# Patent

## Title
Recombinant tumor specific antibody and use thereof

## Abstract

The invention provides a family of antibodies that specifically bind the human epithelial cell adhesion molecule. The antibodies comprise modified variable regions, more specially, modified framework regions, which reduce their immunogenicity when administered to a human. The antibodies, when coupled to the appropriate moiety, may be used in the diagnosis, prognosis and treatment of cancer.

## Background
RELATED APPLICATIONS
This application is a divisional application of U.S. Ser. No. 10/138,727, filed May 3, 2002 now U.S. Pat. No. 6,969,517, which claims the benefit of and priority to U.S. Ser. No. 60/288,564, filed May 3, 2001, the disclosures of each of which are incorporated by reference herein.


FIELD OF THE INVENTION
The invention relates generally to recombinant antibodies. More particulary, the invention relates to recombinant antibodies that specifically bind human Epithelial Cell Adhesion Molecule, and to their use as diagnostic, prognostic and therapeutic agents.
BACKGROUND OF THE INVENTION
There has been significant progress in the development of antibody-based therapies over the years. For example, investigators have identified not only a variety of cancer-specific markers but also a variety of antibodies that bind specifically to those markers. Antibodies can be used to deliver certain molecules, for example, a toxin or an immune stimulatory moiety, for example, a cytokine, to a cancer cell expressing the marker so as to selectively kill the cancer cell (see, e.g., U.S. Pat. Nos. 5,541,087; and 5,650,150).
The KS-1⁄4 antibody is a mouse-derived monoclonal antibody directed against human epithelial cell adhesion molecule (EpCAM). EpCAM is expressed at very low levels on the apical surface of certain epithelial cells. For example, EpCAM is expressed on intestinal cells on the cell surface facing toward ingested food and away from the circulation, where it would not be accessible to most proteins and cells of the immune system (Balzar et al. [1999] J. Mol. Med. 77:699-712).
Under certain circumstances, however, EpCAM is highly expressed on certain cells, for example, tumor cells of epithelial origin. Typically, these tumor cells have lose their polarity with the result that EpCAM is expressed over the entire surface of the cell. Thus, EpCAM is a convenient tumor-specific marker for directing antibody-based immune-stimulatory moieties to tumor cells (Simon et al. [1990] Proc. Nat. Acad. Sci. USA 78:2755-2759; Perez et al. [1989] J. Immunol. 142:3662-3667).
However, antibodies can have an associated immunogenicity in the host mammal. This is more likely to occur when the antibodies are not autologous. Consequently, the effectiveness of antibody-based therapies often is by an immunogenic response directed against the antibody. The immunogenic response typically is increased when the antibody is derived in whole or in part from a mammal different than the host mammal, e.g., when the antibody is derived from a mouse and the recipient is a human. Accordingly, it may be helpful to modify mouse-derived antibodies to more closely resemble human antibodies, so as to reduce or minimize the immunogenicity of the mouse-derived antibody.
Although a variety of approaches have been developed, including, for example, chimeric antibodies, antibody humanization and antibody veneering, Accordingly, there is a need in the art for antibodies that bind to cancer specific markers and that have reduced immunogenicity when administered to a human. Further, there is a need in the art for antibodies that deliver toxins or immune stimulatory moieties, for example, as fusion proteins or immune conjugates to a cancer specific marker to selectively kill the tumor cell.
SUMMARY OF THE INVENTION
The present invention is based, in part, upon the identification of recombinant antibodies that specifically bind human EpCAM but are less immunogenic in humans than the template, murine anti-EpCAM antibodies. In particular, the invention provides recombinant KS antibodies in which the amino acid sequences defining one or more framework regions and/or complementarity determining regions have been modified to reduce their immunogenicity in humans.
As used herein, the terms “antibody” and “immunoglobulin” are understood to mean (i) an intact antibody (for example, a monoclonal antibody or polyclonal antibody), (ii) antigen binding portions thereof, including, for example, an Fab fragment, an Fab′ fragment, an (Fab′)2 fragment, an Fv fragment, a single chain antibody binding site, an sFv, (iii) bi-specific antibodies and antigen binding portions thereof, and (iv) multi-specific antibodies and antigen binding portions thereof.
As used herein, the terms “bind specifically,” “specifically bind” and “specific binding” are understood to mean that the antibody has a binding affinity for a particular antigen of at least about 106 M−1, more preferably, at least about 107 M−1, more preferably at least about 108 M−1, and most preferably at least about 1010 M−1.
As used herein, the terms “Complementarity-Determining Regions” and “CDRs” are understood to mean the hypervariable regions or loops of an immunoglobulin variable region that interact primarily with an antigen. The immunoglobulin heavy chain variable region (VH) and immunoglobulin light chain variable region (VL) both contain three CDRs interposed between framework regions, as shown in FIG. 1. For example, with reference to the amino acid sequence defining the immunoglobulin light chain variable of the KS-1⁄4 antibody as shown in SEQ ID NO: 1, the CDRs are defined by the amino acid sequences from Ser24 to Leu33 (CDR1), from Asp49 to Ser55 (CDR2), and from His88 to Thr96 (CDR3). With reference to the amino acid sequence defining the immunoglobulin heavy chain variable region of the KS-1⁄4 antibody as shown in SEQ ID NO: 2, the CDRs are defined by the amino acid sequences from Gly26 to Asn35 (CDR1), from Trp50 to Gly66 (CDR2), and from Phe99 to Tyr105 (CDR3). The corresponding CDRs of the other antibodies described herein are shown in FIGS. 1A-1C after alignment with the corresponding KS-1⁄4 heavy or light chain sequence.
As used herein, the terms “Framework Regions” and “FRs” are understood to mean the regions an immunoglobulin variable region adjacent to the Complementarity-Determining Regions. The immunoglobulin heavy chain variable region (VH) and immunoglobulin light chain variable region (VL) both contain four FRs, as shown in FIG. 1. For example, with reference to the amino acid sequence defining the immunoglobulin light chain variable of the of the KS-1⁄4 antibody as shown in SEQ ID NO: 1, the FRs are defined by the amino acid sequences from Gln1 to Cys23 (FR1), from Trp34 to Phe 48 (FR2), from Gly56 to Cys87 (FR3), and from Phe97 to Lys106 (FR4). With reference to the amino acid sequence defining the immunoglobulin heavy chain variable region of the KS-1⁄4 antibody as shown in SEQ ID NO: 2, the FRs are defined by the amino acid sequences from Gln1 to Ser25 (FR1), from Trp36 to Gly49 (FR2), from Arg67 to Arg98 (FR3), and from Trp 106 to Ser 116 (FR4). The FRs of the other antibodies described herein are shown in FIGS. 1A-1C after alignment with the corresponding KS-1⁄4 heavy or light chain sequence.
As used herein, the term “KS antibody” is understood to mean an antibody that binds specifically to the same human EpCAM antigen bound by murine antibody KS-1⁄4 expressed by a hybridoma (see, for example, Cancer Res. 1984, 44 ((2):681-7). The KS antibody preferably comprises (i) an amino acid sequence of SASSSVSY (amino acids 24-31 of SEQ ID NO: 1) defining at least a portion of an immunoglobulin light chain CDR1 sequence, (ii) an amino acid sequence of DTSNLAS (amino acids 49-55 of SEQ ID NO: 1) defining at least a portion of an immunoglobulin light chain CDR2 sequence, (iii) an amino acid sequence of HQRSGYPYT (amino acids 88-96 of SEQ ID NO: 1) defining at least a portion of an immunoglobulin light chain CDR3 sequence, (iv) an amino acid sequence of GYTFTNYGMN (amino acids 26-35 of SEQ ID NO: 2) defining at least a portion of an immunoglobulin heavy chain CDR1 sequence, (v) an amino acid sequence of WINTYTGEPTYAD (amino acids 50-62 of SEQ ID NO: 2) defining at least a portion of an immunoglobulin heavy chain CDR2 sequence, or (vi) an amino acid sequence of SKGDY (amino acids 101-105 of SEQ ID NO: 2) defining at least a portion of an immunoglobulin heavy chain CDR3 sequence, or any combination of the foregoing.
In one aspect, the invention provides a recombinant antibody that specifically binds EpCAM, wherein the antibody comprises an amino acid sequence, a portion of which defines a framework region in an immunoglobulin VL domain. In one embodiment, the framework region (FR1) is defined by amino acid residues 1-23 of SEQ ID NO: 5, wherein Xaa1 is Q or E, Xaa3 is L or V, Xaa10 is I or T, Xaa11 is M or L, Xaa13 is A or L, Xaa18 is K or R, or Xaa21 is M or L, provided that at least one of the amino acid residues at positions Xaa1, Xaa3, Xaa10, Xaa11, Xaa13, Xaa18, or Xaa21 is not the same as the amino acid at the corresponding position in SEQ ID NO: 1. The amino acids at each of the positions are denoted by the standard single letter code.
In another embodiment, the framework region (FR2) is defined by amino acid residues 34-48 of SEQ ID NO: 5, wherein Xaa41 is S or Q, Xaa42 is S or A, Xaa45 is P or L, or Xaa46 is W or L, provided that at least one of the amino acid residues at positions Xaa41, Xaa42, Xaa45, or Xaa46 is not the same as the amino acid at the corresponding position in SEQ ID NO: 1.
In another embodiment, the framework region (FR3) is defined by amino acid residues 56-87 of SEQ ID NO: 5, wherein Xaa57 is F or I, Xaa69 is S or D, Xaa71 is S or T, Xaa73 is I or T, Xaa77 is M or L, Xaa79 is A or P, Xaa82 is A or F, or Xaa84 is T or V, provided that at least one of the amino acid residues at positions Xaa57, Xaa69, Xaa71, Xaa73, Xaa77, Xaa79, Xaa82, or Xaa84 is not the same as the amino acid at the corresponding position in SEQ ID NO: 1.
In another aspect, the invention provides a recombinant antibody that specifically binds EpCAM, wherein the antibody comprises an amino acid sequence, a portion of which defines a framework region in an immunoglobulin VL domain. In one embodiment, the framework region (FR1) is defined by amino acid residues 1-25 of SEQ ID NO: 6, wherein Xaa2 is I or V, Xaa9 is P or A, Xaa11 is L or V, or Xaa17 is T or S, provided that at least one of the amino acid residues at positions Xaa2, Xaa9, Xaa11 or Xaa17 is not the same as the amino acid at the corresponding position in SEQ ID NO: 2.
In another embodiment, the framework region (FR2) is defined by amino acid residues 36-49 of SEQ ID NO: 6, wherein Xaa38 is K or R, Xaa40 is T or A, or Xaa46 is K or E, provided that at least one of the amino acid residues at positions Xaa38, Xaa40, Xaa46 is not the same as the amino acid at the corresponding position in SEQ ID NO: 2.
In another embodiment, the framework region (FR3) is defined by amino acid residues 67-98 of SEQ ID NO: 6, wherein Xaa68 is F or V, Xaa69 is A or T, Xaa70 is F or I, Xaa73 is E or D, Xaa76 is A or T, Xaa80 is F or Y, Xaa83 is I or L, Xaa84 is N or S, Xaa85 is N or S, Xaa88 is N, A or S, Xaa91 is M or T, or Xaa93 is T or V, provided that at least one of the amino acid residues at positions Xaa68, Xaa69, Xaa70, Xaa73, Xaa76, Xaa80, Xaa83, Xaa84, Xaa85, Xaa88, Xaa91 or Xaa93 is not the same as the amino acid at the corresponding position in SEQ ID NO: 2. In another embodiment, the framework region (FR4) is defined by amino acid residues 106-116 of SEQ ID NO: 6, wherein Xaa108 is Q or T.
In another embodiment, the immunoglobulin VL domain comprises an FR1 sequence selected from the group consisting of: (i) amino acid residues 1-23 of SEQ ID NO: 9; and (ii) amino acid residues 1-23 of SEQ ID NO: 8. In another embodiment, the immonoglobulin VH domains comprises an FR sequence defined by amino acid residues 1-25 of SEQ ID NO: 18 and or an FR sequence defined by amino acid residues 67-98 of SEQ ID NO: 18. More preferably, the VL domain comprises an amino acid sequence defined by amino acids 1-106 of SEQ ID NO: 9 and/or the VH domain comprises an amino acid sequence defined by amino acids 1-116 of SEQ ID NO: 18.
Furthermore, the antibody optionally may include an amino acid sequence defining at least a portion of a CDR sequence including, for example, (i) amino acid residues 24-31 of SEQ ID NO: 1; (ii) amino acid residues 49-55 of SEQ ID NO: 1; and/or (iii) amino acid residues 88-96 of SEQ ID NO: 1. Similarly, the antibody optionally may include an amino acid sequence defining at least a portion of a CDR sequence including, for example, (i) amino acid residues 26-35 of SEQ ID NO: 2; (ii) amino acid residues 50-62 of SEQ ID NO: 2; and/or iii) amino acid residues 101-105 of SEQ ID NO: 2.
In another embodiment, the antibody comprises the antigen targeting portion of an antibody-cytokine fusion protein. The cytokine preferably is an interleukin and more preferably is interleukin-2.
In another aspect, the invention provides an expression vector encoding at least a portion of the antibody of the invention. In a preferred embodiment, the expression vector comprises the nucleotide sequence set forth in SEQ ID NO: 40.
In another aspect, the invention provides a method of diagnosing, prognosing and/or treating a human patient having a disease associated with over-expression of EpCAM (for example, a disease in which EpCAM is present at a higher level in diseased tissue relative to tissue without that disease). The method comprises administering one of the antibodies of the invention to an individual in need of such diagnosis, prognosis or treatment.
The antibody optionally includes a diagnostic and/or therapeutic agent attached thereto. The agent may be fused to the antibody to produce a fusion protein. Alternatively, the agent may be chemically coupled to the antibody to produce an immuno-conjugate. It is contemplated that the agent may include, for example, a toxin, radiolabel, cytokine, imaging agent or the like. In a preferred embodiment, the antibody of the invention is fused as a fusion protein to a cytokine. Preferred cytokines preferably include interleukins such as interleukin-2 (IL-2), IL-4, IL-5, IL-6, IL-7, IL-10, IL-12, IL-13, IL-14, IL-15, IL-16 and IL-18, hematopoietic factors such as granulocyte-macrophage colony stimulating factor (GM-CSF), granulocyte colony stimulating factor (G-CSF) and erythropoeitin, tumor necrosis factors (TNF) such as TNFα, lymphokines such as lymphotoxin, regulators of metabolic processes such as leptin, interferons such as interferon α, interferon β, and interferon γ, and chemokines. Preferably, the antibody-cytokine fusion protein displays cytokine biological activity.



DESCRIPTION OF THE DRAWINGS
FIGS. 1A, 1B and 1C show an alignment of light and heavy chain variants and consensus sequences of KS antibodies. The immunoglobulin Framework Regions (FR1-FR4) are denoted by -. The immunoglobulin Complementarity Determining Regions (CDR1-CDR3) are denoted by *. Individual KS antibody light chain V region segments are referred to as “VK,” wherein K refers to the fact that the light chain is a kappa chain. Individual KS antibody heavy chain V region segments are referred to as “VH.” Substitutable amino acids are denoted by “X” in the consensus sequences.



DETAILED DESCRIPTION OF THE INVENTION
The present invention provides recombinant antibodies that specifically bind human Epithelial Cell Adhesion Molecule (EpCAM). Preferred antibodies of the invention have altered variable regions that result in reduced immunogenicity in humans. Antibody variable regions of the invention are particularly useful to target antibodies and antibody fusion proteins to tumor tissues that over-express EpCAM in human patients. In preferred embodiments, an antibody of the invention is fused to a cytokine to produce an immuno-cytokine.
Protein Sequences of the Invention
The present invention discloses a family of antibody variable region or V region sequences that, when appropriately heterodimerized, bind to human epithelial cell adhesion molecule (EpCAM) also known as KS antigen or KSA. Preferred proteins of the invention are useful for treating human patients as described herein. Accordingly, preferred KS antibody variants are humanized, deimmunized, or both, in order to reduce their immunogenicity when administered to a human. According to the invention, murine KS antibodies can be deimmunized or humanized, for example, by using deimmunization methods in which potential T cell epitopes are eliminated or weakened by introduction of mutations that reduce binding of a peptide epitope to an MHC Class II molecule (see, for example WO98/52976, and WO00/34317), or by using methods in which non-human T cell epitopes are mutated so that they correspond to human self epitopes that are present in human antibodies (see, for example, U.S. Pat. No. 5,712,120).
I. Variable Light Chain
The recombinant anti-EpCAM antibody has an immunoglobulin variable light chain sequence having the following amino acid sequence:








(SEQ ID NO: 3)









X-I-X-L-T-Q-S-P-A-X-X-X-X-S-P-G-X-X-X-T-X-T-C-S-A-



 


S-S-S-V-S-T-X-L-W-Y-X-Q-K-P-G-X-X-P-K-X-X-I-X-D-T-


 


S-N-L-A-S-G-X-P-X-R-F-S-G-S-G-T-X-Y-X-L-X-I-X-S-X-


 


E-X-E-D-X-A-X-Y-Y-C-H-Q-R-S-G-Y-P-Y-T-F-G-G-G-T-K-


 


X-E-I-K.






In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin light chain FR1, which is represented by residues 1 to 23 of SEQ ID NO: 3, namely, X-I-X-L-T-Q-S-P-A-X-X-X-X-S-P-G-X-X-X-T-X-T-C. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the FR1 region: Q or E at position Xaa1; L or V at position Xaa3; I, T or S at position Xaa10; M or L at position Xaa11; S or A at position Xaa12; A, L or V at position Xaa13; E or Q at position Xaa17, K or R at position Xaa18, V or A at position Xaa19; and, M, L or I at position Xaa21. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitutions in the FR1 region: E at position Xaa1; V at position Xaa3; T or S at position Xaa10; L at position Xaa11; A at position Xaa12; L or V at position Xaa13; Q at position Xaa17, R at position Xaa18, A at position Xaa19; and, L or I at position Xaa21.
In another embodiment, the recombinant anti-EpCAM antibody of the invention has an amino acid sequence defining an immunoglobulin light chain CDR1, which is represented by residues 24 to 33 of SEQ ID NO: 3, namely S-A-S-S-S-V-S-T-X-L. More particularly, the recombinant anti-EpCAM antibody of the invention has one of the following amino acids in the CDR1 region: M or I at position Xaa32. More preferably, the recombinant anti-EpCAM antibody has an amino acid substitution in the CDR1 region, for example, I at position Xaa32.
In another embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin light chain FR2, which is represented by residues 34 to 48 of SEQ ID NO: 3, namely W-Y-X-Q-K-P-G-X-X-P-K-X-X-I-X. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the FR2 region: Q or L at position Xaa36; S or Q at position Xaa41; S, A or P at position Xaa42; P or L at position Xaa45; W or L at position Xaa46; and, F or Y at position Xaa48. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitutions in the FR2 region: L at position Xaa36; Q at position Xaa41; A or P at position Xaa42; L at position Xaa45; L at position Xaa46; and, Y at position Xaa48.
In another embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin light chain FR3, which is represented by residues 56 to 87 of SEQ ID NO: 3, namely, G-X-P-X-R-F-S-G-S-G-S-G-T-X-Y-X-L-X-I-X-S-X-E-X-E-D-X-A-X-Y-Y-C. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the FR3 region: F or I at position Xaa57; A or S at position Xaa59; S, D or T at position Xaa69; I or T at position Xaa71; I or T at position Xaa73; S or N at position Xaa75; M or L at position Xaa77; A or P at position Xaa79; A or F at position Xaa82; and, T or V at position Xaa84. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitution in the FR3 region: I at position Xaa57; S at position Xaa59; D or T at position Xaa69; T at position Xaa71; T at position Xaa73; N at position Xaa75; L at position Xaa77; P at position Xaa79; F at position Xaa82; and, V at position Xaa84.
In another embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin light chain FR4, which is represented by residues 97 to 106 of SEQ ID NO: 3, namely, F-G-G-G-T-K-X-E-I-K. More particularly, the recombinant anti-EpCAM antibody of the invention has at least one of the following amino acids in the FR4 region, for example, L or V at position Xaa103. Accordingly, the recombinant anti-EpCAM antibody of the invention has an amino acid substitution in the FR4 region, for example, V at position Xaa103.
II. Variable Heavy Chain
The recombinant anti-EpCAM antibody has an immunoglobulin variable heavy chain sequence having the following amino acid sequence:







(SEQ ID NO: 4)








Q-X-Q-L-V-Q-S-G-X-E-X-K-K-P-G-X-X-V-K-I-S-C-K-A-S-



 


G-Y-T-F-T-N-Y-G-M-N-W-V-X-Q-X-P-G-X-G-L-X-W-M-G-W-


 


I-N-T-Y-T-G-E-P-T-Y-A-D-X-F-X-G-R-X-X-X-X-X-X-T-S-


 


X-S-T-X-X-L-Q-X-X-X-L-R-X-E-D-X-A-X-Y-F-C-V-R-F-X-


 


S-K-G-D-Y-W-G-X-G-T-X-V-T-V-S-S






In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy chain FR1, which is represented by residues 1 to 25 of SEQ ID NO: 4, namely Q-X-Q-L-V-Q-S-G-X-E-X-K-K-P-G-X-X-V-K-I-S-C-K-A-S. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the FR1 region: I or V at position Xaa2; P or A at position Xaa9; L or V at position Xaa11; E or S at position Xaa16; and, T or S at position Xaa17. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitutions in the FR1 region: V at position Xaa2; A at position Xaa9; V at position Xaa11; S at position Xaa16; and, S at position Xaa17.
In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy chain FR2, which is represented by residues 36 to 49 of SEQ ID NO: 4, W-V-X-Q-X-P-G-X-G-L-X-W-M-G. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the FR2 region: K or R at position Xaa38; T or A at position Xaa40; K or Q at position Xaa43; and, K or E at position Xaa46. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitutions in the FR2 region: R at position Xaa38; A at position Xaa40; Q at position Xaa43; and, E at position Xaa46.
In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy chain CDR2, which is represented by residues 50 to 66 of SEQ ID NO: 4, namely W-I-N-T-Y-T-G-E-P-T-Y-A-D-X-F-X-G. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the CDR2 region: D or K at position Xaa63; and, K or Q at position Xaa65. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitutions in the CDR2 region: K at position Xaa63; and, Q at position Xaa65.
In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy chain FR3, which is represented by residues 67 to 98 of SEQ ID NO: 4, namely R-X-X-X-X-X-X-T-S-X-S-T-X-X-L-Q-X-X-X-L-R-X-E-D-X-A-X-Y-F-C-V-R. More particularly, the recombinant anti-EpCAM antibody of the invention has at least one of the following amino acids in the FR3 region: F or V at position Xaa68, A, T or V at position Xaa69; F or I at position Xaa70; S or T at position Xaa71; L or A at position Xaa72; E or D at position Xaa73; A or T at position Xaa76; A or L at position Xaa79; F or Y at position Xaa80; I or L at position Xaa83; N or S at position Xaa84; N or S at position Xaa85; N, A or S at position Xaa88; M or T at position Xaa91; and, T or V at position Xaa93. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitutions in the FR3 region: V at position Xaa68, T or V at position Xaa69; I at position Xaa70; T at position Xaa71; A at position Xaa72; D at position Xaa73; T at position Xaa76; L at position Xaa79; Y at position Xaa80; L at position Xaa83; S at position Xaa84; S at position Xaa85; A or S at position Xaa88; T at position Xaa91; and, V at position Xaa93.
In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy chain CDR3, which is represented by residues 99 to 105 of SEQ ID NO: 4, namely F-X-S-K-G-D-Y. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the CDR3 region, for example, I or M at position Xaa100. More preferably, the recombinant anti-EpCAM antibody has an amino acid substitution in the CDR3 region, for example, M at position Xaa100.
In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy chain FR4, which is represented by residues 106 to 116 of SEQ ID NO: 4, namely W-G-X-G-T-X-V-T-V-S-S. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the FR4 region: Q or T at position Xaa108; and, S or T at position X111. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitutions in the FR4 region: T at position Xaa108; and, T at position X111.
III. Refined Variable Light Chain
In another embodiment, the recombinant anti-EpCAM antibody has an immunoglobulin variable light chain sequence having the following amino acid sequence:








(SEQ ID NO: 5)









X-I-X-L-T-Q-S-P-A-X-X-S-X-S-P-G-E-X-V-T-X-T-C-S-A-



 


S-S-S-V-S-Y-M-L-W-Y-Q-Q-K-P-G-X-X-P-K-X-X-I-F-D-T-


 


S-N-L-A-S-G-X-P-A-R-F-S-G-S-G-S-G-T-X-Y-X-L-X-I-S-


 


S-X-E-X-E-D-X-A-X-Y-Y-C-H-Q-R-S-G-Y-P-Y-T-F-G-G-G-


 


T-K-L-E-I-K






In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin light chain FR1, which is represented by residues 1 to 23 of SEQ ID NO: 5, namely X-I-X-L-T-Q-S-P-A-X-X-S-X-S-P-G-E-X-V-T-X-T-C. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the FR1 region: Q or E at position Xaa1; L or V at position Xaa3; I or T at position Xaa10; M or L at position Xaa11; A or L at position Xaa13; K or R at position Xaa18; and, M or L at position Xaa2 1. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitutions in the FR1 region: E at position Xaa1; V at position Xaa3; T at position Xaa10; L at position Xaa11; L at position Xaa13; R at position Xaa18; and, L at position Xaa21.
In another preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin light FR1 having at least one of the following amino acids in the FR1 region: Q or E at position Xaa1; A or L at position Xaa11; and, M or L at position Xaa21. More preferably, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin light FR1 having at least one of the following substitutions in the FR1 region: E at position Xaa1; L at position Xaa11; and, L at position Xaa21.
In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin light chain FR2, which is represented by residues 34 to 48 of SEQ ID NO: 5, namely W-Y-Q-Q-K-P-G-X-X-P-K-X-X-I-F. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the FR2 region: S or Q at position Xaa41; S or A at position Xaa42; P or L at position Xaa45; and, W or L at position Xaa46. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitutions in the FR2 region: Q at position Xaa41; A at position Xaa42; L at position Xaa45; and, L at position Xaa46.
In another preferred embodiment, the recombinant anti-EpCAM antibody of the invention has an amino acid sequence defining an immunoglobulin light FR2 having at least one of the following amino acids in the FR2 region: S or A at position Xaa42; P or L at position Xaa45; and, W or L at position Xaa46. More preferably, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin light FR2 having at least one of the following substitutions in the FR2 region: A at position Xaa42; L at position Xaa45; and, L at position Xaa46.
In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin light chain FR3, which is represented by residues 56 to 87 of SEQ ID NO: 5, namely G-X-P-A-R-F-S-G-S-G-S-G-T-X-Y-X-L-X-I-S-S-X-E-X-E-D-X-A-X-Y-Y-C. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the FR3 region: F or I at position Xaa57; S or D at position Xaa69; S or T at position Xaa71; I or T at position Xaa73; M or L at position Xaa77; A or P at position Xaa79; A or F at position Xaa82; and, T or V at position Xaa84. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitution in the FR3 region: I at position Xaa57; D at position Xaa69; T at position Xaa71; T at position Xaa73; L at position Xaa77; P at position Xaa79; F at position Xaa82; and, V at position Xaa84.
In another preferred embodiment, the recombinant anti-EpCAM antibody of the invention has an amino acid sequence defining an immunoglobulin light FR3 having at least one of the following amino acids in the FR3 region: F or I at position Xaa57; S or D at position Xaa69; A or P at position Xaa79; A or F at position Xaa82; and, T or V at position Xaa84. More preferably, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin light FR3 having at least one of the following substitutions in the FR3 region: I at position Xaa57; D at position Xaa69; P at position Xaa79; F at position Xaa82; and, V at position Xaa84.
IV. Refined Variable Heavy Chain
The recombinant anti-EpCAM antibody has an immunoglobulin variable heavy chain sequence having the following amino acid sequence:








(SEQ ID NO: 6)









Q-X-Q-L-V-Q-S-G-X-E-X-K-K-P-G-E-X-V-K-I-S-C-K-A-S-



 


G-Y-T-F-T-N-Y-G-M-N-W-V-X-Q-X-P-G-K-G-L-X-W-M-G-W-


 


I-N-T-Y-T-G-E-P-T-Y-A-D-X-F-X-G-R-X-X-X-S-L-X-T-S-


 


X-S-T-A-X-L-Q-X-X-X-L-R-X-E-D-X-A-X-Y-F-C-V-R-F-I-


 


S-K-G-D-Y-W-G-Q-G-T-S-V-T-V-S-S






In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy chain FR1, which is represented by residues 1 to 25 of SEQ ID NO: 6, namely Q-X-Q-L-V-Q-S-G-X-E-X-K-K-P-G-E-X-V-K-I-S-C-K-A-S. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the FR1 region: I or V at position Xaa2; P or A at position Xaa9; L or V at position Xaa11; and, T or S at position Xaa17. Accordingly, a recombinant anti-EpCAM antibody of the invention has at least one of the following amino acid substitution in the FR1 region: V at position Xaa2; A at position Xaa9; V at position Xaa11; and, S at position Xaa17.
In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy FR1 having at least one of the following amino acids in the FR1 region: I or V at position Xaa2; P or A at position Xaa9; and, L or V at position Xaa11. Accordingly, a recombinant anti-EpCAM antibody of the invention has an amino acid sequence defining an immunoglobulin heavy FR1 having at least one of the following substitutions in the FR1 region: V at position Xaa2; A at position Xaa9; and, V at position Xaa11.
In another embodiment, a recombinant anti-EpCAM antibody of the invention has an amino acid sequence defining an immunoglobulin heavy chain FR2, which is represented by residues 36 to 49 of SEQ ID NO: 6, namely W-V-X-Q-X-P-G-K-G-L-X-W-M-G. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitution in the FR2 region: K or R at position Xaa38; T or A at position Xaa40; and, K or E at position Xaa46. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitution in the FR2 region: R at position Xaa38; A at position Xaa40; and, E at position Xaa46.
In another preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy FR2 having the following amino acids in the FR1 region, for example, K or E at position Xaa46. More preferably, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy FR2 having an amino acid substitution in the FR1 region, for example, E at position Xaa46.
In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy chain CDR2, which is represented by residues 50 to 66 of SEQ ID NO: 6, namely W-I-N-T-Y-T-G-E-P-T-Y-A-D-X-F-X-G. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the CDR2 region: D or K at position Xaa63; and, K or Q at position Xaa65. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitutions in the CDR2 region: K at position Xaa63; and, Q at position Xaa65.
In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy chain FR3, which is represented by residues 67 to 98 of SEQ ID NO: 6, namely R-X-X-X-S-L-X-T-S-X-S-T-A-X-L-Q-X-X-X-L-R-X-E-D-X-A-X-Y-F-C-V-R. More particularly, the recombinant anti-EpCAM antibody of the invention has at least one of the following amino acids in the FR3 region: F or V at position Xaa68; A or T at position Xaa69; F or I at position Xaa70; E or D at position Xaa73; A or T at position Xaa76; F or Y at position Xaa80; I or L at position Xaa83; N or S at position Xaa84; N or S at position Xaa85; N, A or S at position Xaa88; M or T at position Xaa91; and, T or V at position Xaa93. More preferably, the recombinant anti-EpCAM antibody has at least one of the following amino acid substitutions in the FR3 region: V at position Xaa68; T at position Xaa69; I at position Xaa70; D at position Xaa73; T at position Xaa76; Y at position Xaa80; L at position Xaa83; S at position Xaa84; S at position Xaa85; A or S at position Xaa88; T at position Xaa91; and, V at position Xaa93.
In another preferred embodiment, the recombinant anti-EpCAM antibody of the invention has an amino acid sequence defining an immunoglobulin heavy chain FR3 having at least one of the following amino acids in the FR3 region: F or V at position Xaa68; E or D at position Xaa73; N or S at position Xaa84; N or S at position Xaa85; N or A at position Xaa88; and, T or V at position Xaa93. More preferrably, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy FR3 having at least one of the following substitutions in the FR3 region: V at position Xaa68; D at position Xaa73; S at position Xaa84; S at position Xaa85; A at position Xaa88; and, V at position Xaa93.
In a preferred embodiment, the recombinant anti-EpCAM antibody has an amino acid sequence defining an immunoglobulin heavy chain FR4, which is represented by residues 106 to 116 of SEQ ID NO: 6, namely W-G-X-G-T-S-V-T-V-S-S. More particularly, the recombinant anti-EpCAM antibody has at least one of the following amino acids in the FR4 region, for example, Q or T at position Xaa108. More preferably, the recombinant anti-EpCAM antibody has an amino acid substitution in the FR4 region, for example, T at position Xaa108.
Accordingly, preferred V regions contain substitutions in FR domains of VH and/or VK regions corresponding to murine KS-1⁄4 variable regions. In addition, preferred V regions of the invention do not include insertions or deletions of amino acids relative to the murine KS-1⁄4 variable regions.
Preferred variants include proteins having variable regions with greater than 80% identity/homology murine KS-1⁄4. The amino acid sequence of murine KS variable region or a portion thereof may be used as a reference sequence to determine whether a candidate sequence possesses sufficient amino acid similarity to have a reasonable expectation of success in the methods of the present invention. Preferably, variant sequences are at least 70% similar or 60% identical, more preferably at least 75% similar or 65% identical, and most preferably 80% similar or 70% identical to a murine KS variable heavy or light chain FR or CDR.
To determine whether a candidate peptide region has the requisite percentage similarity or identity to a murine KS sequence, the candidate amino acid sequence and murine KS sequence are first aligned using the dynamic programming algorithm described in Smith and Waterman (1981) J. Mol. Biol. 147:195-197, in combination with the BLOSUM62 substitution matrix described in FIG. 2 of Henikoff and Henikoff (1992) PNAS 89:10915-10919. For the present invention, an appropriate value for the gap insertion penalty is −12, and an appropriate value for the gap extension penalty is −4. Computer programs performing alignments using the algorithm of Smith-Waterman and the BLOSUM62 matrix, such as the GCG program suite (Oxford Molecular Group, Oxford, England), are commercially available and widely used by those skilled in the art. Once the alignment between the candidate and reference sequence is made, a percent similarity score may be calculated. The individual amino acids of each sequence are compared sequentially according to their similarity to each other. If the value in the BLOSUM62 matrix corresponding to the two aligned amino acids is zero or a negative number, the pairwise similarity score is zero; otherwise the pairwise similarity score is 1.0. The raw similarity score is the sum of the pairwise similarity scores of the aligned amino acids. The raw score is then normalized by dividing it by the number of amino acids in the smaller of the candidate or reference sequences. The normalized raw score is the percent similarity. Alternatively, to calculate a percent identity, the aligned amino acids of each sequence are again compared sequentially. If the amino acids are non-identical, the pairwise identity score is zero; otherwise the pairwise identity score is 1.0. The raw identity score is the sum of the identical aligned amino acids. The raw score is then normalized by dividing it by the number of amino acids in the smaller of the candidate or reference sequences. The normalized raw score is the percent identity. Insertions and deletions are ignored for the purposes of calculating percent similarity and identity. Accordingly, gap penalties are not used in this calculation, although they are used in the initial alignment.
The invention also discloses methods for assaying the expression of KS antibodies from cells such as mammalian cells, insect cells, plant cells, yeast cells, other eukaryotic cells or prokaryotic cells (see Example 1). In a preferred method, KS antibody V regions are expressed as components of an intact human antibody, and the expression of the antibody from a eukaryotic cell line assayed by an ELISA that detects the human Fc region. To precisely quantify binding of a KS antibody to EpCAM, a Biacore assay may be used.
Treatment of Human Disease with KS Antibody Fusion Proteins
The invention also discloses the sequences of KS antibody-IL2 fusion proteins that are useful in treating human disease, such as cancer. Certain KS antibody-IL2 fusion proteins, such as KS-1⁄4-IL2 (see, for example, Construct 3 in Example X), may be used to treat human patients with cancer, with surprisingly little immune response against the antibody.
It is found that, during treatment of human cancers with KS-1⁄4(VH2/VK1)-IL2, even less immunogenicity is seen than with KS-1⁄4(Construct 3)-IL2. Specifically, during a clinical trial, patients with anti-idiotypic antibodies and antibody directed against the antibody-IL2 junction or against the IL-2 moiety are seen at an even lower frequency than with KS-1⁄4(Construct 3)-IL2. Antibody variable regions of the invention can also be fused to other cytokines, for example, interleukins 1, 2, 6, 10, or 12; interferons alpha and beta; TNF, and INF gamma. The invention may be more fully understood by reference to the following non-limiting examples
EXAMPLES
Example 1
Methods and Reagents for Expressing KS Antibodies and Assaying Their Antigen-Binding Activity
1A. Cell Culture and Transfection
The following general techniques were used in the subsequent Examples. For transient transfection, plasmid DNA was introduced into human kidney 293 cells by co-precipitation of plasmid DNA with calcium phosphate [Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y.].
In order to obtain stably transfected clones, plasmid DNA was introduced into the mouse myeloma NS/O cells by electroporation. NS/O cells were grown in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum. About 5×106 cells were washed once with PBS and resuspended in 0.5 ml phosphate buffer solution (PBS). Ten μg of linearized plasmid DNA was then incubated with the cells in a Gene PulserTM Cuvette (0.4 cm electrode gap, BioRad) for 10 minutes on ice. Electroporation was performed using a Gene PulserTM (BioRad) with settings at 0.25 V and 500 μF. Cells were allowed to recover for 10 minutes on ice, after which they were resuspended in growth medium and then plated onto two 96-well plates. Stably transfected clones were selected by growth in the presence of 100 nM methotrexate (MTX), which was introduced two days post-transfection. The cells were fed every 3 days for two to three more times, and MTX-resistant clones appeared in 2 to 3 weeks. Supernatants from clones were assayed by anti-human Fc ELISA to identify high producers [Gillies et al. (1989) J. Immunol. Methods 125:191]. High producing clones were isolated and propagated in growth medium containing 100 1 nM MTX.
1B. ELISAs
Three different ELISAs were used to determine the concentrations of protein products in the supernatants of MTX-resistant clones and other test samples. The anti-huFc ELISA was used to measure the amount of human Fc-containing proteins, e.g., chimeric antibodies. The anti-hu kappa ELISA was used to measure the amount of kappa light chain (of chimeric or human immunoglobulins). The anti-muFc ELISA was used to measure the amount of muFc-containing proteins in test samples (see Example 1C below).
The anti-huFc ELISA is described in detail below.
A. Coating Plates
ELISA plates were coated with AffiniPure goat anti-human IgG (H+L) (Jackson Immuno Research) at 5 μg/ml in PBS, and 100 μl/well in 96-well plates (Nunc-Immuno plate Maxisorp). Coated plates were covered and incubated at 4° C. overnight. Plates were then washed 4 times with 0.05% TweenTM (TweenTM 20) in PBS, and blocked with 1% BSA/1% goat senlm in PBS, 200 μl/well. After incubation with the blocking buffer at 37° C. for 2 hours, the plates were washed 4 times with 0.05% TweenTM in PBS and tapped dry on paper towels.
B. Incubation with Test Samples and Secondary Antibody
Test samples were diluted to the proper concentrations in sample buffer, which contained 1% BSA/1% goat serum/0.05% TweenTM in PBS. A standard curve was prepared with a chimeric antibody (with a human Fc), the concentration of which was known. To prepare a standard curve, serial dilutions are made in the sample buffer to give a standard curve ranging from 125 ng/ml to 3.9 ng/ml. The diluted samples and standards were added to the plate, 100 μd/well, and the plate incubated at 37° C. for 2 hours.
After incubation, the plate was washed 8 times with 0.05% TweenTM in PBS. To each well was then added 100 μl of the secondary antibody, the horse radish peroxidase (HRP) -conjugated anti-human IgG (Jackson Immuno Research), diluted around 1:120,000 in the sample buffer. The exact dilution of the secondary antibody had to be determined for each lot of the HRP-conjugated anti-human IgG. After incubation at 37° C. for 2 hours, the plate was washed 8 times with 0.05% TweenTM in PBS.
C. Development
The substrate solution was added to the plate at 100 μl/well. The substrate solution was prepared by dissolving 30 mg of o-phenylenediamine dihydrochloride (OPD) (1 tablet) into 15 ml of 0.025 M citric acid/0.05M Na2HPO4 buffer, pH 5, which contained 0.03% of freshly added H2O2. The color was allowed to develop for 30 minutes at room temperature in the dark. The developing time was subject to change, depending on lot to lot variability of the coated plates, the secondary antibody, etc. The color development in the standard curve was observed to determine when to stop the reaction. The reaction was stopped by adding 4N H2SO4, 100 μl/well. The plate was read by a plate reader, which was set at both 490 nm and 650 nm and programmed to subtract off the background OD at 650 nm from the OD at 490 nm.
The anti-hu kappa ELISA followed the same procedure as described above, except that the secondary antibody used was horse radish peroxidase-conjugated goat anti-hu kappa (Southern Biotechnology Assoc. Inc., Birmingham, Ala.), used at 1:4000 dilution.
The procedure for the anti-muFc ELISA was also similar, except that ELISA plates were coated with AffiniPure goat anti-murine IgG (H+L) (Jackson Immuno Research) at 5 μg/ml in PBS, and 100 μl/well; and the secondary antibody was horse radish peroxidase-conjugated goat anti-muIgG, Fcγ (Jackson ImmunoResearch), used at 1:5000 dilution.
1C. Cloning of the KS Antigen (KSA, EpCAM) and Expression of the Soluble Form as Human EpCAM-Murine Fc
Messenger RNA (MRNA) was prepared from LnCAP cells using DynabeadsTM mRNA Direct Kit (Dynal, Inc., Lake Success, N.Y.) according to the manufacturer's instructions. After first strand CDNA synthesis with oligo(dT)) and reverse transcriptase, full length CDNA encoding epithelial cell adhesion molecule (also known as KS antigen or KSA), was cloned by polymerase chain reaction (PCR). The sequences of the PCR primers were based on the published sequence described in Perez and Walker (1989) J. Immunol. 142:3662-3667. The sequence of the sense primer is TCTAGAGCAGCATGGCGCCCCCGCA (SEQ ID NO: 27), and the sequence of the nonsense prime: is CTCGAGTTATGCATTGAGTTCCCT (SEQ ID NO: 28), where the translation initiation codon and the anti-codon of the translation stop codon are denoted in bold, and the restriction sites Xbal (TCTAGA) and Xhol (CTCGAG) are underlined. The PCR product was cloned and the correct KSA sequence was confirmed by sequencing several independent clones. The CDNA sequence of the KSA from LnCAP was essentially identical to the published sequence of KSA from UCLA-P3 cells (Perez and Walker, 1989). However, at amino acid residue number 115, the nucleotide sequence from LnCAP was ATG rather than ACG (Met instead of Thr, and at amino acid residue number 277, the nucleotide sequence from LnCAP was ATA rather than ATG (IIe instead of Met).
Binding of KS-1⁄4 antibody to recombinant KSA was demonstrated by immunostaining. Surface expression of KSA was obtained by transfecting cells, e.g., CT26, B16, etc., with full length KSA in a suitable mammalian expression vector (pdCs, as described in U.S. Pat. No. 5,541,087), followed by immunostaining with the KS-1⁄4 antibody. For the expression of KSA as a soluble antigen, the portion of the cDNA encoding the transmembrane domain of the KSA was deleted. To facilitate expression, detection, and purification, the soluble KSA was expressed as a KSA-muFc, the construction of which is described as follows. The 780 bp XbaI-EcoRI restriction fragment encoding the soluble KSA was ligated to the AflII-XhoI fragment encoding the muFc (U.S. Pat. No. 5,726,044) via a linker-adaptor:










(SEQ ID NO: 29)











5′  AA TTC TCA ATG CAG GGC       3′




 










(SEQ ID NO: 30)











3′       G AGT TAC GTC CCG AAT T 5′







The XbaI-XhoI fragment encoding soluble KSA-muFc was ligated to the pdCs vector. The resultant expression vector, pdCs-KSA-muFc, was used to transfect cells and stable clones expressing KSA-muFc were identified by anti-muFc ELISA.
1D. Measurement of Antigen Binding
KSA-muFc in conditioned medium was first purified by Protein A chromatography according to supplier's protocol (Repligen, Cambridge, Mass.). Purified KSA-muFc was used to coat 96-well plates (Nunc-Immuno plate, Maxisorp) at 5 μg/ml in PBS, and 100 μl/well. The assay was similar to the ELISA procedure described in Example 1B. Briefly, coated plates were covered and incubated at 4° C. overnight. Plates then were washed and blocked. Test samples were diluted to the proper concentrations in the sample buffer, added to the plate at 100 μl/well, and the plate was incubated at 37° C. for 1 hour. After incubation, the plate was washed 8 times with 0.05% Tween in PBS. To each well was then added 100 μl of the secondary antibody, the horse radish peroxidase-conjugated anti-human IgG (Jackson Immuno Research), diluted around 1:120,000 in the sample buffer. The plate was then developed and read as described in Example 1B.
1E. Measurement of On-Rates and Off-Rates of KS-1⁄4 Antibodies from EpCAM using a Biacore Assay.
The affinity of KS-1⁄4 and KS-IL2 molecules for the antigen EpCAM were measured by surface plasmon resonance analysis of the antibody-antigen interaction, using a BiacoreTM machine (Biacore International AR, Uppsala, Sweden). EpCAM-murineFc was coupled to a CM5 sensor chip using an nmine coupling protocol supplied by the manufacturer. KS-1⁄4 and KS-IL2 at concentrations varying between 25 nm and 200 nM were then passed over the chip, whereby binding to the chip was observed. Using the built-in curve-fitting routines of the BiacoreTM software, the on-rate, off-rate, association and dissociation constants were calculated.
1F. Measurement of Binding Affinities of KS-1⁄4 Antibodies Using Cell Lines Expressing EpCAM
Purified KS-1⁄4 antibodies were iodinated with 125I using standard techniques, and increasing concentrations of labeled protein were incubated with the EpCAM-positive cell line PC-3. Saturation binding curves were generated and the dissociation constants were determined by Scatchard analysis.
Example 2
Cloning of cDNAs Encoding VH and VK of Mouse KS-1⁄4 and Construction of Vector for the Expression of KS-1⁄4 Hybridoma-Derived Antibody
Messenger RNA prepared from the mouse KS-1⁄4-expressing hybridoma (obtained from R. Reisfeld, Scripps Research Institute) was reverse transcribed with oligo(dT) and then used as templates for PCR to amplify the sequences encoding the variable region of the heavy chain (VH) and the variable region of the light chain (VK). The PCR primers were designed based on published sequences (Beavers et al., ibid.). The PCR primers for VH had the following sequences:








(SEQ ID NO: 31)









VH forward primer (5′) GACTCGAGCCCAAGTCTTAGACATC



(3′) 


 








(SEQ ID NO: 32)









VH reverse primer (5′) CAAGCTTACCTGAGGAGACGGTGACTG



ACGTTC (3′),






where the CTCGAG and AAGCTT sequences represent the XhoI and HindIII restriction sites, respectively, used for ligating the VH into the expression vector (see below); and the TAC in the reverse primer would introduce GTA, the splice donor consensus sequence, in the sense strand of the PCR product.

The PCR primers for VK had the following sequences:








(SEQ ID NO: 33)








VK forward primer (5′) GATCTAGACAAGATGGATTTTCAAGTG


(3′)


 








(SEQ ID NO: 34)








VK reverse primer (5′) GAAGATCTTACGTTTTATTTCCAGCTT


GG (3′)






where the TCTAGA and AGATCT sequences represent the XbaI and BglII restriction sites, respectively, used for ligating the VK into the expression vector (see below); ATG is the translation initiation codon of the light chain; and the TAC in the reverse primer would introduce GTA, the splice donor consensus sequence, in the sense strand of the PCR product.

The PCR products encoding the VH and VK of the mouse KS-1⁄4 antibody were cloned into pCRII vector (Invitrogen, Carlsbad, Calif.). Several VH and VK clones were sequenced and the consensus sequence of each determined. The VH and VK sequences were inserted in a stepwise fashion into the expression vector pdHL7. The ligations took advantage of the unique XhoI and HindIII sites for the VH, and the unique XbaI and BglII/BamHI sites for the VK (the unique BglII in the VK insert and the unique BamHI in the vector have compatible overhangs). The resultant construct is called pdHL7-hybridoma chKS-1⁄4, which already contained transcription regulatory elements and human Ig constant region sequences for the expression of chimeric antibodies (Gillies et al. (1989) J. Immunol. Methods 125:191).
The expression vector pdHL7 was derived from pdHL2 [Gillies et al. (1991) Hybridoma 10:347-356], with the following modifications: in the expression vector pdHL2, the transcriptional units for the light chain and the heavy chain-cytokine consisted of the enhancer of the heavy chain immunoglobulin gene and the metallothionein promoter. In pdHL7, these two transcriptional units consisted of the CMV enhancer-promoter [Boshart et al. (1985) Cell 41:521-530]. The DNA encoding the CMV enhancer-promoter was derived from the AflIII-HindIII fragment of the commercially available pcDNAI (Invitrogen Corp., San Diego, Calif.).
Example 3
Expression Studies of Murine KS-1⁄4 Antibodies
This example discusses expression studies performed using an antibody expression plasmid encoding the V region sequences disclosed in U.S. Pat. No. 4,975,369.
3A. Plasmid Construction
To directly compare the chimeric antibodies encoded by the Hybridoma KS-1⁄4 sequence and those sequences described in U.S. Pat. No. 4,975,369, the cDNA encoding the VH sequence described in U.S. Pat. No. 4,975,369 was synthesized. This was then ligated into the pdHL7 expression vector already containing the VK of KS-1⁄4.
In order to construct the VH sequence described in U.S. Pat. No. 4,975,369, an NdeI-HindIII fragment encoding part of the VH sequence was obtained by total chemical synthesis. Overlapping oligonucleotides were chemically synthesized and ligated. The ligated duplex was then subcloned into a XbaI-HindIII pBluescript vector (Stratagene, LaJolla, Calif.).
This DNA encodes the protein sequence IQQPQNMRTM (residues 83-92 of SEQ ID NO:35) of U.S. Pat. No. 4,975,369. Immediately 3′ to the coding sequence is the splice donor site beginning with gta. The ctag at the 5′ end of the top strand is the overhang for the XbaI cloning site. The XbaI site was created only for cloning into the polylinker of the pBluescript vector. It was followed immediately by the NdeI restriction site (CATATG). The agct at the 5′ end of the bottom strand is the overhang of the HindIII cloning site. This HindIII sticky end is later ligated to the HindIII site in the intron preceding the Cγl gene [Gillies et al. (1991) Hybridoma 10:347-356].
After sequence verification, the NdeI-HindIII restriction fragment was isolated. This, together with the XhoI-NdeI fragment encoding the N-terminal half of VH, was then ligated to the XhoI-HindIII digested pdHL7 expression vector containing the VK of KS-1⁄4. The resultant construct, pdHL7-'369 chKS-1⁄4, contained the VK and VH described in U.S. Pat. No. 4,975,369 (referred to as U.S. Pat. No. 4,975,369 chKS-1⁄4).
3B. Comparison of Hybridoma chKS-1⁄4 and U.S. Pat. No. 4,975,369 chKS-1⁄4 Antibodies
The plasmid DNAs pdHL7-hybridoma chKS-1⁄4 and pdHL7-'369 chKS-1⁄4 were introduced in parallel into human kidney 293 cells by the calcium phosphate coprecipitation procedure mentioned above. Five days post-transfection, the conditioned media were assayed by anti-huFc ELISA and kappa ELISA (see Example 1 for ELISA procedures) and the results are summmarized in Table 1.











TABLE 1







Antibody
huFc ELISA
Kappa ELISA









Hybridoma chKS-1/4
254 ng/mL
200 ng/mL



U.S. Pat. No.
 14 ng/mL
 0 ng/mL



4,975,369 chKS-1/4










The results indicated that hybridoma chKS-1⁄4 was expressed and secreted normally, and that the secreted antibody consisted of roughly equimolar amounts of heavy and light chains, within the accuracies of the two different ELISAs. On the other hand, only a low level of heavy chain was detected in the conditioned medium for the U.S. Pat. No. 4,975,369 chKS-1⁄4 antibody, and no kappa light chain was associated with it.
Western blot analysis was performed on the total cell lysates and the conditioned media of the two transiently transfected cell lines. The procedures for Western blot analysis were as described in (Sambrook et al. (1989), supra). In order to analyze the total cell lysates, the transfected cells were lysed, centrifuged to remove the debris, and the lysate from the equivalent of 5×105 cells applied per lane. To analyze the conditioned media, the protein product from 300 μL of the conditioned medium was first purified by Protein A Sepharose chromatography prior to SDS-PAGE under reducing conditions. After Western blot transfer, the blot was hybridized with a horseradish peroxidase-conjugated goat anti-human IgG, Fcγ (Jackson ImmunoResearch), used at 1:2000 dilution.
The Western blot transfer showed that under the conditions used, the heavy chain was detected in both the conditioned media and the lysed cells of the transfection with pdHL7-hybridoma chKS-1⁄4. This result indicates that the heavy chain of the chKS-1⁄4 antibody was produced in the cells and secreted efficiently (together with the light chain). On the other hand, the heavy chain from the transfection with pdHL7-'369 chKS-1⁄4 was detected only in the cell lysate but not in the conditioned media. This result indicated that although a comparable level of heavy chain was produced inside the cell, it was not secreted. This finding was consistent with the ELISA data, which showed that there was no kappa light chain associated with the small amount of secreted heavy chain in the U.S. Pat. No. 4,975,369 chKS-1⁄4 antibody. It is understood that immunoglobulin heavy chains typically are not normally secreted in the absence of immunoglobulin light chains [Hendershot et al. (1987) Immunology Today 8:111].
In addition to the foregoing, NS/0 cells were transfected by electroporation with the plasmids pdHL7-Hybridoma chKS-1⁄4 and pdHL7-U.S. Pat. No. 4,975,369 chKS-1⁄4 in parallel. Stable clones were selected in the presence of 100 nM MTX, as described in Example 1, and the conditioned media of the MTX-resistant clones in 96-well plates was assayed by anti-huFc ELISA, as described in Example 1. The results are summarized in Table 2.










TABLE 2






Total num-





ber of clones

Highest level


Antibody
screened
Mode*
of expression*




















Hybridoma
80
0.1-0.5
μg/mL (41)
10-50
μg/mL (4)


chKS-1/4


U.S.
47
0-10
ng/mL (36)
0.1-0.4
μg/mL (4)


Pat. No.


4,975,369


chKS-1/4





(*The numbers in parentheses denote the number of clones in the mode or the number expressing the highest levels of product, as determined by anti-Fc ELISA.)






When screened at the 96-well stage, the majority of the clones obtained with the pdHL7-hybridoma chKS-1⁄4 construct produced about 100 ng/mL to 500 ng/mL of antibody, with the best clones producing about 10-50 μg/mL. On the other hand, the majority of the clones obtained with the pdHL7-'369 chKS-1⁄4 construct produced about 0 ng/mL to 10 ng/mL of antibody, with the best producing about 300-400 ng/mL. To examine the composition and binding properties of the U.S. Pat. No. 4,975,369 chKS-1⁄4 antibody, it was necessary to grow up the clones that produced at 300-400 ng/mL. Two of these clones were chosen for expansion. However, their expression levels were found to be very unstable. By the time the cultures were grown up to 200 mL, the expression levels of both clones had dropped to about 20 ng/mL, as assayed by anti-Fc ELISA. When the same conditioned media were assayed by the anti-kappa ELISA, no kappa light chain was detected, as was the case in transient expression in 293 cells.
The following experiment indicated that no detectable kappa light chain was associated with the U.S. Pat. No. 4,975,369 chKS-1⁄4 heavy chain. Briefly, 50 mL each of the conditioned media from each of the clones was concentrated by Protein A chromatography. The eluate were assayed by anti-Fc ELISA and anti-kappa ELISA. As a control, conditioned medium from a hybridoma chKS-1⁄4-producing clone was treated the same way and assayed at the same time. The ELISA results are summarized in Table 3.











TABLE 3







Antibody
huFc ELISA
Kappa ELISA









Hybridoma chKS-1/4
 42 μg/mL
44 μg/mL



U.S. Pat. No. 4,975,369
253 ng/mL
 0 ng/mL



chKS-1/4-clone 1



U.S. Pat. No. 4,975,369
313 ng/mL
 0 ng/mL



chKS-1/4-clone 21










The results showed that there was indeed no detectable kappa light chain associated with the U.S. Pat. No. 4,975,369 chKS-1⁄4 heavy chain. Furthermore, the hybridoma chKS-1⁄4 antibody was shown to bind KS antigen at 10-20 ng/mL, whereas the U.S. Pat. No. 4,975,369 antibody from both clones and concentrated to 253 and 313 ng/mL, still did not bind KS antigen (see Example 9 for measurement of binding to KS antigen.)
Example 4
Expression and Characterization of Variant KS Antibodies
Mutations that significantly lower the expression or the affinity of an antibody for a target molecule are expected to be less effective for therapeutic purposes in humans. Some approaches to reducing immunogenicity, such as “veneering,” “humanization,” and “deimmunization” involve the introduction of many amino acid substitutions, and may disrupt binding of an antibody to an antigen (see, e.g., U.S. Pat. Nos. 5,639,641; and 5,585,089; and PCT Publication Nos. WO 98/52976; WO 00/34317). There is a need in the art for classes of antibody sequences that will bind to epithelial cell adhesion molecule, but which are distinct from the original mouse monoclonal antibodies that recognize this antigen.
Various combinations of KS-1⁄4 heavy and light chain variable (“V”) regions were tested for their ability to be expressed, and for their ability to bind to EpCAM. These results are summarized in Tables 4-6 and described below.







TABLE 4





Sequences of KS-1/4 antibody heavy and light chain V regions.















Light chains:










        10        20        30        40        50        60




         |          |          |          |         |          |


VK0
QILLTQSPAIMSASPGEKVTMTCSASSSVSYMLWYQQKPGSSPKPWIFDTSNLASGFPAR


VK1
QIVLTQSPASLAVSPGQRATITCSASSSVSYILWYQQKPGQPPKPWIFDTSNLASGFPSR


VK6
EIVLTQSPATLSLSPGERVTLTCSASSSVSYMLWYQQKPGQAPKLLIFDTSNLASGIPAR


VK7
QILLTQSPAIMSASPGERVTMTCSASSSVSYMLWYQQKPGSSPKPWIFDTSNLASGFPAR


VK8
EIVLTQSPATLSLSPGERVTLTCSASSSVSYMLWYQQKPGSSPKPWIFDTSNLASGFPAR


 











        70        80        90       100





         |          |          |         |


VK0
FSGSGSGTSYSLIISSMEAEDAATYYCHQRSGYPYTFGGGTKLEIK
(SEQ ID NO: 1)


VK1
FSGSGSGTSYTLTINSLEAEDAATYYCHQRSGYPYTFGGGTKVEIK
(SEQ ID NO: 11)


VK6
FSGSGSGTDYTLTISSLEPEDFAVYYCHQRSGYPYTFGGGTKLEIK
(SEQ ID NO: 7)


VK7
FSGSGSGTSYSLIISSMEPEDAATYYCHQRSGYPYTFGGGTKLEIK
(SEQ ID NO: 8)


VK8
FSGSGSGTSYSLIISSMEAEDAATYYCHQRSGYPYTFGGGTKLEIK
(SEQ ID NO: 9)







Heavy chains:










        10        20        30        40        50        60




         |          |          |          |         |          |


VH0
QIQLVQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQTPGKGLKWMGWINTYTGEPTY


VH1
QIQLVQSGPELKKPGSSVKISCKASGYTFTNYGMNWVRQAPGKGLKWMGWINTYTGEPTY


VH2
QIQLVQSGPELKKPGSSVKISCKASGYTFTNYGMNWVRQAPGKGLKWMGWINTYTGEPTY


VH2.5
QIQLVQSGPELKKPGSSVKISCKASGYTFTNYGMNWVRQAPGKGLKWMGWINTYTGEPTY


VH6
QVQLVQSGAEVKKPGESVKISCKASGYTFTNYGMNWVRQAPGKGLEWMGWINTYTGEPTY


VH7
QIQLVQSGAEVKKPGETVKISCKASGYTFTNYGMNWVKQTPGKGLKWMGWINTYTGEPTY


VH369
QIQLVQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQTPGKGLKWMGWINTYTGEPTY


 











        70        80         90        100       110





         |          |           |          |         |


VH0
ADDFKGRFAFSLETSASTAFLQINNLRNE.DMATYFCVRFISKGDYWGQGTSVTVSS
(SEQ ID NO: 2)


VH1
ADDFKGRFTITAETSTSTLYLQLNNLRSE.DTATYFCVRFMSKGDYWGQGTTVTVSS
(SEQ ID NO: 21)


VH2
ADDFKGRFTITAETSTSTLYLQLNNLRSE.DTATYFCVRFISKGDYWGQGTTVTVSS
(SEQ ID NO: 22)


VH2.5
ADDFKGRFTITAETSTSTLYLQLNNLRSE.DTATYFCVRFISKGDYWGTGTTVTVSS
(SEQ ID NO: 19)


VH6
AQKFQGRVTISLDTSTSTAYLQLSSLRAE.DTAVYFCVRFISKGDYWGQGTSVTVSS
(SEQ ID NO: 17)


VH7
ADDFKGRFAFSLETSTSTAFLQINNLRSE.DTATYFCVRFISKGDYWGQGTSVTVSS
(SEQ ID NO: 18)


VH369
ADDFKGRFAFSLETSASTAFLQIqqpqnmrtMATYFCVRFISKGDYWGQGTSVTVSS
(SEQ ID NO: 35)

















TABLE 5





Sequences of KS-1/4 antibody variants and CDR3 heavy chain



variants with single amino acid insertions.


















VH2 partial seq.:
. . . ATYFCVRF I S K GDYWGQG. . .
(amino acid residues



92-109 of SEQ ID NO: 22)


 


VH2.1:
. . . ATYFCVRF IIS K GDYWGQG. . .
(SEQ ID NO: 36)


 


VH2.2:
. . . ATYFCVRF IVS K GDYWGQG. . .
(SEQ ID NO: 37)


 


VH2.3:
. . . ATYFCVRF I SAK GDYWGQG. . .
(SEQ ID NO: 38)


 


VH2.4:
. . . ATYFCVRF I S KTGDYWGQG. . .
(SEQ ID NO: 39)
















TABLE 6







Expression levels and binding activity of variant KS-1/4 antibodies.










Expression
EpCAM affinity












Transient (*)
Stable (*)
Relative



Contruct
(in ng/mL)
(in μg/mL)
binding (**)
Kd (nM)














Group 1






VK0/VH0 (Hybridoma chKS-1/4)

10-50
  1x
1.0 × 10−9


VK0/VH′369 (′369 chKS-1/4)

      0.1-0.4 (***)
>>30x


VK8/VH7 (Construct 3)

10-50

1.0 × 10−9


VK6/VH6 (Construct 1)
300

n.d.


VK7/VH7 (Construct 2)
30


VK8/VH7-IL2

10-50

1.0 × 10−9


VK1/VH1-IL2

10-50

7.9 × 10−9


VK1/VH2-IL2

10-50

3.1 × 10−9


Group 2


VK8/VH7 (Construct 3; control)
1500

     1x


VK0/VH1
1500

     8x


VK1/VH7
1500

     1x


VK1/VH1
1500

     2x


VK1/VH2
1500

1x-2x


VK1/VH1-IL2
1500

     5x


VK1/VH2-IL2
1500

    1.5x


VK1/VH2.5-IL2
1500

3x-4x


Group 3


VK8/VH7-IL2 (control)
760

     1x


VK1/VH1-IL2
350

     2x


VK1/VH2.1-IL2
290

   >10x


VK1/VH2.2-IL2
270

   >10x


VK1/VH2.3-IL2
190

     7x


VK1/VH2.4-IL2
210

     3x





(*) Routinely achievable levels.


(**) “Relative Binding” is expressed as the fold-increase in protein concentration required to reach an equivalent level of binding. Thus, a larger number reflects a lower affinity for EpCAM.


(***) Kappa light chain was not detectable by ELISA (equivalent to background); therefore, functional antibodies were not expressed.


(**) n.d. = not detectable


In Group 2 and Group 3, the relative binding activity of each protein was normalized to the control shown in the first line for that group. The ELISA assay is primarily a reflection of off-rates, based on amount of protein bound after several rounds of washes. It is used as a rapid screen to rule out poor binders, but is not a precise measure of affinity. In Group 3, VH2 variants VH2.1-VH2.4 were compared with VH1 to determine if amino acid insertions might result in improved relative binding.






The sequences are related as follows. As described in the examples, the VH0 and VK0 sequences were derived from PCR amplification from a hybridoma cell line that expresses the original mouse-derived KS-1⁄4 (SEQ ID NO: 1 and SEQ ID NO: 2). VH-'369 is the VH sequence disclosed in U.S. Pat. No. 4,975,369. Sequences VH1, VH2, VH2.1-2.4 VK1, and VK2 were derived either using deimmunization technology where potential T cell epitopes are eliminated or weakened by introduction of mutations that reduce binding of a peptide epitope to an MHC Class II molecule, or by changing non-human T cell epitopes so that they correspond to human self-epitopes that are present in human antibodies. The design of these constructs is further described and analyzed below. Constructs of Table 6 were generated by transfecting mammalian cells with combinations of nucleic acids that expressed the corresponding heavy and light chain V regions. Sequences VH6, VH7, VK6, VK7, and VK8 were generated by changing surface residues of the hybridoma KS-1⁄4 to human counterparts as described below, with the purpose of removing potential human B cell epitopes. Constructs 1 through 3 were generated by transfecting mammalian cells with combinations of nucleic acids that expressed heavy and light chain V regions VH6, VH7, VK6, VK7, and VK8 as described in Table 4 and below.
4A. Characterization of KS Antibodies with Fewer Human T Cell Epitopes
Sequences VH2.1-VH2.5 were made to test whether certain amino acid insertions and substitutions in the region of the KS-1⁄4 heavy chain CDR3 could be tolerated. Expression vectors for the light and heavy chain combinations VK0/VH1, VK1/VH7, VK1/VH1, VK1/VH2, VK1/VH1-IL2, VK1/VH2-IL2, and VK1/VH2.5-IL2 were constructed and the corresponding antibodies and antibody-IL2 fusion proteins expressed and tested according to methods described in the preceding examples.
Specifically, sequences VH1, VH2, VK1, and VK2 were obtained by total chemical synthesis. For each of these sequences, a series of overlapping oligonucleotides that span the entire coding and complementary strands of these regions were chemically synthesized, phosphorylated, and ligated. The ligated duplex molecules were then amplified by PCR with appropriate primers to the fragment ends, introduced into pCRII vector (Invitrogen, Carlsbad, Calif.) and the sequences verified. These DNA fragments were then introduced into the expression vector pdHL7 at appropriate sites to generate the complete heavy (“H”) chain and light (“L”) chain, respectively.
Sequence VH2.5 was derived from VH2 by the modification of a single codon to obtain a Thr rather than a Gln at position 108 (Table 4), using standard molecular biology techniques.
The antibodies were tested by ELISA (Table 6) and using surface plasmon resonance (BiacoreTM machine and software) to compare their ability to bind to EpCAM. Results of the ELISA experiments were considered to reflect primarily off-rate and not on-rate, and to be generally less precise, such that a poor ELISA result was generally used to exclude certain constructs from further consideration. However, antibodies that showed good binding by the ELISA test needed to be characterized further.
Results of the surface plasmon resonance analysis were as follows:
















Fusion Protein
kon (M−1 s−1)
koff (s−1)
KD (M)









VK8/VH7-IL2
3.1 × 105
3.2 × 10−4
1.0 × 10−9



VK1/VH2-IL2
1.7 × 105
5.3 × 10−4
3.1 × 10−9



VK1/VH1-IL2
2.8 × 105
2.2 × 10−3
7.9 × 10−9










Because the off-rate of VK1/VH1-IL2 was much faster than for VK1/V2-IL2 or VK8/VH7-IL2, VK1/VH1-IL2 was considered to be a less useful fusion protein.
Considering that VK1/VH1-IL2 and VK1/VH1-IL2 differ only by the methionine/isoleucine difference at VH position 100 in CDR3, the enhanced off-rate of VK1/VH1-IL2 compared to VK1/VH2-IL2 suggests that this position makes a hydrophobic contact with EpCAM, and that the slightly longer methionine side-chain makes a less effective contact. In the field of protein-protein interactions, it is generally thought that hydrophobic interactions play a major role in determining off-rates but a much less significant role in determining on-rates.
4B. Characterization of KS-1⁄4 Variants with Single Amino Acid Insertions
The importance of the CDR3 sequence in the heavy chain V region for the affinity of the KS antibody to EpCAM was determined with a series of variants that contained an amino acid insertion or substitution in this region. Sequences VH2.1, VH2.2, VH2.3, and VH2.4 were generated by manipulation of an expression vector encoding VH2 and VK1 using standard recombinant DNA techniques. The resulting expression vectors were transfected into NS/0 cells and secreted antibody proteins purified as described in preceding examples.
It was found that the VH1 variant was suboptimal compared to the VH2 variant, indicating that the isoleucine in CDR3 could not be substituted with methionine. The next goal was to test whether insertion of an amino acid in CDR3 could yield a KS-1⁄4 heavy chain V region with better binding characteristics than VH1. The data in Table 6 compare the binding of VK1/VH2.1, VK1/VH2.2, VK1/VH2.3, and VK1/VH2.4, with VK1/VH1. It was found that none of the constructs with an amino acid insertion in the KS-1⁄4 VH CDR3 showed improved antigen binding compared to VH1, rather, antigen binding activity of the insertion mutants was either somewhat decreased or profoundly decreased.
These results indicate that insertion of amino acids in CDR3 generally is deleterious to the antigen binding activity of KS-1⁄4 heavy chain V regions. When this data is analyzed, some general conclusions emerge. Specifically, the segment of KS-1⁄4 VH amino acid at positions 84 to 108, consisting of the amino acids Asn-Asn-Leu-Arg-Asn-Glu-Asp-Met-Ala-Thr-Tyr-Phe-Cys-Val-Arg-Phe-Ile-Ser-Lys-Gly-Asp-Tyr-Trp-Gly-Gln (residues 84 to 108 of SEQ ID NO:2), is important for KS-1⁄4 antigen binding. This segment includes a framework segment, Asn-Asn-Leu-Arg-Asn-Glu-Asp-Met-Ala-Thr-Tyr-Phe-Cys-Val-Arg (residues 84-98 of SEQ ID NO :2), which is generally tolerant to single and multiple amino acid substitutions, but not tolerant to amino acid insertions, which may have a deleterious effect on expression and assembly. In addition, the data suggests that for the amino acids at positions 86, 91, 93, 94, and 95, it is preferable to have hydrophobic amino acids for an antibody that is efficiently expressed and binds to EpCAM.
Insertion of an amino acid in the V.sub.H CDR3 segment, consisting of Phe-Ile-Ser-Lys-Gly-Asp-Tyr (residues 99-105 of SEQ ID NO:2), is generally deleterious to the EpCAM antigen-binding function of a KS-1⁄4 antibody, although some insertions can be tolerated with only partial loss of activity. Similarly, substitution of these positions is also generally deleterious to binding of the EpCAM antigen, although some insertions can be tolerated with only partial loss of activity.
4C. Construction of Active Derivatives of KS-1⁄4 Antibodies with Mouse Surface Residues Converted to Their Human Counterparts
Antibodies were prepared by substituting amino acids within the KS-1⁄4 antibody with amino acids commonly found in human antibodies in order to minimize the immunogenicity of the mouse-derived V regions. Preferred KS derivatives also retained specific binding affinity for human EpCAM.
Construct 1. It was found that the KS-1⁄4 light chain most closely resembled human consensus subgroup III, and the heavy chain most closely resembled subgroup I. Based on these similarities, a conceptual sequence consisting of the human consensus subgroup amino acids and KS-1⁄4-derived CDRs and non-consensus amino acids was generated. For this and the following constructs a three-dimensional model was generated using a Silicon GraphicsTM Workstation and Biosym molecular modeling software.
Inspection of the three-dimensional model revealed that certain human-derived amino acids were close to the CDRs and were likely to influence their conformation. Based on this analysis, in the light chain, human Ser22, Arg44, and Phe66 were changed back to Thr, Lys, and Tyr, respectively. In the heavy chain, it was believed such changes were unnecessary. In the final design for Construct 1, the light chain had 18 human amino acids not found in the mouse light chain, and the heavy chain had 22 human amino acids not found in the mouse heavy chain.
DNAs for expression of Construct 1 were created using synthetic oligonucleotides. The Construct 1 protein was efficiently expressed but was found to be more than 10-fold less active in an EpCAM binding assay.
Construct 2. A less aggressive approach was then taken, by which only the following changes were introduced:
Light chain: K18R, A79P
Heavy chain: P9A, L11V, A76T, N88S, M91T
DNAs for expression of Construct 2 were created using synthetic oligonucleotides and standard recombinant DNA techniques. The Construct 2 protein was not efficiently expressed. It was further found that the combination of Construct 2 light chain and mouse KS-1⁄4 heavy chain was not efficiently expressed, while the combination of Construct 2 heavy chain and mouse KS-1⁄4 light chain was efficiently expressed. Thus, the expression defect appeared to lie in the Construct 2 light chain.
Construct 3. Based on the apparent expression defect in the Construct 2 light chain, a new light chain was constructed by fusing the N-terminal portion of the light chain of Construct 1 with the C-terminal portion of the mouse light chain. The KpnI site, which encodes the amino acids at positions 35 and 36, was used. When this light chain was combined with the Construct 2 heavy chain, efficient expression and no significant loss of binding was observed.
Because Construct 3 resulted in an antibody with superior properties in terms of protein expression and affinity for the antigen when compared to Construct 1 or 2, DNA sequences of Construct 3 were inserted into pdHL7s-IL2, resulting in pdHL7s-VK8/VH7-IL2, which is disclosed as SEQ ID NO: 40. For expression purposes, this plasmid DNA was electroporated into mouse myeloma cells NS/0 to produce a stably transfected cell line as described in Example 1A. Culture medium taken from stable clones was then assayed for antibody expression in an ELISA coated with human Fc, as described in Example 1B. The amino acid sequences of the heavy and light chain for this antibody fusion protein are shown in SEQ ID NO: 41 and SEQ ID NO: 42, respectively.
In addition, the binding of iodinated VK8/VH7 and VK8/VH7-IL2 to EpCAM expressed on the surface of PC-3 tumor cells was compared to binding of iodinated VK0/VH0-IL2, using methods described in Example 1F. Within experimental error, essentially identical binding affinities were found for VK8/VH7 and VK0/VH0, and for VK8/VH7-IL2 and VK0/VH0-IL2.
4D. Structure-Function Relationships Useful in Constructing Active KS-1⁄4 Antibodies
Taken together, the antigen binding activities of KS-1⁄4 antibodies and fusion proteins with the disclosed V region sequences provide guidance in designing sequences of KS-1⁄4 antibodies to EpCAM, as well as for proper expression and secretion of KS-1⁄4 antibodies. In particular, the KS-1⁄4 heavy and light chain V regions can tolerate multiple amino acid substitutions and retain activity, provided that these amino acid substitutions are outside the CDRs. The KS-1⁄4 heavy and light chain V regions do not generally appear to tolerate amino acid insertions, especially within CDRs or in framework regions between CDRs.
For example, if the hybridoma KS-1⁄4 sequence is taken to be a starting, “wild-type” sequence, the data indicate that the heavy chain V region can tolerate amino acid substitutions at positions 9, 11, 16, 17, 38, 40, 69, 70, 71, 72, 76, 79, 80, 83, 88, 91, and 111 with little or no loss of activity. Similarly, the light chain can tolerate amino acid substitutions at positions 1, 3, 10, 11, 12, 13, 17, 18, 19, 21, 41, 42, 59, 71, 73, 75, 77, and 103 with little or no loss of activity. These changes are outside the CDRs of KS-1⁄4 heavy and light chain V regions. The 17 clearly acceptable heavy chain amino acid substitutions represent about 21% of the amino acid positions outside the CDRs, and about 68% of the amino acid positions outside the CDRs for which an amino acid substitution was attempted. Similarly, the eighteen clearly acceptable light chain amino acid substitutions represent about 23% of the amino acid positions outside the CDRs, and about 72% of the amino acid positions outside the CDRs for which an amino acid substitution was attempted. There were only two examples of an amino acid substitution outside of a CDR that resulted in a significantly less useful protein: the substitution Ala79Pro in the light chain, which appeared to have a negative impact on expression; and the substitution Q108T in the heavy chain, which had a negative impact on antigen binding. Thus, an amino acid substitution can be introduced into a KS-1⁄4 antibody heavy chain or light chain sequence outside of a CDR, and there is a high probability that the substitution will result in an active protein.
Mutations involving the substitution of an amino acid in a CDR often have a negative impact on antigen binding. For example, the substitution I100M in the heavy chain reduces binding by about 8-fold. Mutations that involve the insertion of an amino acid generally have a negative impact on the utility of a KS-1⁄4 sequence. For example, the VH-'369 heavy chain V region is unable to assemble into a proper antibody with a light chain, as described herein. The VH2.1 to 2.4 mutations have an insertion of an amino acid in CDR3 of the heavy chain V region, and each of these mutations has a negative impact on antigen binding.
Example 5
Immunogenicity of a KS Antibody (Construct 3)-IL2 Fusion Protein in Humans
In a human clinical trial, twenty two patients received one or more treatment regimes, with each treatment regime comprising three consecutive daily 4-hour intraveous infusions of KS antibody (Construct 3)-IL2. Each treatment regime was separated by a month (Weber et al. (2001). Proc. Am. Soc. Clin. Oncology 20:259a.). Serum samples were harvested from each patient before and after each treatment regime and tested for antibody reactivity against the whole KS Antibody (Construct 3)-IL2 molecule or the Fc-IL2 component (without the Fv region). No reactivity was observed in any of the pre-immune sera. The results indicated that only 4 patients experienced any significant immune response against either the Fv regions alone, or both the Fv regions and the Fc-IL2 component. Furthermore, these responses did not appear to be boosted upon subsequent exposure to huKS-IL2.
It is believed that the use of the antibody-IL2 fusion protein constitutes a particularly stringent test of the immunogenicity of the V region, because the interleukin-2 moiety has an adjuvant effect. Accordingly, the results indicate that the KS Antibody (Construct 3) may be administered to humans with only a small number of recipients apparently developing an antibody response to the KS antibody (Construct 3)-IL2 fusion protein. These results are particularly encouraging in view of the fact that the KS antibody (Construct 3) contains a variable region that is almost entirely murine in origin but with a few amino acid residues replaced with the corresponding human amino acid residues.
EQUIVALENTS
The invention may be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting on the invention described herein. The scope of the invention is thus indicated by the appended claims rather than by the foregoing description, and all changes which come within the meaning and range of equivalency of the claims are intended to be embraced therein.
INCORPORATION BY REFERENCE
The disclosure of each of the patent documents and scientific publications disclosed herein, are incorporated by reference into this application in their entirety.

## Claims

1. An anti-EpCAM protein comprising an antibody that binds human EpCAM, said antibody comprising an immunoglobulin light chain variable region comprising (i) amino acid residues 24-31 of SEQ ID NO:1; (ii) amino acid residues 49-55 of SEQ ID NO:1; and (iii) amino acid residues 88-96 of SEQ ID NO:1; and further comprising an amino acid sequence defining an immunoglobulin light chain framework region selected from the group consisting of: (i) amino acid residues 1-23 of SEQ ID NO:8; and (ii) amino acid residues 1-23 of SEQ ID NO:9.

2. The anti-EpCAM protein of claim 1, wherein the antibody comprises amino acids 1-106 of SEQ ID NO:9.

3. The anti-EpCAM protein of claim 1, wherein the antibody has a Kd for EpCAM of at least 10−8 M.

4. The anti-EpCAM protein of claim 1, wherein the protein comprises a cytokine.

5. The anti-EpCAM protein of claim 4, wherein the cytokine is IL-2.

6. An anti-EpCAM protein, wherein the protein comprises an antibody that binds human EpCAM, said antibody comprising an immunoglobulin heavy chain variable region comprising (i) amino acid residues 26-35 of SEQ ID NO:2; (ii) amino acid residues 50-62 of SEQ ID NO:2; and (iii) amino acid residues 101-105 of SEQ ID NO:2; and further comprising an amino acid sequence defining an immunoglobulin heavy chain framework region selected from the group consisting of: (i) amino acid residues 1-25 of SEQ ID NO:18; and (ii) amino acid residues 67-98 of SEQ ID NO:18.

7. The anti-EpCAM protein of claim 6, wherein the antibody comprises amino acids 1-116 of SEQ ID NO:18.

8. The anti-EpCAM protein of claim 6, wherein the antibody has a Kd for EpCAM of at least 10−8 M.

9. The anti-EpCAM protein of claim 6, wherein the protein comprises a cytokine.

10. The anti-EpCAM protein of claim 9, wherein the cytokine is IL-2.

11. An anti-EpCAM protein, wherein the protein comprises an antibody that binds human EpCAM, said antibody comprising an antibody light chain comprising the amino acid sequence defined by residues 1-106 of SEQ ID NO:9 and an antibody heavy chain comprising the amino acid sequence defined by residues 1-116 of SEQ ID NO:18.

12. The anti-EpCAM protein of claim 11, wherein the protein comprises a cytokine.

13. The anti-EpCAM protein of claim 12, wherein the cytokine is IL-2.

14. A humanized or deimmunized anti-EpCAM protein suitable for administering into a human patient for treating a disease associated with EpCAM over-expression, wherein the protein comprises an antibody that binds human EpCAM, said antibody comprising an immunoglobulin light chain variable region comprising (i) amino acid residues 24-31 of SEQ ID NO:1; (ii) amino acid residues 49-55 of SEQ ID NO:1; and (iii) amino acid residues 88-96 of SEQ ID NO:1; and further comprising an amino acid sequence defining an immunoglobulin light chain framework region selected from the group consisting of: (i) amino acid residues 1-23 of SEQ ID NO:8; and (ii) amino acid residues 1-23 of SEQ ID NO:9.

15. A humanized or deimmunized anti-EpCAM protein suitable for administering into a human patient for treating a disease associated with EpCAM over-expression, wherein the protein comprises an antibody that binds human EpCAM, said antibody comprising an immunoglobulin heavy chain variable region comprising (i) amino acid residues 26-35 of SEQ ID NO:2; (ii) amino acid residues 50-62 of SEQ ID NO:2; and (iii) amino acid residues 101-105 of SEQ ID NO:2; and further comprising an amino acid sequence defining an immunoglobulin heavy chain framework region selected from the group consisting of: (i) amino acid residues 1-25 of SEQ ID NO:18; and (ii) amino acid residues 67-98 of SEQ ID NO:18.

16. A humanized or deimmunized anti-EpCAM protein suitable for administering into a human patient for treating a disease associated with EpCAM over-expression, wherein the protein comprises an antibody that binds human EpCAM, said antibody comprising an antibody light chain comprising the amino acid sequence defined by residues 1-106 of SEQ ID NO:9 and an antibody heavy chain comprising the amino acid sequence defined by residues 1-116 of SEQ ID NO:18.