Glycan-Interacting Compounds and Methods of Use

Abstract

The present invention provides glycan-interacting antibodies and methods for producing glycan-interacting antibodies useful in the treatment and prevention of human disease, including cancer. Such glycan-interacting antibodies include humanized antibodies, derivatives and fragments thereof as well as related compositions and kits. Methods of using glycan-interacting antibodies for treatment and diagnosis are included.

What is claimed is: 
     
         1 . An antibody, wherein said antibody comprises a heavy chain variable domain (VH) with a CDR-H3 complementarity determining region having at least 50% amino acid sequence identity to an amino sequence selected from the group consisting of SEQ ID NOs: 115, 114, 116-120, 140, and 141. 
     
     
         2 . The antibody of  claim 1 , wherein the VH comprises:
 a CDR-H1 having at least 50% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 105, 106, and 136; and   a CDR-H2 having at least 60% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 107-113, and 137-139.   
     
     
         3 . An antibody, wherein said antibody comprises a light chain variable domain (VL) with a CDR-L3 having at least 50% amino acid sequence identity to an amino sequence selected from the group consisting of SEQ ID NOs: 89, 91, 93, 95-98, 101-103, 133-135, and 148. 
     
     
         4 . The antibody of  claim 3 , wherein the VL comprises:
 a CDR-L1 having at least 50% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 121-129, and 142-146; and   a CDR-L2 having at least 50% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 77, 79-81, 83-86, 88, 130-132, and 147.   
     
     
         5 . The antibody of any of  claims 1-4  comprising at least one human framework region having an amino acid sequence with at least 70% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 206-216. 
     
     
         6 . An antibody comprising a VH having at least 70% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 220-224, 230-234, 237-241, 249-253, and 256-260. 
     
     
         7 . An antibody comprising a VL having at least 70% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 217-219, 225-229, 235, 236, 242-248, 254, and 255. 
     
     
         8 . The antibody of  claim 6  or  7 , wherein said antibody comprises:
 a VH having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 220-224; and 
 a VL having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 217-219. 
 
     
     
         9 . The antibody of  claim 6  or  7 , wherein said antibody comprises:
 a VH having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 237-241; and 
 a VL having at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 235 and 236. 
 
     
     
         10 . The antibody of any of  claims 1-9 , wherein said antibody comprises an isotype selected from the group consisting IgG1, IgG2a, IgG2b, IgG2c, IgG3, and IgG4. 
     
     
         11 . The antibody of any of  claims 1-10 , wherein said antibody is a human or humanized antibody. 
     
     
         12 . The antibody of any of  claims 1-10 , wherein said antibody is a human IgG1 antibody. 
     
     
         13 . A construct encoding the antibody of any of  claims 1-12 . 
     
     
         14 . A cell comprising the construct of  claim 13 . 
     
     
         15 . A vector comprising the construct of  claim 13 . 
     
     
         16 . An antibody produced by the cell of  claim 14 . 
     
     
         17 . The antibody of any of  claims 1-12 , wherein said antibody binds to cell-associated STn with a half maximal effective concentration (EC50) of from about 0.01 nM to about 30 nM. 
     
     
         18 . The antibody of any of  claims 1-12 , wherein said antibody is conjugated to a therapeutic agent. 
     
     
         19 . The antibody of  claim 18 , wherein said therapeutic agent is a cytotoxic agent. 
     
     
         20 . The antibody of  claim 19 , wherein said cytotoxic agent is selected from the group consisting of monomethyl auristatin E (MMAE) and monomethyl auristatin F (MMAF). 
     
     
         21 . The antibody of  claim 20 , wherein the cytotoxic agent is MMAE and wherein said antibody is capable of killing an STn-associated cell with a half-maximal inhibitory concentration (IC50) of from about 0.1 nM to about 20 nM. 
     
     
         22 . A method of treating cancer comprising administering the antibody of any of  claims 1-12  or  17-21 . 
     
     
         23 . The method of  claim 22 , wherein said cancer comprises at least one tumor. 
     
     
         24 . The method of  claim 23 , wherein the volume of said at least one tumor is reduced. 
     
     
         25 . The method of  claim 24 , wherein the volume of said at least one tumor is reduced by at least 20%. 
     
     
         26 . The method of any of  claims 23-25 , wherein said at least one tumor comprises at least one tumor cell, wherein said at least one tumor cell comprises at least one tumor-associated carbohydrate antigen (TACA). 
     
     
         27 . The method of  claim 26 , wherein said at least one TACA comprises sialyl(α2,6)N-acetylgalactosamine (STn). 
     
     
         28 . The method of any of  claims 22-27 , wherein said cancer comprises one or more of breast cancer, colon cancer, pancreatic cancer, lung cancer, cervical cancer, ovarian cancer, stomach cancer, prostate cancer, and liver cancer. 
     
     
         29 . The method of any of  claims 22-28 , wherein the antibody is administered in combination with a chemotherapeutic agent and/or therapeutic antibody. 
     
     
         30 . The method of  claim 29 , wherein the chemotherapeutic agent is selected from at least one of fluoropyrimidine, oxaliplatin, and irinotecan. 
     
     
         31 . The method of  claim 28  or  29 , wherein the therapeutic antibody is selected from at least one of bevacizumab and anti-epidermal growth factor receptor (EGFR) antibody. 
     
     
         32 . The method of any of  claims 22-31 , wherein the antibody is administered at a dose of from about 0.1 mg/kg to about 30 mg/kg. 
     
     
         33 . The method of  claim 32 , wherein the antibody is administered at a dose of from about 2.5 mg/kg to about 5 mg/kg. 
     
     
         34 . The method of  claim 32  or  33 , wherein the antibody is detectable in at least one subject sample obtained from about 1 day after treatment to about 1 month after treatment. 
     
     
         35 . The method of  claim 34 , wherein the antibody is conjugated with MMAE, and wherein the drug to antibody ratio (DAR) of said MMAE to said antibody changes by less than 50% in said at least one subject sample. 
     
     
         36 . A method of screening a cell or sample for the presence of at least one TACA, said method comprising contacting the cell or sample with the antibody of any of  claims 1-12 . 
     
     
         37 . The method of  claim 36 , wherein said at least one TACA comprises STn. 
     
     
         38 . The method of  claim 36  or  37 , wherein said sample is a biological sample, said biological sample obtained from a subject. 
     
     
         39 . The method of  claim 38 , wherein said subject has or is suspected of having cancer. 
     
     
         40 . The method of  claim 38  or  39 , wherein said biological sample comprises one or more of a cell, a tissue, a tissue section, and a body fluid. 
     
     
         41 . The method of any of  claims 36-40 , wherein said antibody comprises a detectable label. 
     
     
         42 . The method of any of  claim 36-40 , wherein said antibody is detected using a detection agent. 
     
     
         43 . The method of  claim 42 , wherein said detection agent is a secondary antibody. 
     
     
         44 . The method of  claim 43 , wherein said secondary antibody comprises a detectable label. 
     
     
         45 . A method of diagnosing cancer in a subject comprising screening a sample according to the method of any of  claims 38-44 . 
     
     
         46 . The method of  claim 45 , wherein said method is part of a companion diagnostic. 
     
     
         47 . The method of  claim 46 , wherein said companion diagnostic is used for one or more of stratifying cancer severity, stratifying cancer risk, selecting a subject for a clinical trial, developing a therapeutic regimen, modulating a therapeutic regimen, increasing treatment safety, and modulating treatment effectiveness. 
     
     
         48 . The method of any of  claims 36-40 , wherein said sample comprises a protein array. 
     
     
         49 . The method of  claim 48 , wherein said protein array comprises one or more antibodies configured to bind one or more proteins, wherein at least one of said one or more proteins present in said sample. 
     
     
         50 . A kit for carrying out the method of any of  claims 36-49 , said kit comprising the antibody of any of  claims 1-12 . 
     
     
         51 . The kit of  claim 50  comprising a secondary antibody. 
     
     
         52 . The kit of  claim 51 , wherein said secondary antibody comprises a detectable label. 
     
     
         53 . A composition comprising one or more of the antibody of any of  claims 1-12  and  17-21 . 
     
     
         54 . The composition of  claim 53  comprising at least one excipient. 
     
     
         55 . The composition of  claim 54 , wherein said at least one excipient comprises a pharmaceutically acceptable excipient. 
     
     
         56 . The composition of  claim 53 , wherein said composition comprises an antibody-coated agent. 
     
     
         57 . The composition of  claim 56 , wherein said antibody-coated agent comprises one or more of a particle, a nanoparticle, a protein, a fusion-protein, a lipid, a liposome, and a cell. 
     
     
         58 . The composition of  claim 56  or  57 , wherein said antibody is an antibody fragment. 
     
     
         59 . The composition of  claim 58 , wherein said antibody fragment is selected from one or more of an Fab fragment and a single chain Fv. 
     
     
         60 . A modified cell comprising a synthetic construct, wherein said synthetic construct encodes a factor, wherein said factor modulates cellular STn levels. 
     
     
         61 . The modified cell of  claim 60 , wherein said factor comprises at least one factor involved in STn synthesis. 
     
     
         62 . The modified cell of  claim 61 , wherein said at least one factor is selected from at least one of (Alpha-N-Acetyl-Neuraminyl-2,3-Beta-Galactosyl-1,3)-N-Acetylgalactosaminide, Alpha-2,6-Sialyltransferase I (ST6GalNAc I), T-synthase, and Core 1 Beta3-Galactosyltransferase-Specific Molecular Chaperone (COSMC). 
     
     
         63 . The modified cell of any of  claims 60-62 , wherein said modified cell comprises elevated STn levels when compared with at least one unmodified cell. 
     
     
         64 . The modified cell of  claim 60 , wherein said factor reduces expression of ST6GalNAC. 
     
     
         65 . The modified cell of  claim 64 , wherein said factor is an inhibitory ribonucleic acid (RNA) molecule. 
     
     
         66 . The modified cell of any of  claims 60-65 , wherein said modified cell is a modified ovarian tumor cell. 
     
     
         67 . The modified cell of  claim 66 , wherein said modified ovarian tumor cells is selected from one or more of a SKOV3 cell, an OVCAR3 cell, an OVCAR4 cell, a BRCA1 mutant tumor cell, and a non-BRCA1 mutant tumor cell. 
     
     
         68 . A method of characterizing binding of an antibody, said method comprising contacting a glycan array with said antibody, wherein said glycan array includes a plurality of glycans. 
     
     
         69 . The method of  claim 68 , wherein said glycan array comprises a panel of glycans, wherein said panel of glycans consists of one or more of each of:
 Neu5Acα6GalNAcαO(CH2)2CH2NH2;   Neu5Gcα6GalNAcαO(CH2)2CH2NH2;   Neu5Acα6Galβ4GlcNAcβO(CH2)2CH2NH2;   Neu5Gcα6Galβ4GlcNAcβO(CH2)2CH2NH2;   Neu5Acα6Galβ4GlcβO(CH2)2CH2NH2;   Neu5Gcα6Galβ4GlcβO(CH2)2CH2NH2;   Neu5Acα6GalβO(CH2)2CH2NH2;   Neu5Gcα6GalβO(CH2)2CH2NH2;   GaINAcaO(CH2)2CH2NH2;   Galβ3GalNAcβO(CH2)2CH2NH2;   Gal3βGalNAcαO(CH2)2CH2NH2;   Neu5Acα3Galβ1-3GalNAcαO(CH2)2CH2NH2; and   Neu5Gcα3Galβ1-3GalNAcαO(CH2)2CH2NH2.   
     
     
         70 . The method of  claims 68  or  69 , wherein each of said plurality of glycans are part of a neoglycolipid probe.