Cancer neoepitopes

Abstract

Certain universal neoepitopes and cancer specific neoepitopes and methods therefor are presented that may be used in immunotherapy and cancer diagnosis. Preferred therapeutic and diagnostic compositions include antibodies or fragments thereof that bind to neoepitopes on cancer cells.

1 . A method of directing an agent to a cancer cell, comprising:
 contacting the cancer cell with an antibody or fragment thereof that binds to a cancer neoepitope in an AGGF1 (angiogenic factor with g-patch and FHA domains 1) protein, and wherein the cancer neoepitope is formed by a V202L mutation in the AGGF1 protein.   
     
     
         2 . The method of  claim 1  wherein the cancer cell is selected form the group consisting of a BRCA (breast cancer) cell, a CESC (cervical squamous cell carcinoma) cell, a HNSC (head and neck squamous cell carcinoma) cell, a LIHC (liver hepatocellular carcinoma) cell, a LUAD (lung adenocarcinoma) cell, a LUSC (lung squamous cell carcinoma) cell, an OV (ovarian cancer) cell, a READ (renal adenocarcinoma) cell, a STAD (stomach adenocarcinoma) cell, a THCA (thyroid carcinoma) cell, and a UCEC (uterine corpus endometrioid carcinoma) cell. 
     
     
         3 . The method of  claim 1  wherein the antibody or fragment thereof comprises an IgG antibody, a Fab, a F(ab′) 2 , and a scFv, or a synthetic antibody. 
     
     
         4 . The method of  claim 1  wherein the antibody or fragment thereof further comprises a therapeutic agent, or a radiologic agent or an imaging agent. 
     
     
         5 - 6 . (canceled) 
     
     
         7 . The method of  claim 1  wherein the antibody or fragment thereof is further coupled to a portion of a T-cell receptor. 
     
     
         8 . The method of  claim 1  wherein the antibody or fragment thereof is further coupled to cytotoxic T-cell or an NK cell. 
     
     
         9 . (canceled) 
     
     
         10 . The method of  claim 1  wherein the antibody or fragment thereof is produced in a process comprising a step of immunizing a mammal with a peptide having SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3. 
     
     
         11 . The method of  claim 1  wherein the cancer neoepitope has a sequence of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3. 
     
     
         12 - 16 . (canceled) 
     
     
         17 . An antibody or fragment thereof that binds to a cancer neoepitope in an AGGF1 protein, wherein the cancer neoepitope is formed by a V202L mutation in the AGGF1 protein, and wherein the cancer neoepitope has a sequence of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3. 
     
     
         18 . The antibody or fragment of  claim 17  wherein the antibody is an IgG antibody or wherein the antibody or fragment further comprises a portion of a T-cell receptor, or wherein the antibody or fragment is configured as a scFv, optionally further comprising a therapeutic or diagnostic agent. 
     
     
         19 - 24 . (canceled) 
     
     
         25 . A method of directing an agent to a breast cancer cell, comprising:
 contacting the cancer cell with an antibody or fragment thereof that binds to a cancer neoepitope having a sequence of any one of SEQ ID NO:4 to SEQ ID NO:28, of any one of SEQ ID NO:29 to SEQ ID NO:53, of any one of SEQ ID NO:54 to SEQ ID NO:78, or of any one of SEQ ID NO:79 to SEQ ID NO:103.   
     
     
         26 . The method of  claim 25  wherein the cancer cell is a triple negative breast cancer cell, and wherein the neoepitope has a sequence of any one of SEQ ID NO:4 to SEQ ID NO:28. 
     
     
         27 . The method of  claim 25  wherein the cancer cell is a ER (estrogen receptor) positive breast cancer cell, and wherein the neoepitope has a sequence of any one of SEQ ID NO:29 to SEQ ID NO:53. 
     
     
         28 . The method of  claim 25  wherein the cancer cell is a PR (progesterone receptor) positive breast cancer cell, and wherein the neoepitope has a sequence of any one of SEQ ID NO:54 to SEQ ID NO:78. 
     
     
         29 . The method of  claim 25  wherein the cancer cell is a HER2 (human epidermal growth factor receptor 2) positive breast cancer cell, and wherein the neoepitope has a sequence of any one of SEQ ID NO:79 to SEQ ID NO:103. 
     
     
         30 . The method of  claim 25  wherein the antibody or fragment thereof comprises an IgG antibody, a Fab, a F(ab′) 2 , and a scFv. 
     
     
         31 . The method of  claim 25  wherein the antibody or fragment thereof further comprises a therapeutic agent, an imaging agent, or a radiologic agent. 
     
     
         32 . The method of  claim 25  wherein the antibody or fragment thereof is further coupled to a portion of a T-cell receptor. 
     
     
         33 . The method of  claim 25  wherein the antibody or fragment thereof is further coupled to cytotoxic T-cell or an NK cell. 
     
     
         34 . The method of  claim 25  wherein the antibody or fragment thereof is produced in a process comprising a step of immunizing a mammal with any one of a peptide having SEQ ID NO:4 to SEQ ID NO:103. 
     
     
         35 - 49 . (canceled)