US20150132272A1 - Compositions and methods for diminishing an immune response - Google Patents

Compositions and methods for diminishing an immune response Download PDF

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US20150132272A1
US20150132272A1 US14/407,627 US201314407627A US2015132272A1 US 20150132272 A1 US20150132272 A1 US 20150132272A1 US 201314407627 A US201314407627 A US 201314407627A US 2015132272 A1 US2015132272 A1 US 2015132272A1
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cells
lag
cell
cd49b
disease
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Richard A. Flavell
Nicola Gagliani
Silvia Gregori
Samuel Huber
Chiara Francesca Magnani
Maria Grazia Roncarolo
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Fondazione Telethon
Ospedale San Raffaele SRL
Yale University
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Ospedale San Raffaele SRL
Yale University
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    • C12N5/0602—Vertebrate cells
    • C12N5/0634—Cells from the blood or the immune system
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    • A61K35/14—Blood; Artificial blood
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    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
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    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61K39/46—Cellular immunotherapy
    • A61K39/462—Cellular immunotherapy characterized by the effect or the function of the cells
    • A61K39/4621—Cellular immunotherapy characterized by the effect or the function of the cells immunosuppressive or immunotolerising
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
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    • A61K39/46433—Antigens related to auto-immune diseases; Preparations to induce self-tolerance
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    • A61K39/4643—Vertebrate antigens
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    • C12N2501/00—Active agents used in cell culture processes, e.g. differentation
    • C12N2501/20—Cytokines; Chemokines
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    • C12N2501/20—Cytokines; Chemokines
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    • C12N2501/50—Cell markers; Cell surface determinants
    • C12N2501/515—CD3, T-cell receptor complex

Definitions

  • Tr1 T regulatory type 1 cells were discovered in peripheral blood of severe combined immunodeficiency patients with long-term mixed chimerism after HLA-mismatched fetal liver hematopoietic stem cell transplant (HSCT) (Roncarolo et al., 1988, J Exp Med 167, 1523-1534; Bacchetta et al., 1994, J Exp Med 179, 493-502). Tr1 cells have strong immunosuppressive capacity in several immune-mediated diseases (Roncarolo and Battaglia, 2007, Nat Rev Immunol 7, 585-598; Roncarolo et al., 2011, Immunol Rev 241, 145-163; Pot et al., 2011, Semin Immunol 23, 202-208).
  • Tr1-mediated suppression The secretion of high levels of IL-10, and the killing of myeloid antigen-presenting cells (APCs) via Granzyme B are the main mechanisms of Tr1-mediated suppression (Groux et al., 1997, Nature 389, 737-742; Magnani et al., 2011 Eur J Immunol 41, 1652-1662). To date specific biomarkers for Tr1 cells have not been identified, limiting their study and clinical application. Tr1 cells are distinguished from T helper (T H )1, T H 2, and T H 17 cells by their unique cytokine profile and the regulatory function. Tr1 cells secrete higher levels of IL-10 than IL-4 and IL-17, the hallmark cytokines of T H 2 and T H 17 cells, respectively.
  • Tr1 cells also secrete low levels IL-2 and, depending on the local cytokine milieu, can produce variable levels of IFN- ⁇ , together, the key T H 1 cytokines (Roncarolo et al., 2011, Immunol Rev 241, 145-163).
  • FOXP3 is not a biomarker for Tr1 cells since its expression is low and transient upon activation.
  • IL-10-producing Tr1 cells express ICOS (Haringer et al., 2009, J Exp Med 206, 1009-1017) and PD-1 (Akdis et al., 2004, J Exp Med 199, 1567-1575), but these markers are not specific (Marchnard et al., 2007, Nat Immunol 8, 931-941).
  • CD49b the ⁇ 2 integrin subunit of the very-late-activation antigen (VLA)-2
  • VLA very-late-activation antigen
  • Lymphocyte activation gene-3 (LAG-3), a CD4 homolog that binds with high affinity to MHC class II molecules, is expressed by murine IL-10-producing CD4 + T cells (Okamura et al., 2009, Proc Natl Acad Sci USA 106, 13974-13979), but also by activated effector T cells (Workman and Vignali, 2005, J Immunol 174, 688-695; Bettini et al., 2011, J Immunol 187, 3193-3498; Bruniquel et al., 1998, Immunogenetics 48, 116-124; Lee et al., 2012, Nat Immunol 13, 991-999) and by FOXP3 + regulatory T cells (Tregs) (Camisaschi et al., 2010, J Immunol 184, 6545-6551).
  • Tr1 cells express CD226 (DNAM-1), which is involved in the specific killing of myeloid APCs (Magnani et al., 2011 Fur J Immunol 41, 1652-1662). Overall, none of the abovementioned markers has been confirmed to be selective for Tr1 cells.
  • Tr1 cell-based clinical approaches are still largely limited by the inability to transfer a pure population of these cells. Moreover, a high frequency of Tr1 cells has been correlated with a positive outcome after HSCT (Bacchetta et al., 1994, J Exp Med 179, 493-502; Serafini et al., 2009, Haematologica 94, 1415-1426), but the absence of suitable markers has made the clinical screening of this type of Tr1 cells impossible. Hence, the availability of specific biomarkers of Tr1 cells would facilitate the transition of therapies targeting Tr1 cells from bench to bedside.
  • compositions and methods to identify and purify Tr1 cells there is a need in the art for compositions and methods to identify and purify Tr1 cells.
  • the present invention satisfies this unmet need.
  • the invention described herein is based in part upon the discovery that T regulatory type 1 (Tr1) cells express particular cell surface markers that allow for their selection, enrichment, isolation, purification and administration.
  • the invention is a composition comprising an enriched population of T regulatory type 1 (Tr1) cells, wherein the Tr1 cells in the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3.
  • the Tr1 cells also express the cell surface marker CD226.
  • the Tr1 cells express the cell surface marker CD226 at a level greater than the level of CD226 expressed by a comparator cell population.
  • the comparator cell population is at least one selected from the group consisting of CD49b-LAG-3 ⁇ T cells and TH0 cells.
  • the Tr1 cells do not constitutively express high levels of Foxp3, as compared with the level of Foxp3 on a comparator cell selected from the group consisting of a CD25bright T cell and a Foxp3+ Treg cell.
  • greater than 90% of the cells in the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3.
  • greater than 95% of the cells in the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3.
  • Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3. In another embodiment, wherein greater than 99% of the cells in the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3.
  • the invention is a method of isolating an enriched population of Tr1 cells from a biological sample of a subject including the steps of obtaining a T cell-containing biological sample of a subject, and isolating cells from the biological sample of the subject that express the cell surface markers CD4, CD49b, and LAG-3.
  • the method includes the additional step of removing cells that express high levels of Foxp3 from the enriched population of Tr1 cells.
  • the method includes the additional step of isolating cells from the biological sample of the subject that express the cell surface marker CD226.
  • the cells express the cell surface marker CD226 at a level greater than the level of CD226 expressed by a comparator cell population.
  • the comparator cell population is at least one selected from the group consisting of CD49b-LAG-3 ⁇ T cells and TH0 cells. In some embodiments, greater than 90% of the cells in the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3. In some embodiments, greater than 95% of the cells in the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3. In some embodiments, greater than 98% of the cells in the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3. In some embodiments, greater than 99% of the cells in the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3.
  • the step of isolating cells from the biological sample of the subject employs the use of antibody that specifically binds to a cell surface marker.
  • the cell surface marker is at least one selected from the group consisting of CD4, CD49b, and LAG-3.
  • the step of cells from the biological sample of the subject employs the use of fluorescence-activated cell sorting (FACS).
  • FACS fluorescence-activated cell sorting
  • the biological sample is at least one selected from the group consisting of blood, bone marrow, cord blood, lymph, thymus, and spleen.
  • the invention is a method of treating or preventing a disease or disorder in a subject in need thereof, the method comprising administering to the subject an effective amount of Tr1 cells that express the cell surface markers CD4, and CD49b, and TAG-3.
  • the disease or disorder is at least one selected from the group consisting of an inflammatory disease and disorder, an autoimmune disease or disorder, and a disease or disorder associated with transplantation.
  • the disease or disorder is at least one selected from the group consisting of allergy, asthma, inflammatory bowel disease, autoimmune entheropathy, Addision's disease, alopecia areata, ankylosing spondylitis, autoimmune hepatitis, autoimmune parotitis, Crohn's disease, diabetes mellitus, dystrophic epidermolysis bullosa, epididymitis, glomerulonephritis, Graves' disease, Guillain-Barr syndrome, Hashimoto's disease, hemolytic anemia, systemic lupus erythematosus, multiple sclerosis, myasthenia gravis, pemphigus vulgaris, psoriasis, rheumatic fever, rheumatoid arthritis, sarcoidosis, scleroderma, Sjogren's syndrome, spondyloarthropathies, thyroiditis, vasculitis, vitiligo, myxedem
  • the invention is a method of inhibiting alloreactive T cells in a subject in need thereof, the method including the step of contacting the alloreactive T cells with an effective amount of Tr1 cells that express the cell surface markers CD4, and CD49b, and LAG-3.
  • the invention is a method of inhibiting a T cell mediated immune response in a subject in need thereof, the method including the step of contacting at least one T-lymphocyte with an effective amount of Tr1 cells that express the cell surface markers CD4, and CD49b, and LAG-3.
  • the inhibited T cell mediated immune response is an effector T cell activity and the at least one T-lymphocyte is a CD4+ T-lymphocyte.
  • the inhibited T cell mediated immune response is a cytotoxic T-lymphocyte (CTL) activity and the at least one T-lymphocyte is a cytotoxic T-lymphocyte.
  • CTL cytotoxic T-lymphocyte
  • the invention is a method of generating an immunomodulatory effect in a subject having an alloreactive response, inflammatory response, or autoimmune response, including the step of administering to said subject an effective amount of CD4+CD49+LAG-3+ Tr1 cells.
  • the invention is a method of preventing or treating an alloreactive response, inflammatory response, or autoimmune response in :subject, including the step of administering to said subject, prior to onset of the alloreactive response, inflammatory response, or autoimmune response, an effective amount of CD4+CD49+LAG-3+ Tr1 cells to prevent said response.
  • the invention is a composition comprising CD4+CD49+LAG-3+ Tr1 cells for use in treating or preventing a disease or disorder in a subject in need thereof, wherein the disease or disorder is at least one selected from the group consisting of an inflammatory disease and disorder, an autoimmune disease or disorder, and a disease or disorder associated with transplantation.
  • the invention is a composition comprising CD4+CD49+LAG-3+ Tr1 cells for use in treating or preventing a disease or disorder in a subject in need thereof, wherein the disease or disorder is at least one selected from the group consisting of allergy, asthma, inflammatory bowel disease, autoimmune entheropathy, Addision's disease, alopecia areata, ankylosing spondylitis, autoimmune hepatitis, autoimmune parotitis, Crohn's disease, diabetes mellitus, dystrophic epidermolysis bullosa, epididymitis, glomerulonephritis, Graves' disease, Guillain-Barr syndrome, Hashimoto's disease, hemolytic anemia, systemic lupus erythematosus, multiple sclerosis, myasthenia gravis, pemphigus vulgaris, psoriasis, rheumatic fever, rheumatoid arthritis, sarcoidosis, s
  • the invention is a composition comprising CD4+CD49+LAG-3+ Tr1 cells for use in inhibiting alloreactive cells in a subject in need thereof.
  • the invention is a composition comprising CD4+CD49+LAG-3+ Tr1 cells for use in inhibiting a T cell mediated immune response in a subject in need thereof.
  • the inhibited T cell mediated immune response is an effector T cell activity.
  • the inhibited T cell mediated immune response is a cytotoxic T-lymphocyte (CTL) activity.
  • CTL cytotoxic T-lymphocyte
  • the invention is a composition comprising CD4+CD49+LAG-3+ Tr1 cells for use in generating an immunomodulatory effect in a subject having an alloreactive response, inflammatory response, or autoimmune response, the method comprising administering to said subject an effective amount of CD4+CD49+LAG-3+ Tr1 cells.
  • the invention is a composition comprising CD4+CD49+LAG-3+ Tr1 cells for use in preventing or treating an alloreactive response, inflammatory response, or autoimmune response in a subject, said method comprising administering to said subject, prior to onset of the alloreactive response, inflammatory response, or autoimmune response, an effective amount of CD4+CD49+LAG-3+ Tr1 cells to prevent said response.
  • FIG. 1 depicts the results of experiments demonstrating the identification of CD49b, LAG-3 and CD226 by gene expression profile of human Tr1 cell clones.
  • HDs Healthy Donors
  • FIG. 1A Following data normalization by standard Robust Multichip Analysis (RMA) protocol and statistical analysis (t test welch without the False Discovery Rate, FDR, correction), Tr1 and T H 0 cell populations were compared at the three time points. Normalized expression values for profiles directly comparing Tr1 vs. T H 0 cell clones at t0, 6 h and 16 h are shown.
  • FIG. 1B-1C Two-dimensional heatmaps of genes differentially expressed (DEGs) encoding for membrane proteins in Tr1 as compared to T H 0 cell clones.
  • DEGs differentially expressed
  • FIG. 1D Heatmap of DEGs in Tr1, as compared to T H 0 cell clones, at the three time points (t0, t6 h, and t16 h) ( FIG. 1B ) and at 6 h and 16 h ( FIG. 1C ) are shown. Red genes are expressed at higher levels compared to the mean signal intensities in all experiments, whereas down-regulated genes are in green, and in black are signal intensities close to the mean expression level. The rows are scaled to have mean zero and standard deviation one. Gene Name, and Gene Symbol are indicated.
  • FIG. 2 depicts the results of experiments demonstrating that the co-expression of CD49b and LAG-3 identifies human Tr1 cells in vivo in healthy donors.
  • FIG. 2A Expression of CD49b and LAG-3 (gated on CD4 + CD45RA ⁇ T cells) in blood of HDs. Dot plots of 1 representative donor out of 23 donors are presented (left and middle panels); percentages of cells in each quadrant are indicated. Percentages of CD49b ⁇ LAG-3 ⁇ , CD49b ⁇ LAG-3 + , and CD49b ⁇ LAG-3 + T cells in each donor analysed are shown (right panel).
  • FIG. 2 depicts the results of experiments demonstrating that the co-expression of CD49b and LAG-3 identifies human Tr1 cells in vivo in healthy donors.
  • FIG. 2A Expression of CD49b and LAG-3 (gated on CD4 + CD45RA ⁇ T cells) in blood of HDs. Dot plots of 1 representative donor out of 23 donors are presented (left and middle panels); percentage
  • FIG. 3 depicts the results of experiments demonstrating that co-expression of CD49b and LAG-3 identifies Tr1 cells in anti-CD3 treated mice.
  • T cells were isolated from the small intestine of anti-CD3 treated mice.
  • FIG. 3A Expression of CD49b and LAG-3 measured on CD4 + TCR ⁇ + Foxp3 RFP ⁇ IL-10 eGFPbright or IL-10 eGFP ⁇ T cells (left panel). Percentages of cells in each quadrant are indicated.
  • FIG. 3B IL-10 eGFP frequency and MFI in the indicated T cell populations (gated on CD4 + TCR ⁇ + Foxp3 RFP ) isolated from the small intestine of anti-CD3 treated mice. Representative dot plots from 1 experiment out of 5 are shown (left panel). In each experiment 2 to 5 mice were pooled.
  • FIG. 3C Mean ⁇ SEM of IL-10 eGFP+ cell frequencies among the indicated T cell populations obtained in 5 independent experiments is shown. ** P ⁇ 0.005.
  • FIG. 3D Concentration levels of IL-10, IL-4, IFN- ⁇ and IL-17A in culture supernatants of the indicated FACS-sorted T cell populations (gated on CD4 + TCR ⁇ + Foxp3 RFP ⁇ ) from the small intestine of anti-CD3 treated mice (Mean ⁇ SEM) and the ratios of IL-10 vs.
  • IL-4, IFN- ⁇ and IL-17A in 1 representative experiment out of 3 are shown.
  • cells isolated from 5 mice were pooled before FACS-sorting.
  • Each experiment contains at least 3 replicates of the same sample for each population. * P ⁇ 0.05, ** P ⁇ 0.005, *** P ⁇ 0.0005. When not indicated differences were not statistically different.
  • FIG. 4 depicts the results of experiments demonstrating the in vitro and in vivo regulatory activity of murine CD4 + CD49b + LAG-3 + T cells.
  • FIG. 4B eT H 17 (CD4 + TCR ⁇ + Foxp3 RFP ⁇ IL-17A eGFP+ ) cells were isolated from the colon and mesenteric lymph nodes of RAG1 ⁇ / ⁇ mice injected with CD4 + CD45RB High T cells isolated from Foxp3 RFP IL-17A eGFP double reporter mice. The indicated T cell populations were isolated from the small intestine of anti-CD3-treated mice and injected i.p. in combination with eT H 17 (ratio 1:1) into RAG1 ⁇ / ⁇ mice.
  • FIG. 4C Representative endoscopic (upper panels) and histological (lower panels) pictures. Endoscopic ( FIG. 4D ), mass loss ( FIG. 4E ) colitis score were measured. Each dot represents 1 mouse. Lines indicate mean ⁇ SEM. ** P ⁇ 0.005, and *** P ⁇ 0.0005.
  • FIG. 5 depicts the results of experiments demonstrating that co-expression of CD49b and LAG-3 is specific for murine Tr1 cells.
  • FIG. 5A Expression of CD49b and LAG-3 measured on CD4 + TCR ⁇ + IL-4 eGFP+ (T H 2), CD4 + TCR ⁇ + Foxp3 RFP ⁇ IL-17A eGFP+ (T H 17), and CD4 + TCR ⁇ + Foxp3 RFP+ IL-17A eGFP ⁇ (Foxp3 + Tregs) cells isolated from the draining lymph nodes of IL-4 eGFP and Foxp3 RFP IL-17A eGFP mice 10 days after N. brasiliensis infection.
  • FIG. 5B Expression of CD49b and LAG-3 on CD4 + TCR ⁇ + Foxp3 RFP ⁇ IL-10 eGFPbright T cells isolated from the draining lymph nodes of Foxp3 RFP IL-10 eGFP mice infected with N. brasiliensis. Dot plots from 1 representative experiment out of 4 are shown. Percentages of cells in each quadrant are indicated.
  • FIG. 5D Frequencies of CD4 + IL-10 eGFP+ T cells and IL-10 eGFP MFI in the indicated T cell populations (gated on CD4 + TCR ⁇ + Foxp3 RFP ⁇ ) from the draining lymph nodes of Foxp3 RFP IL-10 eGFP mice 10 days after N. brasiliensis infection. Dot plots from 1 representative experiment out of 4 are shown. Percentages of cells in each quadrant are indicated.
  • 5F Suppression mediated by the indicated FACS-sorted T cell populations from the draining lymph nodes of infected Foxp3 RFP IL-10 eGFP mice.
  • One representative experiment out of 3 (left panel) and mean ⁇ SEM of the percentages of suppression obtained in 3 independent experiments (the right panel) are shown, * P ⁇ 0.05 and ** P ⁇ 0.005.
  • FIG. 6 depicts the results of experiments demonstrating that co-expression of CD49b and LAG-3 allows the selection of human Tr1 cells in vitro and the enumeration of Tr1 cells in vivo in tolerant subjects.
  • FIG. 6A Percentages of CD49b + LAG-3 ⁇ , CD49b ⁇ LAG-3 + , and CD49b + LAG-3 + cells in Tr1 (pTr1) and T H 0 cell lines polarized with artificial APC. ** P ⁇ 0.005. When not indicated differences were not statistically different.
  • FIG. 6A Percentages of CD49b + LAG-3 ⁇ , CD49b ⁇ LAG-3 + , and CD49b + LAG-3 + cells in Tr1 (pTr1) and T H 0 cell lines polarized with artificial APC. ** P ⁇ 0.005. When not indicated differences were not statistically different.
  • FIG. 6B Percentages of CD49b + LAG-3 ⁇ , CD49b ⁇ LAG-3 + , and CD49b + LAG-3 + cells in pTr1(DC-10) and T(mDC) cell lines polarized with DC. ** P ⁇ 0.005 and *** P ⁇ 0.0005. When not indicated differences were not statistically different.
  • FIG. 6D Suppression mediated by pTr1 cells and CD49b + LAG-3 + T cells sorted from pTr1 cells (CD49b + LAG-3 + pTr1).
  • FIG. 6E Expression of CD49b and LAG-3 (gated on CD4 + CD45RA ⁇ T cells) in subjects with complete chimerism (CC) and persistent mixed chimerism (PMC) after allogeneic HSCT. Representative dot plots from 1 out of 7 CC and 1 out 11 PMC are shown, percentages of cells in each quadrant are indicated.
  • FIG. 6E Expression of CD49b and LAG-3 (gated on CD4 + CD45RA ⁇ T cells) in subjects with complete chimerism (CC) and persistent mixed chimerism (PMC) after allogeneic HSCT. Representative dot plots from 1 out of 7 CC and 1 out 11 PMC are shown, percentages of cells in each quadrant are indicated.
  • FIG. 7 depicts the results of experiments demonstrating the validation and selection of genes encoding for CD49b, CD226, and LAG-3.
  • Tr1 and T H 0 cell clones isolated from peripheral blood of 2 Healthy Donors (HDs).
  • FIG. 7A Expression of IL-10, GZB, and PD1 determined by the DNA microarray is shown. * P 0.05 and ** P 0.005.
  • FIG. 7B Expression of CD-49b, CD226, and LAG-3 determined by the DNA microarray is shown. ** P 0.005. When not indicated differences were not statistically different.
  • FIG. 7C Expression of CD49b, CD226, and LAG3 in T H 0 and Tr1 cell clones. Following normalization to HPRT and B2M, relative mRNA amounts of T cell clones were adjusted to corresponding expression levels of a calibrator (pool of CD4 + T cell lines from 4 HDs). Numbers represent arbitrary units. ** P 0.005 and *** P 0.0005. When not indicated differences were not statistically different.
  • FIG. 7D IL-10-producing cells purified from pTr1 and T H 0 cell lines were stimulated for 6 h with immobilized anti-CD3 and soluble anti-CD28 mAbs. Expression of the indicated genes was investigated by RT-PCR. Following normalization to HPRT, relative mRNA amounts of T cells were adjusted to corresponding expression levels of a calibrator (pool of CD4 + T cell lines from 4 HDs). Numbers represent arbitrary units, * P 0.05.
  • FIG. 8 depicts the results of experiments demonstrating that CD49b + LAG-3 + T cells are CD25 low and do not express FOXP3.
  • FIG. 8A Expression of CD226 in the indicated T cell populations in peripheral blood of Healthy Donors (HDs). Mean fluorescent intensity (MFI) of CD226 expressed in the indicated T cell populations (gated on CD4 + CD45RA ⁇ T cells) (left panel) and mean ⁇ SEM of the CD226 MFI in the indicated T cell populations relative to the CD226 MFI of CD49b ⁇ LAG-3 ⁇ T cells obtained in 7 donors (right panel) are reported. ** P 0.005.
  • MFI Mean fluorescent intensity
  • FIG. 8C IL-10/IL-4 ratio in the indicated FACS-sorted T cell populations activated with immobilized anti-CD3 and soluble anti-CD28 mAbs for 72 h are shown. Three out of 9 donors tested.
  • FIG. 9 depicts the results of experiments demonstrating that co-expression of CD49b and LAG-3 identities murine Tr1 cells in anti-CD3 treated mice.
  • FIG. 9A Expression of CD226. MFI of CD226 expressed by the indicated T cell populations (gated on CD4 + TCR ⁇ + Foxp3 RFP ⁇ T cells) analyzed 4 h after the second anti-CD3 mAb injection (upper panel) and MFI of CD226 expressed in the indicated T cell populations (gated on CD4 + TCR ⁇ + Foxp3 RFP ⁇ T cells) relative to the expression of CD4 + CD49b ⁇ LAG-3 ⁇ T cells (lower panel) is shown. * P 0.05.
  • FIG. 9B Frequency of the indicated T cell populations (gated on CD4 + TCR ⁇ ⁇ Foxp3 RFP ⁇ T cells) at 4 h (52), 48 h (100) and 96 h (144) after the second anti-CD3 mAb injection.
  • FIG. 9C Expression of the Il10, Il4, Ifng, Il17a, Il2, Tnfa (normalized to Hprt) measured by RT-PCR in the indicated FACS-sorted T cell populations from the small intestine of anti-CD3 treated mice.
  • T H 1 CD4 + TCR ⁇ + IFN- ⁇ Katushka+
  • T H 17 CD4 + TCR ⁇ + IL-17A eGFP+
  • Foxp3 + Treg CD4 + TCR ⁇ + Foxp3 RFP+
  • FIG. 10 depicts the results of experiments demonstrating that CD4 + CD49b + LAG-3 + T cells express AhR. Expression of the indicated transcription factors (normalized to Hprt) measured by RT-PCR in the indicated FACS-sorted T cell populations from the small intestine of anti-CD3 treated mice.
  • T H 1 CD4 + TCR ⁇ + IFN- ⁇ Katushka+
  • T H 17 CD4 + TCR ⁇ + IL-17A eGFP+
  • Foxp3 + Tregs CD4 + TCR ⁇ + Foxp3 RFP+
  • Mean ⁇ SEM of 3 independent experiments is shown. * P 0.05, ** P 0.005, and *** P 0.0005 vs. CD4 + CD49b + LAG-3 + T cells. When not indicated differences were not statistically different.
  • FIG. 11 depicts the results of experiments demonstrating that CD4 + CD49b + LAG-3 + T cells suppress T cell responses in vitro in a dose-dependent manner.
  • Foxp3 RFP IL-10 eGFP double reporter mice were injected i.p. with anti-CD3 mAb at 0 and 48 h.
  • CD4 ⁇ TCR ⁇ + Foxp3 RFP ⁇ CD49b + LAG-3 + T cells were FACS-sorted from the small intestine of anti-CD3 treated mice 4h after the second injection and tested for their ability to suppress the proliferation of responder CD4 + T cells in vitro at the indicated cells ratios. Percentages of suppression are indicated.
  • One representative experiment out of 2 is shown.
  • FIG. 12 depicts the results of experiments demonstrating that the in vivo regulatory activity of murine CD4 + CD49b + LAG-3 + T cells is IL-10 dependent.
  • FIG. 12A eT H 17 (CD4+TCR ⁇ +Foxp3 RFP ⁇ IL-17A eGFP+ ) and Dominant Negative IL-10R-eT H 17 (DNR eTH17) cells were isolated from the colon and mesenteric lymph nodes of RAG1 ⁇ / ⁇ mice injected with CD4 + CD45RB High T cells isolated from either Foxp3 RFP IL-17A eGFP or Dominant Negative IL-10R ⁇ Foxp3 RFP IL-17A eGFP double reporter mice.
  • FIG. 13 depicts the results of experiments demonstrating the in vitro regulatory activity of murine CD4 + CD49b + LAG-3 + T cells isolated from the spleen of anti-CD3 treated mice.
  • FIG. 13A Expression of LAG-3 and CD49b measured on CD4 + TCR ⁇ + Foxp3 RFP ⁇ in cells isolated from the spleen of anti-CD3 treated mice (upper panel) and frequencies of CD4 + IL-10 eGFP+ T cells (gated on CD4+TCR ⁇ + Foxp3 RFP ⁇ ) in the indicated T cell populations (lower panel) are shown. Representative dot plots from 1 experiment out of 5 are shown. In each experiment cells isolated from 2 to 5 mice were pooled.
  • FIG. 13B Mean ⁇ SEM of IL-10 eGFP+ cell frequencies among the indicated T cell populations obtained in 3 independent experiments is shown. In each experiment 2 to 5 mice were pooled. *** P 0.0005.
  • FIG. 13C The indicated FACS-sorted T cell populations (gated on CD4 + TCR ⁇ + Foxp3 RFP ⁇ ) from the spleen of anti-CD3 treated mice were re-stimulated in vitro with anti-CD3 and anti-CD28 mAbs for cytokine production.
  • FIG. 13D The indicate FACS-sorted T cell populations (gated on CD4 + TCR ⁇ + Foxp3 RFP ⁇ ) from the spleen of anti-CD3 treated mice were tested in suppressive assay in the presence or absence of anti-IL-10R mAbs. Percentages of suppression mediated by the indicated T cell populations are reported. * P 0.05, ** P 0.005.
  • FIG. 14 depicts the results of experiments demonstrating that murine CD4 + CD49b + LAG-3 + T cells can be isolated from N. brasiliensis infected mice.
  • FIG. 14B Frequencies of Ly6G cells among CD45 + cells infiltrating the lung at different time points during the infection are shown (Mean ⁇ SEM).
  • FIG. 14C Expression of CD49b and LAG-3 measured on CD4 + TCR ⁇ + IL-4 eGFP ⁇ (T H 2); CD4 + TCR ⁇ + Foxp3 RFP ⁇ IL-17A eGFP+ (T H 17), CD4 ⁇ TCR ⁇ + Foxp3 RFP+ IL-17 eGFP ⁇ (Foxp3 + Tregs), and CD4 ⁇ TCR ⁇ + Foxp3 RFP ⁇ IL-10 eGFP+ (Tr1) cells isolated from the lungs of IL-4 eGFP , Foxp3 RFP IL-17 eGFP , Foxp3 RFP IL-10 eGFP reporter mice infected with N.
  • FIG. 14D Expression of CD49b and LAG-3 on CD4 TCR ⁇ + Foxp3 RFP ⁇ IL-17A eGFP+ (eT H 17) and on CD4 + TCR ⁇ + Foxp3 RFP ⁇ IFN- ⁇ Katushka+ (eT H 1) cells isolated from inflamed colon of RAG1 ⁇ / ⁇ mice transferred with CD4 + CD45RB High T cells isolated either from Foxp3 RFP IL-17A eGFP cells or Foxp3 RFP IFN- ⁇ Katushka double reporter mice. Percentages of cells in each quadrant are indicated. Representative dot plots from 1 experiment out of 3 are shown.
  • FIG. 14E Mean ⁇ SEM of frequencies of the indicated T cell populations obtained in 3-4 independent experiments is shown. In each experiment 2 to 5 mice were pooled. *** P 0.0005. When not indicated differences were not statistically different.
  • FIG. 15 depicts the results of experiments demonstrating that murine CD4 + CD49b + LAG-3 + T cells isolated from N. brasiliensis infected mice expressed high levels of IL-10 and AhR.
  • FIG. 15A Expression of Il10, Il4, Il13, Gata3, Ahr (relative to Hrpt) measured by RT-PCR in the indicated T cell populations isolated from IL-4 eGFP and Foxp3 RFP IL-10 eGFP reporter mice infected with N. brasiliensis.
  • FIG. 16 depicts the results of experiments demonstrating that in vitro differentiated Tr1 cells co-express CD49b and LAG-3.
  • FIG. 16A Expression of the indicated genes (normalized to Hprt) in in vitro differentiated T H 0, iTregs, T H 2, T H 17, T H 1, and Tr1 cells measured by RT-PCR. T H 0 cells were used as internal control and the expression of each gene in each T cell is normalized to T H 0 cells. Mean ⁇ SEM of triplicates are shown. *** P 0.0005. When not indicated differences were not statistically different.
  • FIG. 16A Expression of the indicated genes (normalized to Hprt) in in vitro differentiated T H 0, iTregs, T H 2, T H 17, T H 1, and Tr1 cells measured by RT-PCR.
  • T H 0 cells were used as internal control and the expression of each gene in each T cell is normalized to T H 0 cells. Mean ⁇ SEM of triplicates are shown. *** P 0.0005. When not indicated differences
  • FIG. 16B Expression of CD49b and LAG-3 in the indicated T cells differentiated in vitro after 4 days of culture is shown. Percentages of cells in each quadrant are indicated. Representative dot plots from 1 experiment out of 3 are shown.
  • FIG. 17 depicts the results of experiments demonstrating that CD49b and LAG-3 are expressed over time on in vitro generated Tr1 CD4 ⁇ T cells were isolated from the spleen of wild type mice and in vitro differentiated in Tr1, cells with IL-27 and TGF- ⁇ .
  • FIG. 17A After 5 days CD4 + CD49b + LAG-3 + IL-10 + Tr1 cells were FACS sorted and activated in the presence of anti-CD3 and anti-CD28 mAbs (upper panel) or anti-CD3, anti-CD28, TGF- ⁇ , IL-6 and IL-23 (lower panel).
  • FIG. 17B Sorted Tr1 cells were cultured for 4 days in the presence of anti-CD3, anti-CD28, TGF- ⁇ , IL-6 and IL-23. The expression of IL-10 among CD49b + LAG-3 + and CD49b ⁇ LAG-3 +/ ⁇ is reported.
  • FIG. 18 depicts the results of experiments demonstrating that upon transfer in vivo, CD49b and LAG-3 are expressed on in vitro generated Tr1 cells.
  • CD4 + T cells were isolated from the spleen of wild type mice and in vitro differentiated in Tr1 cells with IL-27 and TGF- ⁇ . After 5 days CD4 + CD49b + LAG-3 + IL-10 + Tr1 cells were FACS sorted transferred into RAG-1 ⁇ / ⁇ mice.
  • FIG. 18A Each mouse was injected i.p. with 10 5 Tr1 cells and treated as depicted in the cartoon.
  • FIG. 18B-C The frequency of the indicated populations was analyzed at the indicated time points by FACS.
  • FIG. 19 depicts the results of experiments demonstrating that co-expression of CD49b and LAG-3 allows the selection of human Tr1 cells in vitro.
  • FIG. 19A Expression of CD49b and LAG-3 in pTr1 and T H 0 cell lines. Dot plots from 1 representative donor out of 7 donors tested is presented. Percentages of cells in each quadrant are indicated.
  • FIG. 19B CD49b + LAG-3 + T cells were FACS-sorted from pTr1(DC-10) cells and were tested for their ability to suppress T cells activated with mDC (responder cells, filled histogram).
  • pTr1(DC-10) cells and CD49b + LAG-3 + T cells sorted from pTr1(DC-10) cells were used to suppress the proliferation of autologous CD4+ T cells activated with mDC.
  • T(mDC) cells were used as control. Percentages of suppression are indicated.
  • One representative experiment out of 3 is shown.
  • FIG. 20 depicts the results of experiments demonstrating the sensitivity and specificity of the co-expression of CD49b and LAG-3 on human CD4 + CD45RA ⁇ T cells.
  • Area under the curve (AUC) were 0.900 and 0.916, respectively.
  • a threshold of 3.64% for CD49b + LAG-3 + T cells gave 81.8% sensitivity and 91.3% specificity when PMC were compared to HDs.
  • a threshold of 2.765% for CD49b + LAG-3 + T cells gave 91% sensitivity and 87.5% specificity when PMC were compared to CC.
  • the present invention is based upon the discovery that T regulatory type 1 (Tr1) cells express particular cell surface markers that allow for their selection, enrichment, isolation, purification and administration.
  • Tr1 T regulatory type 1
  • the ability to use the particular markers described herein to select, enrich, isolate, purify and administer Tr1 cells allows for improved methods of Tr1 therapies for treating a wide variety of diseases and disorders.
  • the invention includes methods of administering Tr1 cells to a subject in need thereof, to treat or prevent a disease or disorder involving an undesired immune response.
  • exemplary diseases and disorders that are treatable or preventable with the Tr1 cell compositions and methods of the invention include, but are not limited to, inflammatory diseases and disorders, autoimmune diseases or disorders, and disorders associated with transplantation, such as transplant rejection and graft versus host disease.
  • the methods of the invention comprise isolating T cells which express one or more Tr1 selective markers.
  • the method comprises selecting T cells which express one or more Tr1 marker selected from the group consisting of CD49b, LAG-3, and CD226 (DNAM-1).
  • the method comprises selecting T cells that co-express CD49b and LAG-3.
  • the method comprises selecting T cells that co-express CD49b, LAG-3, and CD226.
  • the Tr1 cells do not constitutively express high levels of Foxp3, as compared with the level of Foxp3 on a comparator cell selected from the group consisting of a CD25bright T cell and a Foxp3+ Treg cell.
  • the Tr1 cells exhibit IL-10 dependent regulatory activity.
  • an element means one element or more than one element.
  • “About” as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ⁇ 20% or ⁇ 10%, more preferably ⁇ 5%, even more preferably ⁇ 1%, and still more preferably ⁇ 0.1% from the specified value, as such variations are appropriate to perform the disclosed methods.
  • to “alleviate” a disease means reducing the severity of one or more symptoms of the disease.
  • Allogeneic refers to a graft derived from a different animal of the same species.
  • “Alloantigen” is an antigen that differs from an antigen expressed by the recipient.
  • antibody refers to an immunoglobulin molecule, which is able to specifically bind to a specific epitope on an antigen.
  • Antibodies can be intact immunoglobulins derived from natural sources or from recombinant sources and can be immunoactive portions of intact immunoglobulins.
  • Antibodies are typically tetramers of immunoglobulin molecules.
  • the antibodies in the present invention may exist in a variety of forms including, for example, polyclonal antibodies, monoclonal antibodies, Fv, Fab and F(ab).sub.2, as well as single chain antibodies and humanized antibodies (Harlow et al., 1988; Houston et al., 1988; Bird et al., 1988).
  • antigen or “Ag” as used herein is defined as a molecule that provokes an immune response. This immune response may involve either antibody production, or the activation of specific immunologically-competent cells, or both.
  • any macromolecule including virtually all proteins or peptides, can serve as an antigen.
  • antigens can be derived from recombinant or genomic DNA. A skilled artisan will understand that any DNA, which comprises a nucleotide sequences or a partial nucleotide sequence encoding a protein that elicits an immune response therefore encodes an “antigen” as that term is used herein.
  • an antigen need not be encoded solely by a full length nucleotide sequence of a gene. It is readily apparent that the present invention includes, but is not limited to, the use of partial nucleotide sequences of more than one gene and that these nucleotide sequences are arranged in various combinations to elicit the desired immune response. Moreover, a skilled artisan will understand that an antigen need not be encoded by a “gene” at all. It is readily apparent that an antigen can be generated synthesized or can be derived from a biological sample. Such a biological sample can include, but is not limited to a tissue sample, a tumor sample, a cell or a biological fluid.
  • APC antigen presenting cell
  • DCs dendritic cells
  • DC dendritic cell
  • lymphoid or non-lymphoid tissues These cells are characterized by their distinctive morphology, high levels of surface MHC-class II expression.
  • DCs can be isolated from a number of tissue sources. DCs have a high capacity for sensitizing MHC-restricted T cells and are very effective at presenting antigens to T cells in situ.
  • the antigens may be self-antigens that are expressed during T cell development and tolerance, and foreign antigens that are present during normal immune processes.
  • autologous is meant to refer to any material derived from the same individual to which it is later to be re-introduced into the mammal.
  • “combination therapy” is meant that a first agent is administered in conjunction with another agent.
  • “In conjunction with” refers to administration of one treatment modality in addition to another treatment modality.
  • “in conjunction with” refers to administration of one treatment modality before, during, or after delivery of the other treatment modality to the individual. Such combinations are considered to be part of a single treatment regimen or regime.
  • the term “concurrent administration” means that the administration of the first therapy and that of a second therapy in a combination therapy overlap with each other.
  • a “disease” is a state of health of an animal wherein the animal cannot maintain homeostasis, and wherein if the disease is not ameliorated, then the animal's health continues to deteriorate.
  • a “disorder” in an animal is a state of health in which the animal is able to maintain homeostasis, but in which the animal's state of health is less favorable than it would be in the absence of the disorder. Left untreated, a disorder does not necessarily cause a further decrease in the animal's state of health.
  • DNA as used herein is defined as deoxyribonucleic acid.
  • Donor antigen refers to an antigen expressed by the donor tissue to be transplanted into the recipient.
  • Recipient antigen refers to an antigen expressed by the recipient.
  • an “effector cell” refers to a cell which mediates an immune response against an antigen.
  • An example of an effector cell includes, but is not limited to a T cell and a B cell.
  • immune response includes T cell mediated and/or B-cell mediated immune responses.
  • exemplary immune responses include T cell responses, e.g., cytokine production and cellular cytotoxicity, and B cell responses, e.g., antibody production.
  • immune response includes immune responses that are indirectly affected by T cell activation, e.g., antibody production (humoral responses) and activation of cytokine responsive cells, e.g., macrophages.
  • Immune cells involved in the immune response include lymphocytes, such as B cells and T cells (CD4+, CD8+, Th1 and Th2 cells); antigen presenting cells (e.g., professional antigen presenting cells such as dendritic cells, macrophages, B lymphocytes, Langerhans cells, and non-professional antigen presenting cells such as keratinocytes, endothelial cells, astrocytes, fibroblasts, oligodendrocytes); natural killer cells; myeloid cells, such as macrophages, eosinophils, mast cells, basophils, and granulocytes.
  • B cells and T cells CD4+, CD8+, Th1 and Th2 cells
  • antigen presenting cells e.g., professional antigen presenting cells such as dendritic cells, macrophages, B lymphocytes, Langerhans cells, and non-professional antigen presenting cells such as keratinocytes, endothelial cells, astrocytes,
  • MLC Multiple lymphocyte reaction
  • MLR mixed lymphocyte culture
  • MLC multiple lymphocytes
  • the cells are cultured together for a time and under suitable conditions to result in the stimulation of the lymphocytes, including for example, Tr1 cells.
  • Tr1 cells A frequent objective of an MLC is to provide allogeneic stimulation, such as may initiate proliferation of the Tr1 cells; but unless indicated, proliferation during the culture is not required. In the proper context, these terms may alternatively refer to a mixture of cells derived from such a culture.
  • endogenous refers to any material from or produced inside an organism, cell, tissue or system.
  • the immune response can be readily assessed by a plethora of art-recognized methods.
  • the skilled artisan would understand that the amount of the composition administered herein varies and can be readily determined based on a number of factors such as the disease or condition being treated, the age and health and physical condition of the mammal being treated, the severity of the disease, the particular compound being administered, and the like.
  • exogenous refers to any material introduced from or produced outside an organism, cell, tissue or system.
  • epitope is a portion of an antigen that can elicit an immune response, including B and/or T cell responses.
  • An antigen can have one or more epitopes. Most antigens have many epitopes; i.e., they are multivalent. In some examples, an epitope is roughly about 10 amino acids and/or sugars in size. Preferably, the epitope is about 4-18 amino acids, more preferably about 5-16 amino acids, and even more most preferably 6-14 amino acids, more preferably about 7-12, and most preferably about 8-10 amino acids.
  • the three-dimensional structure, rather than the specific linear sequence of the molecule is the main criterion of antigenic specificity and therefore distinguishes one epitope from another.
  • expression as used herein is defined as the transcription and/or translation of a nucleotide sequence.
  • expression vector refers to a vector containing a nucleic acid sequence coding for at least part of a gene product capable of being transcribed. In some cases, RNA molecules are then translated into a protein, polypeptide, or peptide. In other cases, these sequences are not translated, for example, in the production of antisense molecules, siRNA, ribozymes, and the like.
  • Expression vectors can contain a variety of control sequences, which refer to nucleic acid sequences necessary for the transcription and possibly translation of an operatively linked coding sequence in a particular host organism. In addition to control sequences that govern transcription and translation, vectors and expression vectors may contain nucleic acid sequences that serve other functions as well.
  • helper T cell as used herein is defined as an effector T cell whose primary function is to promote the activation and functions of other B and T lymphocytes and or macrophages. Many helper T cells are CD4 T-cells.
  • heterologous as used herein is defined as DNA or RNA sequences or proteins that are derived from the different species.
  • immunoglobulin or “Ig,” as used herein is defined as a class of proteins, which function as antibodies.
  • the five members included in this class of proteins are IgA, IgG, IgM, IgD, and IgE.
  • IgA is the primary antibody that is present in body secretions, such as saliva, tears, breast milk, gastrointestinal secretions and mucus secretions of the respiratory and genitourinary tracts.
  • IgG is the most common circulating antibody.
  • IgM is the main immunoglobulin produced in the primary immune response in most mammals. It is the most efficient immunoglobulin in agglutination, complement fixation, and other antibody responses, and is important in defense against bacteria and viruses.
  • IgD is the immunoglobulin that has no known antibody function, but may serve as an antigen receptor.
  • IgE is the immunoglobulin that mediates immediate hypersensitivity by causing release of mediators from mast cells and basophils upon exposure to allergen.
  • immunological is used herein to refer to increasing at least one parameter of an immune response.
  • immunosuppressive is used herein to refer to reducing at least one parameter of an immune response.
  • Tr1 differentiation refers to any event which results in a detectable increase in the phenotype and/or genotype characteristic of Tr1 cells.
  • a phenotype and/or genotype characteristic of Tr1 cells is the co-expression of CD49b and LAG-3.
  • Another phenotype and/or genotype characteristic of Tr1 cells is immunosuppression.
  • nucleotide sequence encoding an amino acid sequence includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence.
  • the phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some version contain an intron(s).
  • nucleotide as used herein is defined as a chain of nucleotides.
  • nucleic acids are polymers of nucleotides.
  • nucleic acids and polynucleotides as used herein are interchangeable.
  • nucleic acids are polynucleotides, which can be hydrolyzed into the monomeric “nucleotides.” The monomeric nucleotides can be hydrolyzed into nucleosides.
  • polynucleotides include, but are not limited to, all nucleic acid sequences which are obtained by any means available in the art, including, without limitation, recombinant means, i.e., the cloning of nucleic acid sequences from a recombinant library or a cell genome, using ordinary cloning technology and PCR, and the like, and by synthetic means.
  • recombinant means i.e., the cloning of nucleic acid sequences from a recombinant library or a cell genome, using ordinary cloning technology and PCR, and the like, and by synthetic means.
  • polypeptide as used herein is defined as a chain of amino acid residues, usually having a defined sequence. As used herein the term polypeptide is mutually inclusive of the terms “peptide” and “protein.”
  • self-antigen as used herein is defined as an antigen that is expressed by a host cell or tissue.
  • Self-antigens may be tumor antigens, but in certain embodiments, are expressed in both normal and tumor cells. A skilled artisan would readily understand that a self-antigen may be overexpressed in a cell.
  • “specifically binds” refers to the fact that a first compound binds preferentially with a second compound and does not bind in a significant amount to other compounds present in the sample.
  • substantially purified cell is a cell that is essentially free of other cell types.
  • a substantially purified cell also refers to a cell which has been separated from other cell types with which it is normally associated in its naturally occurring state.
  • a population of substantially purified cells refers to a homogenous population of cells. In other instances, this term refers simply to cells that have been separated from the cells with which they are naturally associated in their natural state.
  • the cells are cultured in vitro. In other embodiments, the cells are not cultured in vitro.
  • substantially separated from refers to the characteristic of a population of first substances being removed from the proximity of a population of second substances, wherein the population of first substances is not necessarily devoid of the second substance, and the population of second substances is not necessarily devoid of the first substance.
  • a population of first substances that is “substantially separated from” a population of second substances has a measurably lower content of second substances as compared to the non-separated mixture of first and second substances.
  • the first substance is a particular type of cell identifiable by is expression of cell surface markers.
  • a “population” is used herein to refer to a group of cells having a substantially similar phenotypic characteristic.
  • Transplant refers to a donor tissue, organ or cell, to be transplanted.
  • An example of a transplant may include but is not limited to skin cells or tissue, hematopoietic cells, bone marrow, and solid organs such as heart, pancreas, kidney, lung and liver.
  • T-cell as used herein is defined as a thymus-derived cell that participates in a variety of cell-mediated immune reactions.
  • B-cell as used herein is defined as a cell derived from the bone marrow and/or spleen. B cells can develop into plasma cells which produce antibodies.
  • a “therapeutically effective amount” is the amount of a therapeutic composition sufficient to provide a beneficial effect to a mammal to which the composition is administered.
  • treating refers to the reduction, alleviation or elimination, of at least one sign or symptom of a disease or disorder which is being treated, e.g. alleviation of immune dysfunction or avoidance of transplant rejection, relative to the symptoms prior to treatment.
  • treating or “treatment” includes both therapeutic and prophylactic treatments.
  • a “vector” is a composition of matter which comprises an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell.
  • vectors are known in the art including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses.
  • the term “vector” includes an autonomously replicating plasmid or a virus.
  • the term should also be construed to include non-plasmid and non-viral compounds which facilitate transfer of nucleic acid into cells, such as, for example, polylysine compounds, liposomes, and the like.
  • viral vectors include, but are not limited to, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, and the like.
  • Xenogeneic refers to a graft derived from an animal of a different species.
  • ranges throughout this disclosure, various aspects of the invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. This applies regardless of the breadth of the range.
  • Tr1 cells express specific cell surface markers that allow for their selection, enrichment, isolation, and purification. While certain methods of generating Tr1 cells are known in the art, there has, until now, yet to be a method of producing an enriched population of Tr1 cells for use in research and clinical therapeutic methods. The ability to use the specific markers described herein to select, enrich, isolate, and purify Tr1 cells allows for improved methods of Tr1 therapies for treating a wide variety of diseases and disorders. For example, it is demonstrated herein that Tr1 cells selected, enriched, isolated, and purified by the methods of the invention exhibit immunosuppressive activities both in vitro and in vivo.
  • Tr1 cells selected, enriched, isolated, and purified by the methods of the invention exhibit immunosuppressive activities both in vitro and in vivo.
  • the invention includes methods of administering Tr1 cells to a subject in need thereof, to treat or prevent a disease or disorder involving an undesired immune response.
  • exemplary diseases and disorders that are treatable or preventable with the Tr1 cell compositions and methods of the invention include, but are not limited to, inflammatory diseases and disorders, autoimmune diseases or disorders, and disorders associated with transplantation, such as transplant rejection and graft versus host disease.
  • autoimmune and inflammatory diseases and disorders treatable or preventable with the Tr1 cell compositions and methods of the invention include, but are not limited to, acute and chronic diseases and disorders such as allergy, asthma, inflammatory bowel disease, autoimmune entheropathy, Addision's disease, alopecia areata, ankylosing spondylitis, autoimmune hepatitis, autoimmune parotitis, Crohn's disease, diabetes mellitus, dystrophic epidermolysis bullosa, epididymitis, glomerulonephritis, Graves' disease, Guillain-Barr syndrome, Hashimoto's disease, hemolytic anemia, systemic lupus erythematosus, multiple sclerosis, myasthenia gravis, pemphigus vulgaris, psoriasis, rheumatic fever, rheumatoid arthritis, sarcoidosis, scleroderma, Sjogren's syndrome, spondyloarth
  • the Tr1 cell compositions and methods of the invention are used to treat subjects who have received a transplant, such as a hematopoietic cell transplant, a stein cell transplant, a bone marrow transplant, cord blood transplant, an organ and cell transplant, a blood transfusion, and the like.
  • a transplant such as a hematopoietic cell transplant, a stein cell transplant, a bone marrow transplant, cord blood transplant, an organ and cell transplant, a blood transfusion, and the like.
  • the methods of the invention comprise selecting T cells which express one or more Tr1 selective markers.
  • the method comprises selecting T cells which express one or more Tr1 marker selected from the group consisting of CD49b, LAG-3, and CD226 (DNAM-1).
  • the method comprises selecting T cells that co-express CD49b and LAG-3.
  • the method comprises selecting T cells that co-express CD49b, LAG-3, and CD226.
  • the method comprises selected T cells that express CD49b, LAG-3, and an elevated level of CD226, as compared with the level of CD226 on a comparator cell population, such as CD49b ⁇ LAG-3 ⁇ T cells, or T H 0 cells.
  • the Tr1 cells do not constitutively express high levels of Foxp3, as compared with the level of Foxp3 on a comparator cell selected from the group consisting of a CD25bright T cell and a Foxp3+ Treg cell.
  • the Tr1 cells exhibit IL-10 dependent regulatory activity.
  • the method comprises selecting T cells which express one or more Tr1 markers after the T cells are activated.
  • the invention comprises detecting the level of Tr1 cells in a subject by detecting the absolute number, or the relative amount, of T cells which express Tr1 markers in a sample obtained from the subject.
  • the method comprises detecting T cells which express one or more Tr1 markers selected from the group consisting of CD49b, LAG-3, and CD226.
  • the Tr1 cells do not constitutively express high levels of Foxp3, as compared with the level of Foxp3 on a comparator cell selected from the group consisting of a CD25bright T cell and a Foxp3+ Treg cell.
  • the Tr1 cells exhibit IL-10 dependent regulatory activity.
  • the method can be used to determine if the subject is tolerized or tolerant to a transplantation therapy, including, but not limited to a hematopoietic cell transplantation, such as a hematopoietic stem cell transplantation (HSCT).
  • a transplantation therapy including, but not limited to a hematopoietic cell transplantation, such as a hematopoietic stem cell transplantation (HSCT).
  • the method can be used to monitor the absolute number or relative amount of Tr1 cells in a subject over time, thereby allowing for the prediction of the risk of an adverse immune response.
  • the invention includes methods of and compositions for converting or differentiating non-regulatory T cells into Tr1 cells.
  • the method comprises converting non-regulatory T cells into Tr1 cells that express at least one marker selected from the group consisting of CD49b, LAG-3, and CD226 (DNAM-1).
  • the method comprises converting non-regulatory T cells into Tr1 cells that co-express CD49b and LAG-3.
  • the method comprises converting non-regulatory T cells into Tr1 cells that co-express CD49b, LAG-3, and CD226.
  • the method comprises converting non-regulatory T cells into Tr1 cells that do not constitutively express high levels of Foxp3, as compared with the level of Foxp3 on a comparator cell selected from the group consisting of a CD25bright T cell and a Foxp3+ Treg cell.
  • the method comprises converting non-regulatory T cells into Tr1 cells that exhibit IL-10 dependent regulatory activity.
  • the method of differentiating cells into Tr1 cells includes the step of obtaining non-regulatory T cells of a subject.
  • the non-regulatory T cells of the subject are CD4 + T cells.
  • the non-regulatory T cells the subject are CD4 + CD25 ⁇ T cells.
  • the subject is a mammal, such as a human or a mouse.
  • the method of differentiating cells into Tr1 cells includes the step of culturing the non-regulatory T cells of the subject in the presence of feeder cells.
  • the feeder cells are L cells.
  • the feeder cells are transfected with at least one of CD32, CD80, and CD58.
  • the feeder cells are transfected with at least one of hCD32, hCD80, and hCD58.
  • the method of differentiating cells into Tr1 cells includes the step of culturing the non-regulatory T cells of the subject in the presence of anti-CD3 mAb.
  • the method of differentiating cells into Tr1 cells includes the step of culturing the non-regulatory T cells of the subject in the presence of IL-2, such as rhIL-2.
  • the method of differentiating cells into Tr1 cells includes the step of culturing the non-regulatory T cells of the subject in the presence of IL-15, such as rhIL-15.
  • the differentiated Tr1 cells are polarized. In some embodiments, the differentiated Tr1 cells are polarized by culturing the differentiated Tr1 cells in the presence of at least one of IL-10, such as rhIL-10, and IFN ⁇ -2b, such as rhIFN ⁇ -2b.
  • IL-10 such as rhIL-10
  • IFN ⁇ -2b such as rhIFN ⁇ -2b.
  • the invention also provides methods and compositions for ex vivo conversion and expansion of Tr1 cells from non-Tr1 cells.
  • the expansion methods for Tr1 cells can include the use of a bead- or cell-based artificial antigen-presenting cell. However, any method in the art can be used to expand the Tr1.
  • the present invention provides a method of large-scale conversion and expansion of Tr1 that addresses the low numbers of natural Tr1 cells that can be isolated and expanded.
  • the methods and compositions of the invention are useful for therapeutic purposes, for example, in the prevention and treatment of immune-based disorders and in the prevention and treatment of allograft rejection.
  • Tr1 cells suppress immune responses and play an important role in immunotherapy against inflammation and autoimmune disease and contribute to transplantation tolerance. Some in vivo uses require expansion processes to generate sufficient numbers of Tr1 cells for in vivo therapeutic use.
  • the present invention provides a method of generating an enriched population of immunosuppressive Tr1 cells from the abundant CD4 + T cell population.
  • the majority of the cells of the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3.
  • greater than 90% the cells of the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3.
  • greater than 95% the cells of the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3.
  • greater than 98% the cells of the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3.
  • the cells of the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3. In some embodiments, greater than 99.5% the cells of the enriched population of Tr1 cells express the cell surface markers CD4, and CD49b, and LAG-3.
  • This method allows for the generation of Tr1 cells in sufficient numbers for in vivo infusions.
  • the method can be used both for generating Tr1 cells for research purposes as well as for clinical use by administration to a subject in need thereof.
  • the present invention provides a method of generating a population of immunosuppressive Tr1 cells from the abundant CD4 ⁇ T cell population. This method allows for the generation of Tr1 cells in sufficient numbers for in vivo infusions. The method can be used both for generating Tr1 cells for research purposes as well as for clinical use by administration to a subject in need thereof.
  • CD4 + T cells are obtained from blood (e.g., isolated from PBMC), bone marrow, cord blood, lymphoid tissue, thymus, spleen, or any tissues/organ sample of interest, including, but not limited the pancreas, eye, heart, liver, nerves, intestine, skin, muscle, and joints.
  • the cells bearing the desired markers can be isolated, for instance, by the use of labeled antibodies or ligands with FACS or magnetic particles/bead technologies as known to one of ordinary skill in the art. Accordingly, in some embodiments, the invention provides a method of generating an enriched population of immunosuppressive Tr1 cells which are substantially CD4 + CD49b + LAG-3 + by obtaining a biological sample that also comprises non-Tr1 cells, including, but not limited to, CD4 + , CD4 + CD25 ⁇ , CD4 + CD25 ⁇ CD45RA cells, and converting or differentiating the non-Tr1 cells into Tr1 cells.
  • a biological sample that also comprises non-Tr1 cells, including, but not limited to, CD4 + , CD4 + CD25 ⁇ , CD4 + CD25 ⁇ CD45RA cells, and converting or differentiating the non-Tr1 cells into Tr1 cells.
  • CD49b and/or LAG-3 may be combined with negative selection against cell surface makers specific to non-Tr1 cell types, including, by way of non-limiting examples, CD8, CD11b, CD16, CD19, CD36 and CD56.
  • T cells may conveniently be isolated from the blood e.g. from a peripheral blood mononuclear cell (PBMC) population isolated from blood, or from other blood-derived preparations such as leukopheresis products or from bone marrow, lymph, thymus, spleen or umbilical cord.
  • PBMC peripheral blood mononuclear cell
  • T cell populations may be derived from any appropriate source, including human or animal sources.
  • the invention includes converting or differentiating non-Tr1 cells, or mixed populations of Tr1 cells and non-Tr1 cells, in the presence of a bead- or cell-based artificial antigen-presenting cell system.
  • the cells can be expanded prior to, simultaneously with, and/or subsequent to Tr1 conversion.
  • the cells can be expanded using a bead- or cell-based artificial antigen-presenting cell system before the initial Tr1 conversion stage.
  • the cells can be expanded using a bead- or cell-based artificial antigen-presenting cell system after the initial Tr1 conversion stage but before the selective outgrowth stage that favors proliferation of Tr1s.
  • the cells can be expanded using a bead- or cell-based artificial antigen-presenting cell system after the outgrowth stage but before the imprinting state.
  • the cells can be expanded using a bead- or cell-based artificial antigen-presenting cell system after the imprinting state.
  • Special cell-sized beads e.g., magnetic iron-dextran beads
  • antibodies such as anti-CD3 and/or anti-CD28.
  • the use of anti-CD3 and/or anti-CD28 beads induced robust proliferation of cells.
  • a 3:1 bead:T cell ratio expands and preserves Tr1 function at a desirable level.
  • the ratios of antibodies to CD3 and/or CD28 can be adjusted for optimal results.
  • the beads can easily be removed by passing the cultured cells through a magnetic column. As an added advantage, the culture-expanded Tr1 retain potent functional suppressor activity.
  • the culture-expanded Tr1 of the present invention are capable of suppressing an MLR, with, by way of example, primary CD4 + cells or cultured CD4 + CD25 ⁇ cells as responding T cells.
  • the converted and expanded Tr1 cells inhibit the autologous proliferation of peripheral blood cells.
  • the converted and expanded Tr1 cells block or prevent GVHD, or inhibit or reverse the disease if already in progress.
  • the converted and expanded Tr1 cells are introduced into a different host; whereas in yet another embodiment, the Tr1 cells are established as a cell line for continuous therapeutic use.
  • the host is a human host and the culture-expanded Tr1 cells are human, although animals, including animal models for human disease states, are also included in this invention and therapeutic treatments of such animals are contemplated herein.
  • Tr1 cells can be expanded under appropriate conditions for growth of the Tr1 cells. Growth is allowed to progress for a time period selected according to the final number of T cells required and the rate of expansion of the cells. Passaging of the cells may be undertaken during this period. Such a time period is normally between 3 and 10 days but can be as long as 14 to 20 days or even longer providing the viability and continued proliferation of the T cells is maintained.
  • the invention includes methods of administering Tr1 cells to a subject in need thereof, for the treatment or prevention of a disease or disorder, such as an inflammatory disease or disorder, an autoimmune disease or disorder, or transplantation rejection.
  • a disease or disorder such as an inflammatory disease or disorder, an autoimmune disease or disorder, or transplantation rejection.
  • the ex vivo culture-converted and culture-expanded Tr1 cells can be introduced to the host subject or to another subject by any number of approaches. In some embodiments, they are injected intravenously.
  • the host subject may be treated with agents to promote the in vivo function and survival of the Tr1 cells.
  • the culture-expanded Tr1 may also be introduced in a variety of pharmaceutical formulations.
  • Tr1 cells may contain such normally employed additives as binders, fillers, carriers, preservatives, stabilizing agents, emulsifiers, and buffers. Suitable diluents and excipients are, for example, water, saline, and dextrose, as utilized in the methods described herein.
  • Suitable diluents and excipients are, for example, water, saline, and dextrose, as utilized in the methods described herein.
  • the cells can be converted directly after harvest or the cells can be stored (e.g., by freezing) prior to their expansion, or the cells can be stored (e.g., by freezing) after expansion and prior to their therapeutic administration.
  • the Tr1 cells of the invention can be administered alone, or the Tr1 cells of the invention can be administered in combination with a known immunosuppressive therapy.
  • the methods of the invention thus provide for achieving an immunosuppressive effect in a subject, i.e., a method of preventing or diminishing an immune response.
  • the disease or disorder typified by an aberrant immune response may be an inflammatory or autoimmune disease or disorder, such as allergy, asthma, inflammatory bowel disease, autoimmune entheropathy, Addision's disease, alopecia areata, ankylosing spondylitis, autoimmune hepatitis, autoimmune parotitis, Crohn's disease, diabetes mellitus, dystrophic epidermolysis bullosa, epididymitis, glomerulonephritis, Graves' disease, Guillain-Barr syndrome, Hashimoto's disease, hemolytic anemia, systemic lupus erythematosus, multiple sclerosis, myasthenia gravis, pemphigus vulgaris, psoriasis, rheumatic fever, rheumatoid arthritis,
  • the Tr1 cell compositions and methods of the invention are used to prevent or treat with an inflammatory disease or disorder, or an autoimmune disease or disorder, in a subject in need thereof.
  • inflammatory and autoimmune diseases and disorders preventable or treatable with the compositions and methods of the invention include but are not limited to, allergy, asthma, inflammatory bowel disease, autoimmune entheropathy, Addision's disease, alopecia areata, ankylosing spondylitis, autoimmune hepatitis, autoimmune parotitis, Crohn's disease, diabetes mellitus, dystrophic epidermolysis bullosa, epididymitis, glomerulonephritis, Graves' disease, Guillain-Barr syndrome, Hashimoto's disease, hemolytic anemia, systemic lupus erythematosus, multiple sclerosis, myasthenia gravis, pemphigus vulgaris, psoriasis, rheumatic fever,
  • the Tr1 cell compositions and methods of the invention are used to treat subjects who have received a transplant, such as a hematopoietic cell transplant, a stem cell transplant, a bone marrow transplant, an organ or cell transplant, a blood transfusion, and the like.
  • a transplant such as a hematopoietic cell transplant, a stem cell transplant, a bone marrow transplant, an organ or cell transplant, a blood transfusion, and the like.
  • Conditions in which immune suppression would be advantageous include conditions in which a normal or an activated immune response is disadvantageous to the mammal, e.g. allotransplantation of cells or tissues, to avoid rejection, or in fertility treatments in which inappropriate immune responses have been implicated in failure to conceive and miscarriage.
  • the use of such cells before, during, or after transplantation avoids extensive chronic graft versus host disease which may occur in post-transplant patients.
  • the cells may be converted immediately after harvest or stored (e.g., by freezing) prior to expansion or after
  • the methods of the present invention are particularly useful for humans, but may also be practiced on veterinary subjects.
  • An “individual,” “subject,” “patient” or “host” referred to herein is a vertebrate, preferably a mammal. More preferably, such individual is a human and the culture-expanded cells are human, although animals, including animal models for human disease states, are also included in this invention and therapeutic treatments of such animals are contemplated herein.
  • Such animal models can be used to test and adjust the compositions and methods of this invention, if desired. Certain models involve injecting in-bred animals with established cell populations. Also useful are chimeric animal models, described in U.S. Pat. Nos.
  • Non-human mammals include, but are not limited to, veterinary or farm animals, sport animals, and pets. Accordingly, as opposed to animal models, such animals may be undergoing selected therapeutic treatments.
  • the present invention encompasses a method of reducing and/or eliminating an immune response in a subject with an inflammatory or autoimmune disease or disorder by administering to the subject an amount of Tr1 cells effective to reduce or inhibit an immune response in the subject.
  • the Tr1 cells can be administered to the subject, before, during, or after onset of the disease or disorder.
  • Non-limiting examples of inflammatory and autoimmune diseases and disorders treatable with the compositions and methods of the invention include but are not limited to, allergy, asthma, inflammatory bowel disease, autoimmune entheropathy, Addision's disease, alopecia areata, ankylosing spondylitis, autoimmune hepatitis, autoimmune parotitis, Crohn's disease, diabetes mellitus, dystrophic epidermolysis bullosa, epididymitis, glomerulonephritis, Graves' disease, Guillain-Barr syndrome, Hashimoto's disease, hemolytic anemia, systemic lupus erythematosus, multiple sclerosis, myasthenia gravis, pemphigus vulgaris, psoriasis, rheumatic fever, rheumatoid arthritis, sarcoidosis, scleroderma, Sjogren's syndrome, spondyloarthropathies, thyroiditis, vascu
  • the present invention encompasses a method of reducing and/or eliminating an immune response to a transplant in a recipient by administering to the recipient of the transplant an amount of Tr1 cells effective to reduce or inhibit host rejection of the transplant.
  • the Tr1 cells can be administered to the transplant patient, before transplant, during transplant, or after the transplant has occurred. Without wishing to be bound to any particular theory, the Tr1 cells that are administered to the recipient of the transplant inhibit the activation and proliferation of the recipient's T cells, or induce tolerance.
  • the transplant can include a donor tissue, organ or cell.
  • An example of a transplant may include but is not limited to skin cells or tissue, hematopoietic cells, bone marrow, pancreatic islets, and solid organs such as heart, pancreas, kidney, lung and liver.
  • the method of the invention is a method of inhibiting a T cell mediated immune response, by contacting at least one T cell with an effective amount of CD4+CD49+LAG-3+ Tr1 cells.
  • the T cell mediated immune response inhibited by the methods of the invention is an effector T cell activity.
  • the T cell mediated immune response inhibited by the methods of the invention is cytotoxic T-lymphocyte (CTL) activity.
  • CTL cytotoxic T-lymphocyte
  • the method of the invention is a method of inhibiting at least one alloreactive T cell, by contacting the at least one alloreactive T cell with an effective amount of CD4+CD49+LAG-3+Tr1 cells.
  • the method of the invention is a method of generating an immunomodulatory effect in a subject having alloreactive response, inflammatory response, or autoimmune response, the method comprising administering to said subject an effective amount of CD4+CD49+LAG-3+ Tr1 cells.
  • the method of the invention is a method of preventing an alloreactive response, inflammatory response, or autoimmune response in a subject, said method comprising administering to the subject, prior to onset of the alloreactive response, inflammatory response, or autoimmune response, an effective amount of CD4+CD49+LAG-3+ Tr1 cells to prevent the response.
  • Tr1 cells can be obtained from any source, for example, from the tissue donor, the transplant recipient or an otherwise unrelated source (a different individual or species altogether).
  • the Tr1 cells may be autologous with respect to the T cells (obtained from the same host) or allogeneic with respect to the T cells.
  • the Tr1 cells may be autologous with respect to the transplant to which the T cells are responding to, or the Tr1 cells may be obtained from a mammal that is allogeneic with respect to both the source of the T cells and the source of the transplant to which the T cells are responding to.
  • the Tr1 cells may be xenogeneic to the T cells (obtained from an animal of a different species), for example mouse Tr1 cells may be used to suppress activation and proliferation of human T cells.
  • Tr1 cells can be administered by a route that is suitable under the circumstances.
  • Tr1 cells can be administered systemically, i.e., parenterally, by intravenous injection or can be targeted to a particular tissue or organ, such as bone marrow.
  • Tr1 can be administered via a subcutaneous implantation of cells or by injection of the cells into connective tissue, for example, muscle.
  • Tr1s cells can be suspended in an appropriate diluent, at a concentration of about 5 ⁇ 10 6 cells/ml.
  • Suitable excipients for injection solutions are those that are biologically and physiologically compatible with the Tr1s and with the recipient, such as buffered saline solution or other suitable excipients.
  • the composition for administration can be formulated, produced and stored according to standard methods complying with proper sterility and stability.
  • the dosage of the Tr1 cells varies within wide limits and may be adjusted to the subject's requirements in each particular case.
  • the number of cells used depends on the weight and condition of the recipient, the number and/or frequency of administrations, and other variables known to those of skill in the art.
  • between about 10 5 and about 10 13 Tr1 cells per 100 kg body weight can be administered to the subject. In some embodiments, between about 1.5 ⁇ 10 6 and about 1.5 ⁇ 10 12 cells are administered per 100 kg body weight. In some embodiments, between about 1 ⁇ 10 9 and about 5 ⁇ 10 11 cells are administered per 100 kg body weight. In some embodiments, between about 4 ⁇ 10 9 and about 2 ⁇ 10 11 cells are administered per 100 kg body weight. In some embodiments, between about 5 ⁇ 10 8 cells and about 1 ⁇ 10 10 cells are administered per 100 kg body weight.
  • Tr1 cells are administered to the recipient prior to, contemporaneously with, or after a transplant to reduce and/or eliminate host rejection of the transplant.
  • Tr1s can be used to condition a recipient's immune system to the transplant by administering Tr1s to the recipient, prior to, at the same time as, or following transplantation of the transplant, in an amount effective to reduce, inhibit or eliminate an immune response against the transplant by the recipient's T cells.
  • the Tr1 cells affect the T cells of the recipient such that the T cell response is reduced, inhibited or eliminated when presented with the transplant.
  • host rejection of the transplant may be avoided, or the severity thereof reduced, by administering Tr1 cells to the recipient, prior to, at the same time as, or following transplantation.
  • Tr1 cells are administered to the patient prior to, contemporaneously with, or after the onset of inflammatory or autoimmune diseases to prevent and/or re-establish tolerance.
  • Tr1s can be used to condition a patient's immune system by administering Tr1s to the patient, prior to, at the same time as, or following disease onset, in an amount effective to prevent, reduce, inhibit or eliminate an immune response by the patient's T cells.
  • the Tr1 cells affect the T cells of the patients such that the T cell response is prevented, reduced, inhibited or eliminated.
  • the present invention comprises a method of treating a patient who is undergoing an adverse immune response to a transplant by administering Tr1 cells to the patient in an amount effective to reduce, inhibit or eliminate the immune response to the transplant, also known as host rejection of the transplant.
  • the present invention includes a method of using Tr1 cells as a therapy to inhibit graft versus host disease or graft rejection following transplantation. Accordingly, the present invention encompasses a method of contacting a donor transplant, for example a donor tissue, organ or cell, with Tr1 cells prior to, during, or after transplantation of the transplant into a recipient.
  • the Tr1 cells serve to ameliorate, inhibit or reduce an adverse response by the donor transplant against the recipient.
  • Tr1 cells can be obtained from any source, for example, from the tissue donor, the transplant recipient or an otherwise unrelated source (a different individual or species altogether) for the use of eliminating or reducing an unwanted immune response by a transplant against a recipient of the transplant. Accordingly, Tr1 cells can be autologous, allogeneic or xenogeneic to the tissue donor, the transplant recipient or an otherwise unrelated source.
  • the transplant is exposed to Tr1 cells prior, at the same time, or after transplantation of the transplant into the recipient.
  • Tr1 cells are allogeneic to the recipient and may be derived from the donor or from a source other than the donor or recipient.
  • Tr1 cells autologous to the recipient may be used to suppress an immune response against the transplant.
  • the Tr1 cells may be xenogeneic to the recipient, for example mouse or rat Tr1 cells can be used to suppress an immune response in a human.
  • the donor transplant can be “preconditioned” or “pretreated” by contacting the transplant prior to transplantation into the recipient with Tr1 cells in order to reduce the immunogenicity of the transplant against the recipient, thereby reducing and/or preventing graft versus host disease or graft rejection.
  • the transplant can be contacted with cells or a tissue from the recipient prior to transplantation in order to activate T cells that may be associated with the transplant.
  • the cells or tissue may be removed from the transplant.
  • the treated transplant is then further contacted with Tr1 cells in order to reduce, inhibit or eliminate the activity of the T cells that were activated by the treatment of the cells or tissue from the recipient.
  • the Tr1 cells may be removed from the transplant prior to transplantation into the recipient. However, some Tr1 cells may adhere to the transplant, and therefore, may be introduced to the recipient with the transplant. In this situation, the Tr1 cells introduced into the recipient can suppress an immune response against the recipient caused by any cell associated with the transplant.
  • the treatment of the transplant with Tr1 cells prior to transplantation of the transplant into the recipient serves to reduce, inhibit or eliminate the activity of the activated T cells, thereby preventing restimulation, or inducing hyporesponsiveness of the T cells to subsequent antigenic stimulation from a tissue and/or cells from the recipient.
  • preconditioning or pretreatment of the transplant prior to transplantation may reduce or eliminate the graft versus host response.
  • hematopoietic stem cell transplantation In the context of umbilical cord blood, bone marrow or peripheral blood stem cell (hematopoietic stem cell) transplantation, attack of the host by the graft can be reduced, inhibited or eliminated by preconditioning the donor marrow by using the pretreatment methods disclosed herein in order to reduce the immunogenicity of the graft against the recipient.
  • a donor hematopoietic stem and progenitor cell source can be pretreated with Tr1 cells from any source, preferably with recipient Tr1 cells in vitro prior to the transplantation of the donor marrow into the recipient.
  • the donor marrow is first exposed to recipient tissue or cells and then treated with Tr1 cells.
  • the initial contact of the donor hematopoietic stein and progenitor cell source with recipient tissue or cells function to activate the T cells in the donor marrow.
  • Treatment of the donor marrow with the Tr1 cells induces hyporesponsiveness or prevents restimulation of T cells to subsequent antigenic stimulation, thereby reducing, inhibiting or eliminating an adverse effect induced by the donor marrow on the recipient.
  • a transplant recipient suffering from graft versus host disease or graft rejection may be treated by administering Tr1 cells to the recipient to reduce, inhibit or eliminate the graft versus host disease wherein the Tr1 cells are administered in an amount effective to reduce or eliminate graft versus host disease.
  • the recipient's Tr1 cells may be obtained from the recipient prior to the transplantation and may be stored and/or expanded in culture to provide a reserve of Tr1 cells in sufficient amounts for treating an ongoing graft versus host reaction.
  • Tr1 cells can be obtained from any source, for example, from the tissue donor, the transplant recipient or an otherwise unrelated source (a different individual or species altogether).
  • Tr1 cells of the present invention can be used in conjunction with the use of immunosuppressive drag therapy.
  • An advantage of using Tr1 cells in conjunction with immunosuppressive drugs is that by using the methods of the present invention to ameliorate the severity of the immune response in a subject, such as a transplant recipient, the amount of immunosuppressive drug therapy used and/or the frequency of administration of immunosuppressive drug therapy can be reduced.
  • a benefit of reducing the use of immunosuppressive drug therapy is the alleviation of general immune suppression and unwanted side effects associated with immunosuppressive drug therapy.
  • Tr1 cells of the present invention may be administered into a recipient repeatedly or as a “one-time” therapy for the prevention or treatment of a disease or disorder, such as an autoimmune disease or disorder, an inflammatory disease or disorder, or a disease or disorder associated with transplant, such as host rejection of donor tissue or graft versus host disease.
  • a disease or disorder such as an autoimmune disease or disorder, an inflammatory disease or disorder, or a disease or disorder associated with transplant, such as host rejection of donor tissue or graft versus host disease.
  • a one-time administration of Tr1 cells into the recipient of the transplant eliminates the need for chronic immunosuppressive drug therapy.
  • multiple administrations of Tr1 cells may also be employed.
  • the invention described herein also encompasses a method of preventing or treating transplant rejection and/or graft versus host disease by administering Tr1 cells in a prophylactic or therapeutically effective amount for the prevention, treatment or amelioration of host rejection of the transplant and/or graft versus host disease.
  • a therapeutic effective amount of Tr1 cells is an amount that inhibits or decreases the number of activated T cells, when compared with the number of activated T cells in the absence of the administration of Tr1 cells.
  • an effective amount of Tr1 cells is an amount that inhibits or decreases the number of activated T cells in the recipient of the transplant when compared with the number of activated T cells in the recipient prior to administration of the Tr1 cells.
  • An effective amount of Tr1 cells can be determined by comparing the number of activated T cells in a subject with a disease or disorder prior to the administration of Tr1 cells thereto, with the number of activated T cells present in the subject following the administration of Tr1 cells thereto. A decrease, or the absence of an increase, in the number of activated T cells in the subject, or in the transplant itself, that is associated with the administration of Tr1 cells thereto, indicates that the number of Tr1 cells administered is a therapeutic effective amount of Tr1s.
  • compositions can be further approximated through analogy to compounds known to exert the desired effect.
  • Tr1 T regulatory type 1
  • Tr1 cells are induced in the periphery and play a pivotal role in promoting and maintaining tolerance.
  • the absence of surface markers that uniquely identify Tr1 cells has limited their study and their clinical application.
  • the studies presented herein demonstrate that by gene expression profiling of human Tr1 cell clones, the surface markers CD49b and LAG-3, which are stably and selectively co-expressed on murine and human Tr1 cells, were identified. As described herein, the specificity of these markers is proven in two mouse models of inflammation and in peripheral blood of healthy volunteers.
  • the co-expression of CD49b and LAG-3 enables the isolation of highly suppressive human Tr1 cells from in vitro anergized cultures and, enables tracking Tr1 cells in the peripheral blood of tolerant subjects. As well as being an important finding for the biology of Tr1 cells, the identification of these markers makes Tr1 cells an even more attractive tool for therapeutic interventions.
  • C57BL/6 mice (B6), C57BL/6, RAG1 ⁇ / ⁇ mice, C57BL/6 CD45.1 + and C57BL/6 IL-4 eGFP (4get) mice were purchased from The Jackson Laboratories.
  • Dominant Negative IL-10R mice (Pacciani et al., 2010, J Allergy Clin Immunol 125, 727-736), Foxp3 reporter mice (Wan and Flavell, 2005, Proc Natl Acad Sci USA 102, 5126-5131), IL-17A eGFP reporter mice (Esplugues et al., 2011, Nature 475, 514-518), IL-10 eGFP reporter mice (Kamanaka et al., 2006, Immunity 25, 941-952) and IFN- ⁇ Katushka reporter mice were crossed and generated. Age- and sex-matched littermates between 8 and 12 weeks of age were used.
  • CD4 + T lymphocytes were purified from PBMC by negative selection using the untouched CD4 + T Cell Isolation Kit II (Miltenyi Biotech, Auburn, Calif.), according to manufacturer's instructions. Na ⁇ ve CD4 + CD45RO ⁇ T lymphocytes were purified from CD4 + T lymphocytes by CD45RO MicroBeads (Miltenyi Biotech). The proportion of CD4 + CD45RO ⁇ CD45RA + was consistently greater than 90%.
  • T cell clones were obtained from CD4 + cells by limiting dilution at 0.3 cells/well in the presence of a feeder cell mixture and soluble anti-CD3 mAbs (1 ⁇ g/mL, OKT3, Jansen-Cilag, Raritan, N.J., USA), in X-vivo 15 medium (BioWhittaker, Verviers, Belgium) supplemented with 5% pooled human AB serum (BioWhittaker), 100 U/mL penicillin/streptomycin (BioWhittaker). At day 3, IL-2 (40 U/mL; Chiron, Italia, Milan, Italy) was added.
  • T cell clones were re-stimulated every 14 days with feeder cell mixture and soluble anti-CD3 mAbs (1 ⁇ g/mL). Between stimulations with feeder cells, T cell clones were expanded with rhIL-2 (40 U/mL). Once the T cell clones had been established, rhIL-15 (5 ng/mL, R&D System, Minneapolis, Minn., USA) was added at every change of medium as a Tr1 cell growth factor (Serafini et al., 2009, Haematologica 94, 1415-1426; Bacchetta et al., 2002, Eur J Immunol 32, 2237-2245).
  • Tr1 cell clones were classified based on the cytokine production profile (Romagnani, 1994, Annual review of immunology 12, 227-257). Tr1 cell clones were defined when the ratio between IL-10 and IL-4 was higher than 8, as previously described (Serafini et al., 2009, Haematologica 94, 1415-1426; Bacchetta et al., 2002, Eur J Immunol 32, 2237-2245). All T cell clones were tested in a suppression assay to assess their regulatory activity.
  • Human Tr1 and T H 0 cell lines were differentiated using murine L cells transfected with hCD32, hCD80, and hCD58 and supplemented with anti-CD3 mAb (100 ng/ml; OKT3, Jansen-Cilag, Raritan, N.J., USA) (artificial APCs), as previously described (Levings et al., 2001, J Immunol 166, 5530-5539).
  • CD4 + CD45RO ⁇ T cells were activated by previously plated irradiated (7000 rad) L cells in X-vivo 15 medium (BioWhittaker) supplemented with 5% pooled human AB serum (BioWhittaker), 100 U/mL penicillin/streptomycin (BioWhittaker).
  • T H 0 cell lines were differentiated in the presence of rhIL-2 (100 U/ml; Chiron Italia) and rhIL-15 (1 ng/ml; R&D Systems, Minneapolis, Minn., USA), whereas Tr1 cells were polarized with rhIL-10 (100 U/ml; BD Pharmingen), and rhIFN ⁇ -2b (5 ng/ml; IntronA, Schering Plough Europe, mar, Belgium). After 7 days, cells were re-stimulated under identical conditions for additional 7 days. At the end of the 14 days of culture, T cells were washed, counted, and analyzed for cytokine production. IL-10-producing T cells were purified by IL-10-secretion assay (Miltenyi Biotech), according to the manufacturer's instruction.
  • DC-10 was differentiated as previously described (Gregori et al., 2010, Blood 116, 935-944). Briefly, CD14 ⁇ monocytes were isolated as the adherent fraction of PBMC following incubation for 1 hour in RPMI 1640 (Biowhittaker) supplemented with 10% FCS (Biowhittaker), 100 U/ml penicillin/streptomycin (Bristol-Myers Squibb), and 50 ⁇ M 2 mercaptoethanol (BioRad) (DC medium) at 37° C.
  • adherent monocytes were cultured in 10 ng/ml rhIL-4 (R&D Systems) and 100 ng/ml rhGM-CSF (R&D Systems) in DC medium in the absence (mDC) or presence (DC-10) of 10 ng/ml of rhIL-10 (BD, Bioscience) for 7 days. After 5 days, mDC differentiated in the absence of rhIL-10 were stimulated with 1 ⁇ g/ml of LPS (Sigma Aldrich) for additional 2 days.
  • mDC differentiated in the absence of rhIL-10 were stimulated with 1 ⁇ g/ml of LPS (Sigma Aldrich) for additional 2 days.
  • T(DC-10) cell lines 10 5 DC-10 were cultured with 10 6 allogeneic CD4 + CD45RO ⁇ T cells in 1 ml of X-vivo 15 medium (Biowhittaker), supplemented with 5% pooled AB human serum (Biowhittaker), and 100 U/ml penicillin/streptomycin (Bristol-Myers Squibb). After 6 or 7 days, rhIL-2 (20 U/ml; Chiron Italia) was added, and the cells were expanded for additional 7-8 days. Fourteen days after culture the T cells were collected, washed, and functionally analyzed. As control, T cells differentiated with mDC were used. T cells stimulated with DC-10 are indicated as pTr1(DC-10), and T cells stimulated with mDC as T(mDC).
  • Murine naive CD4 + T cells (CD4 + CD62L hi CD25 ⁇ ) from C57BL/6 mice were activated with plate-bound anti-CD3 (2-5 ⁇ g/ml; 145-2C11) and anti-CD28 (1-2 ⁇ g/ml; PV-1) mAbs.
  • T H 0 cells were differentiated in the presence of anti-IFN- ⁇ (10 ⁇ g/ml) and anti-IL-4 (10 ⁇ g/ml) mAbs.
  • Tr1 cells were differentiated in the presence of murine recombinant IL-27 (25 ng/ml) and TGF- ⁇ (2 ng/ml).
  • T H 2 cells were differentiated in the presence of murine recombinant IL-4 (10 ng/ml) and anti-IFN ⁇ (10 ⁇ g/ml).
  • T H 17 cells were differentiated in the presence of murine recombinant TGF- ⁇ (0.5 ng/ml), IL-6 (10 ng/ml), IL-23 (20 ng/ml), anti-IFN ⁇ (10 ⁇ g/ml), and anti-IL-4 (10 ⁇ g/ml).
  • T H 1 cells were differentiated in the presence of murine recombinant IL-12 (10 ng/ml), IL-2 (50 u/ml), and anti-IL-4 (10 ⁇ g/ml).
  • Tregs cells were differentiated in the presence of murine recombinant TGF- ⁇ (2 ng/ml), IL-2 (50 U/ml), anti-IFN ⁇ (10 ⁇ g/ml) and anti-IL-4 (10 ⁇ g/ml). After four days of culture, T cells were harvested and analyzed.
  • RT-PCR Assay on Demand quantitative Reverse Transcription Polymerase Chain Reaction
  • the High capacity cDNA synthesis Kit (Applied Biosystems) was used for synthesis of cDNA.
  • Real-time PCR analysis was performed using TaqMan® Fast Universal PCR Mater Mix and TaqMan® Gene Expression Assays (Applied Biosystems) on 7500 Fast Real-time PCR system machine (Applied Biosystems). Samples were run in duplicate or triplicate, and relative expression was determined by normalizing to hypoxanthine phosphoribosyltransferase 1 (hrpt) expression.
  • Human T cells (0.2-0.4 ⁇ 10 6 cells/ml) were stimulated with immobilized anti-CD3 mAb (10 ⁇ g/mL; Jansen-Cilag) and soluble anti-CD28 mAb (1 ⁇ g/mL, BD Pharmingen) complete medium.
  • immobilized anti-CD3 mAb 10 ⁇ g/mL; Jansen-Cilag
  • soluble anti-CD28 mAb 1 ⁇ g/mL, BD Pharmingen
  • culture supernatants were harvested after 24 (for IL-2 detection), or 72 hours (for other cytokines) of culture and levels of cytokines were determined by capture ELISA according to the manufacturer's instruction (BD Biosciences). The limits of detection were as follows: IFN- ⁇ : 60 pg/ml; IL-10: 19 pg/ml; IL-4: 9 pg/ml; IL-1.7: 30 pg/ml.
  • Murine T cells (0.3-0.5 ⁇ 10 6 cells/ml) were stimulated for 72 hours with immobilized anti-CD3 mAb (10 ⁇ g/mL; Jansen-Cilag) and soluble anti-CD28 mAb (10 ⁇ g/mL, BD Pharmingen) in complete medium.
  • Cytokines were quantified by Cytometric Bead Array (BD Bioscience) according to the manufacturer's instructions.
  • Murine T cells were stained with anti-CD4, anti-TCR ⁇ , anti-CD45.1, anti-CD45.2, anti-CD49b (clone HMa2), anti-LAG-3 (clone C9B7W), anti-CD226 mAbs all purchased from Biolegend.
  • the staining for CD49b and LAG-3 was performed at 37° C. for 15 minutes and at room temperature for additional 15 minutes.
  • CD4 + T cells were first enriched by magnetic-activated cell sorting beads (MACS; Miltenyi Biotec) and then further purified with a FACSVantage (BD). Purity of sorted cells was higher than 95%.
  • CD4 + T cells were stained with CFSE (Molecular Probes) and were activated with anti-CD3, anti-CD2, and anti-CD28-coated beads (Tr1 Inspector, Miltenyi Biotech, Bergisch Gladbach, Germany), at a ratio of three beads per cell. Suppressor cells were added at a ratio of 1:1. The percentage of divided responder T cells was calculated by gating on CD4 + cells, as described elsewhere (Lyons and Parish, 1994, J Immunol Methods 171, 131-137).
  • CD45.1 + CD4 + CD25 ⁇ T cells were labeled with Cell Trace Violet Cell Proliferation Kit (1 ⁇ M; Invitrogen) and were cultured in a 96-well flat bottom plates (20-50 ⁇ 10 3 cells/well) with or without CD4 + CD49b + LAG-3 + Foxp3 RFP ⁇ , CD4 + CD49b ⁇ LAG-3 + Foxp3 RFP ⁇ , CD4 + CD49b + LAG-3 ⁇ Foxp3 RFP ⁇ and CD4 + CD49b ⁇ LAG-3 ⁇ Foxp3 RFP ⁇ T cells FACS-sorted from the different organs. The ratio between responder and suppressor was 1:1, 2:1, 4:1, 8:1.
  • Irradiated APCs splenocytes MACS depleted for CD4 and CD8 T cells
  • feeder cells 4 ⁇ 10 5 cells/well.
  • Cells were stimulated with 1 ⁇ g/ml of CD3 mAb (2C11).
  • suppression was performed in the presence of anti-IL10R ⁇ (50 ug/ml; clone 1B1) mAb.
  • Cell Trace Violet dilution in CD45.1 ⁇ CD4 + (responder cells) was analyzed by flow cytometry. The percentage of divided responder T cells was calculated as described (Lyons and Parish, 1994, J Immunol Methods 171, 131-137).
  • Colonoscopy was performed in a blinded fashion for colitis scoring via the Coloview system (Karl Storz, Germany) (Huber et al., 2011, Immunity 34, 554-565; Becker et al., 2006, Nature 440, 303-307).
  • colitis scoring was based on granularity of mucosal surface, stool consistence, vascular pattern, translucency of the colon, and fibrin visible (0-3 points for each). For the histology, colons were fixed in Bouin's fixative solution and embedded in paraffin.
  • mice were injected with anti-CD3 (15 ⁇ g, 145-2C11) mAb, isotype antibody, or PBS i.p. two times every other day.
  • IEL intraepithelial lymphocytes
  • LPL lamina propria lymphocytes
  • the transcriptome of human Tr1 cell clones were compared to that of T H 0 cell clones either unstimulated or stimulated for 6 and 16 h.
  • the high expression of IL-10 (Groux et al., 1997, Nature 389, 737-742), GzB (Magnani et al., 2011 Eur J Immunol 41, 1652-1662; Serafini et al., 2009, Haematologica 94, 1415-1426; Grossman et al., 2004, Blood 104, 2840-2848) and PD-1 (Akdis et al., 2004, J Exp Med 199, 1567-1575) ( FIG. 7A ) known to be expressed in Tr1 cells, validated the microarray accuracy.
  • Tr1 and T H 0 cells were similar overall ( FIG. 1A ), but a small number of transcripts were uniquely expressed in Tr1 cell clones ( FIG. 1A ).
  • Seventeen differentially expressed genes (DEGs) were identified in Tr1 as compared to T H 0 cell clones at all time points, and 28 DEGs upon activation ( FIG. 1B , C).
  • DEGs differentially expressed genes
  • FIG. 1B C
  • the 17 DEGs identified in both unstimulated and stimulated Tr1 cells ITGA2 (CD49b) and CD226 were selected according to the p-values and Log2FC ( FIG. 7B ).
  • Tr1 cell clones expressed significantly higher levels of CD49b and LAG-3 than T H 0 cell clones ( FIG. 1D ). All T cell clones expressed CD226, but Tr1 cell clones showed higher mean fluorescence intensity (MFI) than T H 0 cell clones ( FIG. 1D ). Overall, CD49b, CD226, and LAG-3 were identified as putative markers for human Tr1 cells.
  • CD4 + T cells expressing CD49b, LAG-3 and CD226 were next investigated.
  • a small population (2.14 ⁇ 0.25%) of memory CD45RA ⁇ CD4 + T cells co-expressing CD49b, LAG-3 ( FIG. 2A ), and CD226 ( FIG. 8A ) was observed in the peripheral blood of healthy donors (HDs).
  • CD4 + CD49b + LAG-3 + T cells did not express CD25 at high levels and the expression of FOXP3 at mRNA and protein levels was significantly lower than in CD25 bright T cells ( FIG. 8B ).
  • CD4 ⁇ CD49b + LAG-3 + T cells FACS-sorted from peripheral blood of HDs, secreted significantly higher levels of IL-10 compared to CD4 + CD49b ⁇ LAG-3 + , CD4 + CD49b + LAG-3 ⁇ , and CD4 + CD49b ⁇ LAG-3 ⁇ T cells, as well as low amounts of IL-4 ( FIG. 2B ).
  • CD4 + CD49b + LAG-3 + T cells displayed a high IL-10/IL-4 ratio, which is one of the key parameters to distinguish Tr1 from T H 2 cells (Groux et al., 1997, Nature 389, 737-742; Magnani et al., 2011 Eur J Immunol 41, 1652-1662; Serafini et al., 2009, Haematologica 94, 1415-1426; Passerini et al., 2011, Eur J Immunol 41, 1120-1131), ( FIGS. 2B and 8C ). Moreover, CD4 /+ CD49b + LAG-3 + T cells secreted IFN- ⁇ , but not IL-17 ( FIG. 2B ).
  • CD4 + CD49b + LAG-3 + T cells suppressed the proliferation of CD4 + T cells in vitro, which is a key feature of Tr1 cells, at significantly higher levels than the other subsets analysed ( FIG. 2C ).
  • CD4 + CD49b + LAG-3 + T cells represent a subpopulation of CD4 + memory T cells that secrete high amounts of IL-10, do not express high levels of FOXP3, and exert suppressive activity in vitro.
  • IL-10-producing T cells and CD4 + CD49b + LAG-3 + T cells arc largely superimposable.
  • CD4 + CD49b + LAG-3 ⁇ T cells were FACS-sorted and characterized. Without in vitro re-stimulation, CD4 + CD49b + LAG-3 + T cells expressed high levels of Il10 and very low levels of Il4; expression of Ifng, Il2, Tnfa, and Il17a was significantly lower than in T H 1 and T H 17 cells, respectively ( FIG. 9C ).
  • CD4 + CD49b + LAG-3 + T cells secreted large amounts of IL-10, which were five to eight fold higher than IL-4, IL-17A, IL-2, and TNF- ⁇ ( FIGS. 3D and 9D ), and significant amounts of IFN- ⁇ ( FIG. 3D ).
  • CD4 ⁇ CD49b + LAG-3 + T cells expressed Tbx21, Rorc, and Foxp3 at significantly lower levels than T H 1, T H 17, and Foxp3 Treg cells, respectively. Gata3 levels were similar to those of T H 1 and Foxp3 + Treg cells ( FIG. 10 ).
  • CD4 + CD49b + LAG-3 + T cells expressed low levels of Egr2, a transcription factor critically involved in the development of IL-10-producing LAG-3 ⁇ Tr1 cells (Okamura et al., 2009, Proc Natl Acad Sci USA 106, 13974-13979).
  • Ahr a key transcription factor for IL-10 production by Tr1 cells (Apetoh et al., 2010, Nat Immunol 11, 854-861), was significantly higher in CD4 + CD49b + LAG-3 + T cells compared to the other cell subsets analyzed ( FIG. 10 ).
  • CD4 ⁇ Foxp3 RFP ⁇ CD49b + LAG-3 ⁇ T cells from the small intestine of anti-CD3 treated mice suppressed effector T cells in a dose-dependent manner in vitro ( FIGS. 4A and 11 ). Furthermore, using a T cell transfer IBD model (Huber et al., 2011, Immunity 34, 554-565) ( FIG. 4B ), it was demonstrated that CD4 + Foxp3 RFP ⁇ CD49b + LAG-3 + T cells suppressed the colitogenic eT H 17 cells in vivo ( FIGS. 4C , 4 D, and 4 E), in an IL-10 dependent manner ( FIG. 12 ).
  • Tr1 cells accumulated in the spleen of tolerant pancreatic islet transplanted mice (Battaglia et al., 2006, Diabetes 55, 40-49; Gagliani et al., 2011, PLoS One 6, e28434).
  • a population of CD4 + CD49b ⁇ LAG-3 + T cells was found that contained a high frequency of IL-10 eGFP+ cells ( FIGS. 13A and 13B ), displayed a Tr1-cytokine profile ( FIG. 13C ), and suppressed T-cell responses in vitro in a partially IL-10-dependent manner ( FIG. 13D ).
  • CD4 + CD49b + LAG-3 + T cells which accumulate in the intestine and spleen of anti-CD3 treated mice, produce large amounts of IL-10 and have strong suppressive activity in vitro and in vivo.
  • the co-expression of CD49b and LAG-3 on CD4 + T cells therefore identifies Tr1 cells not only in humans but also in mice.
  • IL-4 eGFP reporter mice were infected with N. brasiliensis to examine T H 2 cells.
  • the larvae enter the lung 2-3 days after subcutaneous injection causing haemorrhage and massive inflammation (Chen et al., 2012, Nat Med 18, 260-266) ( FIGS. 14A and 14B ).
  • the adult worms are expelled due to the development of T H 2-type responses Wills-Karp et al., 2012, J Exp Med 209, 607-622; Mohrs et al., 2001, Immunity 15, 303-311).
  • T H 2 CD4 + IL-4 eGFP+
  • LNs draining lymph nodes
  • FIGS. 14C and 14E did not co-express CD49b and LAG-3.
  • N. brasiliensis infection also induces a strong IL-17 response in the lungs, which contributes to inflammation and tissue damage (Chen et al., 2012, Nat Med 18, 260-266). It was observed that both T H 17 (CD4 + Foxp3 RFP ⁇ IL-17A GFP+ ) and Foxp3 + Tregs (CD4 + Foxp3 RFP ⁇ IL-17A GFP ⁇ ) cells were induced by N. brasiliensis. These cells accumulated in the draining LNs and in the lungs and did not co-express CD49b and LAG-3 ( FIGS. 5A , 5 C, 14 C, and 14 E).
  • T H 17 cells do not co-express CD49b and LAG-3, these cells were isolated from the colon of the previously described IBD model (Huber et al., 2011, Immunity 34, 554-565).
  • Colitogenic Foxp3 RFP ⁇ IL-17A eGFP+ cells which include T H 17 and a significant proportion of ‘T H 1+T H 17’ cells (Huber et al., 2011, Immunity 34, 554-565), and CD4 + Foxp3 RFP ⁇ IL-17A eGFP ⁇ T cells, which contained almost 30-40% of IFN- ⁇ -producing T H 1 cells, expressed CD49b, but not LAG-3 ( FIGS. 14D and 14E ).
  • colitogenic T H 1 (Foxp3 RFP ⁇ IFN- ⁇ Katushka+ ) cells did not co-express CD49b and LAG-3 ( FIGS. 14D and 14E ).
  • T H 1, T H 2, T H 17, and Foxp3 + Treg cells do not co-express CD49b and LAG-3 in vivo.
  • IL-10 production increases and contributes to the resolution of inflammation and consequently tissue damage (Chen et al., 2012, Nat Med 18, 260-266), suggesting the induction of Tr1 cells.
  • CD4 ⁇ Foxp3 ⁇ IL-10 + T cells were found in the draining LNs and lung of N. brasiliensis infected mice ( FIGS. 5B , 5 C, 14 C and 14 E).
  • the large majority of CD4 + Foxp3 RFP ⁇ IL-10 GFPbright T cells were CD49b LAG-3 + ( FIGS. 5B and FIG. 4C ).
  • CD4 + T cells co-expressing CD49b and LAG-3 contained the highest frequency of IL-10 eGFP+ cells with the highest MFI ( FIGS. 5D , and 5 E).
  • CD4 + CD49b + LAG-3 + T cells FACS-sorted from draining LNs of infected mice expressed high levels of Il10 mRNA ( FIG. 15S ) and suppressed the proliferation of effector CD4 + T cells in vitro ( FIG. 5F ).
  • CD4 + CD49b + LAG-3 + T cells expressed Il4, Il13, and Gata3 mRNA at levels comparable to those expressed by Foxp3 + Treg cells, but significantly lower than those in T H 2 cells ( FIG. 15A ).
  • Expression of Ahr CD4 + CD49b + LAG-3 ⁇ T cells was high but not selective.
  • Tr1 cells accumulated both in the lungs and draining LNs ( FIGS. 15B and 15C ), which is in line with the described role of IL-10 during resolution of infection (Chen et al., 2012, Nat Med 18, 260-266).
  • the frequency of Tr1 cells ( FIGS. 15B and 15C ) decreased in infected mice over time, but CD49b and LAG-3 were stably co-expressed by CD4 + Foxp3 RFP ⁇ IL-10 GFPbright cells ( FIGS. 15B and 15C ).
  • Tr1 cells differentiated in vitro with IL-27 and TGF- ⁇ were also confirmed in Tr1 cells differentiated in vitro with IL-27 and TGF- ⁇ .
  • CD4 + CD49b + LAG-3 + T cells from the small intestine of anti-CD3 treated mice expression of Erg2, Gata3, Rorct, Tbx21, and Foxp3 was low or undetectable in in vitro-induced Tr1 cells ( FIG. 16A ).
  • Tr1 cells that maintained IL-10 expression stably remained CD49b + LAG-3 + cells ( FIGS. 18A and 18B ).
  • CD49b and LAG-3 are selectively and stably co-expressed by IL-10-producing Tr1 cells, but not by T H 1, T H 2, T H 17, and Foxp3 + Treg cells.
  • Tr1 cells were polarized in the presence of IL-10.
  • the resulting cell population contains only a small proportion of Tr1 cells and is contaminated by a large fraction of non-IL-10-producing T cells (Bacchetta et al., 2010, Haematologica 95, 2134-2143).
  • CD49b + LAG-3 + T cells The frequency of CD49b + LAG-3 + T cells was assessed in a unique cohort of ⁇ -thalassemic subjects in which persistent mixed chimerism (PMC) of donor and host cells after allogeneic HSCT correlates with tolerance and the presence of circulating CD4 + IL-10 + cells (Serafini et al., 2009, Haematologica 94, 1415-1426). Circulating CD49b + LAG-3 + T cells were significantly higher in peripheral blood of subjects with PMC (Andreani et al., 2011, Chimerism 2, 21-22; Andreani et al., 2011, Haematologica 96, 128-133) compared to both HDs or subject with complete chimerism (CC) ( FIGS. 6E and 6F ).
  • PMC persistent mixed chimerism
  • CD49b and LAG-3 identifies human and murine Tr1 cells.
  • CD4 + CD49b + LAG-3 + T cells secrete large amounts of IL-10, display a high IL-10/IL-4 and IL-10/IL-17 ratio, express high levels of CD226, do not express high Foxp3 and possess strong IL-10-dependent regulatory activity.
  • Concomitant expression of CD49b and LAG-3 is specific for Tr1 cells, since T H 1, T H 2, T H 17 and Foxp3 + Treg cells do not co-express these markers.
  • Co-expression of CD49b and LAG-3 can be used to purify human Tr1 cells from in vitro Tr1-polarized cell cultures, and enables tracing of Tr1 cells in tolerant subjects.
  • CD49b has been previously described on effector memory CD4 + T cells (Kassiotis et al., 2006, J Immunol 177, 968-975), T H 17 cells (Boisvert et al., 2010, Eur J Immunol 40, 2710-2719) and IL-10-producing T cells (Charbonnier et al., 2006, J Immunol 177, 3806-3813; Rahmoun al., 2006, Int Arch Allergy Immunol 140, 139-149). The present data shows that CD49b is expressed on Tr1 cells, but also on T H 1, T H 2, T H 17 cells and Foxp3 + Treg cells.
  • LAG-3 is expressed on splenic T cells isolated from na ⁇ ve mice with regulatory function and correlates with IL-10 production (Okamura et al., 2009, Proc Natl Acad Sci USA 106, 13974-13979; Huang et al., 2004, Immunity 21, 503-513).
  • activated T cells also express LAG-3 (Workman and Vignali, 2005, J Immunol 174, 688-695; Bettini et al., 2011, J Immunol 187, 3493-3498; Bruniquel et al., 1998, Immunogenetics 48, 116-124; Lee et al., 2012, Nat Immunol 13, 991-999; Huard et al., 1997, Proc Natl Acad Sci USA 94, 5744-5749). It is shown that murine and human T cells expressing LAG-3 but not CD49b produce IL-4, low amounts of IL-10, are highly proliferative, and do not display significant suppressive activity in vitro.
  • CD49b alone or LAG-3 alone is not sufficient to select a highly enriched population of functional Tr1 cells, or to distinguish these cells from other T H or Treg cell subsets. It is demonstrated herein that the combination of CD49b and LAG-3 is required to identify and select murine and human Tr1 cells, which secrete high levels of IL-10 and have regulatory activity in vitro and in vivo. Both CD49b and LAG-3 are stably expressed on functional Tr1 cells. CD49b is expressed by Tr1 cells irrespectively of their activation, whereas LAG-3 is expressed on Tr1 cells when they produce IL-10 and display suppressor activity. Co-expression of CD49b and LAG-3 distinguishes Tr1 cells from T H 1, T H 2, T H 17 cells during helminth infection and IBD.
  • Tr1 cells in patients has been limited by their ability to produce IL-10 only upon in vitro re-stimulation (Bacchetta et al., 1994, J Exp Med 179, 493-502; Meiler et al., 2008, J Exp Med 205, 2887-2898; Petrich de Marquesini et al., 2010, Diabetologia 53, 1451-1460; Sanda et al., 2008, Clin Immunol 127, 138-143). Moreover, intracellular flow cytometric analysis of IL-10 expression is insensitive and is highly variable according to the type of stimuli.
  • T-cell cloning of circulating CD4 + T cells allows the enumeration of IL-10-producing Tr1 cells in tolerant subjects (Bacchetta et al., 1994, J Exp Med 179, 493-502; Gregori et al., 2011, Methods in molecular biology 677, 31-46).
  • IL-10-producing T cells and of Tr1 cell clones in peripheral blood of allogeneic HSCT transplanted subjects correlated with persistent mixed chimerism and tolerance (Bacchetta et al., 1994, J Exp Med 179, 493-502; Serafini et al., 2009, Haematologica 94, 1415-1426).
  • Tr1 cell-based therapies have become an attractive therapeutic option for inducing/restoring tolerance.
  • Several protocols to generate and expand Tr1 cells in vitro have been developed (Bacchetta et al., 2010, Haematologica 95, 2134-2143; Brun et al., 2009, Int Immunopharmacol 9, 609-613), and proof-of-principle clinical trials demonstrating safety and feasibility of Tr1 cell-infusion have been recently completed (Bacchetta et al., 2009, Blood, 45 (ASH Annual Meeting Abstract; Desreumaux et al., 2012, Gastroenterology 143, 1207-1217 e1201-1202).
  • the cell preparation consisting of antigen-specific IL-10-anergized T cells generated with recombinant IL-10 or DC-10 (Gregori et al., 2010, Blood 116, 935-944; Bacchetta and Gregori, 2010, Hematologica 95, 2134-2143) still contains a subset of contaminating non-Tr1 cells, which could potentially exacerbate the pathogenic clinical condition of patients.
  • the data presented herein show that CD49b and LAG-3 co-expression allows the isolation of Tr1 cells from in vitro Tr1-polarized populations and from antigen-specific IL-10-anergized T cells, thereby rendering their clinical use safer and broadening their clinical application.
  • Tr1 cells are conserved in mice and humans. These markers make it possible to study the in vivo localization of Tr1 cells in physiological conditions, as well as the role of Tr1 cells in subjects with immune-mediated diseases in which a defect in Tr1 cells has been proposed.

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US10260042B2 (en) 2019-04-16
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