Glycan-interacting compounds and methods of use
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.
1. An isolated antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), wherein the antibody comprises a heavy chain variable domain (VH) comprising an amino acid sequence selected from SEQ ID NOs: 237-241, and a light chain variable domain (VL) comprising an amino acid sequence selected from SEQ ID NOs: 235 and 236.
2. The isolated antibody of claim 1 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
3. The isolated antibody of claim 1 , wherein the antibody comprises a human IgG1, IgG2, IgG3, or IgG4 constant region.
4. The isolated antibody of claim 1 , wherein the antibody comprises a human IgG1 constant region.
5. The isolated antibody of claim 2 , wherein the antibody comprises a human IgG1 constant region.
6. The isolated antibody of claim 2 , wherein the antibody binds to cell-associated STn with a half maximal effective concentration (EC50) of from about 0.01 nM to about 30 nM.
7. A pharmaceutical composition comprising the antibody of claim 1 and at least one pharmaceutically acceptable excipient.
8. An isolated nucleic acid that encodes an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), wherein the antibody comprises a heavy chain variable domain (VH) comprising an amino acid sequence selected from SEQ ID NOs: 237-241, and a light chain variable domain (VL) comprising an amino acid sequence selected from SEQ ID NOs: 235 and 236.
9. The isolated nucleic acid of claim 8 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
10. The isolated nucleic acid of claim 8 , wherein the antibody comprises a human IgG1, IgG2, IgG3, or IgG4 constant region.
11. The isolated nucleic acid of claim 8 , wherein the antibody comprises a human IgG1 constant region.
12. The isolated nucleic acid of claim 9 , wherein the antibody comprises a human IgG1 constant region.
13. An isolated host cell that comprises the nucleic acid of claim 8 .
14. An isolated host cell that comprises the nucleic acid of claim 9 .
15. An isolated host cell that expresses the antibody of claim 1 .
16. An isolated host cell that expresses the antibody of claim 2 .
17. A method of producing an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), comprising culturing the host cell of claim 15 under conditions suitable for expressing the antibody.
18. The method of claim 17 , further comprising isolating the antibody.
19. A method of producing an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), comprising culturing the host cell of claim 16 under conditions suitable for expressing the antibody.
20. The method of claim 19 , further comprising isolating the antibody.
21. A method of treating cancer comprising administering to a subject with cancer a therapeutically effective amount of an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), wherein the antibody comprises a heavy chain variable domain (VH) comprising an amino acid sequence selected from SEQ ID NOs: 237-241, and a light chain variable domain (VL) comprising an amino acid sequence selected from SEQ ID NOs: 235 and 236, wherein the antibody comprises an IgG1 or IgG3 constant region, and wherein the cancer comprises STn-positive cancer cells.
22. The method of claim 21 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
23. The method of claim 21 , wherein the antibody comprises a human IgG1 constant region.
24. The method of claim 22 , wherein the antibody comprises a human IgG1 constant region.
25. The method of claim 22 , wherein the antibody binds to cell-associated STn with a half maximal effective concentration (EC50) of from about 0.01 nM to about 30 nM.
26. The method of claim 21 , wherein the cancer is breast cancer, colon cancer, pancreatic cancer, lung cancer, cervical cancer, ovarian cancer, stomach cancer, prostate cancer, or liver cancer.
27. A method of selecting a subject with cancer for treatment with an anti-STn antibody, comprising contacting a sample from the subject with an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn) and comprises a heavy chain variable domain (VH) comprising an amino acid sequence selected from SEQ ID NOs: 237-241, and a light chain variable domain (VL) comprising an amino acid sequence selected from SEQ ID NOs: 235 and 236; and detecting binding of the antibody to STn-expressing cancer cells.
28. The method of claim 27 , further comprising administering an anti-STn antibody to the subject.
29. The method of claim 27 , wherein the sample is a cell, a tissue, a tissue section, a body fluid, serum, or a combination thereof.
30. A kit for screening a biological sample for the presence of STn-expressing cancer cells, comprising the isolated antibody of claim 1 .
31. An antibody-drug conjugate comprising an antibody conjugated to a therapeutic agent, wherein the antibody binds to sialyl(α2,6)N-acetylgalactosamine (STn) and comprises a heavy chain variable domain (VH) comprising an amino acid sequence selected from SEQ ID NOs: 237-241, and a light chain variable domain (VL) comprising an amino acid sequence selected from SEQ ID NOs: 235 and 236.
32. The antibody-drug conjugate of claim 31 , wherein said therapeutic agent is a cytotoxic agent.
33. The antibody-drug conjugate of claim 32 , wherein said cytotoxic agent is monomethyl auristatin E (MMAE) or monomethyl auristatin F (MMAF).
34. The antibody-drug conjugate of claim 33 , wherein the cytotoxic agent is MMAE.
35. The antibody-drug conjugate of claim 31 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
36. The antibody-drug conjugate of claim 32 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
37. The antibody-drug conjugate of claim 33 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
38. The antibody-drug conjugate of claim 34 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
39. A pharmaceutical composition comprising the antibody-drug conjugate of claim 31 and at least one pharmaceutically acceptable excipient.
40. A method of treating cancer comprising administering to a subject with cancer a therapeutically effective amount of an antibody-drug conjugate comprising an antibody conjugated to a cytotoxic agent, wherein the antibody binds to sialyl(α2,6)N-acetylgalactosamine (STn) and comprises a heavy chain variable domain (VH) comprising an amino acid sequence selected from SEQ ID NOs: 237-241, and a light chain variable domain (VL) comprising an amino acid sequence selected from SEQ ID NOs: 235 and 236, and wherein the cancer comprises STn-positive cancer cells.
41. The method of claim 40 , wherein said cytotoxic agent is monomethyl auristatin E (MMAE) or monomethyl auristatin F (MMAF).
42. The method of claim 41 , wherein the cytotoxic agent is MMAE.
43. The method of claim 40 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
44. The method of claim 41 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
45. The method of claim 42 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
46. The method of claim 40 , wherein the cancer is breast cancer, colon cancer, pancreatic cancer, lung cancer, cervical cancer, ovarian cancer, stomach cancer, prostate cancer, or liver cancer.
47. The method of claim 45 , wherein the cancer is breast cancer, colon cancer, pancreatic cancer, lung cancer, cervical cancer, ovarian cancer, stomach cancer, prostate cancer, or liver cancer.
48. A method of killing a STn-expressing cell, comprising contacting the cell with the antibody-drug conjugate of claim 31 .
49. A method of making an antibody-drug conjugate, comprising contacting an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn) with maleimidocaproyl-valine-citruline-p-aminobenzyloxycarbonyl-monomethyl auristatin E (MC-γc-PAB-MMAE), wherein the antibody comprises a heavy chain variable domain (VH) comprising an amino acid sequence selected from SEQ ID NOs: 237-241, and a light chain variable domain (VL) comprising an amino acid sequence selected from SEQ ID NOs: 235 and 236.
50. The method of claim 49 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
51. The method of claim 21 , wherein the cancer is endometrial cancer, gastric cancer, or colorectal cancer.
52. The method of claim 40 , wherein the cancer is endometrial cancer, gastric cancer, or colorectal cancer.
53. The method of claim 45 , wherein the cancer is endometrial cancer, gastric cancer, or colorectal cancer.
54. The isolated antibody of claim 1 , wherein the antibody binds to cell-associated STn with a half maximal effective concentration (EC50) of from about 0.01 nM to about 30 nM.
55. A pharmaceutical composition comprising the antibody of claim 2 and at least one pharmaceutically acceptable excipient.
56. An isolated nucleic acid that encodes a heavy chain variable domain of an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), wherein the heavy chain variable domain (VH) comprises an amino acid sequence selected from SEQ ID NOs: 237-241.
57. The isolated nucleic acid of claim 52 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240.
58. An isolated nucleic acid that encodes a light chain variable domain of an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), wherein the light chain variable domain (VL) comprises an amino acid sequence selected from SEQ ID NOs: 235 and 236.
59. The isolated nucleic acid of claim 54 , wherein the VL comprises the amino acid sequence of SEQ ID NO: 235.
60. The isolated nucleic acid of claim 56 , wherein the antibody comprises a human IgG1, IgG2, IgG3, or IgG4 constant region.
61. The isolated nucleic acid of claim 52 , wherein the antibody comprises a human IgG1 constant region.
62. The isolated nucleic acid of claim 53 , wherein the antibody comprises a human IgG1 constant region.
63. An isolated host cell that comprises a first nucleic acid that encodes a heavy chain variable domain (VH) of an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), wherein the VH comprises an amino acid sequence selected from SEQ ID NOs: 237-241, and a second nucleic acid that encodes a light chain variable domain (VL) of the antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), wherein the VL comprises an amino acid sequence selected from SEQ ID NOs: 235 and 236.
64. The isolated host cell of claim 63 , wherein the VH comprises the amino acid sequence of SEQ ID NO: 240 and the VL comprises the amino acid sequence of SEQ ID NO: 235.
65. The isolated host cell of claim 63 , wherein the antibody comprises a human IgG1, IgG2, IgG3, or IgG4 constant region.
66. The isolated host cell of claim 63 , wherein the antibody comprises a human IgG1 constant region.
67. The isolated host cell of claim 64 , wherein the antibody comprises a human IgG1 constant region.
68. A method of producing an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), comprising culturing the host cell of claim 63 under conditions suitable for expressing the antibody.
69. The method of claim 68 , further comprising isolating the antibody.
70. A method of producing an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), comprising culturing the host cell of claim 64 under conditions suitable for expressing the antibody.
71. The method of claim 70 , further comprising isolating the antibody.
72. The antibody-drug conjugate of claim 31 , further comprising a linker attaching the therapeutic agent to the antibody.
73. The antibody-drug conjugate of claim 34 , further comprising a linker attaching the therapeutic agent to the antibody.
74. The antibody-drug conjugate of claim 35 , further comprising a linker attaching the therapeutic agent to the antibody.
75. The antibody-drug conjugate of claim 38 , further comprising a linker attaching the therapeutic agent to the antibody.
76. The antibody-drug conjugate of claim 72 , wherein the linker is a cleavable linker.
77. The antibody-drug conjugate of claim 73 , wherein the linker is a cleavable linker.
78. The antibody-drug conjugate of claim 74 , wherein the linker is a cleavable linker.
79. The antibody-drug conjugate of claim 75 , wherein the linker is a cleavable linker.
80. The method of claim 40 , wherein the antibody-drug conjugate comprises a linker attaching the cytotoxic agent to the antibody.
81. The method of claim 42 , wherein the antibody-drug conjugate comprises a linker attaching the cytotoxic agent to the antibody.
82. The method of claim 43 , wherein the antibody-drug conjugate comprises a linker attaching the cytotoxic agent to the antibody.
83. The method of claim 45 , wherein the antibody-drug conjugate comprises a linker attaching the cytotoxic agent to the antibody.
84. The method of claim 47 , wherein the antibody-drug conjugate comprises a linker attaching the cytotoxic agent to the antibody.
85. The method of claim 80 , wherein the linker is a cleavable linker.
86. The method of claim 81 , wherein the linker is a cleavable linker.
87. The method of claim 82 , wherein the linker is a cleavable linker.
88. The method of claim 83 , wherein the linker is a cleavable linker.
89. The method of claim 84 , wherein the linker is a cleavable linker.
90. The method of claim 82 , wherein the cancer is endometrial cancer, gastric cancer, or colorectal cancer.
91. The method of claim 83 , wherein the cancer is endometrial cancer, gastric cancer, or colorectal cancer.
92. The method of claim 87 , wherein the cancer is endometrial cancer, gastric cancer, or colorectal cancer.
93. The method of claim 88 , wherein the cancer is endometrial cancer, gastric cancer, or colorectal cancer.