,420,032 and 6,833,252; Belfort et al., Nucleic Acids Res.25:3379-3388, 1997; Dujon et al., Gene 82:115-118, 1989; Perler et al., Nucleic Acids Res.22:1125-1127, 1994; Jasin, Trends Genet.12:224-228, 1996; Gimble et al., J. Mol. Biol.263:163-180, 1996; Argast et al., J. Mol. Biol.280:345-353, 1998). [0135] In certain embodiments, naturally occurring meganucleases may be used to promote site-specific genome modification of a target selected from PD-1, LAG3, TIM3, CTLA4, TIGIT, an HLA-encoding gene, or a TCR component-encoding gene. In other embodiments, an engineered meganuclease having a novel binding specificity for a target gene is used for site-specific genome modification (see, e.g., Porteus et al., Nat. Biotechnol.23:967-73, 2005; Sussman et al., J. Mol. Biol.342:31-41, 2004; Epinat et al., Nucleic Acids Res.31:2952-62, 2003; Chevalier et al., Molec. Cell 10:895-905, 2002; Ashworth et al., Nature 441:656-659, 2006; Paques et al., Curr. Gene Ther.7:49- 66, 2007; U.S. Patent Publication Nos. US 2007/0117128; US 2006/0206949; US 2006/0153826; US 2006/0078552; and US 2004/0002092). In further embodiments, a chromosomal gene knockout is generated using a homing endonuclease that has been modified with modular DNA binding domains of TALENs to make a fusion protein known as a megaTAL. MegaTALs can be utilized to not only knock-out one or more target genes, but to also introduce (knock in) heterologous or exogenous polynucleotides when used in combination with an exogenous donor template encoding a polypeptide of interest.
[0136] In certain embodiments, a chromosomal gene knockout comprises an inhibitory nucleic acid molecule that is introduced into a host cell (e.g., an immune cell) comprising a heterologous polynucleotide encoding an antigen-specific receptor that specifically binds to a tumor associated antigen, wherein the inhibitory nucleic acid molecule encodes a target-specific inhibitor and wherein the encoded target-specific inhibitor inhibits endogenous gene expression (i.e., of PD-1, TIM3, LAG3, CTLA4, TIGIT, an HLA component, or a TCR component, or any combination thereof) in the host immune cell. [0137] A chromosomal gene knockout can be confirmed directly by DNA sequencing of the host immune cell following use of the knockout procedure or agent. Chromosomal gene knockouts can also be inferred from the absence of gene expression (e.g., the absence of an mRNA or polypeptide product encoded by the gene) following the knockout. [0138] Any of the foregoing gene-editing techniques can be used to introduce a polynucleotide of the present disclosure (e.g., encoding a binding protein and/or a CD8 co-receptor polypeptide) into a host cell genome. In some embodiments, a heterologous polynucleotide is introduced into a locus encoding an endogenous TCR component, HLA component, PD-1, LAG-3, Fas, CTLA4, TIM3, or TIGIT, or a safe harbor locus such as Rosa26, AAVS1, CCR5, or the like. In certain embodiments, a heterologous polynucleotide encoding a binding protein and/or encoding a CD8 co-receptor polypeptide is introduced into a host cell TRAC locus. In further embodiments, a chromosomal knockout of a host cell TRBC locus is introduced. [0139] Accordingly, in certain embodiments, a host cell (e.g., modified immune cell) is provided that comprises, in an endogenous TRAC locus, a heterologous polynucleotide encoding a binding protein of the present disclosure, a heterologous polynucleotide encoding a CD8 co-receptor of the present disclosure, or both. In further embodiments, the host cell comprises a chromosomal knockout of an endogenous TRBC locus. [0140] In some embodiments, a modified cell is a CD4+ T cell that comprises a heterologous polynucleotide encoding a binding protein of the present disclosure. In some embodiments, a heterologously encoded TCR of a modified CD4+ T cell is a high- affinity TCR. In particular embodiments, a heterologously encoded TCR of a modified
CD4+ T cell is capable of specifically binding to a peptide:antigen HLA complex on a cell surface independent of CD8 or in the absence of CD8. [0141] In further embodiments, a modified CD4+ T and/or modified CD8+ T cell further comprises a heterologous polynucleotide encoding at least an extracellular portion of a CD8 co-receptor. As shown in the Examples, co-expression of a MAGE- A1-specific binding protein of the present disclosure and at least an extracellular portion of a CD8 co- receptor by a CD4+ T cell can confer a new or improved functionality (e.g., improved cytokine release, CTL response when bound to a MAGE- A1:HLA-expressing target cell) upon the CD4+ T cell. An amino acid sequence of a CD8 co-receptor α-chain is provided in SEQ ID NO:143. Amino acid sequences of five different isoforms of CD8 co-receptor β-chain are provided in SEQ ID NOS:144-148, respectively. In some embodiments, a modified CD4+ T and/or modified CD8+ T cell of this disclosure further comprises a heterologous polynucleotide encoding a full-length CD8 co-receptor receptor β-chain, a heterologous polynucleotide encoding a full-length CD8 co-receptor α-chain, or both. In some embodiments, a CD8 co-receptor α-chain comprises or consists of the amino acid sequence set forth in SEQ ID NO.:143 and a CD8 co-receptor β-chain comprises or consists of the amino acid sequence set forth in any one of SEQ ID NOs.:144-148, preferably SEQ ID NO.:144. [0142] A CD8 co-receptor-encoding polynucleotide may, in some embodiments, be codon-optimized for expression in a host cell. [0143] In certain embodiments, a polynucleotide is provided that encodes (i) a TCR of the present disclosure and one or both of (ii) a CD8 co-receptor α-chain and (iii) a CD8 co-receptor β-chain. It will be appreciated that polynucleotides encoding these encoded polypeptides can be provided in any arrangement or order within a single polynucleotide, or can be present as separate nucleic acid molecules. In particular embodiments, a polynucleotide comprises, in a 5’ to 3’ direction: (i) a polynucleotide encoding a CD8 co-receptor α-chain; (ii) a polynucleotide encoding a CD8 co-receptor β-chain; and (iii) a polynucleotide encoding a TCR α-chain, and (iv) a polynucleotide encoding a TCR β-chain. In some embodiments, a polynucleotide encoding a self- cleaving peptide is disposed between the polynucleotide of (i) and the polynucleotide of (ii), between the polynucleotide of (ii) and the polynucleotide of (iii), and/or between the polynucleotide of (iii) and the polynucleotide of (iv).
[0144] Also provided herein are methods for making a modified CD4+ T cell, wherein the methods comprise transducing a CD4+ T cell with a heterologous polynucleotide encoding a TCR from a CD8+ T cell that is capable of specifically binding a peptide antigen. In certain embodiments, a TCR-encoding polynucleotide used to modify a CD4+ T cell comprises a nucleotide sequence according to a naturally occurring CD8+ T cell, or is a codon-optimized or otherwise engineered variant of such a naturally occurring polynucleotide. Further embodiments of the methods may include transducing the CD4+ T cell with a heterologous polynucleotide encoding at least an extracellular portion of a CD8 co-receptor, which may in some embodiments comprise a CD8α and a CD8β from the CD8+ T cell. Compositions [0145] Also provided herein are compositions (e.g., pharmaceutical compositions) that comprise a modified cell or population thereof as disclosed herein and a pharmaceutically acceptable carrier, diluent, or excipient. Suitable excipients include water, saline, dextrose, glycerol, or the like and combinations thereof. In embodiments, compositions comprising fusion proteins or host cells as disclosed herein further comprise a suitable infusion media. Suitable infusion media can be any isotonic medium formulation, typically normal saline, Normosol R (Abbott) or Plasma-Lyte A (Baxter), 5% dextrose in water, Ringer’s lactate can be utilized. An infusion medium can be supplemented with human serum albumin or other human serum components. Compositions described herein may be presented in unit-dose or multi-dose containers, such as sealed ampoules or vials. Such containers may be frozen to preserve the stability of the formulation until infusion into the patient. [0146] An “effective amount” of a composition refers to an amount sufficient, at dosages and for periods of time needed, to achieve the desired clinical results or beneficial treatment, as described herein. An effective amount may be delivered in one or more administrations. If the administration is to a subject already known or confirmed to have a disease or disease-state, the term “therapeutic amount” may be used in reference to treatment, whereas “prophylactically effective amount” may be used to describe administrating an effective amount to a subject that is susceptible or at risk of developing a disease or disease-state (e.g., recurrence) as a preventative course.
[0147] Compositions may be administered in a manner appropriate to the disease or condition to be treated (or prevented) as determined by persons skilled in the medical art. An appropriate dose and a suitable duration and frequency of administration of the compositions will be determined by such factors as the health condition of the patient, size of the patient (i.e., weight, mass, or body area), the type and severity of the patient’s condition, the particular form of the active ingredient, and the method of administration. In general, an appropriate dose and treatment regimen provide the composition(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit (such as described herein, including an improved clinical outcome, such as more frequent complete or partial remissions, or longer disease-free and/or overall survival, or a lessening of symptom severity). For prophylactic use, a dose should be sufficient to prevent, delay the onset of, or diminish the severity of a disease associated with disease or disorder. Prophylactic benefit of the compositions administered according to the methods described herein can be determined by performing pre-clinical (including in vitro and in vivo studies) and clinical studies and analyzing data obtained therefrom by appropriate statistical, biological, and clinical methods and techniques. [0148] A therapeutically effective dose is an amount of host cells (expressing a binding protein or high affinity recombinant TCR specific for a human MAGE-A1 antigen peptide) used in adoptive transfer that is capable of producing a clinically desirable result (e.g., a sufficient amount to induce or enhance a specific T cell immune response against cells overexpressing MAGE-A1 (e.g., a cytotoxic T cell response) in a statistically significant manner) in a treated human or non-human mammal. The dosage for any one patient depends upon many factors, including the patient’s size, weight, body surface area, age, the particular therapy to be administered, sex, time and route of administration, general health, and other drugs being administered concurrently. Doses will vary, but a preferred dose for administration of a host cell comprising a binding protein, polynucleotide, or recombinant expression vector as described herein is about 107 cells/m2, about 5 x 107 cells/m2, about 108 cells/m2, about 5 x 108 cells/m2, about 109 cells/m2, about 5 x 109 cells/m2, about 1010 cells/m2, about 5 x 1010 cells/m2, or about 1011 cells/m2. In certain embodiments, a unit dose comprises a modified cell as described herein at a dose of about 107 cells/m2 to about 1011 cells/m2.
[0149] In certain embodiments, a unit dose comprises (i) a composition comprising at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% engineered CD4+ T cells, combined with (ii) a composition comprising at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% engineered CD8+ T cells, in about a 1:1 ratio. In further embodiments, a unit dose contains a reduced amount or substantially no naïve T cells (i.e., has less than about 50%, less than about 40%, less than about 30%, less than about 20%, less than about 10%, less than about 5%, or less than about 1% the population of naïve T cells present in a unit dose as compared to a patient sample having a comparable number of PBMCs). [0150] In some embodiments, a unit dose comprises (i) a composition comprising at least about 50% engineered CD4+ T cells, combined with (ii) a composition comprising at least about 50% engineered CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no naïve T cells. In further embodiments, a unit dose comprises (i) a composition comprising at least about 60% modified CD4+ T cells, combined with (ii) a composition comprising at least about 60% modified CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no naïve T cells. In still further embodiments, a unit dose comprises (i) a composition comprising at least about 70% modified CD4+ T cells, combined with (ii) a composition comprising at least about 70% modified CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no naïve T cells. In some embodiments, a unit dose comprises (i) a composition comprising at least about 80% modified CD4+ T cells, combined with (ii) a composition comprising at least about 80% modified CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no naïve T cells. In some embodiments, a unit dose comprises (i) a composition comprising at least about 85% modified CD4+ T cells, combined with (ii) a composition comprising at least about 85% modified CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no naïve T cells. In some embodiments, a unit dose comprises (i) a composition comprising at least about 90% modified CD4+ T cells, combined with (ii) a composition comprising at least about 90% modified CD8+ T cells, in about a 1:1
ratio, wherein the unit dose contains a reduced amount or substantially no naïve T cells. In any of the embodiments described herein, a unit dose comprises equal, or approximately equal numbers, of modified CD45RA- CD3+ CD8+ and modified CD45RA- CD3+ CD4+ TM cells. [0151] In some embodiments, a population comprises engineered CD4+ T cells in combination with CD8+ T cells. In certain embodiments, the CD8+ T cells comprise CD62L+ T cells. In some embodiments, the CD4+ T cells and the CD8+ T cells are present in the population at a ratio of about 1:1. In some embodiments, the population of immune cells comprises NK cells, NK-T cells, macrophages, and/or microglia. [0152] In certain embodiments, a population comprises (i) at least about 50% engineered CD4+ T cells, combined with (ii) at least about 50% engineered CD8+ T cells, in about a 1:1 ratio, and optionally comprises a reduced amount or substantially no naïve T cells. In further embodiments, a population comprises (i) at least about 60% modified CD4+ T cells, combined with (ii) at least about 60% modified CD8+ T cells, in about a 1:1 ratio, wherein the population optionally contains a reduced amount or substantially no naïve T cells. In still further embodiments, a population comprises (i) at least about 70% modified CD4+ T cells, combined with (ii) at least about 70% modified CD8+ T cells, in about a 1:1 ratio, wherein the population optionally contains a reduced amount or substantially no naïve T cells. In some embodiments, a population comprises (i) at least about 80% modified CD4+ T cells, combined with (ii) at least about 80% modified CD8+ T cells, in about a 1:1 ratio, wherein the population optionally contains a reduced amount or substantially no naïve T cells. In some embodiments, a population comprises (i) at least about 85% modified CD4+ T cells, combined with (ii) at least about 85% modified CD8+ T cells, in about a 1:1 ratio, wherein the population optionally contains a reduced amount or substantially no naïve T cells. In some embodiments, a population comprises (i) at least about 90% modified CD4+ T cells, combined with (ii) at least about 90% modified CD8+ T cells, in about a 1:1 ratio, wherein the population optionally contains a reduced amount or substantially no naïve T cells. [0153] The development of suitable dosing and treatment regimens for using the particular compositions described herein in a variety of treatment regimens, including, e.g., parenteral or intravenous administration or formulation. If the subject composition is administered parenterally, the composition may also include sterile aqueous or
oleaginous solution or suspension. Suitable non-toxic parenterally acceptable diluents or solvents include water, Ringer’s solution, isotonic salt solution, 1,3-butanediol, ethanol, propylene glycol or polythethylene glycols in mixtures with water. Aqueous solutions or suspensions may further comprise one or more buffering agents, such as sodium acetate, sodium citrate, sodium borate or sodium tartrate. Of course, any material used in preparing any dosage unit formulation should be pharmaceutically pure and substantially non-toxic in the amounts employed. In addition, the active compounds may be incorporated into sustained-release preparation and formulations. Dosage unit form, as used herein, refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit may contain a predetermined quantity of modified cells or active compound calculated to produce the desired effect in association with an appropriate pharmaceutical carrier. [0154] As used herein, administration of a composition refers to delivering the same to a subject, regardless of the route or mode of delivery. Administration may be continuous or intermittent. Administration may be for treating a subject already confirmed as having a recognized condition, disease or disease state, or for treating a subject susceptible to or at risk of developing such a condition, disease or disease state. Co-administration with an adjunctive therapy may include simultaneous and/or sequential delivery of multiple agents in any order and on any dosing schedule (e.g., modified cells with one or more cytokines; immunosuppressive therapy such as calcineurin inhibitors, corticosteroids, microtubule inhibitors, low dose of a mycophenolic acid prodrug, HDAC inhibitors, DNA hypomethylation agents, or any combination thereof). [0155] In certain embodiments, a plurality of doses of a modified cell or population or composition described herein is administered to the subject, which may be administered at intervals between administrations of about two to about four weeks. Methods of Treatment [0156] In certain aspects, the instant disclosure is directed to methods for treating a hyperproliferative disorder or a condition characterized by MAGE-A1 expression (e.g., aberrant MAGE-A1 expression) by administering to human subject in need thereof a modified cell, composition, or unit dose as disclosed herein (or any combination thereof).
[0157] A condition associated with MAGE-A1 expression includes any disorder or condition in which underactivity, over-activity, or improper activity of a MAGE-A1 cellular or molecular event is present and may be the result of unusually high (with statistical significance) levels of MAGE-A1 expression or inappropriate (i.e., not occurring in healthy cells of the given cell type) expression in afflicted cells (e.g., myeloma cells), relative to normal cells. A subject having such a disorder or condition would benefit from treatment with a composition or method of the presently described embodiments. Some conditions associated with aberrant MAGE-A1 expression thus may include acute as well as chronic disorders and diseases, such as those pathological conditions that predispose the subject to a particular disorder. In certain embodiments, MAGE-A1 in a disease setting (e.g., cancer or proliferative disease or hyperproliferative disease) can be assessed by, for example, sequencing a MAGE-A1 gene locus in a diseased cell or cells, by immunohistochemistry (IHC), or using qPCR or RT-PCR. In some embodiments, diseased cells encode or express a MAGE-A1 comprising the amino acid sequence set forth in SEQ ID NO.:123, optionally comprised in SEQ ID NO.:122. [0158] Some examples of conditions associated with MAGE-A1 expression include proliferative disorders or hyperproliferative disorders, which refer to states of activated and/or proliferating cells (which may also be transcriptionally overactive) in a subject including tumors, neoplasms, cancer, malignancy, etc. In addition to activated or proliferating cells, the hyperproliferative disorder may also include an aberration or dysregulation of cell death processes, whether by necrosis or apoptosis. Such aberration of cell death processes may be associated with a variety of conditions, including cancer (including primary, secondary malignancies as well as metastasis), or other conditions. [0159] The presence of a hyperproliferative disorder or malignant condition in a subject refers to the presence of dysplastic, cancerous and/or transformed cells in the subject, including, for example neoplastic, tumor, non-contact inhibited or oncogenically transformed cells, or the like (e.g., solid cancers; hematologic cancers including lymphomas and leukemias, such as acute myeloid leukemia, chronic myeloid leukemia, etc.), which are known in the art and for which criteria for diagnosis and classification are established (e.g., Hanahan and Weinberg, Cell 144:646, 2011; Hanahan and Weinberg, Cell 100:57, 2000; Cavallo et al., Canc. Immunol. Immunother. 60:319, 2011; Kyrigideis et al., J. Carcinog.9:3, 2010). In certain embodiments, such
cancer cells may be cells of acute myeloid leukemia, B-cell lymphoblastic leukemia, T- cell lymphoblastic leukemia, or myeloma, including cancer stem cells that are capable of initiating and serially transplanting any of these types of cancer (see, e.g., Park et al., Molec. Therap.17:219, 2009). [0160] In certain embodiments, there are provided methods for treating a hyperproliferative disorder, such as a hematological malignancy or a solid cancer, wherein the method comprises administering to a human subject in need thereof a modified cell, composition, or unit dose of the present disclosure. Exemplary hematological malignancies include acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), chronic myelogenous leukemia (CML), chronic eosinophilic leukemia (CEL), myelodysplastic syndrome (MDS), non-Hodgkin’s lymphoma (NHL), or multiple myeloma (MM). [0161] In further embodiments, there are provided methods for treating a hyperproliferative disorder, such as a solid cancer is selected from non-small cell lung cancer (NSCLC), triple negative breast cancer (TNBC), ovarian cancer, malignant melanoma, colon cancer, colorectal adenocarcinoma, colorectal cancer, biliary cancer, bladder cancer, bone and soft tissue carcinoma, brain tumor, breast cancer, cervical cancer, desmoid tumor, embryonal cancer, endometrial cancer, esophageal cancer, gastric cancer, gastric adenocarcinoma, glioblastoma multiforme, gynecological tumor, head and neck squamous cell carcinoma, hepatic cancer, lung cancer, mesothelioma, osteosarcoma, pancreatic cancer, pancreatic ductal adenocarcinoma, primary astrocytic tumor, primary thyroid cancer, prostate cancer, renal cancer, renal cell carcinoma, rhabdomyosarcoma, skin cancer, soft tissue sarcoma, testicular germ-cell tumor, urothelial cancer, uterine sarcoma, or uterine cancer. [0162] As understood by a person skilled in the medical art, the terms, “treat” and “treatment,” refer to medical management of a disease, disorder, or condition of a subject (i.e., patient, host, who may be a human or non-human animal) (see, e.g., Stedman’s Medical Dictionary). In general, an appropriate dose and treatment regimen provide one or more of a binding protein or high affinity recombinant TCR specific for human MAGE-A1 or a host cell expressing the same, and optionally an adjunctive or combination therapy (e.g., a cytokine such as IL-2, IL-15, IL-21, or any combination thereof; a PD-1/PD-L1 axis inhibitor), in an amount sufficient to provide therapeutic or prophylactic benefit. Therapeutic or prophylactic benefit resulting from therapeutic
treatment or prophylactic or preventative methods include, for example an improved clinical outcome, wherein the object is to prevent or retard or otherwise reduce (e.g., decrease in a statistically significant manner relative to an untreated control) an undesired physiological change or disorder, or to prevent, retard or otherwise reduce the expansion or severity of such a disease or disorder. Beneficial or desired clinical results from treating a subject include abatement, lessening, or alleviation of symptoms that result from or are associated the disease or disorder to be treated; decreased occurrence of symptoms; improved quality of life; longer disease-free status (i.e., decreasing the likelihood or the propensity that a subject will present symptoms on the basis of which a diagnosis of a disease is made); diminishment of extent of disease; stabilized (i.e., not worsening) state of disease; delay or slowing of disease progression; amelioration or palliation of the disease state; and remission (whether partial or total), whether detectable or undetectable; overall survival; or prolonging survival when compared to expected survival if a subject were not receiving treatment. In some embodiments, treatment results in a decreased rate of growth and/or decreased spread of and/or decreased rate of spread of cancer cells, a decreased number of cancer cells, a decreased size or density of a tumor, a decreased number of tumors, remission, killing of cancer cells, or any combination thereof. [0163] In some embodiments, treatment results in a partial response (also referred-to as partial remission). In some embodiments, a partial response comprises a decrease in the size of a tumor, or in the extent of cancer in the body, in response to treatment. In some embodiments, treatment results in a complete response (also referred-to as complete remission). In some embodiments, a complete response comprises he disappearance of all signs of cancer in response to treatment. In some embodiments, treatment results in a period of progression-free survival and/or in results an increased duration of progression-free survival (also referred-to as PFS). In some embodiments, PFS comprises a length of time during and after the treatment of a disease, such as cancer, that a patient lives with the disease but it does not get worse. [0164] Subjects in need of the methods and compositions described herein include those who already have the disease or disorder, as well as subjects prone to have or at risk of developing the disease or disorder. Subjects in need of prophylactic treatment include subjects in whom the disease, condition, or disorder is to be prevented (i.e., decreasing the likelihood of occurrence or recurrence of the disease or disorder).
The clinical benefit provided by the compositions (and preparations comprising the compositions) and methods described herein can be evaluated by design and execution of in vitro assays, preclinical studies, and clinical studies in subjects to whom administration of the compositions is intended to benefit, as described in the examples. [0165] In some contexts, a subject receiving therapy according to the present disclosure is negative for or has been identified as negative for expression of HLA B*49:01. In some embodiments, a subject receiving therapy according to the present disclosure is positive for or has been identified as positive for expression of HLA- A*02:01. In further embodiments, the methods comprise, prior to administering a population of modified immune cells, identifying the subject as being negative for expression of HLA-B*49:01 and/or as being positive for expression of HLA-A*02:01. [0166] In some embodiments, the present disclosure provides a method of treating a cancer or disease or disorder that is associated with MAGE-A1 expression in a subject, comprising administering to the subject a population of modified immune cells comprising a binding protein described herein wherein the subject is negative for or has been identified as negative for expression of HLA B*49:01. [0167] A subject is considered “negative for expression of HLA-B*49:01” when the subject has no detectable levels of the HLA-B*49:01 allele as determined by genetic sequencing (e.g., high throughput Next Generation Sequencing (NGS)). This genetic determination of the HLA expression is referred to herein as “HLA typing” and can determined though molecular approaches in a clinical laboratory licensed for HLA typing. In some embodiments, HLA typing is performed using PCR amplification followed by high throughput NGS and subsequent HLA determination. Herein, the HLA haplotype is determined at the major HLA loci (e.g., HLA-A, HLA-B, HLA-C, etc.). [0168] A subject is considered “positive for expression of HLA-A*02:01” when the subject has detectable levels of the HLA-A*02:01 allele as determined by genetic sequencing (e.g., high throughput Next Generation Sequencing (NGS)). This genetic determination of the HLA expression is referred to herein as “HLA typing” and can determined though molecular approaches in a clinical laboratory licensed for HLA typing. In some embodiments, HLA typing is performed using PCR amplification followed by high throughput NGS and subsequent HLA determination. Herein, the
HLA haplotype is determined at the major HLA loci (e.g., HLA-A, HLA-B, HLA-C, etc.). [0169] HLA typing can be performed using any known method, including, for example, protein or nucleic acid testing. Examples of nucleic acid testing include sequence-based typing (SBT) and use of sequence-specific oligonucleotide probes (SSOP) or sequence-specific primers (SSP). In certain embodiments, HLA typing is performed using PCR amplification followed by high throughput Next Generation Sequencing (NGS) and subsequent HLA determination. In some embodiments, sequence typing is performed using a system available through Scisco Genetics (sciscogenetics.com/pages/technology.html, the contents of which is incorporated herein by reference in its entirety). Other methods for HLA typing include, e.g., those disclosed in Mayor et al. PLoS One 10(5):e0127153 (2015), which methods and reagents are incorporated herein by reference. [0170] In some embodiments, a subject receiving cell therapy (or a combination therapy comprising cell therapy) according to the present disclosure has metastatic disease, and/or disease that is confirmed by archival, initial, or subsequent biopsy or other pathologic material. For example, in the case of triple-negative breast cancer (TNBC), in certain embodiments, a subject must meet the American Society of Clinical Oncology – College of American Pathologists (ASCO-CAP) definition of negative estrogen, progesterone, and HER2 receptor expression. [0171] In some embodiments, a subject receiving cell therapy (or a combination therapy comprising cell therapy) according to the present disclosure has measurable disease, for example, defined as at least one target lesion that can be measured in at least one dimension (longest diameter to be recorded) as ≥10 mm, unless lymph node, in which case short axis may be ≥ 15 mm. In some embodiments, baseline imaging (for example, diagnostic CT chest/abdomen/pelvis and imaging of the affected extremity as appropriate), brain imaging (MRI or CT scan) is obtained within 45 days of prior to start of first planned infusion of therapeutic immune cells (e.g., T cells). In some embodiments, MRI can be substituted for CT in subjects unable to have CT contrast. [0172] In some embodiments, a subject receiving cell therapy (or a combination therapy comprising cell therapy) according to the present disclosure has received or is receiving treatment with standard-of-care therapy approved by an appropriate regulatory agency (e.g., FDA, EMA, or the like). In some embodiments, subjects with
NSCLC who have actionable somatic mutations or alterations in EGFR, ROS1 and ALK with approved drug therapy options receive cell therapy or combination therapy only after treatment with targeted therapies for those mutations have been offered or received. In some embodiments, subjects with urothelial carcinoma receive cell therapy or combination therapy according to the present disclosure after prior treatment with enfortumab vedotin-ejfv has been offered or received. [0173] In some embodiments, a subject receiving cell therapy (or a combination therapy comprising cell therapy) has received or is receiving therapy comprising a CPI (immune checkpoint inhibitor, discussed further herein), a PD-1 inhibitor, a PD-L1 inhibitor, and/or a PD-1/PD-L1 axis inhibitor, as described herein. In certain embodiments, a subject has been offered or been previously treated with at least one dose of a PD-L1 axis inhibitor (e.g., PD-1-inhibiting or PD-L1-inhibiting monoclonal antibody such as pembrolizumab, nivolumab, avelumab, atezolizumab, durvalumab, or any combination thereof). In further embodiments, if the prior therapy was received, the subject either developed progression or has detectable disease and has not developed CTCAE grade 3 or higher toxicity while receiving the prior treatment. [0174] In certain embodiments, a subject is receiving or has received CPI, PD-1 inhibitor, PD-L1 inhibitor, and/or a PD-1/PD-L1 axis inhibitor therapy in the neoadjuvant or adjuvant setting. In some embodiments, a first dose of a CPI is administered after a population of modified immune cells is administered, such as within 24 to 72 hours after the population of modified immune cells is administered. [0175] In some embodiments, the CPI or the PD-1/PD-L1 axis inhibitor is selected from atezolizumab, nivolumab, durvalumab, and pembrolizumab. In particular embodiments, the CPI or the PD-1/PD-L1 axis inhibitor comprises atezolizumab. In certain embodiments, the atezolizumab is administered to the subject every three weeks at 1200 mg per administration. In some embodiments, the method comprises administering a PD-L1 inhibitor and the PD-L1 inhibitor is avelumab. [0176] In certain embodiments, a cancer treatable according to the disclosed methods is or comprises a solid tumor. [0177] In certain embodiments, a cancer treatable according to the disclosed methods is or comprises triple negative breast cancer (TNBC), wherein, optionally, the TNBC is metastatic TNBC.
[0178] In certain embodiments, a cancer treatable according to the disclosed methods is or comprises non-small cell lung cancer (NSCLC), wherein, optionally, the NSCLC is metastatic NSCLC. [0179] In certain embodiments, a cancer treatable according to the disclosed methods is or comprises urothelial cancer. In some embodiments, the urothelial cancer is a metastatic urothelial cancer or an advanced urothelial cancer. [0180] In certain embodiments, subjects have received 1 or more prior systemic regimens for metastatic TNBC or NSCLC. In certain such embodiments, any number of prior systemic regimens is contemplated. [0181] In some embodiments, a subject receiving cell therapy (or a combination therapy comprising cell therapy) has an ECOG (Eastern Cooperative Oncology Group) Performance Status of 0, 1, or 2. [0182] In some embodiments, a subject receiving cell therapy (or a combination therapy comprising cell therapy) has not received systemic therapy (e.g., immunotherapy (for example, T-cell infusions, immunomodulatory agents, interleukins, vaccines), small molecule or chemotherapy cancer treatment, other investigational agents) for three or more weeks prior to the cell therapy or combination therapy. [0183] In certain embodiments, a subject receiving cell therapy (or a combination therapy comprising cell therapy) may be receiving or has received biophosphonates but has not received concurrent treatment with a RANK-ligand inhibitor (e.g., denosumab) for eight or more weeks prior to the cell therapy or combination therapy. [0184] In some embodiments, a subject receiving cell therapy (or a combination therapy comprising cell therapy) according to the present disclosure is lymphodepeleted or has undergone or receives a lymphodepletion procedure. Lymphodepletion prior to administration of cell therapy can reduce tumor burden, minimize risk of tumor lysis syndrome, and induce lymphopenia to improve persistence of transferred cells. [0185] As used herein, “lymphodepleted” refers to an, optionally artificially induced, condition or state wherein a subject has a reduced amount of lymphocytes present in blood and/or in bone marrow, as compared to a normal or healthy state of the subject. In some embodiments, a lymphodepleted subject has lymphopenia (also called lymphocytopenia).
[0186] In certain embodiments, a lymphodepleted subject has an amount of lymphocytes in blood and/or in bone marrow that is reduced by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, or more, as compared to the subject when in a normal healthy condition, and/or as compared to a reference subject in a normal healthy condition, and/or as compared to the subject prior to receiving lymphodepleting therapy. [0187] Procedures for inducing lymphodepletion are known, and include, e.g., administering radiation therapy; a lymphodepleting chemotherapy comprising cyclophosphamide, fludarabine, bendamustine, or any combination thereof; anti- thymocyte globulin; or any combination thereof. Lymphodepleting chemotherapy can, in some embodiments, be administered intravenously. [0188] In particular embodiments, lymphodepleting chemotherapy comprises cyclophosphamide, fludarabine, or a combination thereof, wherein, optionally, the lymphodepleting chemotherapy comprises 300 mg/m2 cyclophosphamide and/or 30 mg/m2 fludarabine. [0189] In some embodiments, a method further comprises providing lymphodepletion to the subject, wherein, optionally, the lymphodepletion is provided prior to administering a population of modified immune cells, wherein, further optionally, the lymphodepletion is provided 4 days, 3 days, 2 days, and/or 1 day prior to administering a population of modified immune cells. [0190] In certain embodiments of the presently disclosed methods, a modified cell is capable of promoting an antigen-specific T cell response against a MAGE-A1 in a class I HLA-restricted manner. In some embodiments, a class I HLA-restricted response is transporter-associated with antigen processing (TAP) independent. In some embodiments, an antigen-specific T cell response promoted by a modified cell administered according to the presently disclosed methods comprises at least one of a CD4+ helper T lymphocyte (Th) response and a CD8+ cytotoxic T lymphocyte (CTL) response. In particular embodiments, a CTL response elicited according to the instantly disclosed methods is directed against a cell having aberrant MAGE-A1 expression (e.g., a MAGE-A1+ tumor cell). The level of a CTL immune response may be determined by any one of numerous immunological methods described herein and routinely practiced in the art. The level of a CTL immune response may be determined prior to and
following administration of any one of the herein described MAGE-A1-specific binding proteins expressed by, for example, a T cell. Cytotoxicity assays for determining CTL activity may be performed using any one of several techniques and methods routinely practiced in the art (see, e.g., Henkart et al., “Cytotoxic T-Lymphocytes” in Fundamental Immunology, Paul (ed.) (2003 Lippincott Williams & Wilkins, Philadelphia, PA), pages 1127-50, and references cited therein). [0191] Antigen-specific T cell responses are typically determined by comparisons of observed T cell responses according to any of the herein described T cell functional parameters (e.g., proliferation, cytokine release, CTL activity, altered cell surface marker phenotype, etc.) that may be made between T cells that are exposed to a cognate antigen in an appropriate context (e.g., the antigen used to prime or activate the T cells, when presented by immunocompatible antigen-presenting cells) and T cells from the same source population that are exposed instead to a structurally distinct or irrelevant control antigen. A response to the cognate antigen that is greater, with statistical significance, than the response to the control antigen signifies antigen- specificity. [0192] A biological sample may be obtained from a subject for determining the presence and level of an immune response to a MAGE-A1-derived antigen peptide as described herein. A “biological sample” as used herein may be a blood sample (from which serum or plasma may be prepared), biopsy specimen, body fluids (e.g., lung lavage, ascites, mucosal washings, synovial fluid), bone marrow, lymph nodes, tissue explant, organ culture, or any other tissue or cell preparation from the subject or a biological source. Biological samples may also be obtained from the subject prior to receiving any immunogenic composition, which biological sample is useful as a control for establishing baseline (i.e., pre-immunization) data. [0193] Modified cells of this disclosure are useful, in certain embodiments, in adoptive cell therapies. For example, in some embodiments, a modified cell is modified (e.g., transduced with a recombinant expression vector or polynucleotide of the present disclosure) ex vivo, and then administered to a subject in need thereof. In certain embodiments, modified cell is an allogeneic cell, a syngeneic cell, or an autologous cell (i.e., relative to the subject administered the modified cell). In any of the presently disclosed methods, a modified cell comprises a modified human immune cell selected from a CD4+ T cell, a CD8+ T cell, a CD4- CD8- double negative T cell, a γδ T cell, a
natural killer cell, a dendritic cell, or any combination thereof. In certain embodiments, a modified cell is a T cell, e.g., is a naïve T cell, a central memory T cell, an effector memory T cell, or any combination thereof. [0194] In particular embodiments, a modified cell used in the presently disclosed methods is a CD4+ T cell. In some such embodiments, a modified CD4+ T cell further comprises a heterologous polynucleotide encoding at least an extracellular portion of a CD8 co-receptor, and optionally encodes a complete CD8 α-chain, a complete CD8 β-chain, or both. Such methods may, in certain embodiments, further comprise administering to the subject a CD8+ T cell that is capable of specifically binding to a MAGE-A1 peptide:HLA complex on a cell surface, such as a CD8+ modified T cell according to the present disclosure. [0195] Presently disclosed treatment or prevention methods may include any appropriate method of administering or dosing a modified cell, or a combination therapy. For example, in certain embodiments, a plurality of doses of a modified cell as described herein is administered to the subject, which may be administered at intervals between administrations of about two to about four weeks. In addition, treatment or prevention methods of this disclosure may be administered to a subject as part of a treatment course or regimen, which may comprise additional treatments prior to, or after, administration of the instantly disclosed unit doses, cells, or compositions. In further embodiments, a cytokine is administered sequentially, provided that the subject was administered the recombinant host cell at least three or four times before cytokine administration. In certain embodiments, the cytokine is administered subcutaneously (e.g., IL-2, IL-15, IL-21). In still further embodiments, the subject being treated is further receiving immunosuppressive therapy, such as calcineurin inhibitors, corticosteroids, microtubule inhibitors, low dose of a mycophenolic acid prodrug, or any combination thereof. In yet further embodiments, the subject being treated has received a non-myeloablative or a myeloablative hematopoietic cell transplant, wherein the treatment may be administered at least two to at least three months after the non- myeloablative hematopoietic cell transplant. In some embodiments, subject has been administered one or more of a DNA hypomethylation agent and a HDAC inhibitor, either or both of which may enhance MAGE-A1 expression (see Weon, J.L. and P.R. Potts, Curr Opin Cell Biol, 2015.37: p.1-8) and thereby enhance an adoptive cell therapy targeting MAGE-A1.
[0196] Methods according to the instant disclosure may, in certain embodiments, further include administering one or more additional agents to treat the disease or disorder in a combination therapy. For example, in certain embodiments, a combination therapy comprises administering a modified cell with (concurrently, simultaneously, or sequentially) an immune checkpoint inhibitor. In some embodiments, a combination therapy comprises administering a modified cell with an agonist of a stimulatory immune checkpoint agent. In further embodiments, a combination therapy comprises administering a modified cell with a secondary therapy, such as chemotherapeutic agent, a radiation therapy, a surgery, an antibody, or any combination thereof. [0197] As used herein, the term “immune suppression agent” or “immunosuppression agent” refers to one or more cells, proteins, molecules, compounds, or complexes providing inhibitory signals to assist in controlling or suppressing an immune response. For example, immune suppression agents include those molecules that partially or totally block immune stimulation; decrease, prevent or delay immune activation; or increase, activate, or up regulate immune suppression. Exemplary immunosuppression agents to target (e.g., with an immune checkpoint inhibitor) include PD-1, PD-L1, PD- L2, LAG3, CTLA4, B7-H3, B7-H4, CD244/2B4, HVEM, BTLA, CD160, TIM3, GAL9, KIR, PVR1G (CD112R), PVRL2, adenosine, A2aR, immunosuppressive cytokines (e.g., IL-10, IL-4, IL-1RA, IL-35), IDO, arginase, VISTA, TIGIT, LAIR1, CEACAM-1, CEACAM-3, CEACAM-5, Treg cells, or any combination thereof. [0198] An immune suppression agent inhibitor (also referred to as an immune checkpoint inhibitor (“CPI”)) may be a compound, an antibody, an antibody fragment, or fusion polypeptide (e.g., Fc fusion, such as CTLA4-Fc or LAG3-Fc), an antisense molecule, a ribozyme or RNAi molecule, or a low molecular weight organic molecule. In any of the embodiments disclosed herein, a method may comprise a modified cell with one or more inhibitor of any one of the following immune suppression components, singly or in any combination. [0199] In certain embodiments, a modified cell is used in combination with a PD-1 inhibitor, for example a PD-1-specific antibody or binding fragment thereof, such as pidilizumab, nivolumab, pembrolizumab, MEDI0680 (formerly AMP-514), AMP- 224, tislelizumab, cemiplimab, JTX-1041, spartelizumab, camrelizumab, sintilimab,
toripalimab, dostarlimab, INCMGA00012 aka MGA012, AMP-224, AMP-514, BMS- 936558 or any combination thereof. In certain embodiments, a modified cell of the present disclosure is used in combination with a PD-L1 specific antibody or binding fragment thereof or peptide, such as BMS-936559, durvalumab (MEDI4736), atezolizumab (RG7446), avelumab (MSB0010718C), MPDL3280A, KN035, CK-301, AUNP12, CA-170, BMS-986189, or any combination thereof. PD-1 inhibitors and PD- L1 inhibitors can be referred-to as PD-1/PD-L1 axis inhibitors. In particular embodiments, a CPI, a PD-1/PD-L1 axis inhibitor, a PD-1 inhibitor, and/or a PD-L1 axis inhibitor is administered as a combination with a cell therapy. In further embodiments, the CPI, PD-1/PD-L1 axis inhibitor, PD-1 inhibitor, and/or PD-L1 axis inhibitor is administered following administration of at least a first dose or infusion of a cell therapy. [0200] It will be understood that a subject receiving cell therapy (optionally in combination with CPI, PD-1/PD-L1 axis inhibitor, PD-1 inhibitor, and/or PD-L1 axis inhibitor) of the present disclosure may have previously received or initiated a course of therapy comprising the same or a different CPI, PD-1/PD-L1 axis inhibitor, PD-1 inhibitor, and/or PD-L1 axis inhibitor. It will additionally be understood that in such a circumstance, a first dose of the CPI, PD-1/PD-L1 axis inhibitor, PD-1 inhibitor, and/or PD-L1 axis inhibitor according to a presently disclosed cell therapy or combination method refers to the first dose administered in the context of the combination, e.g., following at least a first dose or infusion of the cell therapy, and does not refer to a dose of the CPI, PD-1/PD-L1 axis inhibitor, PD-1 inhibitor, and/or PD-L1 axis inhibitor in a prior line of therapy (i.e., a line of therapy that preceded or began prior to the cell therapy or combination therapy comprising the cell therapy). [0201] In certain embodiments, a modified cell of the present disclosure is used in combination with a LAG3 inhibitor, such as LAG525, IMP321, IMP701, 9H12, BMS- 986016, or any combination thereof. In certain embodiments, a modified cell is used in combination with an inhibitor of CTLA4. In particular embodiments, a modified cell is used in combination with a CTLA4 specific antibody or binding fragment thereof, such as ipilimumab, tremelimumab, CTLA4-Ig fusion proteins (e.g., abatacept, belatacept), or any combination thereof. In certain embodiments, a modified cell is used in combination with a B7-H3 specific antibody or binding fragment thereof, such as enoblituzumab (MGA271), 376.96, or both. A B7-H4 antibody binding fragment
may be a scFv or fusion protein thereof, as described in, for example, Dangaj et al., Cancer Res.73:4820, 2013, as well as those described in U.S. Patent No.9,574,000 and PCT Patent Publication Nos. WO /201640724A1 and WO 2013/025779A1. In certain embodiments, a modified cell is used in combination with an inhibitor of CD244. In certain embodiments, a modified cell is used in combination with an inhibitor of BLTA, HVEM, CD160, or any combination thereof. Anti-CD-160 antibodies are described in, for example, PCT Publication No. WO 2010/084158. In certain embodiments, a modified cell is used in combination with an inhibitor of TIM3. In certain embodiments, a modified cell is used in combination with an inhibitor of Gal9. In certain embodiments, a modified cell is used in combination with an inhibitor of adenosine signaling, such as a decoy adenosine receptor. [0202] In certain embodiments, a modified cell is used in combination with an inhibitor of A2aR. In certain embodiments, a modified cell is used in combination with an inhibitor of KIR, such as lirilumab (BMS-986015). In certain embodiments, a modified cell is used in combination with an inhibitor of an inhibitory cytokine (typically, a cytokine other than TGFβ) or Treg development or activity. In certain embodiments a modified cell is used in combination with an IDO inhibitor, such as levo-1-methyl tryptophan, epacadostat (INCB024360; Liu et al., Blood 115:3520-30, 2010), ebselen (Terentis et al., Biochem.49:591-600, 2010), indoximod, NLG919 (Mautino et al., American Association for Cancer Research 104th Annual Meeting 2013; Apr 6-10, 2013), 1-methyl-tryptophan (1-MT)-tira-pazamine, or any combination thereof. In certain embodiments, a modified cell is used in combination with an arginase inhibitor, such as N(omega)-Nitro-L-arginine methyl ester (L-NAME), N- omega-hydroxy-nor-l-arginine (nor-NOHA), L-NOHA, 2(S)-amino-6- boronohexanoic acid (ABH), S-(2-boronoethyl)-L-cysteine (BEC), or any combination thereof. In certain embodiments, a modified cell is used in combination with an inhibitor of VISTA, such as CA-170 (Curis, Lexington, Mass.). In certain embodiments, a modified cell is used in combination with an inhibitor of TIGIT such as, for example, COM902 (Compugen, Toronto, Ontario Canada), an inhibitor of CD155, such as, for example, COM701 (Compugen), or both. In certain embodiments, a modified cell is used in combination with an inhibitor of PVRIG, PVRL2, or both. Anti-PVRIG antibodies are described in, for example, PCT Publication No. WO 2016/134333. Anti- PVRL2 antibodies are described in, for example, PCT Publication No. WO
2017/021526. In certain embodiments, a modified cell is used in combination with a LAIR1 inhibitor. In certain embodiments, a modified cell is used in combination with an inhibitor of CEACAM-1, CEACAM-3, CEACAM-5, or any combination thereof. [0203] In certain embodiments, a modified cell is used in combination with an agent that increases the activity (i.e., is an agonist) of a stimulatory immune checkpoint molecule. For example, a modified cell can be used in combination with a CD137 (4- 1BB) agonist (such as, for example, urelumab), a CD134 (OX-40) agonist (such as, for example, MEDI6469, MEDI6383, or MEDI0562), lenalidomide, pomalidomide, a CD27 agonist (such as, for example, CDX-1127), a CD28 agonist (such as, for example, TGN1412, CD80, or CD86), a CD40 agonist (such as, for example, CP- 870,893, rhuCD40L, or SGN-40), a CD122 agonist (such as, for example, IL-2) an agonist of GITR (such as, for example, humanized monoclonal antibodies described in PCT Patent Publication No. WO 2016/054638), an agonist of ICOS (CD278) (such as, for example, GSK3359609, mAb 88.2, JTX-2011, Icos 145-1, Icos 314-8, or any combination thereof). [0204] In any of the embodiments disclosed herein, a method may comprise administering a modified cell with one or more agonist of a stimulatory immune checkpoint molecule, including any of the foregoing, singly or in any combination. [0205] In certain embodiments, a combination therapy comprises a modified cell and a secondary therapy comprising one or more of: an antibody or antigen binding-fragment thereof that is specific for a cancer antigen expressed by the non- inflamed solid tumor, a radiation treatment, a surgery, a chemotherapeutic agent, a cytokine, RNAi, or any combination thereof. [0206] In certain embodiments, a combination therapy method comprises administering a modified cell and further administering a radiation treatment or a surgery. Radiation therapy is well-known in the art and includes X-ray therapies, such as gamma- irradiation, and radiopharmaceutical therapies. Surgeries and surgical techniques appropriate to treating a given cancer in a subject are well-known to those of ordinary skill in the art. [0207] In certain embodiments, a combination therapy method comprises administering a modified cell and further administering a chemotherapeutic agent. A chemotherapeutic agent includes, but is not limited to, an inhibitor of chromatin function, a topoisomerase inhibitor, a microtubule inhibiting drug, a DNA damaging
agent, an antimetabolite (such as folate antagonists, pyrimidine analogs, purine analogs, and sugar-modified analogs), a DNA synthesis inhibitor, a DNA interactive agent (such as an intercalating agent), and a DNA repair inhibitor. Illustrative chemotherapeutic agents include, without limitation, the following groups: anti-metabolites/anti-cancer agents, such as pyrimidine analogs (5-fluorouracil, floxuridine, capecitabine, gemcitabine and cytarabine) and purine analogs, folate antagonists and related inhibitors (mercaptopurine, thioguanine, pentostatin and 2- chlorodeoxyadenosine (cladribine)); antiproliferative/antimitotic agents including natural products such as vinca alkaloids (vinblastine, vincristine, and vinorelbine), microtubule disruptors such as taxane (paclitaxel, docetaxel), vincristin, vinblastin, nocodazole, epothilones and navelbine, epidipodophyllotoxins (etoposide, teniposide), DNA damaging agents (actinomycin, amsacrine, anthracyclines, bleomycin, busulfan, camptothecin, carboplatin, chlorambucil, cisplatin, cyclophosphamide, Cytoxan, dactinomycin, daunorubicin, doxorubicin, epirubicin, examethylmelamineoxaliplatin, iphosphamide, melphalan, merchlorehtamine, mitomycin, mitoxantrone, nitrosourea, plicamycin, procarbazine, taxol, taxotere, temozolamide, teniposide, triethylenethiophosphoramide and etoposide (VP 16)); antibiotics such as dactinomycin (actinomycin D), daunorubicin, doxorubicin (adriamycin), idarubicin, anthracyclines, mitoxantrone, bleomycins, plicamycin (mithramycin) and mitomycin; enzymes (L-asparaginase which systemically metabolizes L-asparagine and deprives cells which do not have the capacity to synthesize their own asparagine); antiplatelet agents; antiproliferative/antimitotic alkylating agents such as nitrogen mustards (mechlorethamine, cyclophosphamide and analogs, melphalan, chlorambucil), ethylenimines and methylmelamines (hexamethylmelamine and thiotepa), alkyl sulfonates -busulfan, nitrosoureas (carmustine (BCNU) and analogs, streptozocin), trazenes— dacarbazinine (DTIC); antiproliferative/antimitotic antimetabolites such as folic acid analogs (methotrexate); platinum coordination complexes (cisplatin, carboplatin), procarbazine, hydroxyurea, mitotane, aminoglutethimide; hormones, hormone analogs (estrogen, tamoxifen, goserelin, bicalutamide, nilutamide) and aromatase inhibitors (letrozole, anastrozole); anticoagulants (heparin, synthetic heparin salts and other inhibitors of thrombin); fibrinolytic agents (such as tissue plasminogen activator, streptokinase and urokinase), aspirin, dipyridamole, ticlopidine, clopidogrel, abciximab; antimigratory agents; antisecretory agents (breveldin); immunosuppressives
(cyclosporine, tacrolimus (FK-506), sirolimus (rapamycin), azathioprine, mycophenolate mofetil); anti-angiogenic compounds (TNP470, genistein) and growth factor inhibitors (vascular endothelial growth factor (VEGF) inhibitors, fibroblast growth factor (FGF) inhibitors); angiotensin receptor blocker; nitric oxide donors; anti- sense oligonucleotides; antibodies (trastuzumab, rituximab); chimeric antigen receptors; cell cycle inhibitors and differentiation inducers (tretinoin); mTOR inhibitors, topoisomerase inhibitors (doxorubicin (adriamycin), amsacrine, camptothecin, daunorubicin, dactinomycin, eniposide, epirubicin, etoposide, idarubicin, irinotecan (CPT-11) and mitoxantrone, topotecan, irinotecan), corticosteroids (cortisone, dexamethasone, hydrocortisone, methylpednisolone, prednisone, and prenisolone); growth factor signal transduction kinase inhibitors; mitochondrial dysfunction inducers, toxins such as Cholera toxin, ricin, Pseudomonas exotoxin, Bordetella pertussis adenylate cyclase toxin, or diphtheria toxin, and caspase activators; and chromatin disruptors. [0208] Cytokines can be used to manipulate host immune response towards anticancer activity. See, e.g., Floros & Tarhini, Semin. Oncol.42(4):539-548, 2015. Cytokines useful for promoting immune anticancer or antitumor response include, for example, IFN-α, IL-2, IL-3, IL-4, IL-10, IL-12, IL-13, IL-15, IL-16, IL-17, IL-18, IL- 21, IL-24, and GM-CSF, singly or in any combination with a modified cell of this disclosure. Further Numbered Embodiments [0209] The present disclosure also provides the following exemplary Embodiments. 1. A method of treating a cancer or disease or disorder that is associated with MAGE-A1 expression in a subject, the method comprising administering to the subject a population of modified immune cells comprising a binding protein, the binding protein comprising: a) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3
amino acid sequences according to SEQ ID NOS.: 45-47, respectively; b) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 30-32, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 27-29, respectively; c) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 36-38, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 33-35, respectively; d) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 42-44, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 39-41, respectively; or e) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 24-26, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 21-23, respectively, wherein the cancer or disease or disorder, or a cell thereof, expresses MAGE- A1, and wherein the subject is negative for or has been identified as negative for expression of HLA B*49:01. 2. The method of Embodiment 1, wherein the method further comprises, prior to administering the population of modified immune cells, identifying the subject as being negative for expression of HLA B*49:01. 3. The method of Embodiment 1 or Embodiment 2, wherein the subject is positive for or has been identified as positive for expression of HLA A*02:01. 4. The method of any one of Embodiments 1-3, wherein the method further comprises, prior to administering the population of modified immune cells, identifying the subject as positive for expression of HLA A*02:01.
5. The method of any one of Embodiments 1-4, wherein the subject is lymphodepleted or has undergone a lymphodepletion procedure. 6. The method of any one of Embodiments 1-5, wherein the method further comprises providing lymphodepletion to the subject, wherein, optionally, the lymphodepletion is provided prior to administering the population of modified immune cells, wherein, further optionally, the lymphodepletion is provided 4 days, 3 days, 2 days, and/or 1 day prior to administering the population of modified immune cells. 7. The method of Embodiment 6, wherein providing lymphodepletion comprises administering a lymphodepleting chemotherapy to the subject. 8. The method of Embodiment 7, wherein the lymphodepleting chemotherapy comprises cyclophosphamide, fludarabine, or a combination thereof, wherein, optionally, the lymphodepleting chemotherapy comprises 300 mg/m2 cyclophosphamide and/or 30 mg/m2 fludarabine. 9. The method of Embodiment 7 or Embodiment 8, wherein the lymphodepleting chemotherapy is administered intravenously to the subject. 10. The method of any one of Embodiments 1-9, wherein the method comprises administering an immune checkpoint inhibitor (CPI) to the subject, wherein, optionally, a first dose of the CPI is administered after the population of modified immune cells is administered, such as within 24 to 72 hours after the population of modified immune cells is administered. 11. The method of any one of Embodiments 1-10, wherein the method comprises administering a PD-1/PD-L1 axis inhibitor to the subject. 12. The method of Embodiment 10 or Embodiment 11, wherein the CPI or the PD-1/PD-L1 axis inhibitor comprises nivolumab, pembrolizumab, durvalumab,
atezolizumab, avelumab, or any combination thereof. 13. The method of any one of Embodiments 1-12, wherein the method comprises administering a PD-1 inhibitor and/or a PD-L1 inhibitor to the subject. 14. The method of Embodiment 13, wherein the method comprises administering a PD-1 inhibitor to the subject. 15. The method of Embodiment 14, wherein the CPI or the PD-1/PD-L1 axis inhibitor is selected from atezolizumab, nivolumab, durvalumab, and pembrolizumab. 16. The method of Embodiment 15, wherein the CPI or the PD-1/PD-L1 axis inhibitor comprises atezolizumab. 17. The method of any one of Embodiments 12-16, wherein the atezolizumab is administered to the subject every three weeks at 1200 mg per administration. 18. The method of any one of Embodiments 13-17, wherein the method comprises administering a PD-L1 inhibitor and the PD-L1 inhibitor is avelumab. 19. The method of any one of Embodiments 1-18, wherein the cancer is or comprises a solid tumor. 20. The method of any one of Embodiments 1-19, wherein the cancer is triple negative breast cancer (TNBC), wherein, optionally, the TNBC is metastatic TNBC. 21. The method of any one of Embodiments 1-19, wherein the cancer is non- small cell lung cancer (NSCLC), wherein, optionally, the NSCLC is metastatic NSCLC.
22. The method of any one of Embodiment 1-19, wherein the cancer is urothelial cancer. 23. The method of Embodiment 22, wherein the urothelial cancer is a metastatic urothelial cancer or an advanced urothelial cancer. 24. The method of any one of Embodiments 1-23, wherein the population of modified immune cells comprises T cells, wherein, optionally, the T cells comprise CD8+ T cells, wherein, further optionally, the CD8+ T cells comprise CD62L+ T cells. 25. The method of any one of Embodiments 1-24, wherein the population of modified immune cells comprises a CD4+ T cells, wherein, optionally, the CD4+ T cells are present in the population in combination with CD8+ T cells, wherein, further optionally, the CD4+ T cells and the CD8+ T cells are present in the population at a ratio of about 1:1. 26. The method of any one of Embodiments 1-25, wherein the population of modified immune cells comprises NK cells, NK-T cells, macrophages, and/or microglia. 27. The method of any one of Embodiments 1-26, wherein the population comprises modified immune cells that are autologous to the subject. 28. The method of any one of Embodiments 1-26, wherein the population comprises modified immune cells that are allogeneic to the subject. 29. The method of any one of Embodiments 1-28, comprising one or more administration of the population of modified immune cells, wherein the population of modified immune cells comprises between 1 × 108 and 5 × 1012 modified immune cells in each of the one or more administration.
30. The method of Embodiment 29, wherein the population of modified immune cells comprises between 5 × 108 and 5 × 109 modified immune cells in each of the one or more administration. 31. The method of Embodiment 29, wherein the population of modified immune cells comprises about 5 × 108 modified immune cells in each of the one or more administration. 32. The method of Embodiment 29, wherein the population of modified immune cells comprises about 5 × 109 modified immune cells in each of the one or more administration. 33. The method of any one of Embodiments 1-32, comprising (1) a first administration comprising the population of modified immune cells comprising about 1 x 109 modified immune cells, and (2) a second, subsequent administration of a population of the modified immune cells that comprises (i) about 1 x 1 x 109 modified immune cells, (ii) about 5 x 108 modified immune cells, or (iii) about 5 x 109 modified immune cells, wherein, optionally, the second, subsequent administration occurs about 6, about 7, about 8, about 9, about 10, about 11, or about 12 weeks after the first administration. 34. The method of any one of Embodiments 1-33, wherein administering the population of modified immune cells and/or administering the CPI and/or administering PD-1/PD-L1 axis inhibitor and/or administering the PD-1 inhibitor and/or administering the PD-L1 inhibitor is repeated at least once. 35. The method of any one of Embodiments 1-34, wherein the binding protein is capable of specifically binding to a KVLEYVIKV (SEQ ID NO: 123): human leukocyte antigen (HLA)-A*02:01 complex. 36. The method of any one of Embodiments 1-35, wherein the Vα domain
has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and the Vβ domain has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively. 37. The method of Embodiment 36, wherein the Vα domain has at least 95% identity to SEQ ID NO: 19, or has at least 95% identity to SEQ ID NO: 19 with the signal peptide removed. 38. The method of Embodiment 36 or 37, wherein the Vα domain has at least 99% identity to SEQ ID NO: 19, or has at least 99% identity to SEQ ID NO: 19 with the signal peptide removed. 39. The method of any one of Embodiments 36-38, wherein the Vα domain comprises the sequence of SEQ ID NO: 19, or comprises the sequence of SEQ ID NO: 19 with the signal peptide removed. 40. The method of any one of Embodiments 36-39, wherein the Vβ domain has at least 95% identity to SEQ ID NO: 17, or has at least 95% identity to SEQ ID NO: 17 with the signal peptide removed. 41. The method of any one of Embodiments 36-40, wherein the Vβ domain has at least 99% identity to SEQ ID NO: 17, or has at least 99% identity to SEQ ID NO: 17 with the signal peptide removed. 42. The method of any one of Embodiments 36-41, wherein the Vβ domain comprises the sequence of SEQ ID NO: 17, or comprises the sequence of SEQ ID NO: 17 with the signal peptide removed. 43. The method of any one of Embodiments 1-42, wherein the binding protein comprises a TCR α chain constant (Cα) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 20, and wherein, optionally, the Vα domain and
the Cα domain together comprise a TCR α chain. 44. The method of any one of Embodiments 1-43, wherein the binding protein comprises a TCR β chain constant (Cβ) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 18, and wherein, optionally, the Vβ domain and the Cβ domain together comprise a TCR β chain. 45. The method of any one of Embodiments 1-44, wherein the method comprises administering the population of modified immune cells to a plurality of subjects, wherein treating comprises inducing a partial response or a complete response in at least 5%, at least 10%, at least 15%, at least 20%, or at least 25% of the plurality of subjects. 46. The method of any one of Embodiments 1-44, wherein treating comprises reducing the severity and/or the duration of a sign or a symptom of the cancer or disease or disorder in the subject. 47. The method of any one of Embodiments 1-45, wherein treating comprises increasing a duration of progression-free survival of the subject or subjects. 48. The method of any one of Embodiments 1-46, wherein treating comprises inducing a remission of the cancer in the subject or subjects. 49. A method of treating a cancer, comprising administering to a subject in need thereof a population of modified cells comprising a binding protein, the binding protein comprising: a) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively; b) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1,
CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 30-32, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 27-29, respectively; c) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 36-38, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 33-35, respectively; d) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 42-44, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 39-41, respectively; or e) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 24-26, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 21-23, respectively, wherein the cancer or a cell thereof expresses MAGE-A1, and wherein: i) the subject is lymphodepleted or has undergone a lymphodepletion procedure; ii) the method further comprises administering a PD-1 inhibitor and/or a PD-L1 inhibitor to the subject; and/or iii) the subject is negative for or has been identified as negative for expression of HLA B*49:01. 50. The method of Embodiment 49, wherein the method further comprises, prior to administering the population of modified immune cells, identifying the subject as being negative for expression of HLA B*49:01. 51. The method of Embodiment 49 or Embodiment 50, wherein the subject is positive for or has been identified as positive for expression of HLA A*02:01. 52. The method of any one of Embodiments 49-51, wherein the method
further comprises, prior to administering the population of modified immune cells, identifying the subject as positive for expression of HLA A*02:01. 53. The method of any one of Embodiments 49-52, wherein the subject is lymphodepleted or has undergone a lymphodepletion procedure. 54. The method of any one of Embodiments 49-53, wherein the method further comprises providing lymphodepletion to the subject, wherein, optionally, the lymphodepletion is provided prior to administering the population of modified immune cells, wherein, further optionally, the lymphodepletion is provided 4 days, 3 days, 2 days, and/or 1 day prior to administering the population of modified immune cells. 55. The method of Embodiment 54, wherein providing lymphodepletion comprises administering a lymphodepleting chemotherapy to the subject. 56. The method of Embodiment 55, wherein the lymphodepleting chemotherapy comprises cyclophosphamide, fludarabine, or a combination thereof, wherein, optionally, the lymphodepleting chemotherapy comprises 300 mg/m2 cyclophosphamide and/or 30 mg/m2 fludarabine. 57. The method of Embodiment 55 or 56, wherein the lymphodepleting chemotherapy is administered intravenously to the subject. 58. The method of any one of Embodiments 49-57, wherein the method comprises administering an immune checkpoint inhibitor (CPI) to the subject, wherein, optionally, a first dose of the CPI is administered after the population of modified immune cells is administered, such as within 24 to 72 hours after the population of modified immune cells is administered. 59. The method of any one of Embodiments 49-58, wherein the method comprises administering a PD-1/PD-L1 axis inhibitor to the subject.
60. The method of Embodiment 58 or 59, wherein the CPI or the PD-1/PD- L1 axis inhibitor comprises nivolumab, pembrolizumab, durvalumab, atezolizumab, avelumab, or any combination thereof. 61. The method of any one of Embodiments 49-60, wherein the method comprises administering a PD-1 inhibitor and/or a PD-L1 inhibitor to the subject. 62. The method of Embodiment 61, wherein the method comprises administering a PD-1 inhibitor to the subject. 63. The method of Embodiment 62, wherein the CPI or the PD-1/PD-L1 axis inhibitor is selected from atezolizumab, nivolumab, durvalumab, and pembrolizumab. 64. The method of Embodiment 63, wherein the CPI or the PD-1/PD-L1 axis inhibitor comprises atezolizumab. 65. The method of any one of Embodiments 60-64, wherein the atezolizumab is administered to the subject every three weeks at 1200 mg per administration. 66. The method of any one of Embodiments 60-65, wherein the method comprises administering avelumab to the subject. 67. The method of any one of Embodiments 49-66, wherein the cancer is or comprises a solid tumor. 68. The method of any one of Embodiments 49-67, wherein the cancer is triple negative breast cancer (TNBC), wherein, optionally, the TNBC is metastatic TNBC. 69. The method of any one of Embodiments 49-67, wherein the cancer is
non-small cell lung cancer (NSCLC), wherein, optionally, the NSCLC is metastatic NSCLC. 70. The method of any one of Embodiments 49-67, wherein the cancer is urothelial cancer. 71. The method of Embodiment 70, wherein the urothelial cancer is a metastatic urothelial cancer or an advanced urothelial cancer. 72. The method of any one of Embodiments 49-71, wherein the population of modified immune cells comprises T cells, wherein, optionally, the T cells comprise CD8+ T cells, wherein, further optionally, the CD8+ T cells comprise CD62L+ T cells. 73. The method of any one of Embodiments 49-72, wherein the population of modified immune cells comprises CD4+ T cells, wherein, optionally, the CD4+ T cells are present in the population in combination with CD8+ T cells, wherein, further optionally, the CD4+ T cells and the CD8+ T cells are present in the population at a ratio of about 1:1. 74. The method of any one of Embodiments 49-73, wherein the population of modified immune cells comprises NK cells, NK-T cells, macrophages, and/or microglia. 75. The method of any one of Embodiments 49-74, wherein the wherein the population comprises modified immune cells that are autologous to the subject. 76. The method of any one of Embodiments 49-74, wherein the wherein the population comprises modified immune cells that are allogeneic to the subject. 77. The method of any one of Embodiments 49-76, comprising one or more administration of the population of modified immune cells, wherein the population of
modified immune cells comprises between 1 × 108 and 5 × 1012 modified immune cells in each of the one or more administration. 78. The method of Embodiment 77, wherein the population of modified immune cells comprises between 5 × 108 and 5 × 109 modified immune cells in each of the one or more administration. 79. The method of Embodiment 77, wherein the population of modified immune cells comprises about 5 × 108 modified immune cells in each of the one or more administration. 80. The method of Embodiment 77, wherein the population of modified immune cells comprises about 5 × 109 modified immune cells in each of the one or more administration. 81. The method of any one of Embodiments 49-80, comprising (1) a first administration comprising the population of modified immune cells comprising about 1 x 109 modified immune cells, and (2) a second, subsequent administration of a population of the modified immune cells that comprises (i) about 1 x 1 x 109 modified immune cells, (ii) about 5 x 108 modified immune cells, or (iii) about 5 x 109 modified immune cells, wherein, optionally, the second, subsequent administration occurs about 6, about 7, about 8, about 9, about 10, about 11, or about 12 weeks after the first administration. 82. The method of any one of Embodiments 49-81, wherein administering the population of modified immune cells and/or administering the CPI and/or administering PD-1/PD-L1 axis inhibitor and/or administering the PD-1 inhibitor and/or administering the PD-L1 inhibitor is repeated at least once. 83. The method of any one of Embodiments 49-82, wherein the binding protein is capable of specifically binding to a KVLEYVIKV (SEQ ID NO: 123): human
leukocyte antigen (HLA)-A*02:01 complex. 84. The method of any one of Embodiments 49-83, wherein the Vα domain has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and the Vβ domain has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively. 85. The method of Embodiment 84, wherein the Vα domain has at least 95% identity to SEQ ID NO: 19, or has at least 95% identity to SEQ ID NO: 19 with the signal peptide removed. 86. The method of Embodiment 84 or 85, wherein the Vα domain has at least 99% identity to SEQ ID NO: 19, or has at least 99% identity to SEQ ID NO: 19 with the signal peptide removed. 87. The method of any one of Embodiments 84-86, wherein the Vα domain comprises the sequence of SEQ ID NO: 19, or comprises the sequence of SEQ ID NO: 19 with the signal peptide removed. 88. The method of any one of Embodiments 84-87, wherein the Vβ domain has at least 95% identity to SEQ ID NO: 17, or has at least 95% identity to SEQ ID NO: 17 with the signal peptide removed. 89. The method of any one of Embodiments 84-88, wherein the Vβ domain has at least 99% identity to SEQ ID NO: 17, or has at least 99% identity to SEQ ID NO: 17 with the signal peptide removed. 90. The method of any one of Embodiments 84-89, wherein the Vβ domain comprises the sequence of SEQ ID NO: 17, or comprises the sequence of SEQ ID NO: 17 with the signal peptide removed.
91. The method of any one of Embodiments 49-90, wherein the binding protein comprises a TCR α chain constant (Cα) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 20, and wherein, optionally, the Vα domain and the Cα domain together comprise a TCR α chain. 92. The method of any one of Embodiments 49-91, wherein the binding protein comprises a TCR β chain constant (Cβ) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 18, and wherein, optionally, the Vβ domain and the Cβ domain together comprise a TCR β chain. 93. The method of any one of Embodiments 49-92, wherein the method comprises administering the population of modified immune cells to a plurality of subjects, wherein treating comprises inducing a partial response or a complete response in at least 5%, at least 10%, at least 15%, at least 20%, or at least 25% of the plurality of subjects. 94. The method of any one of Embodiments 49-93, wherein treating comprises reducing the severity and/or the duration of a sign or a symptom of the cancer in the subject. 95. The method of any one of Embodiments 49-94, wherein treating comprises increasing a duration of progression-free survival of the subject or subjects. 96. The method of any one of Embodiments 49-95, wherein treating comprises inducing a remission of the cancer in the subject or subjects. 97. The method of any one of Embodiments 1-96, wherein the binding protein is encoded by a polynucleotide comprised in modified immune cells of the population, wherein the polynucleotide comprises a sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%
identity to, or comprises or consists of, the polynucleotide sequence set forth in any one of SEQ ID NOs.:151-153. 98. The method of any one of Embodiments 1-96, wherein the binding protein is encoded by a polynucleotide comprised in modified immune cells of the population, wherein the polynucleotide comprises a sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprises or consists of, the polynucleotide sequence set forth in SEQ ID NO.:159. 99. The method of any one of Embodiments 1-98, wherein modified immune cells of the population further comprise a polynucleotide encoding a CD8 co- receptor α chain, a CD8 co-receptor β chain, or both, wherein, optionally, the polynucleotide encoding a CD8 co-receptor α chain has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the polynucleotide sequence set forth in SEQ ID NO.:149 and the polynucleotide encoding a CD8 co-receptor β chain has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprises or consists of, the polynucleotide sequence set forth in SEQ ID NO.:150. 100. An isolated polynucleotide comprising any one or more of: (i) the polynucleotide sequence according to SEQ ID NO.:149; (ii) the polynucleotide sequence according to SEQ ID NO.:150; (iii) the polynucleotide sequence according to SEQ ID NO.:151; (iv) the polynucleotide sequence according to SEQ ID NO.:152; and (v) the polynucleotide sequence according to SEQ ID NO.:153. 101. An isolated polynucleotide comprising the polynucleotide sequence
according to SEQ ID NO.:159. 102. A vector comprising the polynucleotide of Embodiment 100 or 101. 103. The vector of Embodiment 102, wherein the vector comprises a viral vector. 104. The vector of Embodiment 103, wherein the viral vector is a lentiviral vector or a retroviral vector. 105. A host cell comprising the polynucleotide of Embodiment 100 or 101 and/or the vector of any one of Embodiments 102-104. 106. The host cell of Embodiment 105, wherein the host cell comprises a human immune system cell. 107. The host cell of Embodiment 106, wherein the human immune system cell comprises a T cell, a NK cell, a NK-T cell, a macrophage, and/or a microglia. 108. The host cell of Embodiment 107, wherein the T cell comprises a CD8+ T cell, a CD4+ T cell, or both. 109. The host cell of Embodiment 108, wherein the CD8+ T cell is CD62L+. 110. A composition comprising a plurality of host cells according to any one of Embodiments 105-109. 111. A method comprising introducing the polynucleotide of Embodiment 100 or 101 or the vector of any one of Embodiments 102-104 to a host cell, wherein, optionally, the introducing comprises DNA electroporation or viral transduction.
SEQUENCES SEQ ID NO.:1 1388.1 β chain variable domain with signal peptide (amino acid) MGIRLLCRVAFCFLAVGLVDVKVTQSSRYLVKRTGEKVFLECVQDMDHENMF WYRQDPGLGLRLIYFSYDVKMKEKGDIPEGYSVSREKKERFSLILESASTNQTS MYLCASNNRDSYNSPLHFGNGTRLTVT SEQ ID NO.:2 1388.1 β chain constant domain (amino acid) EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVH SGVCTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSEN DEWTQDRAKPVTQIVSAEAWGRADCGFTSVSYQQGVLSATILYEILLGKATLY AVLVSALVLMAMVKRKDF SEQ ID NO.:3 1388.1 α chain variable domain with signal peptide (amino acid) MKPTLISVLVIIFILRGTRAQRVTQPEKLLSVFKGAPVELKCNYSYSGSPELFWY VQYSRQRLQLLLRHISRESIKGFTADLNKGETSFHLKKPFAQEEDSAMYYCALR SGGYQKVTFGTGTKLQVIP SEQ ID NO.:4 1388.1 α chain constant domain (amino acid) DIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRS MDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTN LNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS SEQ ID NO.:5 1388.2 β chain variable domain with signal peptide (amino acid) MGFRLLCCVAFCLLGAGPVDSGVTQTPKHLITATGQRVTLRCSPRSGDLSVYW YQQSLDQGLQFLIQYYNGEERAKGNILERFSAQQFPDLHSELNLSSLELGDSAL YFCASSQGDEKLFFGSGTQLSVL
SEQ ID NO.:6 1388.2 β chain constant domain (amino acid) EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVH SGVCTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSEN DEWTQDRAKPVTQIVSAEAWGRADCGFTSVSYQQGVLSATILYEILLGKATLY AVLVSALVLMAMVKRKDF SEQ ID NO.:7 1388.2 α chain variable domain with signal peptide (amino acid) MKTFAGFSFLFLWLQLDCMSRGEDVEQSLFLSVREGDSSVINCTYTDSSSTYLY WYKQEPGAGLQLLTYIFSNMDMKQDQRLTVLLNKKDKHLSLRIADTQTGDSAI YFCAESIDARLMFGDGTQLVVKP SEQ ID NO.:8 1388.2 α chain constant domain (amino acid) DIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRS MDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTN LNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS SEQ ID NO.:9 1388.3 β chain variable domain with signal peptide (amino acid) MLCSLLALLLGTFFGVRSQTIHQWPATLVQPVGSPLSLECTVEGTSNPNLYWYR QAAGRGLQLLFYSVGIGQISSEVPQNLSASRPQDRQFILSSKKLLLSDSGFYLCA LSTSYEQYFGPGTRLTVT SEQ ID NO.:10 1388.3 β chain constant domain (amino acid) DLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHS GVCTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSEND EWTQDRAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYA VLVSALVLMAMVKRKDSRG SEQ ID NO.:11 1388.3 α chain variable domain with signal peptide (amino acid)
MTRVSLLWAVVVSTCLESGMAQTVTQSQPEMSVQEAETVTLSCTYDTSENNY YLFWYKQPPSRQMILVIRQEAYKQQNATENRFSVNFQKAAKSFSLKISDSQLGD TAMYFCAFMKSHSGYIFGTGTRLKVLA SEQ ID NO.:12 1388.3 α chain constant domain (amino acid) DIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRS MDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTN LNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS SEQ ID NO.:13 17804.1b β chain variable domain with signal peptide (amino acid) MLCSLLALLLGTFFGVRSQTIHQWPATLVQPVGSPLSLECTVEGTSNPNLYWYR QAAGRGLQLLFYSVGIGQISSEVPQNLSASRPQDRQFILSSKKLLLSDSGFYLCA WSVAVNTEAFFGQGTRLTVV SEQ ID NO.:14 17804.1b β chain constant domain (amino acid) EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVH SGVCTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSEN DEWTQDRAKPVTQIVSAEAWGRADCGFTSVSYQQGVLSATILYEILLGKATLY AVLVSALVLMAMVKRKDF SEQ ID NO.:15 17804.1b α chain variable domain with signal peptide (amino acid) MTRVSLLWAVVVSTCLESGMAQTVTQSQPEMSVQEAETVTLSCTYDTSENNY YLFWYKQPPSRQMILVIRQEAYKQQNATENRFSVNFQKAAKSFSLKISDSQLGD TAMYFCAFGEGARLMFGDGTQLVVKP SEQ ID NO.:16 17804.1b α chain constant domain (amino acid) DIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRS MDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTN LNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS
SEQ ID NO.:17 17804.2 aka MA1 β chain variable domain with signal peptide (amino acid), signal peptide shown underlined MLCSLLALLLGTFFGVRSQTIHQWPATLVQPVGSPLSLECTVEGTSNPNLYWYR QAAGRGLQLLFYSIGIDQISSEVPQNLSASRPQDRQFILSSKKLLLSDSGFYLCA WSVTRHNEQFFGPGTRLTVL SEQ ID NO.:18 17804.2 aka MA1 β chain constant domain (amino acid) DLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHS GVCTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSEND EWTQDRAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYA VLVSALVLMAMVKRKDSRG SEQ ID NO.:19 17804.2 aka MA1 α chain variable domain with signal peptide (amino acid), signal peptide shown underlined MLCSLLALLLGTFFEPRTSQELEQSPQSLIVQEGKNLTINCTSSKTLYGLYWYKQ KYGEGLIFLMMLQKGGEEKSHEKITAKLDEKKQQSSLHITASQPSHAGIYLCGA APTYSNYGGSQGNLIFGKGTKLSVKP SEQ ID NO.:20 17804.2 aka MA1 α chain constant domain (amino acid) DIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRS MDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTN LNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS SEQ ID NO.:21 1388.1 β chain CDR1 domain (amino acid) MDHEN SEQ ID NO.:22 1388.1 β chain CDR2 domain (amino acid) SYDVKM SEQ ID NO.:23 1388.1 β chain CDR3 domain (amino acid)
CASNNRDSYNSPLHF SEQ ID NO.:24 1388.1 α chain CDR1 domain (amino acid) YSGSPE SEQ ID NO.:25 1388.1 α chain CDR2 domain (amino acid) HISR SEQ ID NO.:26 1388.1 α chain CDR3 domain (amino acid) CALRSGGYQKVTF SEQ ID NO.:27 1388.2b β chain CDR1 domain (amino acid) SGDLS SEQ ID NO.:28 1388.2b β chain CDR2 domain (amino acid) YYNGEE SEQ ID NO.:29 1388.2b β chain CDR3 domain (amino acid) CASSQGDEKLFF SEQ ID NO.:30 1388.2b α chain CDR1 domain (amino acid) DSSSTY SEQ ID NO.:31 1388.2b α chain CDR2 domain (amino acid) IFSNMDM SEQ ID NO.:32 1388.2b α chain CDR3 domain (amino acid) CAESIDARLMF SEQ ID NO.:33 1388.3 β chain CDR1 domain (amino acid) GTSNPN
SEQ ID NO.:34 1388.3 β chain CDR2 domain (amino acid) SVGIG SEQ ID NO.:35 1388.3 β chain CDR3 domain (amino acid) CALSTSYEQYF SEQ ID NO.:36 1388.3 α chain CDR1 domain (amino acid) TSENNYY SEQ ID NO.:37 1388.3 α chain CDR2 domain (amino acid) QEAYKQQN SEQ ID NO.:38 1388.3 α chain CDR3 domain (amino acid) CAFMKSHSGYIF SEQ ID NO.:39 17804.1b β chain CDR1 domain (amino acid) GTSNPN SEQ ID NO.:40 17804.1b β chain CDR2 domain (amino acid) SVGIG SEQ ID NO.:41 17804.1b β chain CDR3 domain (amino acid) CAWSVAVNTEAFF SEQ ID NO.:42 17804.1b α chain CDR1 domain (amino acid) TSENNYY SEQ ID NO.:43 17804.1b α chain CDR2 domain (amino acid) QEAYKQQN
SEQ ID NO.:44 17804.1b α chain CDR3 domain (amino acid) CAFGEGARLMF SEQ ID NO.:45 17804.2 aka MA1 β chain CDR1 domain (amino acid) GTSNPN SEQ ID NO.:46 17804.2 aka MA1 β chain CDR2 domain (amino acid) SIGID SEQ ID NO.:47 17804.2 aka MA1 β chain CDR3 domain (amino acid) CAWSVTRHNEQFF SEQ ID NO.:48 17804.2 aka MA1 α chain CDR1 domain (amino acid) KTLYG SEQ ID NO.:49 17804.2 aka MA1 α chain CDR2 domain (amino acid) LQKGGEE SEQ ID NO.:50 17804.2 aka MA1 α chain CDR3 domain (amino acid) CGAAPTYSNYGGSQGNLIF SEQ ID NO.:51 18648.2 α chain CDR3 domain (amino acid) CALRGLNYGQNFVF SEQ ID NO.:52 1388.1 β chain variable domain with signal peptide (Native NA) atgggaatcaggctcctctgtcgtgtggccttttgtttcctggctgtaggcctcgtagatgtgaaagtaacccagagctcgagat atctagtcaaaaggacgggagagaaagtttttctggaatgtgtccaggatatggaccatgaaaatatgttctggtatcgacaag acccaggtctggggctacggctgatctatttctcatatgatgttaaaatgaaagaaaaaggagatattcctgaggggtacagtgt ctctagagagaagaaggagcgcttctccctgattctggagtccgccagcaccaaccagacatctatgtacctcTGCGCC AGCAACAACAGAGACAGCTACAACAGCcccctccactttgggaacgggaccaggctcactgtgac
g SEQ ID NO.:53 1388.1 β chain constant domain (Native NA) GAGGACCTGAACAAAGTGTTCCCCCCAGAGGTGGCCGTGTTCGAGCCTTCT GAGGCCGAGATCAGCCACACCCAGAAAGCCACCCTCGTGTGCCTGGCCACC GGCTTTTTCCCCGACCACGTGGAACTGTCTTGGTGGGTCAACGGCAAAGAG GTGCACTCCGGCGTGTGCACCGATCCCCAGCCTCTGAAAGAACAGCCCGCC CTGAACGACAGCCGGTACTGCCTGTCCAGCAGACTGAGAGTGTCCGCCACC TTCTGGCAGAACCCCCGGAACCACTTCAGATGCCAGGTGCAGTTCTACGGC CTGAGCGAGAACGACGAGTGGACCCAGGACAGAGCCAAGCCCGTGACACA GATCGTGTCTGCCGAAGCCTGGGGCAGAGCCGATTGCGGCTTTACCTCCGT GTCCTATCAGCAGGGCGTGCTGAGCGCCACCATCCTGTACGAGATCCTGCT GGGCAAGGCCACACTGTACGCCGTGCTGGTGTCTGCCCTGGTGCTGATGGC CATGGTCAAGCGGAAGGACTTC SEQ ID NO.:54 1388.1 α chain variable domain with signal peptide (Native NA) atgaagcccaccctcatctcagtgcttgtgataatatttatactcagaggaacaagagcccagagagtgactcagcccgagaa gctcctctctgtctttaaaggggccccagtggagctgaagtgcaactattcctattctgggagtcctgaactcttctggtatgtcca gtactccagacaacgcctccagttactcttgagacacatctctagagagagcatcaaaggcttcactgctgaccttaacaaagg cgagacatctttccacctgaagaaaccatttgctcaagaggaagactcagccatgtattacTGCGCCCTGAGAAG CGGCGGCTACCAGAAGGTGACCTTtggaactggaacaaagctccaagtcatccca SEQ ID NO.:55 1388.1 α chain constant domain (Native NA) gatatccagaaccctgaccctgccgtgtaccagctgagagactctaaatccagtgacaagtctgtctgcctattcaccgattttg attctcaaacaaatgtgtcacaaagtaaggattctgatgtgtatatcacagacaaatgtgtgctagacatgaggtctatggacttc aagagcaacagtgctgtggcctggagcaacaaatctgactttgcatgtgcaaacgccttcaacaacagcattattccagaaga caccttcttccccagcccagaaagttcctgtgatgtcaagctggtcgagaaaagctttgaaacagatacgaacctaaactttcaa aacctgtcagtgattgggttccgaatcctcctcctgaaagtggccgggtttaatctgctcatgacgctgcggctgtggtccagct ga
SEQ ID NO.:56 1388.1 β chain variable domain with signal peptide(Codon- optimized NA) ATGGGAATTAGACTGCTGTGCCGGGTGGCCTTCTGCTTCCTGGCTGTGGGAC TGGTGGACGTGAAAGTGACCCAGAGCAGCAGATACCTCGTGAAGCGGACC GGCGAGAAGGTGTTCCTGGAATGCGTGCAGGACATGGACCACGAGAATATG TTCTGGTACAGACAGGACCCCGGCCTGGGCCTGCGGCTGATCTACTTCAGCT ACGACGTGAAGATGAAGGAAAAGGGCGACATCCCCGAGGGCTACAGCGTG TCCAGAGAGAAGAAAGAGCGGTTCAGCCTGATCCTGGAAAGCGCCAGCAC CAACCAGACCAGCATGTACCTGTGCGCCTCCAACAACCGGGACAGCTACAA CAGCCCCCTGCACTTCGGCAACGGCACCAGACTGACCGTGACC SEQ ID NO.:57 1388.1 β chain constant domain (Codon-optimized NA) GAGGACCTGAACAAAGTGTTCCCCCCAGAGGTGGCCGTGTTCGAGCCTTCT GAGGCCGAGATCAGCCACACCCAGAAAGCCACCCTCGTGTGCCTGGCCACC GGCTTTTTCCCCGACCACGTGGAACTGTCTTGGTGGGTCAACGGCAAAGAG GTGCACTCCGGCGTGTGCACCGATCCCCAGCCTCTGAAAGAACAGCCCGCC CTGAACGACAGCCGGTACTGCCTGTCCAGCAGACTGAGAGTGTCCGCCACC TTCTGGCAGAACCCCCGGAACCACTTCAGATGCCAGGTGCAGTTCTACGGC CTGAGCGAGAACGACGAGTGGACCCAGGACAGAGCCAAGCCCGTGACACA GATCGTGTCTGCCGAAGCCTGGGGCAGAGCCGATTGCGGCTTTACCTCCGT GTCCTATCAGCAGGGCGTGCTGAGCGCCACCATCCTGTACGAGATCCTGCT GGGCAAGGCCACACTGTACGCCGTGCTGGTGTCTGCCCTGGTGCTGATGGC CATGGTCAAGCGGAAGGACTTC SEQ ID NO.:58 1388.1 α chain variable domain with signal peptide (Codon- optimized NA) ATGAAGCCCACCCTGATCTCTGTGCTCGTGATCATCTTCATCCTGCGGGGCA CCAGAGCCCAGAGAGTGACACAGCCTGAGAAGCTGCTGAGCGTGTTCAAGG GCGCTCCTGTGGAACTGAAGTGCAACTACAGCTACAGCGGCAGCCCCGAGC TGTTTTGGTACGTGCAGTACAGCCGGCAGAGACTGCAGCTGCTGCTGCGGC ACATCAGCAGAGAGAGCATCAAGGGCTTCACCGCCGATCTGAACAAGGGC
GAGACAAGCTTCCACCTGAAGAAGCCCTTCGCCCAGGAAGAGGACAGCGCC ATGTACTACTGCGCCCTGAGATCCGGCGGCTACCAGAAAGTGACATTTGGC ACCGGCACCAAGCTGCAAGTGATCCCC SEQ ID NO.:59 1388.1 α chain constant domain (Codon-optimized NA) GACATCCAGAACCCCGACCCTGCAGTGTACCAGCTGCGGGACAGCAAGAGc agcgacaagagcgtgtgcctgttcaccgacttcgacagccagaccaacgtgtcccagagcaaggacagcgacgtgtacatc accgataagtgcgtgctggacatgcggagcatggacttcaagagcaacagcgccgtggcctggtccaacaagagcgacttc gcctgcgccaacgccttcaacaacagcattatccccgaggacacattcttcccaagccccgagagcagctgcgacgtgaag ctggtggaaaagagcttcgagacagacaccaacctgaacttccagaacctcagcgtgatcggcttccggatcctgctgctga aggtggccggcttcaacctgctgatgaccctgcggctgtggtccagctga SEQ ID NO.:60 1388.2b β chain variable domain with signal peptide(Native NA) atgggcttcaggctcctctgctgtgtggccttttgtctcctgggagcaggcccagtgGattctggagtcacacaaaccccaaa gcacctgatcacagcaactggacagcgagtgacgctgagatgctcccctaggtctggagacctctctgtgtactggtaccaac agagcctggaccagggcctccagttcctcattcagtattataatggagaagagagagcaaaaggaaacattcttgaacgattct ccgcacaacagttccctgacttgcactctgaactaaacctgagctctctggagctgggggactcagctttgtatttctgtgccag cagccagggggatgaaaaactgttttttggcagtggaacccagctctctgtcttg SEQ ID NO.:61 1388.2b β chain constant domain (Native NA) GAGGACCTGAACAAAGTGTTCCCCCCAGAGGTGGCCGTGTTCGAGCCTTCT GAGGCCGAGATCAGCCACACCCAGAAAGCCACCCTCGTGTGCCTGGCCACC GGCTTTTTCCCCGACCACGTGGAACTGTCTTGGTGGGTCAACGGCAAAGAG GTGCACTCCGGCGTGTGCACCGATCCCCAGCCTCTGAAAGAACAGCCCGCC CTGAACGACAGCCGGTACTGCCTGTCCAGCAGACTGAGAGTGTCCGCCACC TTCTGGCAGAACCCCCGGAACCACTTCAGATGCCAGGTGCAGTTCTACGGC CTGAGCGAGAACGACGAGTGGACCCAGGACAGAGCCAAGCCCGTGACACA GATCGTGTCTGCCGAAGCCTGGGGCAGAGCCGATTGCGGCTTTACCTCCGT GTCCTATCAGCAGGGCGTGCTGAGCGCCACCATCCTGTACGAGATCCTGCT GGGCAAGGCCACACTGTACGCCGTGCTGGTGTCTGCCCTGGTGCTGATGGC
CATGGTCAAGCGGAAGGACTTC SEQ ID NO.:62 1388.2b α chain variable domain with signal peptide (Native NA) atgaagacatttgctggattttcgttcctgtttttgtggctgcagctggactgtatgagtagaGGAGAGGATGTGGA GCAGAGTCTTTTCCtGAGTgTCCGAGAGGGAGACAGcTCCGTTATAAACTGC ACTTACACAGACAGcTCCTCCACCTACTTATACTGGTATAAGCAAGAACCTG GAGCAGgTCTCCAGTTGCTGACGTATATTTTTTCAAATATGGACATGAAACA AGACCAAAGACTCACTGTTCTATTGAATAAAAAGGATAAACATCTGTCTCT GCGCATTGCAGACACCCAGACTGGGGACTCAGCTATCTACTTCTGTGCAGA GAGTATCGATGCCAGACTCATGTTTGGAGATGGAACTCAGCTGGTGGTGAA GCCC SEQ ID NO.:63 1388.2b α chain constant domain (Native NA) gatatccagaaccctgaccctgccgtgtaccagctgagagactctaaatccagtgacaagtctgtctgcctattcaccgattttg attctcaaacaaatgtgtcacaaagtaaggattctgatgtgtatatcacagacaaatgtgtgctagacatgaggtctatggacttc aagagcaacagtgctgtggcctggagcaacaaatctgactttgcatgtgcaaacgccttcaacaacagcattattccagaaga caccttcttccccagcccagaaagttcctgtgatgtcaagctggtcgagaaaagctttgaaacagatacgaacctaaactttcaa aacctgtcagtgattgggttccgaatcctcctcctgaaagtggccgggtttaatctgctcatgacgctgcggctgtggtccagct ga SEQ ID NO.:64 1388.2b β chain variable domain with signal peptide (Codon- optimized NA) ATGGGCTTCAGACTGCTGTGCTGCGTGGCCTTCTGTCTGCTGGGAGCCGGCC CTGTGGATAGCGGCGTGACACAGACACCCAAGCACCTGATCACCGCCACCG GCCAGCGCGTGACACTGAGATGTAGCCCTAGAAGCGGCGACCTGAGCGTGT ACTGGTATCAGCAGAGCCTGGACCAGGGCCTGCAGTTCCTGATCCAGTACT ACAACGGCGAGGAACGGGCCAAGGGCAACATCCTGGAACGGTTCAGCGCC CAGCAGTTCCCCGATCTGCACAGCGAGCTGAACCTGAGCAGCCTGGAACTG GGCGACAGCGCCCTGTACTTCTGTGCCAGTTCTCAGGGCGACGAGAAGCTG TTCTTCGGCAGCGGCACACAGCTGAGCGTGCTG
SEQ ID NO.:65 1388.2b β chain constant domain (Codon-optimized NA) GAAGATCTGAACAAGGTGTTCCCCCCAGAGGTGGCCGTGTTCGAGCCTTCT GAGGCCGAGATCAGCCACACCCAGAAAGCCACCCTCGTGTGCCTGGCCACC GGCTTTTTCCCCGACCACGTGGAACTGTCTTGGTGGGTCAACGGCAAAGAG GTGCACTCCGGCGTGTGCACCGATCCCCAGCCTCTGAAAGAACAGCCCGCC CTGAACGACAGCCGGTACTGCCTGTCCAGCAGACTGAGAGTGTCCGCCACC TTCTGGCAGAACCCCCGGAACCACTTCAGATGCCAGGTGCAGTTCTACGGC CTGAGCGAGAACGACGAGTGGACCCAGGACAGAGCCAAGCCCGTGACCCA GATCGTGTCTGCCGAAGCCTGGGGCAGAGCCGATTGCGGCTTTACCAGCGT GTCCTATCAGCAGGGCGTGCTGAGCGCCACCATCCTGTACGAGATCCTGCT GGGCAAGGCCACCCTGTACGCCGTGCTGGTGTCTGCCCTGGTGCTGATGGC CATGGTCAAGCGGAAGGACTTC SEQ ID NO.:66 1388.2b α chain variable domain with signal peptide (Codon- optimized NA) ATGAAGACCTTCGCCGGCTTCAGCTTCCTGTTCCTGTGGCTGCAGCTGGACT GCATGAGCAGAGGCGAGGACGTGGAACAGAGCCTGTTTCTGTCCGTGCGCG AGGGCGACTCCAGCGTGATCAATTGCACCTACACCGACAGCAGCAGCACCT ACCTGTATTGGTACAAGCAGGAACCCGGCGCTGGCCTGCAGCTGCTGACCT ACATCTTCAGCAACATGGACATGAAGCAGGACCAGCGGCTGACCGTGCTGC TGAACAAGAAGGATAAGCACCTGTCCCTGCGGATCGCCGATACCCAGACAG GCGACTCCGCCATCTACTTTTGCGCCGAGAGCATCGACGCCCGGCTGATGTT TGGAGATGGCACCCAGCTGGTCGTGAAGCCC SEQ ID NO.:67 1388.2b α chain constant domain (Codon-optimized NA) GACATCCAGAACCCCGACCCTGCAGTGTACCAGCTGCGGGACAGCAAGAGc agcgacaagagcgtgtgcctgttcaccgacttcgacagccagaccaacgtgtcccagagcaaggacagcgacgtgtacatc accgataagtgcgtgctggacatgcggagcatggacttcaagagcaacagcgccgtggcctggtccaacaagagcgacttc gcctgcgccaacgccttcaacaacagcattatccccgaggacacattcttcccaagccccgagagcagctgcgacgtgaag ctggtggaaaagagcttcgagacagacaccaacctgaacttccagaacctcagcgtgatcggcttccggatcctgctgctga
aggtggccggcttcaacctgctgatgaccctgcggctgtggtccagctga SEQ ID NO.:68 1388.3 β chain variable domain with signal peptide(Native NA) atgctctgctctctccttgcccttctcctgggcactttctttggggtcagatctcagactattcatcaatggccagcgaccctggtg cagcctgtgggcagcccgctctctctggagtgcactgtggagggaacatcaaaccccaacctatactggtaccgacaggctg caggcaggggcctccagctgctcttctactccgttggtattggccagatcagctctgaggtgccccagaatctctcagcctcca gaccccaggaccggcagttcatcctgagttctaagaagctccttctcagtgactctggcttctatctcTGCGCCCTGAG CACCAGCTACGAGcagtacttcgggccgggcaccaggctcacggtcaca SEQ ID NO.:69 1388.3 β chain constant domain (Native NA) Gacctgaaaaacgtgttcccacccgaggtcgctgtgtttgagccatcagaagcagagatctcccacacccaaaaggccaca ctggtgtgcctggccacaggcttctaccccgaccacgtggagctgagctggtgggtgaatgggaaggaggtgcacagtggg gtctgcacagacccgcagcccctcaaggagcagcccgccctcaatgactccagatactgcctgagcagccgcctgagggtc tcggccaccttctggcagaacccccgcaaccacttccgctgtcaagtccagttctacgggctctcggagaatgacgagtgga cccaggatagggccaaacctgtcacccagatcgtcagcgccgaggcctggggtagagcagactgtggcttcacctccgagt cttaccagcaaggggtcctgtctgccaccatcctctatgagatcttgctagggaaggccaccttgtatgccgtgctggtcagtg ccctcgtgctgatggccatggtcaagagaaaggattccagaggctag SEQ ID NO.:70 1388.3 α chain variable domain with signal peptide (Native NA) atgacacgagttagcttgctgtgggcagtcgtggtctccacctgtcttgaatccggcatgGcccagacagtcactcagtctcaa ccagagatgtctgtgcaggaggcagagactgtgaccctgagttgcacatatgacaccagtgagaataattattatttgttctggt acaagcagcctcccagcaggcagatgattctcgttattcgccaagaagcttataagcaacagaatgcaacggagaatcgtttct ctgtgaacttccagaaagcagccaaatccttcagtctcaagatctcagactcacagctgggggacactgcgatgtatttctgtgc tttcatgaagtcccactccggatacatctttggaacaggcaccaggctgaaggttttagca SEQ ID NO.:71 1388.3 α chain constant domain (Native NA) gatatccagaaccctgaccctgccgtgtaccagctgagagactctaaatccagtgacaagtctgtctgcctattcaccgattttg attctcaaacaaatgtgtcacaaagtaaggattctgatgtgtatatcacagacaaatgtgtgctagacatgaggtctatggacttc aagagcaacagtgctgtggcctggagcaacaaatctgactttgcatgtgcaaacgccttcaacaacagcattattccagaaga
caccttcttccccagcccagaaagttcctgtgatgtcaagctggtcgagaaaagctttgaaacagatacgaacctaaactttcaa aacctgtcagtgattgggttccgaatcctcctcctgaaagtggccgggtttaatctgctcatgacgctgcggctgtggtccagct ga SEQ ID NO.:72 1388.3 β chain variable domain with signal peptide(Codon- optimized NA) ATGCTGTGTTCTCTGCTGGCCCTGCTGCTGGGCACCTTCTTTGGAGTGCGGA GCCAGACCATCCACCAGTGGCCTGCTACACTGGTGCAGCCTGTGGGCAGCC CTCTGAGCCTGGAATGTACCGTGGAAGGCACCAGCAACCCCAACCTGTACT GGTACAGACAGGCCGCTGGCAGAGGCCTGCAGCTGCTGTTTTACAGCGTGG GCATCGGCCAGATCAGCAGCGAGGTGCCCCAGAATCTGAGCGCCAGCAGAC CCCAGGACCGGCAGTTTATCCTGAGCAGCAAGAAGCTGCTGCTGAGCGACA GCGGCTTCTACCTGTGTGCCCTGAGCACCAGCTACGAGCAGTACTTCGGCCC AGGCACCAGACTGACCGTGACC SEQ ID NO.:73 1388.3 β chain constant domain (Codon-optimized NA) GACCTGAAGAACGTGTTCCCCCCAGAGGTGGCCGTGTTCGAGCCTTCTGAG GCCGAGATCAGCCACACCCAGAAAGCCACCCTCGTGTGTCTGGCCACCGGC TTTTACCCCGACCACGTGGAACTGTCTTGGTGGGTCAACGGCAAAGAGGTG CACTCCGGCGTGTGCACCGATCCCCAGCCTCTGAAAGAACAGCCCGCCCTG AACGACAGCCGGTACTGCCTGTCCAGCAGACTGAGAGTGTCCGCCACCTTC TGGCAGAACCCCCGGAACCACTTCAGATGCCAGGTGCAGTTCTACGGCCTG AGCGAGAACGACGAGTGGACCCAGGACAGAGCCAAGCCCGTGACCCAGAT CGTGTCTGCCGAAGCCTGGGGCAGAGCCGATTGCGGCTTTACCAGCGAGAG CTACCAGCAGGGCGTGCTGTCTGCCACCATCCTGTACGAGATCCTGCTGGG AAAGGCCACCCTGTACGCCGTGCTGGTGTCTGCCCTGGTGCTGATGGCCATG GTCAAGCGGAAGGACAGCAGAGGC SEQ ID NO.:74 1388.3 α chain variable domain with signal peptide (Codon- optimized NA) ATGACCCGGGTGTCACTGCTGTGGGCTGTGGTGGTGTCCACCTGTCTGGAAA
GCGGCATGGCCCAGACCGTGACACAGTCCCAGCCTGAGATGAGCGTGCAGG AAGCCGAGACAGTGACCCTGAGCTGCACCTACGACACCTCCGAGAACAACT ACTACCTGTTTTGGTACAAGCAGCCCCCCAGCCGGCAGATGATCCTCGTGAT CAGACAGGAAGCCTATAAGCAGCAGAACGCCACCGAGAACAGATTCAGCG TGAACTTCCAGAAGGCCGCCAAGAGCTTTAGCCTGAAGATCAGCGACAGCC AGCTGGGCGACACCGCCATGTACTTTTGCGCCTTTATGAAGTCCCACAGCGG CTACATCTTCGGCACCGGCACACGGCTGAAAGTGCTGGCT SEQ ID NO.:75 1388.3 α chain constant domain (Codon-optimized NA) GACATCCAGAACCCCGACCCTGCAGTGTACCAGCTGCGGGACAGCAAGAGc agcgacaagagcgtgtgcctgttcaccgacttcgacagccagaccaacgtgtcccagagcaaggacagcgacgtgtacatc accgataagtgcgtgctggacatgcggagcatggacttcaagagcaacagcgccgtggcctggtccaacaagagcgacttc gcctgcgccaacgccttcaacaacagcattatccccgaggacacattcttcccaagccccgagagcagctgcgacgtgaag ctggtggaaaagagcttcgagacagacaccaacctgaacttccagaacctcagcgtgatcggcttccggatcctgctgctga aggtggccggcttcaacctgctgatgaccctgcggctgtggtccagctga SEQ ID NO.:76 17804.1b β chain variable domain with signal peptide(Native NA) atgctctgctctctccttgcccttctcctgggcactttctttggggtcagatctcagactattcatcaatggccagcgaccctggtg cagcctgtgggcagcccgctctctctggagtgcactgtggagggaacatcaaaccccaacctatactggtaccgacaggctg caggcaggggcctccagctgctcttctactccgttggtattggccagatcagctctgaggtgccccagaatctctcagcctcca gaccccaggaccggcagttcatcctgagttctaagaagctccttctcagtgactctggcttctatctctgtgcctggagtgttgcg gtgaacactgaagctttctttggacaaggcaccagactcacagttgta SEQ ID NO.:77 17804.1b β chain constant domain (Native NA) GAGGACCTGAACAAAGTGTTCCCCCCAGAGGTGGCCGTGTTCGAGCCTTCT GAGGCCGAGATCAGCCACACCCAGAAAGCCACCCTCGTGTGCCTGGCCACC GGCTTTTTCCCCGACCACGTGGAACTGTCTTGGTGGGTCAACGGCAAAGAG GTGCACTCCGGCGTGTGCACCGATCCCCAGCCTCTGAAAGAACAGCCCGCC CTGAACGACAGCCGGTACTGCCTGTCCAGCAGACTGAGAGTGTCCGCCACC TTCTGGCAGAACCCCCGGAACCACTTCAGATGCCAGGTGCAGTTCTACGGC
CTGAGCGAGAACGACGAGTGGACCCAGGACAGAGCCAAGCCCGTGACACA GATCGTGTCTGCCGAAGCCTGGGGCAGAGCCGATTGCGGCTTTACCTCCGT GTCCTATCAGCAGGGCGTGCTGAGCGCCACCATCCTGTACGAGATCCTGCT GGGCAAGGCCACACTGTACGCCGTGCTGGTGTCTGCCCTGGTGCTGATGGC CATGGTCAAGCGGAAGGACTTC SEQ ID NO.:78 17804.1b α chain variable domain with signal peptide (Native NA) atgacacgagttagcttgctgtgggcagtcgtggtctccacctgtcttgaatccggcatggcccagacagtcactcagtctcaa ccagagatgtctgtgcaggaggcagagactgtgaccctgagttgcacatatgacaccagtgagaataattattatttgttctggt acaagcagcctcccagcaggcagatgattctcgttattcgccaagaagcttataagcaacagaatgcaacggagaatcgtttct ctgtgaacttccagaaagcagccaaatccttcagtctcaagatctcagactcacagctgggggacactgcgatgtatttcTGC GCCTTCGGCGAGGGCgccagactcatgtttggagatggaactcagctggtggtgaagccc SEQ ID NO.:79 17804.1b α chain constant domain (Native NA) gatatccagaaccctgaccctgccgtgtaccagctgagagactctaaatccagtgacaagtctgtctgcctattcaccgattttg attctcaaacaaatgtgtcacaaagtaaggattctgatgtgtatatcacagacaaatgtgtgctagacatgaggtctatggacttc aagagcaacagtgctgtggcctggagcaacaaatctgactttgcatgtgcaaacgccttcaacaacagcattattccagaaga caccttcttccccagcccagaaagttcctgtgatgtcaagctggtcgagaaaagctttgaaacagatacgaacctaaactttcaa aacctgtcagtgattgggttccgaatcctcctcctgaaagtggccgggtttaatctgctcatgacgctgcggctgtggtccagct ga SEQ ID NO.:80 17804.1b β chain variable domain with signal peptide (Codon-optimized NA) ATGCTGTGTTCTCTGCTGGCCCTGCTGCTGGGCACCTTCTTTGGAGTGCGGA GCCAGACCATCCACCAGTGGCCTGCTACACTGGTGCAGCCTGTGGGCAGCC CTCTGAGCCTGGAATGTACCGTGGAAGGCACCAGCAACCCCAACCTGTACT GGTACAGACAGGCCGCTGGCAGAGGCCTGCAGCTGCTGTTTTACAGCGTGG GCATCGGCCAGATCAGCAGCGAGGTGCCCCAGAATCTGAGCGCCAGCAGAC CCCAGGACCGGCAGTTTATCCTGAGCAGCAAGAAGCTGCTGCTGAGCGACA
GCGGCTTCTACCTGTGCGCTTGGAGCGTGGCCGTGAACACCGAGGCATTCTT TGGGCAGGGCACCCGGCTGACCGTGGTG SEQ ID NO.:81 17804.1b β chain constant domain (Codon-optimized NA) GAAGATCTGAACAAGGTGTTCCCCCCAGAGGTGGCCGTGTTCGAGCCTTCT GAGGCCGAGATCAGCCACACCCAGAAAGCCACCCTCGTGTGCCTGGCCACC GGCTTTTTCCCCGACCACGTGGAACTGTCTTGGTGGGTCAACGGCAAAGAG GTGCACTCCGGCGTGTGCACCGATCCCCAGCCTCTGAAAGAACAGCCCGCC CTGAACGACAGCCGGTACTGCCTGTCCAGCAGACTGAGAGTGTCCGCCACC TTCTGGCAGAACCCCCGGAACCACTTCAGATGCCAGGTGCAGTTCTACGGC CTGAGCGAGAACGACGAGTGGACCCAGGACAGAGCCAAGCCCGTGACCCA GATCGTGTCTGCCGAAGCCTGGGGCAGAGCCGATTGCGGCTTTACCAGCGT GTCCTATCAGCAGGGCGTGCTGTCTGCCACCATCCTGTACGAGATCCTGCTG GGAAAGGCCACCCTGTACGCCGTGCTGGTGTCTGCCCTGGTGCTGATGGCC ATGGTCAAGCGGAAGGACTTC SEQ ID NO.:82 17804.1b α chain variable domain with signal peptide (Codon-optimized NA) ATGACCAGAGTGTCTCTGCTGTGGGCTGTGGTGGTGTCCACCTGTCTGGAAA GCGGCATGGCCCAGACCGTGACACAGTCCCAGCCTGAGATGAGCGTGCAGG AAGCCGAGACAGTGACCCTGAGCTGCACCTACGACACCAGCGAGAACAACT ACTACCTGTTTTGGTACAAGCAGCCCCCCAGCCGGCAGATGATCCTCGTGAT CAGACAGGAAGCCTATAAGCAGCAGAACGCCACCGAGAACAGATTCAGCG TGAACTTCCAGAAGGCCGCCAAGAGCTTCAGCCTGAAGATCAGCGACAGCC AGCTGGGCGACACCGCCATGTACTTTTGCGCCTTTGGCGAGGGCGCCAGAC TGATGTTTGGCGACGGAACCCAGCTGGTCGTGAAGCCC SEQ ID NO.:83 17804.1b α chain constant domain (Codon-optimized NA) GACATCCAGAACCCCGACCCTGCAGTGTACCAGCTGCGGGACAGCAAGAGc agcgacaagagcgtgtgcctgttcaccgacttcgacagccagaccaacgtgtcccagagcaaggacagcgacgtgtacatc accgataagtgcgtgctggacatgcggagcatggacttcaagagcaacagcgccgtggcctggtccaacaagagcgacttc
gcctgcgccaacgccttcaacaacagcattatccccgaggacacattcttcccaagccccgagagcagctgcgacgtgaag ctggtggaaaagagcttcgagacagacaccaacctgaacttccagaacctcagcgtgatcggcttccggatcctgctgctga aggtggccggcttcaacctgctgatgaccctgcggctgtggtccagctga SEQ ID NO.:84 17804.2 aka MA1 β chain variable domain with signal peptide (Native NA) atgctctgctctctccttgcccttctcctgggcactttctttggggtcagatctcagactattcatcaatggccagcgaccctggtg cagcctgtgggcagcccgctctctctggagtgcactgtggagggaacatcaaaccccaacctatactggtaccgacaggctg caggcaggggcctccagctgctcttctactccattggtattgaccagatcagctctgaggtgccccagaatctctcagcctcca gaccccaggaccggcagttcattctgagttctaagaagctcctcctcagtgactctggcttctatctctgtgcctggagtgtaacc aggcacaatgagcagttcttcgggccagggacacggctcaccgtgcta SEQ ID NO.:85 17804.2 β aka MA1 chain constant domain (Native NA) Gacctgaaaaacgtgttcccacccgaggtcgctgtgtttgagccatcagaagcagagatctcccacacccaaaaggccaca ctggtgtgcctggccacaggcttctaccccgaccacgtggagctgagctggtgggtgaatgggaaggaggtgcacagtggg gtctgcacagacccgcagcccctcaaggagcagcccgccctcaatgactccagatactgcctgagcagccgcctgagggtc tcggccaccttctggcagaacccccgcaaccacttccgctgtcaagtccagttctacgggctctcggagaatgacgagtgga cccaggatagggccaaacctgtcacccagatcgtcagcgccgaggcctggggtagagcagactgtggcttcacctccgagt cttaccagcaaggggtcctgtctgccaccatcctctatgagatcttgctagggaaggccaccttgtatgccgtgctggtcagtg ccctcgtgctgatggccatggtcaagagaaaggattccagaggctag SEQ ID NO.:86 17804.2 aka MA1 α chain variable domain with signal peptide (Native NA) ATGCTGTGCAGCCTGCTGGCCCTGCTGCTGGGCACCTTCTTCGAGCCCAGAA CCagccaagaactggagcagagtcctcagtccttgatcgtccaagagggaaagaatctcaccataaactgcacgtcatcaa agacgttatatggcttatactggtataagcaaaagtatggtgaaggtcttatcttcttgatgatgctacagaaaggtggggaaga gaaaagtcatgaaaagataactgccaagttggatgagaaaaagcagcaaagttccctgcatatcacagcctcccagcccagc catgcaggcatctacctctgtggagcagcccctacatactcgaattatggaggaagccaaggaaatctcatctttggaaaagg cactaaactctctgttaaacca SEQ ID NO.:87 17804.2 aka MA1 α chain constant domain (Native NA)
gatatccagaaccctgaccctgccgtgtaccagctgagagactctaaatccagtgacaagtctgtctgcctattcaccgattttg attctcaaacaaatgtgtcacaaagtaaggattctgatgtgtatatcacagacaaatgtgtgctagacatgaggtctatggacttc aagagcaacagtgctgtggcctggagcaacaaatctgactttgcatgtgcaaacgccttcaacaacagcattattccagaaga caccttcttccccagcccagaaagttcctgtgatgtcaagctggtcgagaaaagctttgaaacagatacgaacctaaactttcaa aacctgtcagtgattgggttccgaatcctcctcctgaaagtggccgggtttaatctgctcatgacgctgcggctgtggtccagct ga SEQ ID NO.:88 17804.2 aka MA1 β chain variable domain with signal peptide (Codon-optimized NA) ATGCTGTGTTCTCTGCTGGCTCTGCTGCTGGGCACCTTCTTTGGAGTGCGGA GCCAGACCATCCACCAGTGGCCTGCTACACTGGTGCAGCCTGTGGGCAGCC CTCTGAGCCTGGAATGTACCGTGGAAGGCACCAGCAACCCCAACCTGTACT GGTACAGACAGGCCGCTGGCAGAGGCCTGCAGCTGCTGTTTTACAGCATCG GCATCGACCAGATCAGCAGCGAGGTGCCCCAGAACCTGAGCGCCAGCAGA CCCCAGGACCGGCAGTTTATCCTGAGCAGCAAGAAGCTGCTGCTGAGCGAC AGCGGCTTCTACCTGTGCGCTTGGAGCGTGACCCGGCACAACGAGCAGTTC TTTGGCCCTGGCACCCGGCTGACCGTGCTG SEQ ID NO.:89 17804.2 aka MA1 β chain constant domain (Codon-optimized NA) GACCTGAAGAACGTGTTCCCCCCAGAGGTGGCCGTGTTCGAGCCTTCTGAG GCCGAGATCAGCCACACCCAGAAAGCCACCCTCGTGTGTCTGGCCACCGGC TTTTACCCCGACCACGTGGAACTGTCTTGGTGGGTCAACGGCAAAGAGGTG CACTCCGGCGTGTGCACCGATCCCCAGCCTCTGAAAGAACAGCCCGCCCTG AACGACAGCCGGTACTGCCTGTCCAGCAGACTGAGAGTGTCCGCCACCTTC TGGCAGAACCCCCGGAACCACTTCAGATGCCAGGTGCAGTTCTACGGCCTG AGCGAGAACGACGAGTGGACCCAGGACAGAGCCAAGCCCGTGACCCAGAT CGTGTCTGCCGAAGCCTGGGGCAGAGCCGATTGCGGCTTTACCAGCGAGAG CTACCAGCAGGGCGTGCTGTCTGCCACCATCCTGTACGAGATCCTGCTGGG AAAGGCCACCCTGTACGCCGTGCTGGTGTCTGCCCTGGTGCTGATGGCCATG GTCAAGCGGAAGGACAGCAGAGGC
SEQ ID NO.:90 17804.2 aka MA1 α chain variable domain with signal peptide (Codon-optimized NA) ATGCTGTGCAGCCTGCTGGCCCTGCTGCTGGGAACATTTTTCGAGCCCCGGA CCAGCCAGGAACTGGAACAGAGCCCACAGAGCCTGATCGTGCAGGAAGGC AAGAACCTGACCATCAACTGCACCAGCTCCAAGACACTGTACGGCCTGTAT TGGTATAAGCAGAAGTACGGCGAGGGCCTGATCTTCCTGATGATGCTGCAG AAGGGCGGCGAGGAAAAGAGCCACGAGAAGATCACCGCCAAGCTGGACGA GAAGAAGCAGCAGTCCAGCCTGCACATCACCGCCTCCCAGCCTTCTCACGC CGGCATCTATCTGTGTGGCGCCGCTCCCACCTACAGCAACTATGGCGGCAG CCAGGGCAATCTGATCTTCGGCAAGGGCACCAAGCTGAGCGTGAAGCCC SEQ ID NO.:91 17804.2 aka MA1 α chain constant domain (Codon-optimized NA) GACATCCAGAACCCCGACCCTGCAGTGTACCAGCTGCGGGACAGCAAGAGc agcgacaagagcgtgtgcctgttcaccgacttcgacagccagaccaacgtgtcccagagcaaggacagcgacgtgtacatc accgataagtgcgtgctggacatgcggagcatggacttcaagagcaacagcgccgtggcctggtccaacaagagcgacttc gcctgcgccaacgccttcaacaacagcattatccccgaggacacattcttcccaagccccgagagcagctgcgacgtgaag ctggtggaaaagagcttcgagacagacaccaacctgaacttccagaacctcagcgtgatcggcttccggatcctgctgctga aggtggccggcttcaacctgctgatgaccctgcggctgtggtccagctga SEQ ID NO.:92 1388.1 β chain CDR1 domain (Codon-optimized NA) atggaccacgagaat SEQ ID NO.:93 1388.1 β chain CDR2 domain (Codon-optimized NA) agctacgacgtgaagatg SEQ ID NO.:94 1388.1 β chain CDR3 domain (Codon-optimized NA) tgcgcctccaacaaccgggacagctacaacagccccctgcacttc SEQ ID NO.:95 1388.1 α chain CDR1 domain (Codon-optimized NA)
tacagcggcagccccgag SEQ ID NO.:96 1388.1 α chain CDR2 domain (Codon-optimized NA) cacatcagcaga SEQ ID NO.:97 1388.1 α chain CDR3 domain (Codon-optimized NA) tgcgccctgagatccggcggctaccagaaagtgacattt SEQ ID NO.:98 1388.2b β chain CDR1 domain (Codon-optimized NA) agcggcgacctgagc SEQ ID NO.:99 1388.2b β chain CDR2 domain (Codon-optimized NA) tactacaacggcgaggaa SEQ ID NO.:100 1388.2b β chain CDR3 domain (Codon-optimized NA) tactacaacggcgaggaa SEQ ID NO.:101 1388.2b α chain CDR1 domain (Codon-optimized NA) gacagcagcagcacctac SEQ ID NO.:102 1388.2b α chain CDR2 domain (Codon-optimized NA) atcttcagcaacatggacatg SEQ ID NO.:103 1388.2b α chain CDR3 domain (Codon-optimized NA) tgcgccgagagcatcgacgcccggctgatgttt SEQ ID NO.:104 1388.3 β chain CDR1 domain (Codon-optimized NA) ggcaccagcaaccccaac SEQ ID NO.:105 1388.3 β chain CDR2 domain (Codon-optimized NA) agcgtgggcatcggc
SEQ ID NO.:106 1388.3 β chain CDR3 domain (Codon-optimized NA) tgtgccctgagcaccagctacgagcagtacttc SEQ ID NO.:107 1388.3 α chain CDR1 domain (Codon-optimized NA) acctccgagaacaactactac SEQ ID NO.:108 1388.3 α chain CDR2 domain (Codon-optimized NA) caggaagcctataagcagcagaac SEQ ID NO.:109 1388.3 α chain CDR3 domain (Codon-optimized NA) tgcgcctttatgaagtcccacagcggctacatcttcggc SEQ ID NO.:110 17084.1b β chain CDR1 domain (Codon-optimized NA) ggcaccagcaaccccaac SEQ ID NO.:111 17084.1b β chain CDR2 domain (Codon-optimized NA) agcgtgggcatcggc SEQ ID NO.:112 17084.1b β chain CDR3 domain (Codon-optimized NA) tgcgcttggagcgtggccgtgaacaccgaggcattcttt SEQ ID NO.:113 17084.1b α chain CDR1 domain (Codon-optimized NA) accagcgagaacaactactac SEQ ID NO.:114 17084.1b α chain CDR2 domain (Codon-optimized NA) caggaagcctataagcagcagaac SEQ ID NO.:115 17084.1b α chain CDR3 domain (Codon-optimized NA) tgcgcctttggcgagggcgccagactgatgttt
SEQ ID NO.:116 17084.2 aka MA1 β chain CDR1 domain (Codon-optimized NA) ggcaccagcaaccccaac SEQ ID NO.:117 17084.2 aka MA1 β chain CDR2 domain (Codon-optimized NA) agcatcggcatcgac SEQ ID NO.:118 17084.2 aka MA1 β chain CDR3 domain (Codon-optimized NA) tgcgcttggagcgtgacccggcacaacgagcagttcttt SEQ ID NO.:119 17084.2 aka MA1 α chain CDR1 domain (Codon-optimized NA) aagacactgtacggc SEQ ID NO.:120 17084.2 aka MA1 α chain CDR2 domain (Codon-optimized NA) ctgcagaagggcggcgaggaa SEQ ID NO.:121 17084.2 aka MA1 α chain CDR3 domain (Codon-optimized NA) tgtggcgccgctcccacctacagcaactatggcggcagccagggcaatctgatcttc SEQ ID NO.:122 Human MAGE-A1 (amino acid) MSLEQRSLHCKPEEALEAQQEALGLVCVQAATSSSSPLVLGTLEEVPTAGSTDP PQSPQGASAFPTTINFTRQRQPSEGSSSREEEGPSTSCILESLFRAVITKKVADLV GFLLLKYRAREPVTKAEMLESVIKNYKHCFPEIFGKASESLQLVFGIDVKEADPT GHSYVLVTCLGLSYDGLLGDNQIMPKTGFLIIVLVMIAMEGGHAPEEEIWEELS VMEVYDGREHSAYGEPRKLLTQDLVQEKYLEYRQVPDSDPARYEFLWGPRAL AETSYVKVLEYVIKVSARVRFFFPSLREAALREEEEGV SEQ ID NO.:123 Human MAGE-A1278-286 (amino acid) KVLEYVIKV
SEQ ID NO.:124 Porcine teschovirus-12A (P2A) peptide (amino acid) GSGATNFSLLKQAGDVEENPGP SEQ ID NO.:125 Foot-and-Mouth disease virus 2A (F2A) peptide (amino acid) GSGVKQTLNFDLLKLAGDVESNPGP SEQ ID NO.:126 Equine rhinitis A virus (ERAV) 2A (E2A) peptide (amino acid) QCTNYALLKLAGDVESNPGP SEQ ID NO.:127 Thoseaasigna virus 2A (T2A) peptide (amino acid) LEGGGEGRGSLLTCGDVEENPGPR SEQ ID NO.:128 Porcine teschovirus-12A (P2A) peptide (NA) GGAAGCGGAGCTACTAACTTCAGCCTGCTGAAGCAGGCTGGAGACGTGGAG GAGAACCCTGGACCT SEQ ID NO.:129 Porcine teschovirus-12A (P2A) peptide (CO-NA) GGTTCCGGAGCCACGAACTTCTCTCTGTTAAAGCAAGCAGGAGACGTGGAA GAAAACCCCGGTCCC SEQ ID NO.:130 Foot-and-Mouth disease virus 2A (F2A) peptide (NA) GGAAGCGGAGTGAAACAGACTTTGAATTTTGACCTTCTCAAGTTGGCGGGA GACGTGGAGTCCAACCCTGGACCT SEQ ID NO.:131 Equine rhinitis A virus (ERAV) 2A (E2A) peptide (NA) GGAAGCGGACAGTGTACTAATTATGCTCTCTTGAAATTGGCTGGAGATGTT GAGAGCAACCCTGGACCT SEQ ID NO.:132 Thoseaasigna virus 2A (T2A) peptide (NA) GGAAGCGGAGAGGGCAGAGGAAGTCTGCTAACATGCGGTGACGTCGAGGA GAATCCTGGACCT
SEQ ID NO.:133 Glycine-serine linker (aa) GGGGSGGGGSGGGGS SEQ ID NO.:134 Glycine-serine linker (aa) GSTSGGGSGGGSGGGGSS SEQ ID NO.:135 sgRNA Forward Oligo: TRAC_sgRNA_pLenti_F1 CACCGGAGAATCAAAATCGGTGAAT SEQ ID NO.:136 sgRNA Reverse Oligo: TRAC_sgRNA_pLenti_R1 AAACATTCACCGATTTTGATTCTCC SEQ ID NO.:137 sgRNA Forward Oligo: PD1_sgRNA_F1 CACCGCAGTTGTGTGACACGGAAG SEQ ID NO.:138 sgRNA Reverse Oligo: PD1_sgRNA_R1 AAACCTTCCGTGTCACACAACTGC SEQ ID NO.:139 sgRNA Forward Oligo: CTLA4_sgRNA_F1CACCGGCAAAGGTGAGTGAGACTTT SEQ ID NO.:140 sgRNA Reverse Oligo: CTLA4_sgRNA_R1 AAACAAAGTCTCACTCACCTTTGCC SEQ ID NO.:141 sgRNA Forward Oligo: LAG3_sgRNA_F1 CACCGgtttctgcagccgctttggg SEQ ID NO.:142 sgRNA Reverse Oligo: LAG3_sgRNA_R2 AAACcccaaagcggctgcagaaacC
SEQ ID NO.:143 CD8 co-receptor α chain (aa) SQFRVSPLDRTWNLGETVELKCQVLLSNPTSGCSWLFQPRGAAASPTFLLYLSQ NKPKAAEGLDTQRFSGKRLGDTFVLTLSDFRRENEGYYFCSALSNSIMYFSHFV PVFLPAKPTTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACDIYI WAPLAGTCGVLLLSLVITLYCNHRNRRRVCKCPRPVVKSGDKPSLSARYV SEQ ID NO.:144 CD8 co-receptor β chain isoform 1 (aa) LQQTPAYIKVQTNKMVMLSCEAKISLSNMRIYWLRQRQAPSSDSHHEFLALWD SAKGTIHGEEVEQEKIAVFRDASRFILNLTSVKPEDSGIYFCMIVGSPELTFGKGT QLSVVDFLPTTAQPTKKSTLKKRVCRLPRPETQKGPLCSPITLGLLVAGVLVLL VSLGVAIHLCCRRRRARLRFMKQFYK SEQ ID NO.:145 CD8 co-receptor β chain isoform 2 (aa) LQQTPAYIKVQTNKMVMLSCEAKISLSNMRIYWLRQRQAPSSDSHHEFLALWD SAKGTIHGEEVEQEKIAVFRDASRFILNLTSVKPEDSGIYFCMIVGSPELTFGKGT QLSVVDFLPTTAQPTKKSTLKKRVCRLPRPETQKGPLCSPITLGLLVAGVLVLL VSLGVAIHLCCRRRRARLRFMKQLRLHPLEKCSRMDY SEQ ID NO.:146 CD8 co-receptor β chain isoform 3 (aa) (aa)LQQTPAYIKVQTNKMVMLSCEAKISLSNMRIYWLRQRQAPSSDSHHEFLAL WDSAKGTIHGEEVEQEKIAVFRDASRFILNLTSVKPEDSGIYFCMIVGSPELTFG KGTQLSVVDFLPTTAQPTKKSTLKKRVCRLPRPETQKGPLCSPITLGLLVAGVL VLLVSLGVAIHLCCRRRRARLRFMKQKFNIVCLKISGFTTCCCFQILQISREYGF GVLLQKDIGQ SEQ ID NO.:147 CD8 co-receptor β chain isoform 4 (aa) LQQTPAYIKVQTNKMVMLSCEAKISLSNMRIYWLRQRQAPSSDSHHEFLALWD SAKGTIHGEEVEQEKIAVFRDASRFILNLTSVKPEDSGIYFCMIVGSPELTFGKGT QLSVVDFLPTTAQPTKKSTLKKRVCRLPRPETQKGPLCSPITLGLLVAGVLVLL VSLGVAIHLCCRRRRARLRFMKQKFNIVCLKISGFTTCCCFQILQISREYGFGVL LQKDIGQ
SEQ ID NO.:148 CD8 co-receptor β chain isoform 5 (aa) LQQTPAYIKVQTNKMVMLSCEAKISLSNMRIYWLRQRQAPSSDSHHEFLALWD SAKGTIHGEEVEQEKIAVFRDASRFILNLTSVKPEDSGIYFCMIVGSPELTFGKGT QLSVVDFLPTTAQPTKKSTLKKRVCRLPRPETQKGPLCSPITLGLLVAGVLVLL VSLGVAIHLCCRRRRARLRFMKQPQGEGISGTFVPQCLHGYYSNTTTSQKLLNP WILKT SEQ ID NO.:149 Polynucleotide encoding CD8 co-receptor α chain, with signal peptide (nt) Atggctctgcctgtgacagctctgctgctgcctctggctctgcttctgcatgccgctagacccagccagttcagagtgtcccct ctggacagaacctggaacctgggcgagacagtggaactgaagtgccaggtgctgctgagcaatcctaccagcggctgcag ctggctgtttcagcctagaggtgctgccgcctctcctacctttctgctgtacctgagccagaacaagcccaaggccgccgaag gactggacacccagagattcagcggcaagagactgggcgacaccttcgtgctgaccctgagcgacttcagaagagagaac gagggctactacttctgcagcgccctgagcaacagcatcatgtacttcagccacttcgtgcccgtgtttctgcccgccaagcct acaacaacccctgctcctagacctcctacaccagctcctacaatcgccagccagcctctgtctctgaggccagaagcttgtag acctgctgctggcggagccgtgcatacaagaggactggatttcgcctgcgacatctacatctgggcccctctggctggaacat gtggcgtgctgctgctgtccctggtcatcaccctgtactgcaaccaccggaacaggcggagagtgtgcaagtgccctagacc tgtggtcaagagcggcgacaagccTAGCCTGAGCGCCAGATATGTT SEQ ID NO.:150 Polynucleotide encoding CD8 co-receptor β chain, with signal peptide (nt) atgaggcctagactgtggctgcttctggctgcccagctgacagtgctgcacggcaattctgtcctgcagcagacccctgccta catcaaggtgcagaccaacaagatggtcatgctgagctgcgaggccaagatcagcctgtccaacatgcggatctactggctg cggcagagacaggcccctagctctgatagccaccacgagtttctggccctgtgggattctgccaagggcaccattcacggcg aggaagtggaacaagagaagatcgccgtgttccgggacgccagcagattcatcctgaacctgaccagcgtgaagcccgag gacagcggcatctatttctgcatgatcgtgggcagccccgagctgacatttggcaagggaacacagctgagcgtggtggact tcctgcctactacagcccagcctaccaagaagtctaccctgaagaaacgcgtgtgcagactgcccaggcctgagacacaaa agggccctctgtgcagccctatcacactgggattgctggtggctggcgttctggtcctgctggtgtctctgggagttgccatcca cctgtgctgtagaagaaggcgggccagactgcggttcatgaagcagttctacaaa SEQ ID NO.:151 Polynucleotide encoding 17804.1 aka MA1 TCR β chain, with signal peptide Atgctgtgttctctgctggctctgctgctgggcaccttctttggagtgcggagccagaccatccaccagtggcctgctacactg gtgcagcctgtgggcagccctctgagcctggaatgtaccgtggaaggcaccagcaaccccaacctgtactggtacagacag gccgctggcagaggcctgcagctgctgttttacagcatcggcatcgaccagatcagcagcgaggtgccccagaacctgagc gccagcagaccccaggaccggcagtttatcctgagcagcaagaagctgctgctgagcgacagcggcttctacctgtgcgctt ggagcgtgacccggcacaacgagcagttctttggccctggcacccggctgaccgtgctggacctgaagaacgtgttccccc cagaggtggccgtgttcgagccttctgaggccgagatcagccacacccagaaagccaccctcgtgtgtctggccaccggctt ttaccccgaccacgtggaactgtcttggtgggtcaacggcaaagaggtgcactccggcgtgtgcaccgatccccagcctctg
aaagaacagcccgccctgaacgacagccggtactgcctgtccagcagactgagagtgtccgccaccttctggcagaacccc cggaaccacttcagatgccaggtgcagttctacggcctgagcgagaacgacgagtggacccaggacagagccaagcccgt gacccagatcgtgtctgccgaagcctggggcagagccgattgcggctttaccagcgagagctaccagcagggcgtgctgtc tgccaccatcctgtacgagatcctgctgggaaaggccaccctgtacgccgtgctggtgtctgccctggtgctgatggccatgg tcaagcggaaggacagcagaggc SEQ ID NO.:152 Polynucleotide encoding 17804.1 aka MA1 TCR α chain, with signal peptide Atgctgtgcagcctgctggccctgctgctgggaacatttttcgagccccggaccagccaggaactggaacagagcccacag agcctgatcgtgcaggaaggcaagaacctgaccatcaactgcaccagctccaagacactgtacggcctgtattggtataagc agaagtacggcgagggcctgatcttcctgatgatgctgcagaagggcggcgaggaaaagagccacgagaagatcaccgc caagctggacgagaagaagcagcagtccagcctgcacatcaccgcctcccagccttctcacgccggcatctatctgtgtggc gccgctcccacctacagcaactatggcggcagccagggcaatctgatcttcggcaagggcaccaagctgagcgtgaagcc cgacatccagaaccccgaccctgcagtgtaccagctgcgggacagcaagagcagcgacaagagcgtgtgcctgttcaccg acttcgacagccagaccaacgtgtcccagagcaaggacagcgacgtgtacatcaccgataagtgcgtgctggacatgcgga gcatggacttcaagagcaacagcgccgtggcctggtccaacaagagcgacttcgcctgcgccaacgccttcaacaacagca ttatccccgaggacacattcttcccaagccccgagagcagctgcgacgtgaagctggtggaaaagagcttcgagacagaca ccaacctgaacttccagaacctcagcgtgatcggcttccggatcctgctgctgaaggtggccggcttcaacctgctgatgacc ctgcggctgtggtccagctga SEQ ID NO.:153 Polynucleotide encoding [CD8 co-receptor α chain-modified T2A peptide-CD8 co-receptor β chain-P2A peptide-17804.1 aka MA1 TCRβ chain- P2A peptide-17804.1 aka MA1 TCRα chain (with signal peptides)] atggctctgcctgtgacagctctgctgctgcctctggctctgcttctgcatgccgctagacccagccagttcagagtgtcccctc tggacagaacctggaacctgggcgagacagtggaactgaagtgccaggtgctgctgagcaatcctaccagcggctgcagct ggctgtttcagcctagaggtgctgccgcctctcctacctttctgctgtacctgagccagaacaagcccaaggccgccgaagga ctggacacccagagattcagcggcaagagactgggcgacaccttcgtgctgaccctgagcgacttcagaagagagaacga gggctactacttctgcagcgccctgagcaacagcatcatgtacttcagccacttcgtgcccgtgtttctgcccgccaagcctac aacaacccctgctcctagacctcctacaccagctcctacaatcgccagccagcctctgtctctgaggccagaagcttgtagac ctgctgctggcggagccgtgcatacaagaggactggatttcgcctgcgacatctacatctgggcccctctggctggaacatgt ggcgtgctgctgctgtccctggtcatcaccctgtactgcaaccaccggaacaggcggagagtgtgcaagtgccctagacctg tggtcaagagcggcgacaagcctagcctgagcgccagatatgttGGCAGCGGAGAAGGCAGAGGCTC CCTGCTTACATGCGGCGACGTGGAAGAGAACCCCGGACCTatgaggcctagactgtgg ctgcttctggctgcccagctgacagtgctgcacggcaattctgtcctgcagcagacccctgcctacatcaaggtgcagaccaa caagatggtcatgctgagctgcgaggccaagatcagcctgtccaacatgcggatctactggctgcggcagagacaggcccc tagctctgatagccaccacgagtttctggccctgtgggattctgccaagggcaccattcacggcgaggaagtggaacaagag aagatcgccgtgttccgggacgccagcagattcatcctgaacctgaccagcgtgaagcccgaggacagcggcatctatttct gcatgatcgtgggcagccccgagctgacatttggcaagggaacacagctgagcgtggtggacttcctgcctactacagccca gcctaccaagaagtctaccctgaagaaacgcgtgtgcagactgcccaggcctgagacacaaaagggccctctgtgcagccc tatcacactgggattgctggtggctggcgttctggtcctgctggtgtctctgggagttgccatccacctgtgctgtagaagaagg cgggccagactgcggttcatgaagcagttctacaaaGGCAGCGGCGCCACCAACTTCAGCCTGCT GAAACAAGCCGGCGACGTCGAGGAAAATCCTGGACCTatgctgtgttctctgctggctctg ctgctgggcaccttctttggagtgcggagccagaccatccaccagtggcctgctacactggtgcagcctgtgggcagccctct gagcctggaatgtaccgtggaaggcaccagcaaccccaacctgtactggtacagacaggccgctggcagaggcctgcagc tgctgttttacagcatcggcatcgaccagatcagcagcgaggtgccccagaacctgagcgccagcagaccccaggaccgg cagtttatcctgagcagcaagaagctgctgctgagcgacagcggcttctacctgtgcgcttggagcgtgacccggcacaacg agcagttctttggccctggcacccggctgaccgtgctggacctgaagaacgtgttccccccagaggtggccgtgttcgagcct tctgaggccgagatcagccacacccagaaagccaccctcgtgtgtctggccaccggcttttaccccgaccacgtggaactgt
cttggtgggtcaacggcaaagaggtgcactccggcgtgtgcaccgatccccagcctctgaaagaacagcccgccctgaacg acagccggtactgcctgtccagcagactgagagtgtccgccaccttctggcagaacccccggaaccacttcagatgccaggt gcagttctacggcctgagcgagaacgacgagtggacccaggacagagccaagcccgtgacccagatcgtgtctgccgaag cctggggcagagccgattgcggctttaccagcgagagctaccagcagggcgtgctgtctgccaccatcctgtacgagatcct gctgggaaaggccaccctgtacgccgtgctggtgtctgccctggtgctgatggccatggtcaagcggaaggacagcagag gcGGTTCCGGAGCCACGAACTTCTCTCTGTTAAAGCAAGCAGGAGACGTGGA AGAAAACCCCGGTCCCatgctgtgcagcctgctggccctgctgctgggaacatttttcgagccccggaccagc caggaactggaacagagcccacagagcctgatcgtgcaggaaggcaagaacctgaccatcaactgcaccagctccaagac actgtacggcctgtattggtataagcagaagtacggcgagggcctgatcttcctgatgatgctgcagaagggcggcgaggaa aagagccacgagaagatcaccgccaagctggacgagaagaagcagcagtccagcctgcacatcaccgcctcccagccttc tcacgccggcatctatctgtgtggcgccgctcccacctacagcaactatggcggcagccagggcaatctgatcttcggcaag ggcaccaagctgagcgtgaagcccgacatccagaaccccgaccctgcagtgtaccagctgcgggacagcaagagcagcg acaagagcgtgtgcctgttcaccgacttcgacagccagaccaacgtgtcccagagcaaggacagcgacgtgtacatcaccg ataagtgcgtgctggacatgcggagcatggacttcaagagcaacagcgccgtggcctggtccaacaagagcgacttcgcct gcgccaacgccttcaacaacagcattatccccgaggacacattcttcccaagccccgagagcagctgcgacgtgaagctggt ggaaaagagcttcgagacagacaccaacctgaacttccagaacctcagcgtgatcggcttccggatcctgctgctgaaggtg gccggcttcaacctgctgatgaccctgcggctgtggtccagctga SEQ ID NO.:154 modified T2A peptide with GSG linker GSGEGRGSLLTCGDVEENPGP SEQ ID NO.:155 Meganuclease motif LAGLIDADG SEQ ID NO.:156 Meganuclease motif GIY-YIG SEQ ID NO.:157 Meganuclease motif PD-(D/E)XK SEQ ID NO.:158 TCR Cβ domain EDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVH SGVCTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSEN DEWTQDRAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLY AVLVSALVLMAMVKRKDSRG SEQ ID NO.:159 Polynucleotide encoding [CD8 co-receptor α chain-modified T2A peptide-CD8 co-receptor β chain-P2A peptide-17804.1 aka MA1 TCRβ chain- P2A peptide-17804.1 aka MA1 TCRα chain (with signal peptides)] atggctctgcctgtgacagctctgctgctgcctctggctctgcttctgcatgccgctagacccagccagttcagagtgtcccctc tggacagaacctggaacctgggcgagacagtggaactgaagtgccaggtgctgctgagcaatcctaccagcggctgcagct ggctgtttcagcctagaggtgctgccgcctctcctacctttctgctgtacctgagccagaacaagcccaaggccgccgaagga ctggacacccagagattcagcggcaagagactgggcgacaccttcgtgctgaccctgagcgacttcagaagagagaacga gggctactacttctgcagcgccctgagcaacagcatcatgtacttcagccacttcgtgcccgtgtttctgcccgccaagcctac aacaacccctgctcctagacctcctacaccagctcctacaatcgccagccagcctctgtctctgaggccagaagcttgtagac ctgctgctggcggagccgtgcatacaagaggactggatttcgcctgcgacatctacatctgggcccctctggctggaacatgt ggcgtgctgctgctgtccctggtcatcaccctgtactgcaaccaccggaacaggcggagagtgtgcaagtgccctagacctg tggtcaagagcggcgacaagcctagcctgagcgccagatatgttGGCAGCGGAGAAGGCAGAGGCTC
CCTGCTTACATGCGGCGACGTGGAAGAGAACCCCGGACCTatgaggcctagactgtgg ctgcttctggctgcccagctgacagtgctgcacggcaattctgtcctgcagcagacccctgcctacatcaaggtgcagaccaa caagatggtcatgctgagctgcgaggccaagatcagcctgtccaacatgcggatctactggctgcggcagagacaggcccc tagctctgatagccaccacgagtttctggccctgtgggattctgccaagggcaccattcacggcgaggaagtggaacaagag aagatcgccgtgttccgggacgccagcagattcatcctgaacctgaccagcgtgaagcccgaggacagcggcatctatttct gcatgatcgtgggcagccccgagctgacatttggcaagggaacacagctgagcgtggtggacttcctgcctactacagccca gcctaccaagaagtctaccctgaagaaacgcgtgtgcagactgcccaggcctgagacacaaaagggccctctgtgcagccc tatcacactgggattgctggtggctggcgttctggtcctgctggtgtctctgggagttgccatccacctgtgctgtagaagaagg cgggccagactgcggttcatgaagcagttctacaaaGGCAGCGGCGCCACCAACTTCAGCCTGCT GAAACAAGCCGGCGACGTCGAGGAAAATCCTGGACCTatgctgtgttctctgctggctctg ctgctgggcaccttctttggagtgcggagccagaccatccaccagtggcctgctacactggtgcagcctgtgggcagccctct gagcctggaatgtaccgtggaaggcaccagcaaccccaacctgtactggtacagacaggccgctggcagaggcctgcagc tgctgttttacagcatcggcatcgaccagatcagcagcgaggtgccccagaacctgagcgccagcagaccccaggaccgg cagtttatcctgagcagcaagaagctgctgctgagcgacagcggcttctacctgtgcgcttggagcgtgacccggcacaacg agcagttctttggccctggcacccggctgaccgtgctggacctgaagaacgtgttccccccagaggtggccgtgttcgagcct tctgaggccgagatcagccacacccagaaagccaccctcgtgtgtctggccaccggcttttaccccgaccacgtggaactgt cttggtgggtcaacggcaaagaggtgcactccggcgtgtgcaccgatccccagcctctgaaagaacagcccgccctgaacg acagccggtactgcctgtccagcagactgagagtgtccgccaccttctggcagaacccccggaaccacttcagatgccaggt gcagttctacggcctgagcgagaacgacgagtggacccaggacagagccaagcccgtgacccagatcgtgtctgccgaag cctggggcagagccgattgcggctttaccagcgagagctaccagcagggcgtgctgtctgccaccatcctgtacgagatcct gctgggaaaggccaccctgtacgccgtgctggtgtctgccctggtgctgatggccatggtcaagcggaaggacagcagag gcGGTTCCGGAGCCACGAACTTCTCTCTGTTAAAGCAAGCAGGAGACGTGGA AGAAAACCCCGGTCCCatgctgtgcagcctgctggccctgctgctgggaacatttttcgagccccggaccagc caggaactggaacagagcccacagagcctgatcgtgcaggaaggcaagaacctgaccatcaactgcaccagctccaagac actgtacggcctgtattggtataagcagaagtacggcgagggcctgatcttcctgatgatgctgcagaagggcggcgaggaa aagagccacgagaagatcaccgccaagctggacgagaagaagcagcagtccagcctgcacatcaccgcctcccagccttc tcacgccggcatctatctgtgtggcgccgctcccacctacagcaactatggcggcagccagggcaatctgatcttcggcaag ggcaccaagctgagcgtgaagcccgacatccagaaccccgaccctgcagtgtaccagctgcgggacagcaagagcagcg acaagagcgtgtgcctgttcaccgacttcgacagccagaccaacgtgtcccagagcaaggacagcgacgtgtacatcaccg ataagtgcgtgctggacatgcggagcatggacttcaagagcaacagcgccgtggcctggtccaacaagagcgacttcgcct gcgccaacgccttcaacaacagcattatccccgaggacacattcttcccaagccccgagagcagctgcgacgtgaagctggt ggaaaagagcttcgagacagacaccaacctgaacttccagaacctcagcgtgatcggcttccggatcctgctgctgaaggtg gccggcttcaacctgctgatgaccctgcggctgtggtccagc EXAMPLES EXAMPLE 1 GENERATION OF HIGH-AFFINITY TCRS SPECIFIC FOR CANCER EPITOPES [0210] Generation of high-affinity TCRs for use in adoptive cell therapies is difficult due to thymic selection, wherein TCRs with high-affinity for self-antigens (e.g., MART1 and MAGE-A1) are removed and, therefore, relatively rare as compared to TCRs specific for foreign antigens (see, e.g., Figures 1A and 1B).
[0211] As shown in Figures 2A and 2B, a screening and enrichment process was developed to identify high-affinity TCRs specific for MAGE-A1. Briefly, CD8+ T cells from peripheral blood mononuclear cells (PBMCs) of 12 healthy donors were stimulated once with peptide-pulsed autologous DCs and twice with peptide-pulsed autologous PBMCs, in the presence of IL-2, IL-7, IL-15 and IL-21, to obtain polyclonal MAGE-A1-specific CD8+ T cell lines. The stimulated cell lines from all donors were pooled and sorted several times using limited concentrations MAGE-A1 peptide:MHC multimers, which produced enriched populations of high-affinity T cell clones. TCRβ genes from the populations were sequenced to the frequency of TCRs in pooled and individual pMHC sorts. [0212] Figure 3 shows exemplary data from a series of pMHC sorts that enriched for T cells expressing TCRβ CDR3 specific for the MAGE-A1 antigen. High- affinity clones identified from the pool strongly bound MAGE-A1:MHC, correlating with lower EC50 (Figures 4A, 4B). EXAMPLE 2 IN VITRO FUNCTIONALITY OF A MAGE-A1-SPECIFIC TCR [0213] A high-affinity MAGE-A1-specific CD8+ T cell clone “MA2” generated using the method of Example 1 (Figure 5A) was selected for further testing. As shown in Figure 5B, MA2+ CD8+ T cells selectively produced cytokines when co-cultured with MAGE-A1-expressing HAL-A*0201+ U266 multiple myeloma cells (effector to target (E:T) ratio of 10:1, 4 hrs). In a standard 4 hr. Cr51-release assay, MA2+ T cells were capable of killing target cells in the presence or absence of exogenous IFN-γ and MAGE-A1 peptide (Figure 5C). EXAMPLE 3 MAGE-A1-SPECIFIC CD8 TCR BINDS TETRAMER INDEPENDENT OF CD8 [0214] CD8+ TCRs recognize antigens presented by class I HLA molecules, while CD4+ TCRs recognize antigens presented in the context of class II HLA. To test whether the high-affinity MA2 TCR could bind MAGE-A1:HLA I independent of CD8, CD4+ T cells were transduced with MA2 TCR (see, e.g., schematic diagrams of Figures 6A and 6B). As shown in Figures 7A and 7B, CD4+ T cells transduced with MA2 TCR bound MAGE-A1:HLA tetramers with an affinity that was comparable (~5-fold
difference in Bmax) to MA2 CD8+ T cells. However, as shown in Figure 7C, the transformed CD4+ T cells did not kill target cells in vitro. EXAMPLE 4 FUNCTIONAL TESTING OF AN ENGINEERED CD4+ T CELL EXPRESSING A MAGE-A1- SPECIFIC CD8 TCR AND CD8 CO-RECEPTOR [0215] Next, the ability of a CD8+ co-receptor to improve functionality of high- affinity CD8+ T cell-derived-TCR-expressing CD4+ T cells was investigated (see, e.g., Figure 6A). As illustrated in the diagram of Figure 8A, CD4+ T cells were transduced with both a high- affinity Class-I-restricted MAGE-A1-specific TCR ("MA1", having Vα, Cα, Vβ, and Cβ amino acid sequences according to SEQ ID NOs.:19, 20, 17, and 18, respectively) and a CD8 co-receptor. Figure 8B shows that a greater proportion of CD4+ T cells transduced with both exogenous CD8 TCR and CD8 co-receptor produced cytokines in response to antigen, as compared to CD4+ T cells transduced with the exogenous CD8 TCR alone. Figure 8C shows that the dually transduced CD4+ T cells surprisingly exhibited cytolytic activity against MEL526 target cells, at rates comparable to CD8+ T cells expressing the same high- affinity TCR. As shown in Figure 8D, the dually transduced CD4+ T cells also proliferated more robustly following stimulation with antigen than MA1+ CD4+ cells without CD8. [0216] These data show that high-affinity MAGE-A1-specific TCRs of the present disclosure, and CD8+ and CD4+ T cells expressing the same, are useful for targeting and killing MAGE-A1-expressing cancer cells and have use in cellular immunotherapies against MAGE-A1-expressing diseases. EXAMPLE 5 IN VITRO FUNCTION AND IN VIVO EFFICACY OF A MAGE-A1-SPECIFIC TCR [0217] A TCR having Vα, Cα, Vβ, and Cβ amino acid sequences according to SEQ ID NOs.:19 (it will be understood that the signal peptide (amino acids 1-18 of SEQ ID NO.:19) is removed prior to expression at a T cell surface), 20, 17 (it will be
understood that the signal peptide (amino acids 1-17 of SEQ ID NO.:17) is removed prior to expression at a T cell surface), and 18, respectively, is specific to the Class I HLA-A*02:01-restricted MAGE-A1278-287 epitope (KVLEYVIKV; SEQ ID NO.:123) identified by mass spectrometry on the surface of KS24 breast cancer cells. This TCR, is referred to herein as the “MA1” TCR. Specifically, the MA1 TCR comprises a TCRα chain comprising SEQ ID NO.:19 and SEQ ID NO.:20, with the signal peptide (amino acids 1-18 of SEQ ID NO.:19) removed prior to expression at a host cell surface, and a TCRβ chain comprising SEQ ID NO.:17 and SEQ ID NO.:18, with the signal peptide (amino acids 1-17 of SEQ ID NO.:17) removed prior to expression at the host cell surface. [0218] T cells transduced with a lentivirus expressing the MA1 TCR and CD8 co-receptor polypeptides are referred to herein as “MagIC TCR-T”. [0219] T cell products for murine experiments were generated in accordance with T cell products designed for infusion into human patients. Briefly, PBMC first underwent a positive magnetic bead selection for CD4+. The flow through containing a majority of CD8+ T cells was then positively selected for CD62L+ cells. This assures that CD8+ T cell subsets demonstrating improved in vivo persistence, including naïve, central memory and stem cell memory CD8+ cells, are selected for transduction with the MAGE-A1-specific TCR. Pooled CD4+ and CD4-CD62L+ cells at a ratio of 1:3 obtained from frozen PBMC of three individual healthy donors were then stimulated with IL-2 and TransActTM (αCD3/CD28; Miltenyi) two days prior to transduction with a PRRLSIN lentivirus encoding the MA1 TCR and human CD8 co-receptor polypeptides (SEQ ID NOs.:143 and 144) to produce MagIC TCR-T. MagIC TCR-T cell products were harvested on day 14 post-stimulation. MagIC TCR-T cell products from all three donors specifically both killed low-density MAGE-A1-expressing breast cancer line HS578T (Figure 9A) and high-density MAGE-A1 expressing melanoma cell line me275 (Figure 9B) over a period of 5 days (IncuCyteTM assay). For the breast cancer killing assay, MagIC TCR-T cells were re-challenged once, at 24 hours. For the melanoma killing assay, MagIC TCR-T cells were re-challenged twice, at 24 and 48 hours. [0220] An immunodeficient NSG xenograft mouse model of MAGE-A1+ myeloma was utilized to test in vivo efficacy of MagIC TCR-T. Briefly, mice were engrafted with 2x106 U266 myeloma cells (i.v.) 7 days prior to MagIC TCR-T cell
transfer. The U266 myeloma cell line was selected due to its native HLA- A*02:01expression, MAGE-A1 protein expression, and ability grow specifically and consistently in the bone marrow as a xenograft in NSG mice. Furthermore, serial tumor burden assessments in individual mice can be performed by serum quantification of secreted IgE by the U266 cells. To evaluate in vivo efficacy of each T cell population, 15x106 MagIC TCR- CD8+, CD4+, or bulk CD8+ and CD4+ T cells were transferred separately, and all showed tumor control (Figure 10A). All groups containing MagIC TCR-T cells demonstrated in vivo persistence and tumor control, resulting in eradication of U266 cells in tumor engrafted mice (Figure 10B). [0221] These results show that MagIC TCR- CD8+ and CD4+ T cells have potent in vivo anticancer activity. EXAMPLE 6 IDENTIFICATION OF HLA-B49*01 AS A SELECTION CRITERIA [0222] To assess safety and specificity of MagIC TCR-T cell therapy, unbiased testing was performed using a panel of commercially available HLA-A2-positive induced pluripotent stem cell (IPSC) derived human cell lines, cryopreserved normal human bronchial fibroblasts, normal human bronchial and renal epithelial cell lines. These cell lines reflected critical tissues including heart/cardiac, lung, endothelium, liver/hepatocytes, brain (astrocytes and GABA neurons), and kidney (renal epithelium). As these cell lines do not all express HLA-A*02:01, they were lentivirally transduced with HLA-A2 prior to co-culture with MagIC-TCR-T cells. [0223] MagIC-TCR T cells did not express detectable IFNγ or exhibit cytotoxicity against healthy human cell lines expressing self-peptides presented by HLA-A*02:01, as measured by live cell imaging when co-cultured in the presence of all tested cell lines with or without upregulation of HLA molecules and alterations in peptide processing by pretreatment with IFNγ (Figures 11A-11B). [0224] A bank of EBV-transformed human lymphoblastoid cell lines (LCL), which express abundant class I HLA including 60 of the most common human HLA alleles covering >95% of individuals, was used to assess the possibility of class I HLA alloreactivity of MagIC TCR-T cells. These HLA alleles are summarized in Table 1. Briefly, this assay assesses for alloreactivity of the MagIC-TCR T cells to other HLA types, since human subjects have 6 HLA I alleles; “alloreactivity” can also be described
in this context as “non-specific cross-reactivity”. As these B cell lineage-derived LCLs do not express MAGE-A1, they would not be expected to trigger recognition by MagIC TCR-T unless loaded with cognate peptide. Reactivity of the MagIC TCR T cells to twenty-six lines representing >60 of the most common HLA types was assessed in co- culture systems using the LCL cell lines and (1) a nur77- reporter jurkat cell line expressing CD8 and the MagIC-TCR construct or (2) normal donor-derived MagIC- TCR T cells, via an interferon-gamma (IFN ^) cytokine release assay. Results for the 26 cell lines are shown in Figure 12A. As shown, an IFN ^ response was observed with only one HLA-B allele – HLA-B*4901. This alloreactivity is noted in Table 1 below in bold and italicized text. Table 1: HLA typing of cell lines tested
[0225] Reactivity to HLA-B*49:01 was confirmed by positive recognition of the HLA- *02:01-negative, HLA-B*49:01-positive Namalwa cell line (Figures12B). [0226] Patients expressing HLA-B*49:01 are excluded from clinical trials using MagIC TCR T cells. In other words, patients to receive therapy are selected as negative for expression of HLA-B*49:01 and positive for HLA-A*02:01. EXAMPLE 7 DOSING STUDY [0227] A phase I, open-label interventional study investigating MagIC TCR-T for treatment of up to 15-18 HLA-A*02:01 positive, HLA-B*49:01 negative patients with metastatic TNBC, urothelial carcinoma, or NSCLC is performed. In the phase 1 portion of the trial, T cells are administered. In the phase 1/2 portion of the trial, following T cell infusion, atezolizumab is administered and provided as standard of care. In the event atezolizumab is not available, another FDA-approved PD1-axis inhibitor for the specific clinical indication is substituted (e.g., durvalumab or pembrolizumab for NSCLC, or avelumab, durvalumab, or pembrolizumab for urothelial cancer). The study design is illustrated in Figure 13. [0228] This study evaluates the safety of adoptive T cell therapy using MagIC TCR-T (“safe” defined in the study as an observed treatment-related unexpected grade 3 (CTCAE v5.0) or higher toxicity rate consistent with a true rate <= 35%). This study also evaluates clinical activity of MagIC TCR-T (clinical activity defined as an observed response rate that statistically exceeds 5%). Without treatment, metastatic TNBC, urothelial cancer or NSCLC are near uniformly fatal. Response rates to TNBC specifically in the setting of post-treatment progression are unknown as no clinical trials have been reported in this setting. [0229] Participants must be HLA-A*02:01-positive to ensure recognition by infused transgenic T cells of antigen-MHC complexes, and HLA-B*49:01-negative to avoid potential adverse off-target activity. HLA typing is determined though a molecular approach in a clinical laboratory licensed for HLA typing. HLA typing is performed using PCR amplification followed by high throughput Next Generation Sequencing (NGS) and subsequent HLA determination using a system available through Scisco Genetics (sciscogenetics.com/pages/technology.html, the contents of which is incorporated herein by reference in its entirety).
[0230] Exclusion Criteria: Participants expressing HLA-B*49:01 are excluded due to the risk of alloreactivity. [0231] Following confirmation of eligibility based on HLA typing and MAGE- A1 expression on the tumor, patients undergo leukapheresis. Leukapheresis collection is performed on each patient to obtain peripheral blood mononuclear cells (PBMCs) for the production of the MagIC TCR-T investigational product. [0232] The cell product includes both CD8+ and CD4+ transgenic T cells. Dose is measured based on quantity of transgenic CD3+ cells binding to HLA-A2-MAGE-A1 tetramer. Purity is required to be at least 10% of cells transgenic for the TCR and is expected to range from 20-80%, more typically from 30-50%. Although a 1:1 ratio of CD8+ and CD4+ transgenic T cells in the final product is targeted, cells are co-cultured and there is inherent variability in infused products. [0233] In both phases of the trial, lymphodepleting chemotherapy is administered to subjects prior to T-cell infusion to reduce tumor burden, minimize the risk of tumor lysis syndrome, and induce lymphopenia to improve T-cell persistence. [0234] Unless clinical circumstances suggest otherwise, both phases of the trial use a low cyclophosphamide dose (300 mg/m2 for 3 days) and fludarabine (30 mg/m2 for 3 days) (the combination of cyclophosphamide and fludarabine is sometimes referred-to as “Cy/Flu”). Lymphodepletion is administered intravenously (IV) on days -4, -3, and -2 before each investigational T cell infusion. The Dose Assessment Committee (DAC) may recommend lymphodepletion de-escalation in the event of dose-limiting toxicity (DLT) attributable to Cy/Flu. Standard supportive care therapies (e.g., anti-emetics) are provided as-needed. [0235] T cells are delivered to the patient as a frozen product, which is thawed immediately prior to infusion. T cells are infused intravenously over approximately 15- 20 minutes via nonfiltered tubing at the specified dose. The infusion bag is gently mixed periodically during the infusion. [0236] For dose escalation, doses are initially 1 billion (1 x 109) (DL1) and 5 billion (5 x 109) (DL2) MAGE-A1-specific TCR transgenic CD3+ T cells for full dose infusion. All patients included in this study are adults and are thus expected to have similar body surface areas, permitting use of flat rather than weight-based dosing. [0237] In the Phase 1 portion of the trial, patients receive either 1 or 2 infusions of MagIC TCR-T starting at 1x109 (one billion) transgenic CD3+ TCR+ cells. At each
cell dose level, one patient receives cell therapy without prior lymphodepletion, and if no DLT is observed, the next three patients receive cell therapy with prior lymphodepletion. [0238] The first four patients receive 1 x 109 CD3+TCR+ cells (DL1) during their first infusion. Approximately 12 weeks following the first infusion, restaging, and evaluation of peripheral blood persistence of infused transgenic T cells is performed. Patients are provided a second infusion of transgenic T cells at the same dose (DL1) as the first infusion if there are no DLT and no evidence for progression by RECIST criteria. [0239] If all four of these patients complete the first infusion without DLT, the next four patients receive the next dose level of 5 x 109 CD3+TCR+ cells (DL2) in their first infusion. Approximately 12 weeks following the first infusion, restaging, and evaluation of peripheral blood persistence of infused transgenic T cells is performed. Patients are provided a second infusion of transgenic T cells at the same dose (DL2) as the first infusion if there are no DLT and no evidence for progression by RECIST criteria. [0240] If there is toxicity observed at DL1 that is attributable to cellular therapy following review by the DAC, the next four patients receive 5 x 108 CD3+TCR+ cells (DL-1), with the first patient receiving cellular therapy only and the next three patients receiving lymphodepletion followed by cellular therapy. The targeted recommended Phase 2 dose (RP2D) is 5 x 109 CD3+TCR+ cells with lymphodepletion; however, a lower dose may be selected by the DAC for the RP2D based on the totality of toxicity data. [0241] The Phase 1/2 portion of the trial builds on the RP2D with the addition of PD-1/PD-L1-axis therapy (atezolizumab 1200mg IV q3weeks). Atezolizumab is a fully humanized monoclonal antibody which targets human PD-L1 and inhibits its interaction with its receptors. Atezolizumab is administered as standard of care starting 24-72 hours after the T cell infusion. [0242] Of note, patients enrolled to this portion of the trial must have previously been offered or received a PD-1 axis inhibitor. If received, they must have either developed progression or still have detectable disease, and not have developed serious adverse events. If no DLT are observed with the addition of PD-1/PD-L1-axis therapy, up to 6 patients may be treated with the cell product:PD-1/PD-L1 axis combination. The
DAC reviews the data after every 2 patients in this portion of the study and, if PD- 1/PD-L1-axis attributable toxicity is observed, expansion of the number of patients at RP2D may continue without PD-1/PD-L1-axis therapy. [0243] At any dose level per the trial phases described above, if one patient experiences a DLT, three additional patients may be recruited at that dose level (7 patients total). As long as no additional DLT are observed (i.e., as long as 2 or more patients in the total of 7 patients do not experience a DLT), escalation may proceed to the next dose level. If 2 or more of the 7 patients experience a DLT, de-escalation (if possible) to the lower dose takes place [0244] Any patient experiencing treatment-related grade 3 or 4 toxicity (except for anticipated toxicity) immediately stops receiving T cell infusions and/or atezolizumab. The patient receives treatment as appropriate for their condition and continues to be followed for response/outcome. [0245] The various embodiments described above can be combined to provide further embodiments. All of the U.S. patents, U.S. patent application publications, U.S. patent applications, foreign patents, foreign patent applications and non-patent publications referred to in this specification and/or listed in the Application Data Sheet, including U.S. Provisional Patent Application No.63/088,389, filed on October 6, 2020, are incorporated herein by reference, in their entirety. Aspects of the embodiments can be modified, if necessary to employ concepts of the various patents, applications and publications to provide yet further embodiments. [0246] These and other changes can be made to the embodiments in light of the above- detailed description. In general, in the following claims, the terms used should not be construed to limit the claims to the specific embodiments disclosed in the specification and the claims, but should be construed to include all possible embodiments along with the full scope of equivalents to which such claims are entitled. Accordingly, the claims are not limited by the disclosure.
Claims
CLAIMS What is claimed is: 1. A method of treating a cancer or disease or disorder that is associated with MAGE-A1 expression in a subject, the method comprising administering to the subject a population of modified immune cells comprising a binding protein, the binding protein comprising: a) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively; b) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 30-32, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 27-29, respectively; c) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 36-38, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 33-35, respectively; d) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 42-44, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 39-41, respectively; or e) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 24-26, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 21-23, respectively, wherein the cancer or disease or disorder, or a cell thereof, expresses MAGE- A1, and wherein the subject is negative for or has been identified as negative for expression of HLA B*49:01.
2. The method of claim 1, wherein the method further comprises, prior to administering the population of modified immune cells, identifying the subject as being negative for expression of HLA B*49:01.
3. The method of claim 1 or claim 2, wherein the subject is positive for or has been identified as positive for expression of HLA A*02:01.
4. The method of any one of claims 1-3, wherein the method further comprises, prior to administering the population of modified immune cells, identifying the subject as positive for expression of HLA A*02:01.
5. The method of any one of claims 1-4, wherein the subject is lymphodepleted or has undergone a lymphodepletion procedure.
6. The method of any one of claims 1-5, wherein the method further comprises providing lymphodepletion to the subject, wherein, optionally, the lymphodepletion is provided prior to administering the population of modified immune cells, wherein, further optionally, the lymphodepletion is provided 4 days, 3 days, 2 days, and/or 1 day prior to administering the population of modified immune cells.
7. The method of claim 6, wherein providing lymphodepletion comprises administering a lymphodepleting chemotherapy to the subject.
8. The method of claim 7, wherein the lymphodepleting chemotherapy comprises cyclophosphamide, fludarabine, or a combination thereof, wherein, optionally, the lymphodepleting chemotherapy comprises 300 mg/m2 cyclophosphamide and/or 30 mg/m2 fludarabine.
9. The method of claim 7 or claim 8, wherein the lymphodepleting chemotherapy is administered intravenously to the subject.
10. The method of any one of claims 1-9, wherein the method comprises administering an immune checkpoint inhibitor (CPI) to the subject, wherein, optionally, a first dose of the CPI is administered after the population of modified immune cells is administered, such as within 24 to 72 hours after the population of modified immune cells is administered.
11. The method of any one of claims 1-10, wherein the method comprises administering a PD-1/PD-L1 axis inhibitor to the subject.
12. The method of claim 10 or claim 11, wherein the CPI or the PD-1/PD-L1 axis inhibitor comprises nivolumab, pembrolizumab, durvalumab, atezolizumab, avelumab, or any combination thereof.
13. The method of any one of claims 1-12, wherein the method comprises administering a PD-1 inhibitor and/or a PD-L1 inhibitor to the subject.
14. The method of claim 13, wherein the method comprises administering a PD-1 inhibitor to the subject.
15. The method of claim 14, wherein the CPI or the PD-1/PD-L1 axis inhibitor is selected from atezolizumab, nivolumab, durvalumab, and pembrolizumab.
16. The method of claim 15, wherein the CPI or the PD-1/PD-L1 axis inhibitor comprises atezolizumab.
17. The method of any one of claims 12-16, wherein the atezolizumab is administered to the subject every three weeks at 1200 mg per administration.
18. The method of any one of claims 13-17, wherein the method comprises administering a PD-L1 inhibitor and the PD-L1 inhibitor is avelumab.
19. The method of any one of claims 1-18, wherein the cancer is or comprises a solid tumor.
20. The method of any one of claims 1-19, wherein the cancer is triple negative breast cancer (TNBC), wherein, optionally, the TNBC is metastatic TNBC.
21. The method of any one of claims 1-19, wherein the cancer is non-small cell lung cancer (NSCLC), wherein, optionally, the NSCLC is metastatic NSCLC.
22. The method of any one of claim 1-19, wherein the cancer is urothelial cancer.
23. The method of claim 22, wherein the urothelial cancer is a metastatic urothelial cancer or an advanced urothelial cancer.
24. The method of any one of claims 1-23, wherein the population of modified immune cells comprises T cells, wherein, optionally, the T cells comprise CD8+ T cells, wherein, further optionally, the CD8+ T cells comprise CD62L+ T cells.
25. The method of any one of claims 1-24, wherein the population of modified immune cells comprises a CD4+ T cells, wherein, optionally, the CD4+ T cells are present in the population in combination with CD8+ T cells, wherein, further optionally, the CD4+ T cells and the CD8+ T cells are present in the population at a ratio of about 1:1.
26. The method of any one of claims 1-25, wherein the population of modified immune cells comprises NK cells, NK-T cells, macrophages, and/or microglia.
27. The method of any one of claims 1-26, wherein the population comprises modified immune cells that are autologous to the subject.
28. The method of any one of claims 1-26, wherein the population comprises modified immune cells that are allogeneic to the subject.
29. The method of any one of claims 1-28, comprising one or more administration of the population of modified immune cells, wherein the population of modified immune cells comprises between 1 × 108 and 5 × 1012 modified immune cells in each of the one or more administration.
30. The method of claim 29, wherein the population of modified immune cells comprises between 5 × 108 and 5 × 109 modified immune cells in each of the one or more administration.
31. The method of claim 29, wherein the population of modified immune cells comprises about 5 × 108 modified immune cells in each of the one or more administration.
32. The method of claim 29, wherein the population of modified immune cells comprises about 5 × 109 modified immune cells in each of the one or more administration.
33. The method of any one of claims 1-32, comprising (1) a first administration comprising the population of modified immune cells comprising about 1 x 109 modified immune cells, and (2) a second, subsequent administration of a population of the modified immune cells that comprises (i) about 1 x 1 x 109 modified immune cells, (ii) about 5 x 108 modified immune cells, or (iii) about 5 x 109 modified immune cells, wherein, optionally, the second, subsequent administration occurs about 6, about 7, about 8, about 9, about 10, about 11, or about 12 weeks after the first administration.
34. The method of any one of claims 1-33, wherein administering the population of modified immune cells and/or administering the CPI and/or administering
PD-1/PD-L1 axis inhibitor and/or administering the PD-1 inhibitor and/or administering the PD-L1 inhibitor is repeated at least once.
35. The method of any one of claims 1-34, wherein the binding protein is capable of specifically binding to a KVLEYVIKV (SEQ ID NO: 123): human leukocyte antigen (HLA)-A*02:01 complex.
36. The method of any one of claims 1-35, wherein the Vα domain has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and the Vβ domain has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively.
37. The method of claim 36, wherein the Vα domain has at least 95% identity to SEQ ID NO: 19, or has at least 95% identity to SEQ ID NO: 19 with the signal peptide removed.
38. The method of claim 37, wherein the Vα domain has at least 99% identity to SEQ ID NO: 19, or has at least 99% identity to SEQ ID NO: 19 with the signal peptide removed.
39. The method of claim 38, wherein the Vα domain comprises the sequence of SEQ ID NO: 19, or comprises the sequence of SEQ ID NO: 19 with the signal peptide removed.
40. The method of any one of claims 36-39, wherein the Vβ domain has at least 95% identity to SEQ ID NO: 17, or has at least 95% identity to SEQ ID NO: 17 with the signal peptide removed.
41. The method of claim 40, wherein the Vβ domain has at least 99% identity to SEQ ID NO: 17, or has at least 99% identity to SEQ ID NO: 17 with the signal peptide removed.
42. The method of claim 41, wherein the Vβ domain comprises the sequence of SEQ ID NO: 17, or comprises the sequence of SEQ ID NO: 17 with the signal peptide removed.
43. The method of any one of claims 1-42, wherein the binding protein comprises a TCR α chain constant (Cα) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 20, and wherein, optionally, the Vα domain and the Cα domain together comprise a TCR α chain.
44. The method of any one of claims 1-43, wherein the binding protein comprises a TCR β chain constant (Cβ) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 18, and wherein, optionally, the Vβ domain and the Cβ domain together comprise a TCR β chain.
45. The method of any one of claims 1-44, wherein the method comprises administering the population of modified immune cells to a plurality of subjects, wherein treating comprises inducing a partial response or a complete response in at least 5%, at least 10%, at least 15%, at least 20%, or at least 25% of the plurality of subjects.
46. The method of any one of claims 1-44, wherein treating comprises reducing the severity and/or the duration of a sign or a symptom of the cancer or disease or disorder in the subject.
47. The method of any one of claims 1-45, wherein treating comprises increasing a duration of progression-free survival of the subject or subjects.
48. The method of any one of claims 1-46, wherein treating comprises inducing a remission of the cancer in the subject or subjects.
49. A method of treating a cancer, comprising administering to a subject in
need thereof a population of modified cells comprising a binding protein, the binding protein comprising: a) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively; b) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 30-32, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 27-29, respectively; c) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 36-38, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 33-35, respectively; d) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 42-44, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 39-41, respectively; or e) a T cell receptor (TCR) α chain variable (Vα) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 24-26, respectively, and a TCR β chain variable (Vβ) domain having CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 21-23, respectively, wherein the cancer or a cell thereof expresses MAGE-A1, and wherein: i) the subject is lymphodepleted or has undergone a lymphodepletion procedure; ii) the method further comprises administering a PD-1 inhibitor and/or a PD-L1 inhibitor to the subject; and/or iii) the subject is negative for or has been identified as negative for expression of HLA B*49:01.
50. The method of claim 49, wherein the method further comprises, prior to
administering the population of modified immune cells, identifying the subject as being negative for expression of HLA B*49:01.
51. The method of claim 49 or claim 50, wherein the subject is positive for or has been identified as positive for expression of HLA A*02:01.
52. The method of any one of claims 49-51, wherein the method further comprises, prior to administering the population of modified immune cells, identifying the subject as positive for expression of HLA A*02:01.
53. The method of any one of claims 49-52, wherein the subject is lymphodepleted or has undergone a lymphodepletion procedure.
54. The method of any one of claims 49-53, wherein the method further comprises providing lymphodepletion to the subject, wherein, optionally, the lymphodepletion is provided prior to administering the population of modified immune cells, wherein, further optionally, the lymphodepletion is provided 4 days, 3 days, 2 days, and/or 1 day prior to administering the population of modified immune cells.
55. The method of claim 54, wherein providing lymphodepletion comprises administering a lymphodepleting chemotherapy to the subject.
56. The method of claim 55, wherein the lymphodepleting chemotherapy comprises cyclophosphamide, fludarabine, or a combination thereof, wherein, optionally, the lymphodepleting chemotherapy comprises 300 mg/m2 cyclophosphamide and/or 30 mg/m2 fludarabine.
57. The method of claim 55 or 56, wherein the lymphodepleting chemotherapy is administered intravenously to the subject.
58. The method of any one of claims 49-57, wherein the method comprises
administering an immune checkpoint inhibitor (CPI) to the subject, wherein, optionally, a first dose of the CPI is administered after the population of modified immune cells is administered, such as within 24 to 72 hours after the population of modified immune cells is administered.
59. The method of any one of claims 49-58, wherein the method comprises administering a PD-1/PD-L1 axis inhibitor to the subject.
60. The method of claim 58 or 59, wherein the CPI or the PD-1/PD-L1 axis inhibitor comprises nivolumab, pembrolizumab, durvalumab, atezolizumab, avelumab, or any combination thereof.
61. The method of any one of claims 49-60, wherein the method comprises administering a PD-1 inhibitor and/or a PD-L1 inhibitor to the subject.
62. The method of claim 61, wherein the method comprises administering a PD-1 inhibitor to the subject.
63. The method of claim 62, wherein the CPI or the PD-1/PD-L1 axis inhibitor is selected from atezolizumab, nivolumab, durvalumab, and pembrolizumab.
64. The method of claim 63, wherein the CPI or the PD-1/PD-L1 axis inhibitor comprises atezolizumab.
65. The method of any one of claims 60-64, wherein the atezolizumab is administered to the subject every three weeks at 1200 mg per administration.
66. The method of any one of claims 60-65, wherein the method comprises administering avelumab to the subject.
67. The method of any one of claims 49-66, wherein the cancer is or
comprises a solid tumor.
68. The method of any one of claims 49-67, wherein the cancer is triple negative breast cancer (TNBC), wherein, optionally, the TNBC is metastatic TNBC.
69. The method of any one of claims 49-67, wherein the cancer is non-small cell lung cancer (NSCLC), wherein, optionally, the NSCLC is metastatic NSCLC.
70. The method of any one of claims 49-67, wherein the cancer is urothelial cancer.
71. The method of claim 70, wherein the urothelial cancer is a metastatic urothelial cancer or an advanced urothelial cancer.
72. The method of any one of claims 49-71, wherein the population of modified immune cells comprises T cells, wherein, optionally, the T cells comprise CD8+ T cells, wherein, further optionally, the CD8+ T cells comprise CD62L+ T cells.
73. The method of any one of claims 49-72, wherein the population of modified immune cells comprises CD4+ T cells, wherein, optionally, the CD4+ T cells are present in the population in combination with CD8+ T cells, wherein, further optionally, the CD4+ T cells and the CD8+ T cells are present in the population at a ratio of about 1:1.
74. The method of any one of claims 49-73, wherein the population of modified immune cells comprises NK cells, NK-T cells, macrophages, and/or microglia.
75. The method of any one of claims 49-74, wherein the wherein the population comprises modified immune cells that are autologous to the subject.
76. The method of any one of claims 49-74, wherein the wherein the population comprises modified immune cells that are allogeneic to the subject.
77. The method of any one of claims 49-76, comprising one or more administration of the population of modified immune cells, wherein the population of modified immune cells comprises between 1 × 108 and 5 × 1012 modified immune cells in each of the one or more administration.
78. The method of claim 77, wherein the population of modified immune cells comprises between 5 × 108 and 5 × 109 modified immune cells in each of the one or more administration.
79. The method of claim 77, wherein the population of modified immune cells comprises about 5 × 108 modified immune cells in each of the one or more administration.
80. The method of claim 77, wherein the population of modified immune cells comprises about 5 × 109 modified immune cells in each of the one or more administration.
81. The method of any one of claims 49-80, comprising (1) a first administration comprising the population of modified immune cells comprising about 1 x 109 modified immune cells, and (2) a second, subsequent administration of a population of the modified immune cells that comprises (i) about 1 x 1 x 109 modified immune cells, (ii) about 5 x 108 modified immune cells, or (iii) about 5 x 109 modified immune cells, wherein, optionally, the second, subsequent administration occurs about 6, about 7, about 8, about 9, about 10, about 11, or about 12 weeks after the first administration.
82. The method of any one of claims 49-81, wherein administering the population of modified immune cells and/or administering the CPI and/or administering
PD-1/PD-L1 axis inhibitor and/or administering the PD-1 inhibitor and/or administering the PD-L1 inhibitor is repeated at least once.
83. The method of any one of claims 49-82, wherein the binding protein is capable of specifically binding to a KVLEYVIKV (SEQ ID NO: 123): human leukocyte antigen (HLA)-A*02:01 complex.
84. The method of any one of claims 49-83, wherein the Vα domain has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 48-50, respectively, and the Vβ domain has CDR1, CDR2, and CDR3 amino acid sequences according to SEQ ID NOS.: 45-47, respectively.
85. The method of claim 84, wherein the Vα domain has at least 95% identity to SEQ ID NO: 19, or has at least 95% identity to SEQ ID NO: 19 with the signal peptide removed.
86. The method of claim 85, wherein the Vα domain has at least 99% identity to SEQ ID NO: 19, or has at least 99% identity to SEQ ID NO: 19 with the signal peptide removed.
87. The method of claim 86, wherein the Vα domain comprises the sequence of SEQ ID NO: 19, or comprises the sequence of SEQ ID NO: 19 with the signal peptide removed.
88. The method of any one of claims 84-87, wherein the Vβ domain has at least 95% identity to SEQ ID NO: 17, or has at least 95% identity to SEQ ID NO: 17 with the signal peptide removed.
89. The method of claim 88, wherein the Vβ domain has at least 99% identity to SEQ ID NO: 17, or has at least 99% identity to SEQ ID NO: 17 with the signal peptide removed.
90. The method of claim 89, wherein the Vβ domain comprises the sequence of SEQ ID NO: 17, or comprises the sequence of SEQ ID NO: 17 with the signal peptide removed.
91. The method of any one of claims 49-90, wherein the binding protein comprises a TCR α chain constant (Cα) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 20, and wherein, optionally, the Vα domain and the Cα domain together comprise a TCR α chain.
92. The method of any one of claims 49-91, wherein the binding protein comprises a TCR β chain constant (Cβ) domain having at least 95%, at least 99%, or 100% identity to SEQ ID NO: 18, and wherein, optionally, the Vβ domain and the Cβ domain together comprise a TCR β chain.
93. The method of any one of claims 49-92, wherein the method comprises administering the population of modified immune cells to a plurality of subjects, wherein treating comprises inducing a partial response or a complete response in at least 5%, at least 10%, at least 15%, at least 20%, or at least 25% of the plurality of subjects.
94. The method of any one of claims 49-93, wherein treating comprises reducing the severity and/or the duration of a sign or a symptom of the cancer in the subject.
95. The method of any one of claims 49-94, wherein treating comprises increasing a duration of progression-free survival of the subject or subjects.
96. The method of any one of claims 49-95, wherein treating comprises inducing a remission of the cancer in the subject or subjects.
97. The method of any one of claims 1-96, wherein the binding protein is
encoded by a polynucleotide comprised in modified immune cells of the population, wherein the polynucleotide comprises a sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprises or consists of, the polynucleotide sequence set forth in any one of SEQ ID NOs.:151-153.
98. The method of any one of claims 1-96, wherein the binding protein is encoded by a polynucleotide comprised in modified immune cells of the population, wherein the polynucleotide comprises a sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprises or consists of, the polynucleotide sequence set forth in SEQ ID NO.:159.
99. The method of any one of claims 1-98, wherein modified immune cells of the population further comprise a polynucleotide encoding a CD8 co-receptor α chain, a CD8 co-receptor β chain, or both, wherein, optionally, the polynucleotide encoding a CD8 co-receptor α chain has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the polynucleotide sequence set forth in SEQ ID NO.:149 and the polynucleotide encoding a CD8 co- receptor β chain has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprises or consists of, the polynucleotide sequence set forth in SEQ ID NO.:150.
100. An isolated polynucleotide comprising any one or more of: (i) the polynucleotide sequence according to SEQ ID NO.:149; (ii) the polynucleotide sequence according to SEQ ID NO.:150; (iii) the polynucleotide sequence according to SEQ ID NO.:151; (iv) the polynucleotide sequence according to SEQ ID NO.:152; and
Ĩv) the polynucleotide sequence according to SEQ ID NO.:153.
101. An isolated polynucleotide comprising the polynucleotide sequence according to SEQ ID NO.:159.
102. A vector comprising the polynucleotide of claim 100 or 101.
103. The vector of claim 102, wherein the vector comprises a viral vector.
104. The vector of claim 103, wherein the viral vector is a lentiviral vector or a retroviral vector.
105. A host cell comprising the polynucleotide of claim 100 or 101 and/or the vector of any one of claims 102-104.
106. The host cell of claim 105, wherein the host cell comprises a human immune system cell.
107. The host cell of claim 106, wherein the human immune system cell comprises a T cell, a NK cell, a NK-T cell, a macrophage, and/or a microglia.
108. The host cell of claim 107, wherein the T cell comprises a CD8+ T cell, a CD4+ T cell, or both.
109. The host cell of claim 108, wherein the CD8+ T cell is CD62L+.
110. A composition comprising a plurality of host cells according to any one of claims 105-109.
111. A method comprising introducing the polynucleotide of claim 100 or 101 or the vector of any one of claims 102-104 to a host cell, wherein, optionally, the
introducing comprises DNA electroporation or viral transduction.
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