WO1996013594A1 - Fragments d'anticorps a specificite tumorale, proteines de fusion, et leurs utilisations - Google Patents

Fragments d'anticorps a specificite tumorale, proteines de fusion, et leurs utilisations Download PDF

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WO1996013594A1
WO1996013594A1 PCT/US1995/013811 US9513811W WO9613594A1 WO 1996013594 A1 WO1996013594 A1 WO 1996013594A1 US 9513811 W US9513811 W US 9513811W WO 9613594 A1 WO9613594 A1 WO 9613594A1
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antibody
molecule
region
chain
fusion protein
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PCT/US1995/013811
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WO1996013594A8 (fr
Inventor
Ira Pastan
Itai Benhar
Eduardo A. Padlan
Sun-Hee Jung
Byungkook Lee
Mark Willingham
David Fitzgerald
Ulrich Brinkmann
Lee Pai
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The Government Of The United States Of America, Represented By The Secretary, Department Of Health And Human Services
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Priority claimed from US08/331,397 external-priority patent/US5981726A/en
Priority claimed from US08/331,396 external-priority patent/US5889157A/en
Priority claimed from US08/331,398 external-priority patent/US5608039A/en
Application filed by The Government Of The United States Of America, Represented By The Secretary, Department Of Health And Human Services filed Critical The Government Of The United States Of America, Represented By The Secretary, Department Of Health And Human Services
Priority to AU41355/96A priority Critical patent/AU717611B2/en
Priority to EP95939599A priority patent/EP0796334A1/fr
Priority to JP8514718A priority patent/JPH10508202A/ja
Publication of WO1996013594A1 publication Critical patent/WO1996013594A1/fr
Publication of WO1996013594A8 publication Critical patent/WO1996013594A8/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/34—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against blood group antigens
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K19/00—Hybrid peptides, i.e. peptides covalently bound to nucleic acids, or non-covalently bound protein-protein complexes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

Definitions

  • the subject invention relates to tumor-specific recombinant antibody fragments, to molecules incorporating such fragments such as immunotoxins and to uses thereof.
  • Exemplary embodiments of the invention include immunotoxins comprising Pseudomonas exotoxins fused to the Fv regions of monoclonal antibodies Bl, B3, and B5 which have tumor specificity and which may be used in the treatment of mammalian cancer.
  • Monoclonal antibodies Bl, B3, and B5 are recently isolated murine antibodies directed against a carbohydrate antigen in the Lewis ⁇ ( e ⁇ ) family (Pastan et al. Cancer Res. , 51: 3781-3787 (1991)).
  • the Le y antigens are found on the surface of many mucinous carcinomas of the colon, stomach, ovaries, breast, lung as well as some epidermal carcinomas. Because they react with only a limited number of normal tissues, these antibodies are ideal candidates for use in the treatment and diagnosis of cancer.
  • an antibody or its fragments may be used as the targeting moiety of an immunotoxin.
  • the targeting moiety typically replaces the cell binding domain of a cytotoxin molecule (e.g. domain I of Pseudomonas exotoxin (PE) or the B chain of Diphtheria toxin) and acts to specifically direct the cytotoxin to its target cell (as determined by the specificity of the targeting moiety).
  • PE Pseudomonas exotoxin
  • B chain of Diphtheria toxin a cytotoxin molecule
  • Immunotoxins were first made by chemically coupling antibodies to cytotoxic molecules.
  • monoclonal antibody B3 has been chemically coupled to at least two different forms of Pseudomonas exotoxin (PE) (U.S. Patent 4,545,985).
  • PE Pseudomonas exotoxin
  • One of these is the full length toxin (PE) and the other a truncated derivative (PE40) (Kondo et al., J. Biol. Chem. , 263: 9470-75 (1988) and Pai et al, supra).
  • the chemical modifications can change the antibody and affect its binding to the antigen.
  • the purified immunotoxins are a heterogeneous mixture of antibody-toxin molecules connected to each other via different positions on the antibody and the toxin.
  • Pseudomonas exotoxin for example, can be coupled either to the light- or heavy-chain of the antibody and to different positions on each of these chains.
  • chimeric immunotoxins have been made as recombinant, single chain, antibody-toxin fusion proteins. It has been shown that certain single chain antigen binding proteins made from the Fv portions of the heavy and light chain of antibodies held together by a polypeptide linker can have the same binding properties as their full length two chain counterparts (Bird et al., Science, 242: 423-26 (1988) and Huston et al., Proc. Natl. Acad. Sci. USA, 85: 5879-83 (1988)).
  • fusion proteins composed of single chain antibodies linked to toxins may retain the binding capacity of the single chain antibody as well as the activity of the toxin (Chaudhary et al, Nature, 339: 394-97 (1989); Batra et al, J. Biol. Chem. , 265: 15198-15202 (1990); Batra et al., Proc. Natl. Acad. Sci. USA 86: 8545-8549 (1989); Chaudhary et al , Proc. Natl Acad. Sci. USA 87: 1066-1070 (1990)).
  • Receptor proteins have often been used as immunotoxin targets because they are cell surface proteins which are often overexpressed in various cancers (Brinkmann and Pastan, Biochem. Biophys. Acta. , 1198: 27-45 (1994)) and thus provide cancer-specific targets.
  • single chain immunotoxins have been made consisting of the Fv domain of an antibody directed at the interleukin 2 receptor (Chaudhary et al, Nature, 339: 394-97 (1989) and Batra et al., J. Biol. Chem. 265: 15198-15202 (1990)) or at the transferrin receptor (Batra et al, Proc. Natl. Acad. Sci.
  • the present invention provides for recombinant single chain antibodies and fusion proteins such as immunotoxins employing these antibodies.
  • this invention provides for recombinantly produced antibodies comprising the variable light and heavy (Fv) chain regions of antibodies that have the binding specificity of monoclonal antibodies Bl, B3, or B5. These antibodies provide carcinoma-specific targeting moieties suitable for use in cytotoxic fusion proteins.
  • this invention provides for single-chain antibodies comprising an Fv region of both the variable light (V,_) and variable heavy (V H ) chain regions of an antibody where the single-chain antibody has the binding specificity of monoclonal antibodies Bl, B3, or B5. Particularly preferred are single chain antibodies Bl(Fv), B3(Fv), and B5(Fv).
  • this invention provides for single-chain antibodies comprising an Fv region in which position 95 of V H is mutated to a serine when it is not normally a serine.
  • the single-chain antibodies may be carbohydrate-binding antibodies and more preferably are Le ⁇ -binding antibodies having position 95 of V H mutated to a serine. In most cases position 95 will be a tyrosine before mutation.
  • a particularly preferred antibody is B5(Fv): Y95S, described herein.
  • This invention also provides for single-chain B3 antibodies having various mutations that increase the stability of the antibody.
  • Particularly preferred mutations are in the V L chain and include a mutation of methionine to leucine at position 4 (B3(Fv): M4L, or a mutation of serine to threonine at position 7 (B3(Fv): S7T) or the combination of both mutations (B3(Fv): M4L S7T).
  • this invention provides for chimeric single-chain antibodies comprising a variable heavy chain of a first antibody and a variable light chain of a second antibody where the first and second antibody are different antibodies and the heavy and light chain are recombinantly fused to form a single-chain antibody which specifically binds a Lewis ⁇ carbohydrate antigen.
  • the single-chain antibody has the binding specificity of monoclonal antibody Bl, B3, or B5.
  • the first antibody is Bl, B3, or B5.
  • the second antibody is Bl, B3, or B5.
  • Particularly preferred single chain antibodies include B5V H -B3V L and B3V hinder-B5V L .
  • This invention also provides for recombinantly produced humanized single- chain antibodies comprising humanized variable light and heavy (Fv) regions of antibodies that have the binding specificity of monoclonal antibody Bl, B3 or B5.
  • Fv variable light and heavy
  • These antibodies provide carcinoma-specific targeting moieties suitable for use in cytotoxic fusion proteins.
  • Particularly preferred are humanized single-chain Fv regions of Bl, B3 or B5.
  • the single-chain antibody is a humanized B3(Fv).
  • an antibody comprising a humanized variable heavy chain, more specifically a humanized variable heavy chain having the amino acid sequence designated HumB3V H in Figure 11.
  • Another preferred variant is an antibody comprising a humanized variable light chain, more specifically a humanized variable light chain having the amino acid sequence designated HumB3V L in Figure 11.
  • Yet another preferred humanized antibody is one comprising both a humanized variable light chain and a humanized variable heavy chain.
  • Still yet another preferred humanized antibody is one comprising a humanized variable heavy chain having the amino acid sequence designated HumB3V H in Figure 11 and a humanized variable light chain having the amino acid sequence designated HumB3V L in Figure 11 in which the serine at the position designated as 82b in Figure 11, is replaced with arginine.
  • variable heavy chain region and the variable light chain region may be joined by a linker.
  • linker is (Gly 4 Ser) 3 .
  • This invention also provides for single-chain fusion proteins incorporating any of the above-described single-chain antibodies.
  • the fusion proteins comprise the single chain antibodies recombinantly fused to an effector molecule.
  • the effector molecule may be a cytotoxin such as Pseudomonas exotoxin and more preferably is either PE38, PE40, PE38KDEL, or PE38REDL.
  • the Fv region is a Bl(Fv), a B3(Fv), or a B5(Fv) region or any of the modified Bl(Fv), B3(Fv) or B5(Fv) regions described above.
  • preferred fusion proteins include B3(Fv)-PE38, B3(Fv)-PE40, B3(Fv)-PE38KDEL, B3(Fv)-PE38REDL, Bl(Fv)-PE38, Bl(Fv)-PE40, Bl(Fv)-
  • the fusion proteins may also include a linker between the variable heavy (V H ) and the variable light (VJ chain regions of the Fv fragment.
  • One preferred linker is the peptide linker (Gly 4 Ser) 3 .
  • the fusion proteins may also include a connector between the Fv region and the effector molecule. A particular preferred connector is SGGPEGGS.
  • this invention provides for a pharmaceutical composition
  • a pharmaceutical composition comprising any of the single-chain fusion proteins described above in a concentration sufficient to inhibit tumor cell growth together with a pharmaceutically acceptable carrier.
  • This invention similarly provides for a method of killing or inhibiting the growth of cells bearing a Lewis ⁇ antigen in a patient.
  • the method includes the steps of administering to the patient a pharmaceutical composition comprising any of the fusion proteins described above in an amount sufficient to kill or inhibit the growth of the cells.
  • This invention also provides for a method of detecting the presence or absence of a cell bearing a Lewis ⁇ carbohydrate antigen in a patient, the method comprising the steps of removing a tissue or fluid sample from the patient, adding any of the single-chain antibodies described above to the sample, and detecting for the presence or absence of a binding complex between the antibody and the antigen.
  • this invention provides for a method of improving the binding affinity of antibodies that lack a serine at position 95 of the V H region.
  • the method includes the step of replacing the amino acid at position 95 of V H with a serine.
  • the antibody is preferably a carbohydrate-binding antibody and even more preferably an anti-Le ⁇ antibody.
  • the amino acid to be mutated at position 95 of V H will, in most cases, be a tyrosine.
  • Figure la illustrates the strategy for the cloning of the heavy and light chain Fv genes of monoclonal antibody B3 and the construction of expression vectors (e.g., plasmids) for the expression of B3(Fv) immunotoxins.
  • the cloning strategy is a variation of that previously described (Chaudhary et al., Proc. Natl Acad. Sci. USA, 87: 1066-70 (1990)).
  • the plasmid pVC38H which is used as a vector for construction of immunotoxins from heavy and light chain Fv regions, contains an Ndel and a Hindlll recognition sequence preceding the PE40 gene (Chaudhary et al, supra (1990)).
  • (*) indicates a PCR-generated mutation and was repaired by site directed mutagenesis
  • (L) indicates the region encoding the (Gly 4 Ser) 3 linker (Sequence ID No. 32) which serves to join heavy and light chains of the immunotoxin.
  • Figure lb shows the construction LMB7, the immunotoxin B3(Fv)-PE38 with a "C3 connector" between the Fv region and the PE38 cytotoxin.
  • Figure 2 shows the nucleotide sequences encoding the heavy and light chain Fv region of monoclonal antibody B3 (Sequence ID No. 33).
  • the heavy chain Fv coding region extends from position 30 to 383, the light chain Fv gene from position 433 to 767 and the linker from 384 to 432.
  • the deduced amino acid sequence is shown in plain letters (Sequence ID No. 34); below in italic letters is the protein sequence determined by Edman sequencing of the antibody.
  • the first amino acid encoded by the cloned heavy chain Fv gene is Asp instead of Glu due to the oligonucleotide primer used at position 456-465. This is the region where the PCR cloning artifact was repaired.
  • Figure 3(a) represents the toxicity of B3'(Fv)-PE38KDEL on different cell lines. Cytotoxicity assays were performed as described in Example 7. (b): Inhibition of the cytotoxicity of B3(Fv)-PE38KDEL by monoclonal antibody B3. Competition by monoclonal antibody B3 was performed on A431 cells as described in Example 7. Figure 4 shows the ADP-ribosylation and cytotoxic activities of Bl(Fv)-
  • B5(Fv)-PE38 Antigen binding was estimated by competition of [ 12S I]-B1 IgG (A) or [ 12S I]-B3 IgG (B) binding to A431 cells at 4°C.
  • FIG 6 shows stability data for Bl(Fv)-PE38, B3(Fv)-PE38, and B5(Fv)-PE38.
  • the immunotoxins were diluted in PBS to 0.1 mg/ml and incubated at 37°C for 4 hours.
  • A The molecular forms of the immunotoxins were than analyzed by size exclusion chromatography at 4°C. The monomer peak elutes at 18-20 ml, while the aggregates elute at 11-13 ml. Chromatograms of the proteins prior to incubation at 37°C are shown by broken lines. The proteins after the incubation at 37°C are shown by solid lines.
  • B Cytotoxic activity of immunotoxins before (open symbols) or after (solid symbols) incubation at 37°C. Other details are as in Figure 5(B).
  • Figure 7 shows blood levels of B3(Fv)-PE38KDEL in mice.
  • Balb/c mice were injected intravenously with 10 ⁇ g of B3(Fv)-PE38KDEL and immunotoxin levels were measured at different time periods. Bars indicate the standard deviation.
  • Figure 8 illustrates the effect of B3(Fv)-PE38KDEL on the growth of A431 tumors in nude mice. Mice were injected with 3 x 10 6 A431 cells on day 0 and treated beginning on day 4 with intravenous injections every 12 hrs x 6.
  • B3(Fv)-PE38KDEL (-0-) 0.5 ⁇ g B3(Fv)-PE38KDEL; D: treatment began on day 7 with intravenous injections every 12 hrs x 8. (O) untreated, ( ⁇ ) 5 ⁇ g
  • Figure 9 illustrates the construction of plasmids for expression of B3-B5 chimeric Fv single chain immunotoxins.
  • L indicates the (Gly 4 Ser) 3 linker which connects the V H to the V L in the single-chain Fv configuration.
  • Figure 10 shows the cytotoxic activity of immunotoxins B3(Fv)-PE38,
  • A431 epidermoid carcinoma cells were incubated with aliquots of the immunotoxins which were diluted in PBS +0.2% BSA following incubation at 37°C. 3 H-Leucine was added 20 hours after addition of immunotoxins.
  • Figure 11 illustrates the humanization of B3(Fv). Alignment of the amino acid sequences of (A) B3 V H , 56P1'CL V H and HUMB3V H (Sequence ID Nos. 45, 46 and 47) (B) B3 V L , GM607 V L , and HUMB3V L (Sequence ID Nos. 48, 49 and 50). B3 amino acids that differ from the residues of the corresponding position of the human antibody are indicated by vertical lines above the sequence. Inter-domain residues that were not humanized are indicated by asterisks below the sequence. Heavy chain residue 82b is underlined. Numbers above the sequence indicate the positions of residues that were humanized.
  • Figure 12 illustrates the plasmids utilized for expression of humanized B3(Fv)-PE38 immunotoxins.
  • Single-stranded uracil-containing pULI7 DNA (A) encoding wild type B3(Fv)-PE38 was the template for the mutagenesis according to the method of Kunkel, Proc. Natl. Acad. Sci. USA 82,488-492 (1985).
  • Single stranded uracil-containing pB3V H -HUMV L -PE38 DNA (C) was the template for the generation of pHUMB3(Fv)-PE38.
  • Figure 13 shows the ADP-ribosylation activity, cytotoxicity, and antigen binding of B3(Fv)PE38 and of the humanized variants.
  • ADP-ribosylation activity was determined by the incorporation on M C-NAD into acid precipitable material using elongation factor 2 enriched wheat-germ extract.
  • B Cytotoxicity towards A431 cells was measured by the inhibition of incorporation of pHJ-leucine into cell protein.
  • C Antigen binding was estimated by competition of [ I25 1 B3 IgG binding to A431 cells at 4°C with each immunotoxin.
  • Figure 14 shows the reactivity of pooled monkey anti- B3(Fv)-PE38 sera to B3(Fv)PE38 and humanized variants.
  • B3(Fv)-PE38, B3HUMVH-HUMVL-PE38 and HUMB3(Fv)-PE38 were immobilized on a 96-well microtiter plate.
  • Sera that were preincubated with PE38 as a competitor at a molar ratio of 1000 to 1 over the immobilized proteins were added in an equal volume at a dilution of 1:50.
  • Percent reactivity was calculated by setting the mean reactivity with B3(Fv)-PE38 obtained from four independent experiments to 100% and adjusting the relative reactivities with the humanized variant accordingly.
  • Figure 15 provides the nucleotide and deduced amino acid sequences of Bl heavy (A) and light (B) chains. Underlined nucleotide sequences correspond (at the 5' end) or are complementary (at the 3' end) to the PCR primers which were used to PCR amplify the fragment. The amino acid sequence is in single-letter code; below is the amino acid sequence determined by Edman sequencing shown in italics. CDRs are underlined, and constant region amino acids are struck through.
  • Figure 16 provides the nucleotide and deduced amino acid sequence of B5 heavy chain (A) and the variable region and the beginning of the constant region of the light (B) chain. Other details are as in Figure 15.
  • the struck-through carboxyl-terminal amino acids in the heavy chain correspond to the beginning of the (Gly 4 Ser) 3 linker used to connect the V H and the V L in the single chain configuration.
  • Figure 17 provides the amino acid (peptide) sequence of the B3 single chain Fv. The figure provides the sequences for the V H region, the linker and the V L region respectively. CDRs are in parentheses.
  • Figure 18 provides the amino acid (peptide) sequence of the humanized B3 single-chain Fv. CDRs are in parentheses.
  • the left- hand direction is the amino terminal direction and the right-hand direction is the carboxy- terminal direction.
  • the left-hand direction is the 5' direction and the right-hand direction is the 3' direction.
  • nucleic acid refers to a deoxyribonucleotide or ribonucleotide polymer in either single- or double-stranded form, and unless otherwise limited, would encompass known analogs of natural nucleotides that can function in a manner similar to naturally occurring nucleotides.
  • nucleic acid encoding or “nucleic acid sequence encoding” refers to a nucleic acid which directs the expression of a specific protein or peptide.
  • the nucleic acid sequences include both the DNA strand sequence that is transcribed into RNA and the RNA sequence that is translated into protein.
  • the nucleic acid sequences include both full length nucleic acid sequences as well as shorter sequences derived from the full length sequences. It is understood that a particular nucleic acid sequence includes the degenerate codons of the native sequence or sequences which may be introduced to provide codon preference in a specific host cell.
  • the nucleic acid includes both the sense and antisense strands as either individual single strands or in the duplex form.
  • isolated when referring to recombinantly produced proteins, means a chemical composition which is essentially free of other cellular components. Such a composition is preferably in a homogeneous state although it can be in either a dry or aqueous solution. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography.
  • a protein which is the predominant species present in a preparation is substantially purified. Generally, a substantially purified or isolated protein will comprise more than 80% of all macromolecular species present in the preparation. Preferably, the protein is purified to represent greater than 90% of all macromolecular species present. More preferably the protein is purified to greater than 95%, and most preferably the protein is purified to essential homogeneity, wherein other macromolecular species are not detected by conventional techniques.
  • labeled antibody refers to an antibody bound to a label such that detection of the presence of the label (e.g. as bound to a biological sample) indicates the presence of the antibody.
  • Cytotoxin refers to a molecule that when contacted with a cell brings about the death of that cell.
  • binding specificity when referring to a protein or carbohydrate, refers to a binding reaction which is determinative of the presence of the protein or carbohydrate in the presence of a heterogeneous population of proteins and other biologies.
  • the specified antibodies bind to a particular protein or carbohydrate and do not bind in a significant amount to other proteins or carbohydrates present in the sample.
  • Specific binding to an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein or carbohydrate.
  • antibodies raised to the Le ⁇ antigens may be selected to provide antibodies that are specifically immunoreactive with Le ⁇ proteins and not with other proteins.
  • immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein or carbohydrate.
  • solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein or carbohydrate. See Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York, for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity.
  • recombinant DNA refers to DNA which has been isolated from its native or endogenous source and modified either chemically or enzymaticalry by adding, deleting or altering naturally-occurring flanking or internal nucleotides. Flanking nucleotides are those nucleotides which are either upstream or downstream from the described sequence or sub-sequence of nucleotides, while internal nucleotides are those nucleotides which occur within the described sequence or subsequence.
  • recombinant protein or “recombinantly produced protein” refer to a peptide or protein produced using non-native cells that do not have an endogenous copy of DNA able to express the protein.
  • the cells produce the protein because they have been genetically altered by the introduction of the appropriate nucleic acid sequence.
  • the recombinant protein will not be found in association with proteins and other subcellular components normally associated with the cells producing the protein.
  • Mutations in proteins are designated by nomenclature consisting of the peptide sequence in which the mutation occurs, a representation of the non-mutated amino acid, followed by its position, followed by the representation of the mutated amino acid.
  • a mutation designated B3(Fv)V L S7T is a mutation from serine (S) to threonine (T) at position 7 of the V L chain of B3(Fv).
  • This invention relates to recombinantly produced single chain antibodies.
  • this invention provides for recombinant single chain antibodies that may be joined to one or more effector molecules and, because of their ability to specifically bind to a particular preselected target molecule, these antibodies are useful as targeting moieties which serve to direct the joined effector molecules or compositions to a cell or tissue bearing the preselected target molecule.
  • antibody refers to a protein consisting of one or more polypeptides substantially encoded by immunoglobulin genes or fragments of immunoglobulin genes.
  • the recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as the myriad immunoglobulin variable region genes.
  • Light chains are classified as either kappa or lambda.
  • Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.
  • the basic immunoglobulin (antibody) structural unit is known to comprise a tetramer.
  • Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one "light” (about 25 kD) and one "heavy” chain (about 50-70 kD).
  • the N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition.
  • the terms variable light chain (VJ and variable heavy chain (V H ) refer to these light and heavy chains respectively.
  • Antibodies may exist as intact immunoglobulins, or as modifications in a variety of forms including, for example, an Fv fragment containing only the light and heavy chain variable regions, a Fab or (Fab)' 2 fragment containing the variable regions and parts of the constant regions, a single-chain antibody (Bird et al. , Science 242: 424-426 (1988); Huston et al, Proc. Natl. Acad. Sci. USA 85: 5879-5883 (1988) both incorporated by reference herein), and the like.
  • the antibody may be of animal
  • antibody includes these various forms. Using the guidelines provided herein and those methods well known to those skilled in the art which are described in the references cited above and in such publications as Harlow & Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, (1988) the antibodies of the present invention can be readily made.
  • Fv region refers to a single chain antibody Fv region containing a variable heavy (V H ) and a variable light (VjJ chain.
  • the heavy and light chain may be derived from the same antibody or different antibodies thereby producing a chimeric Fv region.
  • effector molecule or “effector composition” as used herein refer to agents having a particular biological activity which is to be directed to a particular target molecule or a cell bearing a target molecule.
  • effector molecules may include various drugs such as vinblastine, daunomycin and the like, cytotoxins such as native or modified Pseudomonas exotoxin or Diphtheria toxin, encapsulating agents (e.g. , liposomes) which themselves contain pharmacological compositions, radioactive agents such as 125 I, 131 Cs, 32 P, 14 C, 3 H, and 35 S, target moieties and ligands.
  • ligands are molecules capable of reacting with or otherwise recognizing and specifically binding a "target” molecule.
  • Ligands and their respective target molecules represent paired species. Typical paired species include, but are not limited to, enzyme/substrate, receptor/agonist, antibody/antigen, and lectin/carbohydrate.
  • the binding between a ligand and its target may be mediated by covalent or non-covalent interactions or a combination of covalent and non-covalent interactions. When the interaction of the two species produces a non-covalently bound complex, the binding which occurs is typically electrostatic, hydrogen-bonding, or the result of hydrophilic/lipophilic interactions.
  • ligands include, but are not limited to antibodies, lymphokines, cytokines, receptor proteins such as CD4 and CD8, solubilized receptor proteins such as soluble CD4, hormones, growth factors, and the like which specifically bind desired target cells.
  • the choice of the particular effector molecule or composition depends on the particular target molecule or cell and the biological effect it is desired to evoke.
  • the effector molecule may be a cytotoxin where it is desired to bring about death of a particular target cell.
  • the effector molecule may be a conjugated non-lethal pharmacological agent or a liposome containing a non-lethal pharmacological agent.
  • the antibodies may be joined to an effector molecule that is a drug or to a cytotoxin to form an immunotoxin capable of selectively killing particular target cells.
  • cytotoxic compounds include, but are not limited to, ricin, abrin, Pseudomonas exotoxin (PE), Diphtheria toxin (DT), and the like.
  • Preferred toxins are PE or DT.
  • Native PE and DT are highly toxic compounds that typically bring about death through liver toxicity. PE and DT, however, can be modified into a form for use as an immunotoxin by removing the native targeting component of the toxin (e.g. domain la of PE and the B chain of DT) and replacing it with a different antibody targeting moiety.
  • PE Pseudomonas exotoxin
  • modifications may include, but are not limited to, elimination of domain la, various amino acid deletions in domains II and HI, single amino acid substitutions (e.g., replacing Lys with Gin at positions 590 and 606), and the addition of one or more sequences at the carboxyl terminus such as KDEL (Seq. ID No: 51) and REDL (Seq. ID No: 52). See Siegall et al, J. Biol. Chem. 264: 14256-14261 (1989).
  • PE38 refers to a truncated Pseudomonas exotoxin composed of amino acids 253-364 and 381-613 (see commonly assigned U.S. Patent Application Serial Number 07/901,709 filed June 18,1992 incorporated herein by reference.
  • the native C-terminus of PE, REDLK (residues 609-613, Seq ID No: 53), may be replaced with the sequence KDEL, REDL, and Lys-590 and Lys-606 may be each mutated to Gin (see commonly assigned U.S. Patent Application Serial Number 07/522,563 filed May 14, 1990, incorporated herein by reference).
  • DT diphtheria toxin
  • Modifications typically include removal of the targeting domain in the B chain and, more specifically, involve truncations of the carboxyl region of the B chain.
  • the recombinant single chain antibodies of the present invention may be fused to, or otherwise bound to the effector molecule or composition by any method known and available to those in the art.
  • the two components may be chemically bonded together by any of a variety of well-known chemical procedures.
  • the linkage may be by way of heterobifunctional cross-linkers, e.g. SPDP, carbod ⁇ mide, glutaraldehyde, or the like.
  • Production of various immunotoxins is well-known within the art and can be found, for example in "Monoclonal Antibody-Toxin Conjugates:
  • the antibodies of this invention may also be fused to a protein effector molecule by recombinant means such as through the use of recombinant DNA techniques to produce a nucleic acid which encodes both the antibody and the effector molecule and expressing the DNA sequence in a host cell such as E. coli.
  • the DNA encoding the chimeric protein may be cloned in cDNA or in genomic form by any cloning procedure known to those skilled in the art. See for example Sambrook et al. , Molecular Cloning: A Laboratory Manual, Cold Spring Harbor laboratory, (1989), which is herein incorporated by reference.
  • the single chain antibodies of the present invention may be fused or chemically conjugated to a wide variety of effector molecules.
  • the antibody may be conjugated or fused to bacterial or plant toxins, or to other effector agents to treat or diagnose human cancer.
  • radionuclides conjugated to antibodies that bind to tumors can produce cell killing based on the high local concentration of radiation.
  • Chemotherapeutic drugs for example, vinblastine or daunomycin, can be coupled to the antibodies and delivered at high concentration to cells that react with the antibodies.
  • the antibodies of this invention may be utilized to specifically target a vehicle that encapsulates a therapeutic agent.
  • the antibodies may be conjugated to a liposome which itself carries a drug (e.g. doxorubicin) and thereby specifically targets the liposome to a specific tissue or cell.
  • a drug e.g. doxorubicin
  • the antibodies may be recombinantly fused to a membrane- inserting protein and thereby incorporated into the liposome for delivery of therapeutic agents.
  • Fusion or conjugation of the antibodies of this invention to various labels produces a highly specific detectable marker that may be used to detect the presence or absence of cells or tissues bearing the particular molecule to which the antibody is detected.
  • the antibodies may be chemically conjugated or fused to an effector molecule that is another specific binding moiety, e.g. a ligand such as those described above.
  • the composition will act as a highly specific bifunctional linker. This linker may act to bind and enhance the interaction between cells or cellular components to which the fusion protein binds.
  • the fusion protein is a growth factor joined to an antibody or antibody fragment (e.g.
  • the antibody may specifically bind antigen positive cancer cells while the growth factor binds receptors (e.g., JL2 or IL4 receptors) on the surface of immune cells.
  • the fusion protein may thus act to enhance and direct an immune response toward target cancer cells.
  • the antibodies of the present invention may also be utilized as multiple targeting moieties.
  • this invention also provides for compositions in which two or more antibodies are bound to a single effector molecule. Where the effector molecule is a cytotoxin, the presence of two or more antibodies may increase specificity or avidity of binding of the immunotoxin.
  • compositions of this nature may provide two or more kinds of biological activity with a single targeting moiety.
  • the antibodies of this invention are antibodies that specifically bind Lewis ⁇ (Le ⁇ ) carbohydrates (Le ⁇ carbohydrate antigens).
  • the Le ⁇ carbohydrate antigens include natural or synthetic Le ⁇ carbohydrates or fragments thereof that contain epitopes recognizable by Le ⁇ binding antibodies.
  • carbohydrates, glycoproteins and other glycoconjugates which contain or mimic the Le ⁇ carbohydrate or epitopes contained within the Le ⁇ carbohydrate (see, Pastan et al. , Cancer Res., 51: 3781-3787 (1991) and Hoess et al. ,
  • tissue binding specificity refers to the particular distribution of tissues to which an antibody binds and does not bind as determined by immunohistochemical analysis. Methods of determining tissue binding specificity as well as the binding specificities for Bl, B3 and B5 are described in U.S. Patent 5,242,813 (see, especially Tables I, II and III) which is incorporated herein by reference.
  • the antibodies may be derived from the monoclonal antibodies designated Bl, B3, and B5 (see U.S. Patent 5,242,813). These antibodies have been shown to specifically bind to Lewis ⁇ and Lewis ⁇ -related carbohydrate antigens that are typically found on various carcinomas including carcinomas of the breast, colon, cervix, and prostate.
  • the antibodies of this invention may be Fv regions comprising a variable light (VJ and a variable heavy (V H ) chain.
  • the light and heavy chains may be joined directly or through a linker.
  • a linker refers to a molecule that is covalentiy linked to the light and heavy chain and provides enough spacing and flexibility between the two chains such that they are able to achieve a conformation in which they are capable of specifically binding the epitope to which they are directed. Protein linkers are particularly preferred as they may be expressed as an intrinsic component of the fusion protein.
  • Single chain Bl, B3 and B5 Fv regions may be cloned from the hybridoma cell lines Bl, B3 and B5 which were deposited on October 10, 1990 with the American Type Culture Collection (ATCC), 12301 Parklawn Drive, Rockville, MD 20852, where the deposits were granted the accession numbers ATCC HB 10572, HB 10573, and HB 10569, respectively. The deposits were made pursuant to the provisions of the Budapest Treaty.
  • the Fv regions may all be cloned using the same general strategy.
  • poly(A) + RNA extracted from the hybridoma cells is reverse transcribed using random hexamers as primers.
  • the V H and V L domains are amplified separately by two polymerase chain reactions (PCR*).
  • Heavy chain sequences may be amplified using 5' end primers which are designed according to the amino-terminal protein sequences of the Bl, B3 and B5 heavy chains respectively (Sequence Listing ID Nos. 19, 17, and 21 respectively) and 3' end primers according to consensus immunoglobulin constant region sequences (Kabat et al, Sequences of Proteins of
  • Light chain Fv regions are amplified using 5' end primers designed according to the amino-terminal protein sequences of Bl, B3 and B5 light chains respectively (Sequence ID Nos. 20, 18 and 22 respectively) and in combination with the primer C-kappa (Table 1 and Sequence ID No. 14). Suitable primers are specifically illustrated in Examples 1 and 2 although one of skill in the art would recognize that other suitable primers may be derived from the sequence listings provided herein.
  • the crude PCR products are subcloned into a suitable cloning vector.
  • Clones containing the correct size insert by DNA restriction are identified.
  • the nucleotide sequence of the heavy or light chain coding regions may then be determined from double stranded plasmid DNA using sequencing primers adjacent to the cloning site.
  • sequencing primers e.g. the SequenaseTM kit, United States Biochemical Corp., Cleveland, Ohio, USA
  • kits e.g. the SequenaseTM kit, United States Biochemical Corp., Cleveland, Ohio, USA
  • sequence information provided for the Fv regions of Bl, B3, and B5 (Sequence ID Nos. 17-22), nucleic acids encoding these sequences may be obtained using a number of methods well known to those of skill in the art.
  • DNA encoding the Fv regions may be prepared by any suitable method, including, for example, amplification techniques such as ligase chain reaction (LCR) (see Wu and Wallace, Genomics, 4: 560 (1989), Landegren, et al, Science, 241: 1077 (1988) and Barringer, et al, Gene, 89: 117 (1990)), transcription amplification (see Kwoh, et al., Proc. Natl Acad. Sci. USA, 86: 1173 (1989)), and self-sustained sequence replication (see Guatelli, et al., Proc. Natl. Acad. Sci.
  • LCR ligase chain reaction
  • Chemical synthesis produces a single stranded oligonucleotide. This may be converted into double stranded DNA by hybridization with a complementary sequence, or by polymerization with a DNA polymerase using the single strand as a template. While it is possible to chemically synthesize an entire single chain Fv region, it is preferable to synthesize a number of shorter sequences (about 100 to 150 bases) that are later ligated together.
  • subsequences may be cloned and the appropriate subsequences cleaved using appropriate restriction enzymes. The fragments may then be ligated to produce the desired DNA sequence.
  • the sequences may be ligated together, either directly or through a DNA sequence encoding a peptide linker, using techniques well known to those of skill in the art.
  • heavy and light chain regions are connected by a flexible peptide linker (e.g. (Gly 4 Ser) 3 ) which starts at the carboxyl end of the heavy chain Fv domain and ends at the amino terminus of the light chain Fv domain.
  • the entire sequence encodes the Fv domain in the form of a single-chain antigen binding protein.
  • fusion proteins comprising that Fv region may be prepared by methods known to one of skill in the art.
  • the Fv region may be fused directly to the effector molecule (e.g. cytotoxin) or may be joined directly to the cytotoxin through a peptide connector.
  • the peptide connector may be present simply to provide space between the targeting moiety and the effector molecule or to facilitate mobility between these regions to enable them to each attain their optimum conformation.
  • the DNA sequence comprising the connector may also provide sequences (such as primer sites or restriction sites) to facilitate cloning or may preserve the reading frame between the sequence encoding the targeting moiety and the sequence encoding the effector molecule.
  • the design of such connector peptides will be well known to those of skill in the art. However, one particularly preferred connector is the peptide SGGPEGGS (Sequence ID No. 44), designated herein as the C3 connector.
  • immunotoxin fusion proteins involves separately preparing the Fv light and heavy chains and DNA encoding any other protein to which they will be fused and recombining the DNA sequences in a plasmid or other vector to form a construct encoding the particular desired fusion protein.
  • a simpler approach involves inserting the DNA encoding the particular Fv region into a construct already encoding the desired second protein.
  • DNA encoding Bl(Fv), B3(Fv), B5(Fv) or chimeric Fv fusion proteins is most easily prepared by inserting the DNA encoding the Bl, B3, B5 or chimeric Fv regions into constructs already containing DNA encoding the desired cytotoxin.
  • the expression plasmid pVC38H contains the gene from the immunotoxin TGF ⁇ -PE40 under control of the T7 promoter, the T transcription terminator at the 3' end of the PE40 coding region and the single strand replication region F + , to generate single stranded phage DNA by contransfection with (Ml 3) helper phages, if desired to create derivatives of the plasmid by site directed mutagenesis (Chaudhary et al. Proc. Natl. Acad. Sci. USA, 87: 1066-1070 (1990).
  • the plasmid pRK79K encodes the Pseudomonas exotoxin PE38KDEL (Chaudhary, et al. Proc. Natl. Acad. Sci. USA, 87: 308-312 (1990).
  • the DNA sequence encoding the Fv region is inserted into the construct using techniques well known to those of skill in the art.
  • the TGF ⁇ gene is removed and replaced by the B3(Fv) gene in a 3 fragment ligation, using an Ndel/BamHI fragment of the heavy chain coding region and the BamHI/Hindi ⁇ fragment encoding the light chain Fv ( Figure la) as described in Example 1.
  • a plasmid encoding B3(Fv)-PE38 may be produced by removing the PE40 coding region from pULIl from the Hindlll site to an EcoRI site positioned just beyond the PE40 gene and replacing it with a Hindlll/EcoRI fragment from pRK79K described by Chaudhary et al. supra. This approach is described in greater detail in Example 1.
  • a particularly preferred approach involves the use of plasmid pULI7 which encodes the B3(Fv)-PE38 immunotoxin (Benhar et al. Bioconjug. Chem. , 5: 321- 326 (1994)).
  • the V H and V L sequences are PCR amplified using the heavy chain and light chain in their respective plasmids as templates.
  • the amplification primers are designed to have at their ends sequences that are complementary to the translation initiation, peptide linker and Fv-toxin junction (connector) which are common to the single-chain Fv-immunotoxin expression vectors.
  • the PCR products are purified and annealed to a uracil-containing single stranded DNA corresponding to the pULI7
  • DNA prepared by rescue of pULI7 with a helper phage.
  • the annealed PCR products are extended using the single stranded DNA as a template (see, for example, MUTAGENE* mutagenesis protocol, Biorad, Hercules, California, USA).
  • the intact DNA may be used to transform cells and express the new fusion protein.
  • the remaining intact "unmodified" DNA may be digested using a restriction endonuclease which has a unique site in the B3(Fv) template but that is absent from Bl and B5. This destroys any residual B3(Fv) sequences leaving only the modified sequences. This approach is described in greater detail in Example 2.
  • B3 In the form of a single chain Fv immunotoxin, B3 is considerably more stable, however it still undergoes inactivation, mainly by aggregation, especially upon incubation in 0.15 M NaCl, 0.01 M NaPO 4 pH 7.4 at 37°C. In contrast to B3(Fv)-PE38 immunotoxin, B5(Fv)-PE38 is more resistant to inactivation under these conditions (see Figure 6). Based on these observations, the stability of chimeric Fv immunotoxins was examined.
  • chimeric Fv regions containing variable heavy and light chain domains from different, albeit related, antibodies may show significantly greater stability in vitro and in vivo than Fv regions where both the heavy and light domain are derived from the same antibody.
  • a fusion protein comprising a B3 variable heavy region and a B5 variable light region fused together and to PE38 shows higher activity and longer term stability than a B3(Fv)-PE38 fusion protein.
  • V H and V L sequences are PCR amplified using the heavy chain and light chain in their respective plasmids as templates as described.
  • V H and V L DNAs are selected from different antibodies.
  • the DNAs are annealed to a uracil-containing single stranded DNA corresponding to the pULI7 DNA and the synthesis of the chimeric Fv-cytotoxin fusion protein DNA is completed as described above and in Examples 2 and 12.
  • cytotoxin moiety may be used in various chemical conjugates for example, either directly with toxins or other therapeutic agents, with carriers for therapeutic agents such as tiposomes, or with various labels and markers such as fluorescent labels.
  • site directed mutagenesis may be used to identify the differences between the more and less stable forms.
  • the B3V H -B5V L -PE38 immunotoxin shows greater stability than the B3-PE38 (B3V H -B3V L -PE38) immunotoxin.
  • To identify the amino acid residues contributing to the increased stability one performs a sequence analysis to identify those regions of the particular light or heavy region (in this case the V L region) that differ from the corresponding light or heavy chain in the non-chimeric antibody. Once the differences have been identified, mutations reflecting those differences may be systematically introduced into the corresponding region of the non-chimeric antibody.
  • the fusion protein comprises either B3V H -B5V L -PE38 or B3(Fv)-PE38: V L M4T.
  • An unexpected result of the present invention is the discovery that mutations at position 95 of the V H region can alter the binding affinity of the single chain antibody. More specifically, it was discovered that mutations that altered the serine at position 95 in B3(Fv) to tyrosine or to phenylalanine, which are the most common amino acids at this position in other antibodies, reduced the binding affinity of B3(Fv) by approximately 10-fold (see Example 18). Conversely, when the tyrosine at V H 95 in B5(fv) was mutated to serine showed a for-fold increase binding activity as analyzed by cytotoxicity assays. B5(Fv) differed from B3(Fv) in having a completely different binding site. Thus the effect of the mutation is independent of the particular binding site.
  • monoclonal antibodies Bl, B3 and B5 are mouse antibodies
  • repeated administration of either labeled antibodies or the immunotoxins including these antibodies as targeting moieties will result in the formation of anti-mouse antibodies (Parren et al , Hum. Antibod. Hybridomas., 3: 137-145 (1992)), in addition to the production of antibodies to the toxin moiety.
  • This immune response may preclude long term treatment in some cases. Therefore it is desirable to produce less immunogenic molecules.
  • the Fv portion of the mouse antibody is humanized so that it may then be used to replace the Fv portion of the murine antibody in the fusion proteins of the present invention.
  • Humanized antibodies are non-human antibodies in which some or all of the amino acid residues are replaced with the corresponding amino acid residue found in a similar human antibody. Humanization thereby reduces the antigenic potential of the antibody.
  • Antibody variable domains have been humanized by various methods, such as CDR grafting (Riechmann et al., Nature, 332: 323-327 (1988)), replacement of exposed residues (Padlan, Mol. Immunol. 28: 489-498 (1991)) and variable domain resurfacing (Roguska et al , Proc. Natl Acad. Sci. USA, 91: 969-973 (1994), all incorporated by reference.
  • the minimalistic approach of resurfacing is particularly suitable for antibody variable domains which require preservation of some mouse framework residues to maintain maximal antigen binding affinity.
  • the Fv portion is humanized by a method referred to as "framework exchange".
  • framework residues are identified that differ from human framework residues in highly homologous human V H or V L donors. These differing framework residues are then simultaneously mutated to human residues.
  • the mutations are introduced onto a single-stranded DNA template prepared from a single-chain immunotoxin cassette which may be expressed in E. coli and allows the rapid purification and analysis of the resulting humanized variants.
  • This approach combines, yet deviates from the principles of CDR grafting or from the replacement of exposed residues, as some residues that are not normally exposed are humanized, while some other residues that are normally exposed are not humanized. Decisions to preserve certain mouse residues are based on knowledge regarding the effect of mutating these particular residues on the binding affinity of the Fv fragment, or on the possible interactions of these residues with other Fv residues observed in a structural model.
  • humanization is accomplished by aligning the variable domains of the heavy and light chains with the best human homolog identified in sequence databases such as GENBANK or SWISS-PROT using the standard sequence comparison software as described above. Sequence analysis and comparison to a structural model based on the crystal structure of the variable domains of monoclonal antibody McPC603 (Queen et al, Proc. Natl. Acad. Sci. USA, 86: 10029-10033 (1989) and Satow et al , J. Mol. Biol 190: 593-604 (1986)); Protein Data bank Entry IMCP) allows identification of the framework residues that differ between the mouse antibody and its human counterpart.
  • McPC603 Queen et al, Proc. Natl. Acad. Sci. USA, 86: 10029-10033 (1989) and Satow et al , J. Mol. Biol 190: 593-604 (1986)
  • Protein Data bank Entry IMCP allows identification of the framework residues that differ between the mouse antibody and its
  • the mouse residues at B3 V H positions 1, 3, 19 24, 89 and 91 are preserved.
  • residue 82b in B3 V H is mutated to arginine.
  • V H and V L gene segments (e.g. in plasmid pULJ.7) encoding wild type B3(Fv)-PE38 may be independently humanized by site specific mutagenesis (see Example 14).
  • site specific mutagenesis see Example 14
  • One of skill in the art will appreciate that once the Fv region has been cloned and sequenced, alteration of various residues by site specific mutagenesis is routine using standard techniques well known to those of skill in the art (Kunkel, Proc. Natl. Acad. Sci. USA, 82: 488-492 (1985)).
  • the recombinant Fv regions and fusion proteins incorporating these antibody regions may be expressed in a variety of host cells, including E. coli, other bacterial hosts, yeast, and various higher eukaryotic cells such as the COS, CHO and HeLa cells lines and myeloma cell lines.
  • a particularly preferred host is E. coli.
  • the recombinant protein gene will be operably linked to appropriate expression control sequences for each host. For E. coli this includes a promoter such as the T7, tip, or lambda promoters, a ribosome binding site and preferably a transcription termination signal.
  • control sequences will include a promoter and preferably an enhancer derived from immunoglobulin genes, SV40, cytomegalovirus, etc., and a polyadenylation sequence, and may include splice donor and acceptor sequences.
  • the plasmids of the invention can be transferred into the chosen host cell by well-known methods such as calcium chloride transformation for E. coli and calcium phosphate treatment or electroporation for mammalian cells.
  • Cells transformed by the plasmids can be selected by resistance to antibiotics conferred by genes contained on the plasmids, such as the amp, gpt, neo and hyg genes.
  • the recombinant fusion proteins can be purified according to standard procedures of the art, including ammonium sulfate precipitation, affinity columns, column chromatography, gel electrophoresis and the like (see, generally, R. Scopes, Protein Purification, Springer- Verlag, N.Y. (1982), Guider, Methods in Enzymology Vol. 182: Guide to Protein Purification. , Academic Press, Inc. N.Y. (1990)). Substantially pure compositions of at least about 90 to 95% homogeneity are preferred, and 98 to 99% or more homogeneity are most preferred for pharmaceutical uses. Once purified, partially or to homogeneity as desired, the polypeptides may then be used therapeutically.
  • the single chain Fv region or a fusion protein comprising a single chain Fv region may possess a conformation substantially different than the native protein. In this case, it may be necessary to denature and reduce the protein and then to cause the protein to re-fold into the preferred conformation. Methods of reducing and denaturing the protein and inducing re-folding are well known to those of skill in the art. (See, Debinski et al. J. Biol. Chem. , 268: 14065-14070 (1993); Kreitman and Pastan, Bioconjug.
  • Debinski et al. describe the denaturation and reduction of inclusion body proteins in guanidine-DTE. The protein is then refolded in a redox buffer containing oxidized glutathione and L-arginine.
  • a redox buffer containing oxidized glutathione and L-arginine.
  • modifications are well known to those of skill in the art and include, for example, a methionine added at the amino terminus to provide an initiation site, or additional amino acids placed on either terminus to create conveniently located restriction sites or termination codons.
  • the primers used to construct B5(Fv) will introduce a sequence encoding an initiator methionine for expression in E. coli and an Ndel restriction site to facilitate cloning.
  • amino acid substitutions may be made that increase specificity or binding affinity of single chain Fv region and fusion proteins comprising the single chain Fv region, etc.
  • non-essential regions of the molecule may be shortened or eliminated entirely.
  • the recombinant antibodies of the present invention also recognize materials such as surface mucins on tumor cells that would be expected to be shed into the surrounding tissues, picked up by the blood stream, and detectable in blood samples taken from distant sites.
  • Such shed antigens have proven to be useful in the diagnosis of primary and recurrent cancers using antibodies that react to these shed antigens.
  • a currently useful example of this is the CA125 antigen that can be assayed in sera from patients with ovarian cancer to predict recurrence or to confirm a primary diagnosis of tumor.
  • Bl, B3 and B5 may be useful in the diagnosis of tumors.
  • the selective reactivity of these antibodies with certain types of tumor cells may be exploited for anatomic pathological diagnosis of tumors, clarifying the type and origin of tumors, and whether a particular group of cells represents a recurrence of a previous tumor or the development of another primary tumor elsewhere.
  • Such a diagnostic determination can be useful for the subsequent planning of anti-tumor therapy in each particular patient.
  • immunohistochemical pathologic diagnosis in tissue sections e.g. , biopsies
  • cytological preparations e.g. , Pap smears, effusions
  • targeting antibodies could be in the diagnosis of macroscopic foci of a tumor using antibodies Bl, B3 or B5 coupled to radioisotopes that could be detected either by external body scanning (imaging diagnosis) or by localization using radiation detector probes at the time of exploratory surgery.
  • diagnostic methods described above involve contacting a
  • a diagnostic method comprises the steps of (a) removing a tissue or fluid sample from a patient; (b) adding an antibody which includes the Fv region of a heavy chain of a first antibody and the Fv region of a light chain of a second antibody, where the Fv regions are recombinantly fused to form a single molecule that specifically bind a Lewis ⁇ -related carbohydrate antigen; and (c) detecting for the presence or absence of the antibody in the sample.
  • detection is by the detection of a label bound to the antibody.
  • Means of labeling antibodies are well known to those of skill in the art. Labels may be directly linked through a covalent bond or covalentiy through a linking molecule which typically bears reactive sites capable of forming covalent bonds with the label and the antibody respectively.
  • a common approach is to label the antibody and the label with either avidin or streptavidin or biotin which, in turn, bind irreversibly with each other.
  • label refers to a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means.
  • useful labels include radioactive molecules such as 32 P, I4 C, 1 J I, 3 H, and 35 S, fluorescent dyes such as fluorescein or rhodamine, electron-dense reagents, enzymes (as commonly used in an ELISA), luminescent enzymes such as luciferase and the like.
  • the recombinant fusion proteins and pharmaceutical compositions of this invention are useful for parenteral, topical, oral, or local administration, such as by aerosol or transdermally, for prophylactic and/or therapeutic treatment.
  • the pharmaceutical compositions can be administered in a variety of unit dosage forms depending upon the method of administration.
  • unit dosage forms suitable for oral administration include powder, tablets, pills, capsules and lozenges.
  • the fusion proteins and pharmaceutical compositions of this invention when administered orally, must be protected from digestion. This is typically accomplished either by complexing the protein with a composition to render it resistant to acidic and enzymatic hydrolysis or by packaging the protein in an appropriately resistant carrier such as a liposome. Means of protecting proteins from digestion are well known in the art.
  • compositions for administration are particularly useful for parenteral administration, such as intravenous administration or administration into a body cavity or lumen of an organ.
  • the compositions for administration will commonly comprise a solution of the single chain antibody or a fusion protein comprising the single chain antibody dissolved in a pharmaceutically acceptable carrier, preferably an aqueous carrier.
  • a pharmaceutically acceptable carrier preferably an aqueous carrier.
  • aqueous carriers can be used, e.g. , buffered saline and the like. These solutions are sterile and generally free of undesirable matter.
  • These compositions may be sterilized by conventional, well known sterilization techniques.
  • compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like.
  • concentration of single chain antibody, fusion protein, or labeled single chain antibody in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight and the like in accordance with the particular mode of administration selected and the patient's needs.
  • a typical pharmaceutical composition for intravenous administration would be about 0.01 to 100 mg per patient per day.
  • Dosages from 0.1 up to about 1000 mg per patient per day may be used, particularly when the drug is administered to a secluded site and not into the blood stream, such as into a body cavity or into a lumen of an organ.
  • Actual methods for preparing parenterally administrate compositions will be known or apparent to those skilled in the art and are described in more detail in such publications as Remington's Pharmaceutical Science, 15th ed., Mack Publishing Company, Easton, Pennsylvania (1980).
  • compositions containing the present fusion proteins or a cocktail thereof can be administered for therapeutic treatments.
  • compositions are administered to a patient suffering from a disease, in an amount sufficient to cure or at least partially arrest the disease and its complications.
  • An amount adequate to accomplish this is defined as a "therapeutically effective dose.” Amounts effective for this use will depend upon the severity of the disease and the general state of the patient's health.
  • compositions may be administered depending on the dosage and frequency as required and tolerated by the patient.
  • the composition should provide a sufficient quantity of the proteins of this invention to effectively treat the patient.
  • cytotoxic fusion proteins of the present invention are included a variety of disease conditions caused by specific human cells that may be eliminated by the toxic action of the protein.
  • One preferred application is the treatment of cancers, in particular cancers in which the tumor cells express carbohydrate antigens that are members of the Lewis ⁇ family.
  • cancers include, but are not limited to colon, breast, esophagus, bladder, gastric, head and neck, lung and ovarian carcinomas.
  • the fusion proteins may also be used in vitro, for example, in the elimination of harmful cells from bone marrow before transplant where those cells express Lewis ⁇ -related antigens. Kits
  • kits for research or diagnostic purposes typically include one or more containers containing the single chain antibodies of the present invention.
  • research kits comprise containers containing single chain Bl(Fv), B3(Fv), B5(Fv), chimeric Fv, mutated Fv or humanized Fv antibodies in a form suitable for derivatizing with a second molecule, e.g. a label, a drug, a cytotoxin, and the like.
  • the research kits may contain DNA sequences encoding these antibodies.
  • the DNA sequences encoding these antibodies are provided in a plasmid suitable for transfection into and expression by a host cell.
  • the plasmid may contain a promoter (often an inducible promoter) to regulate expression of the DNA in the host cell.
  • the plasmid may also contain appropriate restriction sites to facilitate the insertion of other DNA sequences into the plasmid to produce various fusion proteins.
  • the plasmids may also contain numerous other elements to facilitate cloning and expression of the encoded proteins. Such elements are well known to those of skill in the art and include, for example, selectable markers, initiation codons, termination codons, and the like.
  • Diagnostic kits typically comprise containers containing the antibodies described above.
  • the antibodies are themselves derivatized with a label or, alternatively, they may be bound with a secondary label to provide subsequent detection.
  • labels may include radiolabels, fluorescent labels, enzymatic labels, i.e., horseradish peroxidase (HRP), or the like.
  • the kit may also contain appropriate secondary labels (e.g. a sheep anti- mouse-HRP, or the like).
  • the kit may also contain various reagents to facilitate the binding of the antibodies, the removal of non-specific binding antibodies, and the detection of the bound labels. Such reagents are well known to those of skill in the art.
  • the primer pair B3-H1 and B3-H2 was used for amplification of the heavy chain Fv coding region, while the primer pair B3-L1 and B3-L2 was used for amplification of the light chain Fv coding region (see Table 1 and Sequence ID Nos. 1, 2, 7, and 9).
  • These oligonucleotides have at their 3' ends constant sequences that occur at the beginning and end of mouse Fv DNA. At their 5' ends are restriction endonuclease recognition sites (Ndel, BamHI, Hindlll) for cloning of the PCR products as shown in Fig. la.
  • the products of the amplifications of heavy- and light chain Fv DNA fragments were identified by agarose gel electrophoresis to be DNA fragments between 350 and 400 bp. They were purified from gels, cut with BamHI or HindHJ (Fig. la) and, after purification on a second gel, ligated with HindUI- or BamHI linearized and dephosphorylated pBR322 vector (Bolivar et al, Gene, 2: 95-113 (1977)).
  • the nucleotide sequence of the light- and heavy chain Fv coding region of monoclonal antibody B3 was determined from double stranded plasmid DNA using sequencing primers (New England Biolabs, Beverly, Massachusetts, USA) adjacent to the BamHI or HindlH site of pBR322 and a T7 polymerase sequencing reagent kit (United States Biochemicals, Cleveland, Ohio, USA).
  • Xable 1. PCR primers used to amplify Fv heavy and light chains. The Frl primers were designed according to the amino acid sequences which were determined by Edman degradation, and are indicated in single letter code above the primer sequences. Underlined Met are initiator methionine codons.
  • underlined amino acids in the light chain primers are segments of the peptide linker that fuses V H to V L in the single chain configuration.
  • Underlined nucleotides in BIHFrl and B5HFrl encode the initiator methionine for expression in E. coll, and include an Ndel restriction site.
  • Underlined nucleotides in BlHFr4 and B5HFr4 are complementary to the coding sequence for segments of the peptide linker that fuses V H to V L in the single-chain configuration.
  • Underlined nucleotides in BlLFr4 B5LFr4 are complementary to the coding sequence of the junction between the Fv and PE38 and xnclude a Hlndlll restriction site.
  • TCTGG B3-H2 TGGATAGACTGATGGGGATCCGCCTCCGCCTGAGGAGAC 2
  • Poly(A) + mRNA was prepared from 10 s hybridoma cells and reverse-transcribed using random hexamers as primers to yield first strand cDNA. Separate PCR* reactions were carried out to amplify fragments encompassing heavy chain variable through part of CHI domains, and light chain variable through part of C-kappa.
  • the Bl and B5 V H sequences were amplified using 5' end primers designed according to the amino-terminal protein sequence of the Bl and B5 heavy chains and 3' end primers designed according to consensus immunoglobulin constant region sequences (Kabat et al. (1991) supra.).
  • Bl V H was amplified using 5' end primer BIHFrl and 3' end primer GammaCHl (Table 1, Sequence ID Nos. 3 and 5 respectively).
  • B5 V H was amplified using 5' end primer B5HFrl and 3' end primer B5HFr4 (Table 1, Sequence ID Nos. 4 and 7 respectively).
  • Primer GammaCHl was designed according to consensus IgGl CHI region codons 122-129 while primer BlHFr4 was designed according to the determined nucleotide sequence of codons 109-113 of Bl V render (Kabat et al, (1991) supra.).
  • the Bl and B5 V L sequences were amplified using 5' end primers BILFrl and B5LFrl (Table 1 and Sequence ID Nos. 12 and 13) which were designed according to the amino-terminal protein sequence of Bl and B5 light chains respectively (Sequence ID Nos. 20 and 22) in combination with the primer C-kappa (Table 1, Sequence ID No. 14).
  • Primer C-kappa was designed according to consensus kappa light chain codons 113-120 (Id.). PCR was performed as described by Brinkmann et al. , Proc. Nat. Acad.
  • the crude PCR products were subcloned into a PCR* cloning vector (Invitrogen, San Diego, California, USA) employing blue/white selection. Clones containing the correct size insert by DNA restriction analysis were identified. The nucleotide sequence of the heavy or light chain coding regions was determined from double stranded plasmid DNA using sequencing primers (Invitrogen) adjacent to the PCR* EcoRI cloning site and the SequenaseTM kit (United States Biochemical Corp). Three to five independent clones were sequenced for each amplified DNA segment. The nucleotide sequences of the Bl V H and V L are shown in Sequence ID Nos.
  • Bl differs considerably both in framework and in CDR sequence from both B3 (83.9% identity in V H and 88.9% identity in V L coding sequence) and B5 (86.3% identity in V H and 91.2% identity in V L coding sequence), and does not show high sequence identity to any known anti-carbohydrate antibody in a database search (Devereux et al, Nucleic Acids Res., 12: 387-395 (1984)). All three antibodies have a mouse class m heavy chain and a kappa II light chain (Kabat et al., supra). The differences in sequence between Bl and B3 may explain why they recognize different epitopes of otherwise similar antigens (see, Pastan et al. , Cancer Res. , 51: 3781-3787 (1991) and U.S. Patent No. 5,242,813).
  • the expression plasmid pVC38H contains the gene from the immunotoxin TGF ⁇ -PE40 under control of the T7 promoter (Chaudhary et al, Proc. Natl. Acad. Sci. USA 87: 1066-70 (1990)), the Tc transcription terminator at the 3' end of the PE40 coding region and the single strand replication origin, F + , to generate single stranded phage DNA by cotransfection with (M13) helper phages, if desired, to create derivatives of the plasmid by site directed mutagenesis.
  • the TGF ⁇ coding region in pVC38H has an Ndel recognition site at the 5' end and a HindLII site at the point of connection to the DNA encoding PE40.
  • the TGF ⁇ gene was removed and replaced by the B3(Fv) gene in a 3 - fragment ligation, using an Ndel/BamHI fragment of the heavy chain coding region and the BamHI/Hind ⁇ i fragment encoding the light chain Fv (Fig. la). Because sequence analysis showed a mutation (deletion and frameshift) at the 5' end of the light chain Fv gene due to a sequence repetition in the PCR primer annealing region, site-directed mutagenesis was performed (Kunkel, Proc. Natl. Acad. Sci.
  • B3(Fv)-PE38DKEL To make another B3(Fv) immunotoxin, B3(Fv)-PE38DKEL, the PE40 coding region was removed from pULIl from the Hindm site to an EcoRI site positioned just beyond the PE40 gene, and replaced by a Hindl ⁇ /EcoRI fragment from pRK79K encoding the PE variant PE38KDEL which lacks domain la (amino acids 1-252) and part of domain lb (amino acids 365-380), and also contains an altered carboxyl terminal sequence KDEL (Chaudhary et al, Proc. Natl. Acad. Sci., 87: 308-12 (1990)).
  • the expression plasmid pULI4 for production of B3(Fv) was constructed by removal of the light chain and PE40 coding region from pULIl from BamHI to EcoRI which was replaced by a PCR fragment obtained by amplification of the light chain Fv coding sequence with the primer-pair B3-L3 + B3-L4.
  • the primer B3-L3 (Table 1) is similar to B3Ll,used for cloning of light chain Fv from cDNA and B3-L4 (Table 1) is, in the 3' part for priming the PCR, identical to B3-L2, but, at the 5' end, the Hindm site for fusion to PE-sequences is replaced by translation stop codons followed by an EcoRI recognition sequence.
  • B3(Fv)-PE38 also called LMB7 is one recombinant B3(Fv)-immunotoxin of this invention preferred for use as a cancer therapeutic.
  • the plasmid pULI7 for expression of B3(Fv)PE38 was constructed as follows: Plasmid pULIl contains the Fv region of monoclonal antibody B3 in the form of a single chain Fv containing a (Gly 4 -Ser) 3 peptide linker between V H and V L , fused to PE-40, a truncated form of
  • part of the toxin portion of pULI6 was replaced with a shorter molecule with the same activity, PE38 (lacking domain lb of PE), replacing by subcloning a Sall-EcoRI toxin fragment of pULI6 with the PE38 coding Sall-EcoRI fragment of pCSlO (Siegall et al. J. Biol. Chem., 264: 14256-14261 (1989)).
  • the resulting expression plasmid, which codes for the immunotoxin B3(Fv)-PE38 is pULI7 (Fig. lb).
  • Bl and B5 Fv fragments replaced B3Fv sequences in the expression plasmid pULI7 which encodes the B3(Fv)-PE38 immunotoxin (Benhar et al. Bioconjug. Chem. , 5:321-326 (1994)).
  • the V H sequences were PCR amplified using the heavy chain clones in PCR* plasmids as templates.
  • Primers BIHFrl and 5 '-phosphorylated BlHFr4 were used to amplify B1V H
  • primers B5HFrl and 5'-phosphorylated B5HFr4 were used to amplify B5V H .
  • V L sequences were amplified using the light chain clones in pCR* plasmids as templates.
  • Primers BlLFrl and 5 '-phosphorylated BlLFr4 were used to amplify B1V L
  • primers B5LFrl and 5 '-phosphorylated B5LFr4 were used to amplify B5V L .
  • the primers had at their ends sequences that are complementary to the translation initiation, peptide linker and Fv-toxin junction (connector) which are common to the single-chain Fv-immunotoxin expression vectors.
  • Primers BlLFr4 and B5LFr4 were designed according to the determined nucleotide sequence of codons 102-107 of Bl and B5 V L respectively.
  • the PCR amplifications were performed as described in Example 2.
  • the PCR products were purified using spin columns, combined and annealed to a uracil-containing single-stranded DNA phagemid pULI7 which encodes the single-chain immunotoxin B3(Fv)-PE38.
  • the phagemid was prepared by rescue of pULI7 phagemid with an M13MK07 helper phage (Bio-Rad, Hercules, California, USA).
  • the DNA was extended and ligated according to the MUTA-GENE* mutagenesis kit protocol (Bio-Rad).
  • Plasmid DNA obtained from a pool of transformants from the mutagenesis reaction was digested with a restriction endonuclease which had a unique site in the B3Fv template, but whose site was absent from both Bl and B5.
  • the digested DNA was used to re-transform E. coli cells. Following this extra step mutants were obtained with an efficiency greater than 80%. Correct clones were identified by DNA restriction analysis and verified by DNA sequencing. The resulting immunotoxin clones were named pBl(Fv)-PE38 and pB5(Fv)-PE38.
  • Plasmids were transformed in the expression-host E. coli BL21 (XDE3) (Studier et al. J. Mol. Biol. 189: 113-30 (1986)). The bacteria were grown in superbroth containing 0.2-0.4% glucose, 0.05 % MgSO 4 , and 100 ⁇ g/ml ampicillin, induced in the log phase at OD ⁇ , of 3.0 with 1 mM isopropyl-B-D-thiogalactopyranoside (IPTG) and harvested 90 min later. About 30% of the total protein of the induced cultures was the recombinant expression product which was deposited in inclusion bodies.
  • the purified inclusion bodies contained almost pure recombinant protein, which had the expected size of about 67 kDa for a single chain immunotoxin.
  • the recombinant immunotoxin molecules were solubilized, refolded, purified, and the protein was analyzed as previously described (Chaudhary et al, Nature 339: 394-97 (1989) & Batra et al., J. Biol. Chem. 265: 15198-202 (1990)). Protein concentrations were determined by Bradford assay (Bradford, Anal Biochem. 72: 848-54 (1976)).
  • inclusion bodies were dissolved in 6 M guanidine (HCD/0.1 M Tris(HCl) Ph 8.0/2 mM EDTA and reduced by the addition of solid DTE to a final concentration of 65 Mm at a protein concentration of 10 mg/ml.
  • the solubilized and reduced inclusion body proteins were diluted x 100 into 0.1 M Tris (Hcl) Ph 8.0/0.5 M L-arginine/0.9 Mm oxidized glutathione/2 Mm EDTA and were allowed to refold for 36 hr at 10°C.
  • the refolded proteins were extensively dialyzed against 20 Mm Tris (Hcl) Ph 7.4/2 Mm EDTA/0.1 M Urea.
  • the recombinant single chain immunotoxins inhibited protein synthesis in cells expressing the B3 antigen but not in non-expressing cells, similarly to the previously described results with chemical conjugate of B3 with a truncated form of PE (Pai et al. Proc. Natl. Acad. Sci. USA, 88: 3358-62 (1991)).
  • the relative potencies of the chemical conjugate and the single chain immunotoxins were about the same on the four antigen positive cell lines MCF7, CRL1739, A431 and LNCaP.
  • the most active agent was B3(Fv)-PE38KDEL. Table 1. Activities of B3 immunotoxins on different cell lines. C totoxicity (ID M ) in ng/ml (pM).
  • the recombinant single chain B3-Fv immunotoxins did not affect B3 antigen-negative control cells.
  • B3(Fv)-PE38KDEL has two features that distinguish it from B3(Fv)-PE40.
  • One is that a portion of domain lb encompassing amino acids 365-380 is deleted. This removes the disulfide bond formed between cysteine residues at positions 372 and 379, which might form disulfide bonds with other cysteines during the renaturation process and thereby result in the creation of inactive chimeric toxins.
  • the second feature is that the carboxyl terminus of the toxin is changed from the original sequence REDLK to KDEL. When the disulfide bond was removed in other molecules, the increase in activity was small.
  • TGF ⁇ -PE38 is only 50% more active than TGF ⁇ -PE40 (see Siegall et al, J. of Biol. Chem. 264: 14256-14261 (1989)).
  • IL6PE38 is no more active than IL6-PE40.
  • Changing REDLK to KDEL usually only produces a two to three fold increase in activity of chimeric toxins.
  • ADP-Ribosvlation Activity The ADP-ribosylation activity of each of the immunotoxins was to tested to verify that they were of equal enzymatic activity. ADP-ribosylation activity was determined by the incorporation on [ C]-NAD into acid-precipitable material using elongation factor 2 enriched wheat-germ extract (Collier and Kandel, /. Biol. Chem., 246: 1496-1503 (1971)). As shown in Fig. 4(A), B3(Fv)-PE38, which was used as a reference molecule, Bl(Fv)-PE38 and B5(Fv)-PE38 had similar ADP-ribosylation activities.
  • Cytotoxicity towards A431 cells was measured by the inhibition of incorporation of [ 3 H]-leucine into cell protein, following 2 hours or 20 hours of incubation of the cells with serial dilutions of immunotoxins in PBS + 0.2% BSA (see Brinkmann. et al. , Proc. Natl. Acad. Sci. USA, 88: 8616-8620 (1991)).
  • B3(Fv)-PE38 has an IC JO of 2.8 ng/ml and 2.0 ng/ml following 2 or 20 hours incubation respectively.
  • Bl(Fv)-PE38 has an IC 50 of 0.6 ng/ml and 0.3 ng/ml following 2 or 20 hours incubation respectively.
  • B5(Fv)-PE38 has an IC-50 of 120 ng/ml and 20 ng/ml following 2 or 20 hours incubation respectively.
  • B3(Fv)-PE38, Bl(Fv)-PE38, and B5(Fv)-PE38 had the same spectrum of recognition of the cancer cell lines tested albeit having different levels of cytotoxic activity toward the antigen-positive cells, which correlates with the binding affinity of each immunotoxin toward its cellular binding site.
  • These cell lines differ in their level of B3 or Bl antigen expression (Pastan et al, 1991; Brinkmann et al, 1993; see Table 3).
  • Bl(Fv)-PE38 competed for the binding of [ 1 5 I]-B1 IgG to A431 cells by 50% at 1.3 ⁇ U, and for the binding of [ , 5 I]-B3 IgG by 50% at 1.7 ⁇ M.
  • B3(Fv)-PE38 competed for the binding of [ 125 rj-Bl IgG to A431 cells by 50% at 2.7 ⁇ M, and for the binding of [ l25 rj-B3 IgG by 50% at 2.5 ⁇ M.
  • B5(Fv)-PE38 competed for the binding of [ !25 I]-B1 IgG to A431 cells by 50% at about 50-100 ⁇ M.
  • Bl IgG competed by 50% for the binding of m l labeled Bl IgG at 110 nM and B3 IgG competed by 50% for the binding of 125 I labeled B3 IgG at 200 nM (not shown).
  • Bl(Fv)-PE38 The activities of the immunotoxins varied with Bl(Fv)-PE38 being the most potent.
  • Bl(Fv)-PE38 had an IC JO of 0.3 ng/ml on A431 cells, and B5(Fv)-PE38 was the least potent, with an IC 50 of 20 ng/ml on A431 cells.
  • the antigen binding assays (Fig. 5) showed that apparently Bl and B5 recognize the same antigen as B3, because all three immunotoxins compete for the binding of 125 I labeled Bl IgG and B3 IgG. However, the possibility of each recognizing a different epitope of a mutual antigen can not be excluded. A clear correlation was observed between each immunotoxins' antigen binding affinity and its cytotoxic potency. The relative low affinity of B5(Fv)-PE38 is consistent with its being derived from an IgM.
  • the stability of the Bl(Fv)-, B3(Fv)- and B5(Fv) immunotoxins following heat treatment was determined by incubation at 0.1 mg/ml in PBS at 37°C for 4 hours, followed by analytical chromatography on a TSK G3000SW (TosoHaas) column, to separate the monomers from the aggregates. Cytotoxic activities of aliquots of heat treated immunotoxins were determined as described above, and compared to the activities of the untreated immunotoxins.
  • Bl(Fv)-PE38 is more stable, as indicated by the fact that its cytotoxic activity following 20 hours incubation on A431 cells is twice the activity following a 2 hour incubation, and by its reduced aggregation and inactivation following incubation at 37°C. B5(Fv)-PE38 may be the most stable as its cytotoxic activity following 20 hours incubation on A431 cells is six fold higher than the activity after a 2 hour incubation.
  • B5(Fv)-PE38 seems to aggregate as much as Bl(Fv)-PE38 in the absence of antigen, but, when incubated with cells, it appears to be more resistant than both Bl(Fv)-PE38 and B3(Fv)-PE38 to inactivation following incubation at 37°C. Since the antigen binding studies were done at 4°C for three hours, conditions under which all three immunotoxins are stable, the relative binding affinities of the immunotoxins best correlate with their relative cytotoxic activities following a 2 hour incubation period.
  • Example 10 Assay of Blood Levels of B3(Fvi-PE38KDEL in Mice
  • Six week old (19-20 gm) female Balb/c mice were injected with 10 ⁇ g of B3(Fv)-PE38KDEL in the tail vein. Blood was drawn at various time intervals and the level of the immunotoxin measured by incubating serum with A431 cells and measuring inhibition of protein synthesis. A standard curve was made with pure B3(Fv)-PE38KDEL and the blood level of immunotoxin (which is shown in Figure 7) calculated using this curve.
  • Example 11 Anti-tumor Activity of B3fFv)-PE38KDEL in Nude Mice Bearing a Human
  • B3(Fv)-PE38 immunotoxins comprising chimeric Fv regions in which the light and heavy chains were derived from different antibodies were constructed as described below.
  • DNA encoding the variable regions of the heavy and light chains of B5 was prepared from mRNA obtained from B5 hybridoma cells as described in Example 2.
  • the V H and V L fragments were PCR amplified using phosphorylated primers to enable the ligation of extended PCR products (see Example 2).
  • the resulting PCR products were used as "primers” in a "domain shuffling" scheme where they replaced the corresponding B3(Fv) V H or V L regions or both, generating single chain Fv-toxin expression plasmids having B3V H -B5V L , B5V H -B3V L , and B5Fv ( Figure 9).
  • Plasmids encoding B3(Fv)-PE38, B5V render-B5V L -PE38, B5V H -B3V L -PE38,
  • B5(Fv)-PE38 or mutated B3(Fv)-PE38 were expressed and the fusion protein purified as described in Example 6. Typically, monomeric proteins were recovered that were over 95% pure.
  • cytotoxic activity of B3(Fv)-PE38 and its derivatives was assessed, according to the method of Brinkmann et al, Proc. Nat. Acad. Sci. USA 88: 8616-8620 (1991), by measuring the incorporation of [ 3 H]-leucine by various human carcinoma cell lines after treatment with serial dilutions of the immunotoxin in phosphate buffered saline (PBS) containing 0.2% BSA as described in Example 8.
  • PBS phosphate buffered saline
  • B3(Fv)-PE38 When tested on A431 cells, which strongly bind monoclonal antibody B3, B3(Fv)-PE38 has an IC*, of 2.8 ng/ml and 2.0 ng/ml following 2 or 20 hours incubation respectively.
  • B3V favour-B5V L -PE38 and B3(Fv)-PE38 V L : M4L S7T are more active and have identical IC so s of 0.6 ng/ml and 0.3 ng/ml following 2 or 20 hours incubation respectively.
  • B5(Fv)-PE38 is much less active with an IC 50 of 120 ng/ml and 20 ng/ml following 2 or 20 hours incubation respectively.
  • B5V favor-B3V L -PE38 has an IC JO of 200 ng/ml and 120 ng/ml following 2 or 20 hours incubation respectively (data not shown).
  • B3V H -B5V L -PE38, and B3(Fv)PE38;V L M4L S7T were tested and compared to that of B3(Fv)-PE38 by determination of their respective levels of aggregation and inactivation at 37°C as described in Example 9. All three immunotoxins were principally monomeric before incubation at 37° C. After one hour of incubation in PBS at 37°C, about half of B3V hinder-B5V L -PE38 and B3(Fv)PE38 V L : M4L S7T were aggregated, whereas B3(Fv)-PE38 was about 75% aggregated.
  • B3(Fv)-PE38 had an IC 50 of 8 ng/ml which is 25% of its cytotoxic activity before treatment. After 2 hours at 37°C, it had an ICw of 200 ng/ml which is about 1 % of its cytotoxic activity before treatment.
  • Both B3V H -B5V L -PE38 and B3(Fv)-PE38: V L M4L S7T cytotoxic activities after one hour at 37°C in PBS were similar to their pretreatment activities. After 2 hours they showed an IC JO of 3.5 ng/ml which is 12% of their cytotoxic activity before treatment.
  • the lower IC 50 of the chimera and the mutant can be explained by the fact that both are more stable that the wild type B3(Fv)-PE38. This improved stability was evident from their slower aggregation and loss of cytotoxic activity upon incubation in PBS at 37°C. Very little B3(Fv)-PE38 monomer survives a 2 hours incubation, whereas the stabilized variants survive for a longer time. This correlates with the fact that while B3(Fv)-PE38 cytotoxic activity is only slightly increased if A431 cells are expressed to it for 20 hours instead of two hours, whereas the stabilized variants show a 3 fold increase upon a 20 hour incubation when compared to a 2 hour incubation on A431 cells.
  • the apparent Kd is 2.33 x 10- 6 for B3(Fv)-PE38 and 1.84 x 10" 6 for B3(Fv)-PE38: V L M4L S7T. This data correlates with binding data obtained by competition with 125 I B3 IgG.
  • Example 1 Humanization of the B3(Fv) Antibody B3(Fv) was humanized by a process of "framework exchange". As will be explained in detail below, the variable domains of the heavy and light chains were aligned with human antibody sequences and, by comparison of each domain with its best human homolog, framework residues that differed between the mouse B3 and its human homolog were identified. Eleven framework residues in V H and eight in V L were changed by site-specific mutagenesis to human residues and introduced simultaneously into a pre-assembled single-chain Fv (scFv) expression cassette.
  • scFv pre-assembled single-chain Fv
  • a structural model of B3(Fv) was constructed based on the crystal structure of the variable domains of monoclonal antibody McPC603 (Satow et al. ,J. Mol. Biol , 190: 593-604 (1986); Abola et al , pp. 107-132 in Crystallographic databases-information content, Software Systems, Scientific Application, eds. Allen, Bergerhoff, & Sievers, Data Comm. of the Intl. Union of Crystallogr. , Bonn (1987); Protein Data bank Entry IMCP), which was modified and refined by an energy minimization algorithm using the program CHARMM (Brooks et al. , J. Comput. Chem. , 4: 187-217 (1983)) version 22.
  • the V H of the human fetal immunoglobulin 56P1'CL (Schroeder et al., Science, 238: 791-793 (1987)) had the highest overall sequence identity and had the highest identity in the framework regions.
  • the alignment of B3 V H with 59P1'CL VH is shown in Figure 11(A).
  • the V L of the human IgM GM607 (Klobeck et al , Nature, 309, 73-76 (1984)) (SWISSPROT file sw:kv2e-human) scored fourth in overall sequence identity (77.7%), but had the highest identity in the framework regions.
  • the alignment of B3 V L with GM603 V L is shown in Figure 11(B).
  • the human antibodies chosen also had similarity to B3(Fv) in the sequence of the complementarity determining region loops (CDRs), and had the same CDR length which further indicates that they belong to a similar structural group, and possibly have a similar canonical structure of the CDR loops (Chothia et al. , J. Biol. Chem. 227: 799-817 (1992); Williams et al , Eur. J. Immunol. 23: 1456-1461 (1993)).
  • CDRs complementarity determining region loops
  • B3 V H and V L gene segments in plasmid pULI7 (Fig. 13(A)) encoding wild type B3(Fv)-PE38 was selected for modification via site-directed mutagenesis.
  • Uracil-containing single-stranded DNA was prepared by rescue of our F+ origin containing plasmids with an M13KO7 helper phage and was used as a template for site-specific mutagenesis (Kunkel, Proc. Natl Acad. Sci. USA, 82: 488-492 (1985)).
  • the complete nucleotide sequence of the gene encoding B3(Fv)-PE38 has been described (Brinkmann, et al. , Proc. Natl. Acad. Sci. USA, 88: 8616-8620 (1991)). Mutagenic oligonucleotides used and the mutation, they are listed in Table 4.
  • B3 V H and V L gene segments in plasmid pULI7 (Fig. 12(A)), encoding wild type B3(Fv)-PE38, were independently humanized by site specific mutagenesis.
  • a set of four oligonucleotides was used to simultaneously introduce the mutations into each segment, with most of the oligonucleotides changing more than one mouse to human codon.
  • the mutations introduced were LI IV and G16R, T40A, E42G and R44G, A74S and R75K, S82aN, R82bS, K83R and S84A.
  • the resulting plasmid was PB3HUMV H -V L -PE38 (Fig. 12(B)).
  • pB3HUMV H -V L -PE38 (Fig. 12(C)) was used as a template for a second mutagenesis with the combined heavy chain mutagenic oligonucleotides generating plasmid pHUMV H -HUMV L -PE38 (Fig. 12(D)), which encodes the humanized B3(Fv) single-chain immunotoxin.
  • the residues that were mutated are identified in Fig. 11 by their numbers.
  • Expression plasmids encoding B3(Fv)-PE38 or its humanized derivatives were introduced into E. coli strain BL21 ( ⁇ DE3) (Studier et al. J. Mol. Biol. 189, 113-130 (1986)) and the recombinant proteins were expressed as inclusion bodies as described in Example 6.
  • the single-chain immunotoxins were obtained by solubilization and refolding of inclusion body protein as described and subsequently purified as described in Example 6. Typically, the monomeric proteins were obtained at over 95% purity, as determined by non-reducing SDS-PAGE of the product.
  • Table 4 Oligonucleotides utilized for site directed mutagenesis and the mutations they introduced. Restriction sites which were introduced into these oligonucleotides to facilitate identification of mutated clones are underlined.
  • B3(Fv)-PE38 had an IC*, of 1.8 ng/ml on A431 cells which express high levels of the B3 antigen.
  • B3V H -HUMV L -PE38 had a similar cytotoxic activity, while B3HUMV H -V L -PE38 (HUM H ) and B3-HUMV H -HUMV L -PE38 (HUMford +L ) had IC 50 s of about 4.4 ng/ml.
  • B3(Fv)-PE38 caused a change in antigen specificity
  • the same cytotoxic assay was done on additional cell tines.
  • B3(Fv)-PE38 and all the humanized variants had the same spectrum of recognition of the cell lines used. These cell lines differ in their level of B3 antigen expression (Brinkmann et al, Proc. Natl. Acad. Sci. USA, 90: 7538-7542 (1993). This result indicates that the antigen binding specificity of the B3(Fv) was not altered by the humanizing process.
  • the specific antigen binding affinity of the B3(Fv) immunotoxins was further analyzed by determination of the binding affinity of B3(Fv)-PE38 and the humanized variants to B3 antigen bearing cells by a competition assay, in which increasing concentrations of each immunotoxin were used to compete for the binding of [ 125 I]-B3 IgG to A431 cells at 4°C.
  • a competition assay in which increasing concentrations of each immunotoxin were used to compete for the binding of [ 125 I]-B3 IgG to A431 cells at 4°C.
  • both B3(Fv)-PE38 and HUM L blocked the binding of [ 125 I]-B3 antibody to A431 cells by 50% at 1-2 ⁇ M.
  • HUM H and HUM2 H+L had a lower affinity, and competed by 50% at 4-5 ⁇ M.
  • the results from the cytotoxicity and the binding assays indicate that the humanized B3(Fv) suffered a 2-3 fold loss in antigen binding affinity and
  • Cytotox c ty data are given as IC*, values, the concentration of immunotoxin that causes a 50% nh b t on of protei synthesis following it's incubation on the cells for 20 hours.
  • Expression level e ⁇ timatior of the B3 antigen is based on immunofluore ⁇ cence. +++, strong; + weak; -, not detected.
  • the immunotoxins used are B3(Fv)PE38, B3V fate- HUMV L -PE38 (HUM L ), B3HUMV H -V L -PE38 (HUM H ), B3HUMV fate-HUMV L -PE38 (HUMific +L ), HUMB3(Fv)-PE38 (HUMFv). All cell lines excej L929 are of human origin.
  • residue 82b in HUM H+L was mutated to arginine by site-specific mutagenesis.
  • the resulting molecule is named HUMB3(Fv)-PE38.
  • the protein was purified to near homogeneity and was subjected to activity and binding assays. As shown in Figure 13(A), its ADP-ribosylation activity did not differ significantly from that of the other immunotoxins. Moreover, as shown in Figures 13(B), 13(C), and Table 5, its cytotoxic and antigen binding activities were improved relative to HUM H+L and were similar to those of the original B3(Fv)-PE38 immunotoxin.
  • Example 17 Reactivity with Sera from Monkevs Immunized with B3fFv)-PE38
  • Sera obtained from monkeys that had been immunized with B3(Fv)-PE38 contain antibodies to PE38 as well as a lower reactivity with B3Fv.
  • sera from four Cynomolgus monkeys containing specific anti B3(Fv)-PE38 titers (Id.) were pooled and used in an ELISA assay on plates that were coated with B3(Fv)-PE38, HUM H+L , or HUMFv (B3HUMFv).
  • B5 Fv binds like B3 Le ⁇ but contains a different antibody binding site, and in addition contains the "conserved" tyrosine in position V H 95. Exchange of this tyrosine to serine was done by site directed mutagenesis (Kunkel, et al 1985) supra.).
  • the resulting B5(Fv)-ser V H 95 mutant molecule (designated B5(Fv): V H Y95S) showed 4-fold increase in specific binding activity as analyzed by cytotoxicity assays, from which the (relative) affinities can be deduced.
  • the V H tyrosine to serine 95 mutation not only increases the affinity of B3(Fv) but also of one other Le ⁇ binding antibody and probably others. Since the mechanism by which the ser 95 causes increased affinity is most likely facilitation of induced fit binding, it is expected that this mutation can also increase the affinity of certain other antibodies, in cases where induced fit will generate increased interactions between the antibody and the antigen.
  • MOLECULE TYPE DNA (primer) ( ix) FEATURE:
  • MOLECULE TYPE DNA (primer) ( ix ) FEATURE :
  • GCA 363 INFORMATION FOR SEQ ID NO:20:
  • MOLECULE TYPE DNA (primer) ( ix) FEATURE:
  • GGCCAGTCTC CACAGCTGCT GATCTACAAA GTTTCCAACC GATTTTCTGG GGTCCCAGAC 600
  • Val Ala Tyr lie Ser Asn Asp Asp Ser Ser Ala Ala Tyr Ser Asp Thr 50 55 60
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE protein
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • Ala Tyr lie Ser Asn Asp Asp Ser Ser Ala Ala Tyr Ser Asp Thr Val 50 55 60
  • Lye Gly Arg Phe Thr lie Ser Arg A ⁇ p Asn Ser Lye A ⁇ n Thr Leu Tyr 65 70 75 80
  • Ala Tyr lie Ser A ⁇ n A ⁇ p A ⁇ p Ser Ser Ala Ala Tyr Ser A ⁇ p Thr Val 50 55 60
  • a ⁇ p lie Val Met Thr Gin Ser Pro Leu Ser Leu Pro Val Thr Pro Gly 1 5 10 15
  • Glu Pro Ala Ser lie Ser Cys Arg Ser Ser Gin Ser Leu Leu His Ser 20 25 30

Abstract

Cette invention se rapporte à des anticorps monochaînes recombinés, qui sont capables de se fixer spécifiquement à un antigène d'hydrate de carbone apparenté aux antigènes de LewisY, ainsi qu'à des protéines de fusion comprenant ces anticorps. Cette invention concerne plus particulièrement les régions Fv monochaîne (scFv) des anticorps monoclonaux B1, B3 et B5, les régions Fv monochaîne humanisées de ces anticorps B1, B3 et B5, ainsi que des protéines de fusion comprenant ces régions scFv. L'invention présente également un certain nombre de mutations stabilisantes de l'anticorps monoclonal B3 se fixant aux antigènes de LewisY. Cette invention concerne en outre des procédés permettant de détecter des cellules portant un antigène de LewisY chez un patient, ainsi que des procédés pour détruire des cellules portant un antigène de LewisY chez un patient ou pour empêcher la croissance de telles cellules. Cette invention se rapporte également à un procédé permettant d'améliorer l'affinité de fixation d'anticorps auxquels ilmanque une sérine à la position 95 de la région V¿H?, ce procédé impliquant la mutation de la position 95 sur une sérine.
PCT/US1995/013811 1994-10-28 1995-10-26 Fragments d'anticorps a specificite tumorale, proteines de fusion, et leurs utilisations WO1996013594A1 (fr)

Priority Applications (3)

Application Number Priority Date Filing Date Title
AU41355/96A AU717611B2 (en) 1994-10-28 1995-10-26 Tumor-specific antibody fragments, fusion proteins, and uses thereof
EP95939599A EP0796334A1 (fr) 1994-10-28 1995-10-26 Fragments d'anticorps a specificite tumorale, proteines de fusion, et leurs utilisations
JP8514718A JPH10508202A (ja) 1994-10-28 1995-10-26 腫瘍特異性抗体断片、融合タンパク質、およびそれらの使用

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US08/331,397 US5981726A (en) 1990-10-12 1994-10-28 Chimeric and mutationally stabilized tumor-specific B1, B3 and B5 antibody fragments; immunotoxic fusion proteins; and uses thereof
US08/331,398 1994-10-28
US08/331,396 1994-10-28
US08/331,396 US5889157A (en) 1990-10-12 1994-10-28 Humanized B3 antibody fragments, fusion proteins, and uses thereof
US08/331,398 US5608039A (en) 1990-10-12 1994-10-28 Single chain B3 antibody fusion proteins and their uses
US08/331,397 1994-10-28

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US7763719B2 (en) 1998-10-31 2010-07-27 The United States Of America As Represented By The Department Of Health And Human Services Variants of humanized anti-carcinoma MAb CC49
US6818749B1 (en) 1998-10-31 2004-11-16 The United States Of America As Represented By The Department Of Health And Human Services Variants of humanized anti carcinoma monoclonal antibody cc49
US7256004B2 (en) 1998-10-31 2007-08-14 United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Variants of humanized anti-carcinoma monoclonal antibody CC49
WO2000026394A1 (fr) * 1998-10-31 2000-05-11 The Government Of The United States Of America As Represented By The Secretary, Department Of Health And Human Services Variants de l'anticorps monoclonal anti-carcinome de type humain cc49
US8029788B2 (en) 1998-10-31 2011-10-04 The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Variants of humanized anti-carcinoma MAb CC49
EP1434800A2 (fr) * 2001-09-14 2004-07-07 Fraunhofer-Gesellschaft Zur Förderung Der Angewandten Forschung E.V. Immunoglobuline dotee d'un squelette particulier ; methodes de fabrication et d'utilisation
EP1434800A4 (fr) * 2001-09-14 2006-05-10 Fraunhofer Ges Forschung Immunoglobuline dotee d'un squelette particulier ; methodes de fabrication et d'utilisation
WO2003076465A2 (fr) * 2002-03-11 2003-09-18 Universite De Sherbrooke Fonction de l'antigene tumoral ca 125 et utilisations associees
WO2003076465A3 (fr) * 2002-03-11 2003-11-13 Univ Sherbrooke Fonction de l'antigene tumoral ca 125 et utilisations associees
US7569673B2 (en) 2002-06-28 2009-08-04 The United States Of America As Represented By The Department Of Health And Human Services Humanized anti-tag 72 cc49 for diagnosis and therapy of human tumors
US8835167B2 (en) 2002-06-28 2014-09-16 The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Humanized anti-tag 72 CC49 for diagnosis and therapy of human tumors
US7919607B2 (en) 2002-06-28 2011-04-05 The United States Of America As Represented By The Department Of Health And Human Services Nucleic acids encoding humanized anti-tag 72 CC49 antbodies
US8535890B2 (en) 2002-06-28 2013-09-17 The United of America as represented by the Secretary of the Department of Health and Human Services Methods to determine immunogenicity of humanized anti-tag 72 CC49 antibodies
US7589181B2 (en) 2003-08-29 2009-09-15 The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Minimally immunogenic variants of SDR-grafted humanized antibody CC49 and their use
US7915396B2 (en) 2003-08-29 2011-03-29 The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Nucleic acid molecules encoding minimally immunogenic variants of SDR-grafted humanized antibody CC49
EP2322551A2 (fr) * 2004-12-22 2011-05-18 Amgen, Inc Compositions conprenant anti-IGF-1R Anticorps et Méthodes pour leur Production
US10336820B2 (en) 2008-02-20 2019-07-02 Amgen Inc. Antibodies directed to angiopoietin-1 and angiopoietin-2 and uses thereof
WO2021019095A1 (fr) * 2019-07-31 2021-02-04 Scancell Limited Éléments de liaison

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AU4135596A (en) 1996-05-23
CA2203236A1 (fr) 1996-05-09
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WO1996013594A8 (fr) 2000-04-06
EP0796334A1 (fr) 1997-09-24

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