Combination anti-CSF1R and anti-PD-1 antibody combination therapy for pancreatic cancer

1. A method of treating pancreatic cancer in a subject, wherein the cancer has been determined to be microsatellite-stable (MSS), and wherein the cancer has been determined to have: (a) a tumor mutation burden (TMB) of less than 20 mutations/megabase, less than 15 mutations/megabase, or less than 10 mutations/megabase, as determined with a comprehensive genomic profiling assay, and/or (b) a TMB of less than 400, less than 300 or less than 200 missense mutations as determined by whole exome sequencing (WES), comprising administering to the subject 2, 3, or 4 mg/kg of an anti-CSF1R antibody once every two weeks and 400-600 mg of an anti-PD-1 antibody once every four weeks,

wherein the anti-CSF1R antibody comprises a heavy chain comprising a heavy chain (HC) CDR1 having the sequence of SEQ ID NO: 5, an HC CDR2 having the sequence of SEQ ID NO: 6, and an HC CDR3 having the sequence of SEQ ID NO: 7, and a light chain comprising a light chain (LC) CDR1 having the sequence of SEQ ID NO: 8, a LC CDR2 having the sequence of SEQ ID NO: 9, and a LC CDR3 having the sequence of SEQ ID NO: 10; and

wherein the anti-PD-1 antibody comprises a heavy chain comprising a heavy chain (HC) CDR1 having the sequence of SEQ ID NO: 28, an HC CDR2 having the sequence of SEQ ID NO: 30, and an HC CDR3 having the sequence of SEQ ID NO: 32, and a light chain comprising a light chain (LC) CDR1 having the sequence of SEQ ID NO: 35, a LC CDR2 having the sequence of SEQ ID NO: 37, and a LC CDR3 having the sequence of SEQ ID NO: 39.

2. A method of treating pancreatic cancer in a subject, wherein the cancer has been determined to be microsatellite-stable (MSS), and wherein the cancer has been determined to have: (a) a tumor mutation burden (TMB) of less than 20 mutations/megabase, less than 15 mutations/megabase, or less than 10 mutations/megabase, as determined with a comprehensive genomic profiling assay, and/or (b) a TMB of less than 400, less than 300 or less than 200 missense mutations as determined by whole exome sequencing (WES), comprising administering to the subject 2, 3, or 4 mg/kg of an anti-CSF1R antibody once every two weeks and 400-600 mg of an anti-PD-1 antibody once every four weeks in combination with chemotherapy comprising gemcitabine or 5-fluorouracil (5-FU),

wherein the anti-CSF1R antibody comprises a heavy chain comprising a heavy chain (HC) CDR1 having the sequence of SEQ ID NO: 5, an HC CDR2 having the sequence of SEQ ID NO: 6, and an HC CDR3 having the sequence of SEQ ID NO: 7, and a light chain comprising a light chain (LC) CDR1 having the sequence of SEQ ID NO: 8, a LC CDR2 having the sequence of SEQ ID NO: 9, and a LC CDR3 having the sequence of SEQ ID NO: 10; and

wherein the anti-PD-1 antibody comprises a heavy chain comprising a heavy chain (HC) CDR1 having the sequence of SEQ ID NO: 28, an HC CDR2 having the sequence of SEQ ID NO: 30, and an HC CDR3 having the sequence of SEQ ID NO: 32, and a light chain comprising a light chain (LC) CDR1 having the sequence of SEQ ID NO: 35, a LC CDR2 having the sequence of SEQ ID NO: 37, and a LC CDR3 having the sequence of SEQ ID NO: 39.

3. The method of claim 2 , wherein the subject is administered 4 mg/kg of the anti-CSF1R antibody once every two weeks and 450-500 mg the anti-PD-1 antibody once every four weeks.

4. The method of claim 3 , wherein the subject is administered 4 mg/kg of the anti-CSF1R antibody once every two weeks and 480 mg the anti-PD-1 antibody once every four weeks.

5. The method of claim 2 , wherein the subject is administered chemotherapy comprising gemcitabine and nab-paclitaxel.

6. The method of claim 2 , wherein the subject is administered chemotherapy comprising FOLFOX.

7. The method of claim 2 , wherein the anti-CSF1R antibody and/or the anti-PD-1 antibody is a Fab, an Fv, an scFv, a Fab′, or a (Fab′) 2 fragment.

8. The method of claim 2 , wherein (a) the anti-PD-1 antibody heavy chain comprises a heavy chain variable region comprising the sequence of SEQ ID NO: 23 and wherein the anti-PD-1 antibody light chain comprises a light chain variable region comprising the sequence of SEQ ID NO: 25; (b) the anti-PD-1 antibody comprises a heavy chain comprising the sequence of each of SEQ ID NOs: 23 and 24 and wherein the anti-PD-1 antibody comprises a light chain comprising the sequence of each of SEQ ID NOs: 25 and 26; or (c) the anti-PD-1 antibody is nivolumab.

9. The method of claim 2 , wherein (a) the anti-CSF1R antibody comprises a heavy chain variable region comprising the sequence of SEQ ID NO: 11 and wherein the anti-CSF1R antibody comprises a light chain variable region comprising the sequence of SEQ ID NO: 12; (b) the anti-CSF1R antibody comprises a heavy chain comprising the sequence of SEQ ID NO: 13 and wherein the anti-CSF1R antibody comprises a light chain comprising the sequence of SEQ ID NO: 14; or (c) the anti-CSF1R antibody is cabiralizumab.

10. The method of claim 2 , wherein the subject meets one or more of the following criteria:

has previously failed treatment with a standard therapy for pancreatic cancer or is not indicated for treatment with a standard therapy;

has previously received a PD-1/PD-L1 inhibitor therapy;

is a PD-1/PD-L1 inhibitor inadequate responder;

is refractory to a PD-1/PD-L1 inhibitor, e.g., after at least 2 doses;

has a localized adenocarcinoma of the pancreas;

has metastatic adenocarcinoma of the pancreas;

does not have active pancreatitis or ascites of Grade 2 or higher;

has a pancreatic tumor that is PD-L1 positive;

has reduced circulating CD14 + CD16 ++ nonclassical monocytes after at least one dose of each of the anti-CSF1R antibody and the anti-PD-antibody; and

has a pancreatic cancer that has progressed after at least one gemcitabine-based or 5-fluorouracil-based chemotherapy regimen.

11. The method of claim 2 , wherein the subject has advanced pancreatic cancer.

12. A method of treating cancer in a subject, wherein the cancer has been determined to be microsatellite-stable (MSS), and wherein the cancer has been determined to have: (a) a tumor mutation burden (TMB) of less than 20 mutations/megabase, less than 15 mutations/megabase, or less than 10 mutations/megabase, as determined with a comprehensive genomic profiling assay, and/or (b) a TMB of less than 400, less than 300 or less than 200 missense mutations as determined by whole exome sequencing (WES), comprising:

a) Administering to the subject at least one dose of an anti-CSF1R antibody and an anti-PD-1 antibody, wherein the expression level of at least one marker gene is determined to increase following the administration, the at least one marker gene comprising one or more of: CCL19, CCL5, CCL8, CCR7, CD86, CXCL10, CXCL11, CXCL13, CXCL9, IFNG, IL23A, STAT1, TNF, CD72, CD79A, CD79B, MS4A1, TNFRSF17, CD3D, CD8A, CD8B, GZMM, APOL3, CTSW, GNLY, GZMA, GZMH, KLRB1, KLRD1, KLRK1, NKG7, PRF1, BTLA, CD244, CD96, CTLA4, LAGS, PDCD1, TIGIT, and FOXP3; and

b) continuing to administer the anti-CSF1R antibody and anti-PD-1 antibody to the subject.

13. The method of claim 12 , further comprising measuring the expression level of one or more of CSF1R, CSF-1 and IL-34, wherein increases in CSF-1 and IL-34 expression levels following administration indicate that the subject is responsive to treatment with the anti-CSF1R antibody and anti-PD-1 antibody while a decrease in CSF1R expression level indicates that the subject is not responsive to treatment with the anti-CSF1R antibody and anti-PD-1 antibody.

14. The method of claim 12 , wherein the at least one marker gene comprises:

a. at least one pro-inflammatory marker gene comprising: CCL19, CCL5, CCL8, CCR7, CD86, CXCL10, CXCL11, CXCL13, CXCL9, IFNG, IL23A, STAT1, and TNF;

b. at least one B cell marker comprising: CD72, CD79A, CD79B, MS4A1, and TNFRSF17;

c. at least one CD8 T cell marker comprising: CD3D, CD8A, and CD8B;

d. at least one effector T cell cytolytic marker comprising: GZMM, APOL3, CTSW, GNLY, GZMA, GZMH, KLRB1, KLRD1, KLRK1, NKG7, and PRF1; and/or

e. at least one effector T cell receptor marker comprising: BTLA, CD244, CD96, CTLA4, LAGS, PDCD1, TIGIT, and FOXP3.

15. A method of treating cancer in a subject, wherein the cancer has been determined to be microsatellite-stable (MSS), and wherein the cancer has been determined to have: (a) a tumor mutation burden (TMB) of less than 20 mutations/megabase, less than 15 mutations/megabase, or less than 10 mutations/megabase, as determined with a comprehensive genomic profiling assay, and/or (b) a TMB of less than 400, less than 300 or less than 200 missense mutations as determined by whole exome sequencing (WES), comprising: a) administering to the subject at least one dose of an anti-CSF1R antibody and an anti-PD-1 antibody, wherein the expression level of at least one marker gene comprising one or both of CSF-1 and IL-34 is determined to increase following the administration, and b) continuing to administer the anti-CSF1R antibody and anti-PD-1 antibody to the subject.