Antigen Binding Molecules That Bind EGFR, Vectors Encoding Same, and Uses Thereof

Abstract

The present invention relates to antigen binding molecules (ABMs). In particular embodiments, the present invention relates to recombinant monoclonal antibodies, including chimeric, primatized or humanized antibodies specific for human EGFR. In addition, the present invention relates to nucleic acid molecules encoding such ABMs, and vectors and host cells comprising such nucleic acid molecules. The invention further relates to methods for producing the ABMs of the invention, and to methods of using these ABMs in treatment of disease. In addition, the present invention relates to ABMs with modified glycosylation having improved therapeutic properties, including antibodies with increased Fc receptor binding and increased effector function.

1 . An isolated polynucleotide comprising:
 (a)(i) a sequence selected from the group consisting of: SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:122, and SEQ ID NO:124; and (ii) a sequence selected from the group consisting of: SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, and SEQ ID NO:126; and (iii) SEQ ID NO:108;   (b)(i) SEQ ID NO:114; and (ii) a sequence selected from the group consisting of SEQ ID NO:116 and SEQ ID NO:118; and (iii) SEQ ID NO:119;   (c) a sequence having at least 80% identity to a sequence selected from the group consisting of SEQ ID NO:4; SEQ ID NO:6; SEQ ID NO:8; SEQ ID NO:10; SEQ ID NO:12; SEQ ID NO:14; SEQ ID NO:16; SEQ ID NO:18; SEQ ID NO:20; SEQ ID NO:22; SEQ ID NO:24; SEQ ID NO:26; SEQ ID NO:28; SEQ ID NO:30; SEQ ID NO:32; SEQ ID NO:34; SEQ ID NO:36; SEQ ID NO:38; SEQ ID NO:40, and SEQ ID NO:120;   (d) a sequence having at least 80% identity to a sequence selected from the group consisting of SEQ ID NO:46; SEQ ID NO:50; SEQ ID NO:52;   (e) a sequence that encodes a polypeptide having a sequence selected from the group consisting of SEQ ID NO:3; SEQ ID NO:5; SEQ ID NO:7; SEQ ID NO:9; SEQ ID NO:11; SEQ ID NO:13; SEQ ID NO:15; SEQ ID NO:17; SEQ ID NO:19; SEQ ID NO:21; SEQ ID NO:23; SEQ ID NO:25; SEQ ID NO:27; SEQ ID NO:29; SEQ ID NO:31; SEQ ID NO:33; SEQ ID NO:35; SEQ ID NO:37; SEQ ID NO:39; and SEQ ID NO:121; or   (f) a sequence that encodes a polypeptide having a sequence selected from the group consisting of SEQ ID NO:45, SEQ ID NO:49, and SEQ ID NO:51.   
     
     
         2 - 40 . (canceled) 
     
     
         41 . An expression vector comprising an isolated polynucleotide according to  claim 1 . 
     
     
         42 . (canceled) 
     
     
         43 . A host cell comprising the expression vector of  claim 41 . 
     
     
         44 - 46 . (canceled) 
     
     
         47 . A polypeptide comprising a sequence derived from the rat ICR62 antibody and a sequence derived from a heterologous peptide. 
     
     
         48 . An antigen binding molecule comprising the polypeptide of  claim 47 . 
     
     
         49 - 54 . (canceled) 
     
     
         55 . The polypeptide according to  claim 47 , wherein said polypeptide comprises:
 (a)(i) a polypeptide having a sequence selected from the group consisting of SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:123, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, and SEQ ID NO:125; and (ii) a polypeptide having a sequence selected from the group consisting of SEQ ID NO:75 SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:127, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, and SEQ ID NO:105; and (iii) a polypeptide having the sequence of SEQ ID NO:107;   (b)(i) a polypeptide having a sequence of SEQ ID NO:111 or SEQ ID NO:113; and (ii) a polypeptide having a sequence of SEQ ID NO:115; and (iii) a polypeptide having a sequence of SEQ ID NO:117;   (c) a sequence selected from the group consisting of SEQ ID NO: 1; SEQ ID NO:3; SEQ ID NO:5; SEQ ID NO:7; SEQ ID NO:9; SEQ ID NO:11; SEQ ID NO:13; SEQ ID NO:15; SEQ ID NO:17; SEQ ID NO:19; SEQ ID NO:21; SEQ ID NO:23; SEQ ID NO:25; SEQ ID NO:27; SEQ ID NO:29; SEQ ID NO:31; SEQ ID NO:33; SEQ ID NO:35; SEQ ID NO:37; SEQ ID NO:39; and SEQ ID NO:121, or a variant thereof; or   (d) a sequence selected from the group consisting of SEQ ID NO: 43, SEQ ID NO:45, SEQ ID NO:49, and SEQ ID NO:51, or a variant thereof.   
     
     
         56 - 95 . (canceled) 
     
     
         96 . A method of producing an antigen binding molecule, which is capable of competing with the rat ICR62 antibody for binding to human EGFR, and wherein said antigen binding molecule is chimeric; said method comprising
 (a) culturing the host cell of  claim 43  in a medium under conditions allowing the expression of said polynucleotide encoding said antigen binding molecule; and   (b) recovering said antigen binding molecule.   
     
     
         97 - 98 . (canceled) 
     
     
         99 . A pharmaceutical composition comprising the antigen binding molecule according to  claim 48  and a pharmaceutically acceptable carrier. 
     
     
         100 . A method for treating an EGFR-related disorder comprising:
 (a) predicting a response to anti-EGFR therapy in a human subject by assaying a sample from the human subject before therapy with one or a plurality of reagents that detect expression and/or activation of predictive biomarkers for cancer;   (b) determining a pattern of expression and/or activation of one or more of said predictive biomarkers, wherein the pattern predicts the human subject's response to the anti-EGFR therapy; and   (c) administering to a human subject who is predicted to respond the anti-EGFR directed therapy a therapeutically effective amount of the composition of  claim 99 .   
     
     
         101 . The method of  claim 100 , wherein the predictive biomarker is a growth factor receptor, or a growth factor receptor-related downstream signaling molecule. 
     
     
         102 . The method of  claim 101 , wherein the growth factor receptor is EGFR, phosphorylated EGFR, HER2/neu, HER3, or any combination thereof, and the growth factor receptor-related downstream signaling molecules is selected from the group consisting of Akt, RAS, RAF, MAPK, ERK1, ERK2, PKC, STAT3, and STATS. 
     
     
         103 - 105 . (canceled) 
     
     
         106 . A method for targeting cells expressing EGFR in a subject comprising administering to said subject the pharmaceutical composition of  claim 99 . 
     
     
         107 - 109 . (canceled) 
     
     
         110 . A method of treating a cell proliferation disorder treatable by blocking EGFR-mediated signaling comprising administering a therapeutically effective amount of the pharmaceutical composition of  claim 99  to a human subject in need thereof. 
     
     
         111 . A method for detecting in vivo or in vitro the presence of EGFR in a sample comprising:
 (a) contacting a sample to be tested, optionally with a control sample, with the antigen binding molecule of  claim 48  under conditions that allow for formation of a complex between the antigen binding molecule and EGFR; and   (b) detecting said antigen binding molecule-EGFR complexes.   
     
     
         112 . A host cell engineered to express at least one nucleic acid encoding a polypeptide having β(1,4)-N-acetylglucosaminyltransferase III activity in an amount sufficient to modify the oligosaccharides in the Fc region of a polypeptide produced by said host cell, wherein said polypeptide is the antigen binding molecule according to  claim 48 . 
     
     
         113 - 169 . (canceled) 
     
     
         170 . A method for producing an antigen binding molecule having modified oligosaccharides in a host cell, said method comprising:
 (a) culturing a host cell engineered to express at least one nucleic acid encoding a polypeptide having β(1,4)-N-acetylglucosaminyltransferase III activity under conditions which permit the production of said antigen binding molecule, and which permit the modification of the oligosaccharides present on the Fc region of said antigen binding molecule; and   (b) isolating said antigen binding molecule wherein said antigen binding molecule is capable of competing with the ICR62 antibody for binding to EGFR and wherein said antigen binding molecule or fragment thereof is chimeric.   
     
     
         171 - 207 . (canceled) 
     
     
         208 . A method of treating an EGFR-related disorder in a subject in need of such treatment comprising administering to said subject the antigen binding molecule of  claim 48  in an amount of about 1.0 mg/kg to about 15 mg/kg. 
     
     
         209 - 238 . (canceled) 
     
     
         239 . The antigen binding molecule according to  claim 48 , wherein said antigen binding molecule, when administered to a mammalian subject at concentrations above one microgram per milliliter of serum does not cause a clinically significant level of toxicity in said mammalian subject. 
     
     
         240 - 241 . (canceled) 
     
     
         242 . A method of treating an EGFR-related disorder in a mammal in need of treatment thereof, said method comprising administering to said mammal the antigen binding molecule according to  claim 48 , wherein said treatment results in serum concentrations of said antigen binding molecule between about 1 and about 100 μg/ml for a period of at least 4 weeks, and wherein said treatment does not cause a clinically significant level of toxicity in said mammal. 
     
     
         243 - 244 . (canceled) 
     
     
         245 . A method of inhibiting ligand binding to EGFR, comprising contacting EGFR with the antigen binding molecule according to  claim 48 .