Identification of tumor-protective epitopes for the treatment of cancers

Abstract

Described herein are methods of identifying tumor-specific epitopes from the cancer tissue DNA of cancer patients using both DNA sequencing and bioinformatics techniques. The identification of tumor-specific epitopes provides pharmaceutical compositions with a limited number of tumor-specific peptides suitable for personalized genomics-driven immunotherapy of human cancer. Specifically disclosed herein is a novel index called the Differential Agretopic Index (DAI) for the epitope which allows prediction of whether immunization with a particular epitope will be protective against the tumor. Pharmaceutical compositions and methods of administration are also included.

1 . A method of identifying tumor epitopes in a cancer patient, comprising
 sequencing at least a portion of the cancer patient's RNA or DNA in both a healthy tissue and a cancer tissue, to produce a healthy tissue RNA or DNA sequence and a cancer tissue RNA or DNA sequence,   comparing the healthy tissue RNA or DNA sequence and the cancer tissue RNA or DNA sequence and identifying differences between the healthy tissue RNA or DNA sequence and the cancer tissue RNA or DNA sequence to produce a difference DNA marker set,   analyzing the difference DNA marker set to produce a tumor-specific epitope set, wherein the tumor-specific epitope set comprises one or more tumor-specific epitopes,   providing a numerical score called the Differential Agretopic Index for each epitope in the tumor-specific epitope set, wherein the Differential Agretopic Index is calculated by subtracting a score for a normal epitope from a score for the tumor-specific epitope,   optionally producing a pharmaceutical composition comprising a pharmaceutically acceptable carrier and one or more tumor-specific epitope peptides, or one or more polypeptides containing the tumor-specific epitopes, or polynucleotides encoding the one or more tumor-specific epitope peptides, wherein the one or more tumor-specific epitope peptides are selected from the tumor-specific epitope set based on the Differential Agretopic Index, and   optionally administering the pharmaceutical composition to the cancer patient.   
     
     
         2 . The method of  claim 1 , wherein sequencing is transcriptome sequencing. 
     
     
         3 . The method of  claim 1 , wherein DNA or RNA sequencing is high-throughput sequencing. 
     
     
         4 . The method of  claim 1 , wherein analyzing the difference DNA marker set to produce a tumor-specific epitope set is independent of whether one or more tumor-specific epitopes are related to cancer-causing pathways. 
     
     
         5 . The method of  claim 1 , wherein analyzing the difference DNA marker set to produce a tumor-specific epitope set comprises using a predictive algorithm that determines the binding of epitope peptides to MHC molecules to produce an MHC-restricted tumor-specific epitope set. 
     
     
         6 . The method of  claim 1 , further comprising ranking the tumor specific-epitope set by the Differential Agretopic Index for each epitope in the set. 
     
     
         7 . The method of  claim 6 , further comprising using the ranking by Differential Agretopic Index to identify a subset of 10 to 50 top-ranked tumor specific-epitopes. 
     
     
         8 . The method of  claim 1 , wherein the pharmaceutical composition comprises one or more polypeptides comprising 1 to 100 tumor-specific epitopes, one or more polypeptides containing 1 to 100 tumor-specific epitopes, or one or more polynucleotides encoding 1 to 100 tumor-specific epitope peptides from the tumor-specific epitope set. 
     
     
         9 . The method of  claim 1 , wherein the pharmaceutical composition comprises one or more peptides comprising 3 to 20 tumor-specific epitopes, one or more polypeptides containing 3 to 20 tumor-specific epitopes, or one or more polynucleotides encoding 3 to 20 tumor-specific epitope peptides from the tumor-specific epitope set. 
     
     
         10 . The method of  claim 1 , wherein the pharmaceutical composition further comprises an adjuvant. 
     
     
         11 . The method of  claim 1 , wherein the pharmaceutical composition further comprises one or more immune-modulating agents. 
     
     
         12 . The method of  claim 11 , wherein the immune-modulating agent is a TLR ligand or an antibody. 
     
     
         13 . The method of  claim 1 , wherein the cancer patient is suffering from a solid or liquid cancer. 
     
     
         14 . The method of  claim 1 , further comprising treating the cancer patient with radiation therapy, chemotherapy, surgery, or a combination thereof. 
     
     
         15 . The method of  claim 1 , wherein administering comprises mixing or pulsing the one or more tumor-specific epitope peptides, one or more polypeptides containing the tumor-specific epitopes, or one or more polynucleotides encoding the one or more tumor-specific epitope peptides, with cells from the cancer patient, and administering the mixed or pulsed cells to the cancer patient. 
     
     
         16 . A pharmaceutical composition produced by the method of  claim 1 . 
     
     
         17 . A pharmaceutical composition comprising a pharmaceutically acceptable carrier and one or more tumor-specific epitope peptides from a tumor-specific epitope set or one or more polypeptides containing the tumor-specific epitopes, or polynucleotides encoding the one or more tumor-specific epitope peptides, wherein the one or more tumor-specific epitope peptides are selected from the tumor-specific epitope set, wherein the tumor-specific epitope set does not include epitopes from known cancer-causing pathways, and wherein the tumor-specific epitope set is specific to a tumor from a cancer patient. 
     
     
         18 . The pharmaceutical composition of  claim 17 , wherein the pharmaceutical composition comprises 1 to 100 tumor-specific epitope peptides or polynucleotides from the tumor-specific epitope set. 
     
     
         19 . The pharmaceutical composition of  claim 17 , further comprising an adjuvant. 
     
     
         20 . The pharmaceutical composition of  claim 17 , wherein the pharmaceutical composition further comprises one or more immune-modulating agents. 
     
     
         21 . The pharmaceutical composition of  claim 20 , wherein the immune-modulating agent is a TLR ligand or an antibody. 
     
     
         22 . The pharmaceutical composition of  claim 17 , wherein the cancer patient is suffering from a solid or liquid cancer. 
     
     
         23 . A method of treating a cancer patient comprising administering the composition of  claim 17  to the cancer patient. 
     
     
         24 . The method of  claim 23 , further comprising treating the cancer patient with radiation therapy, chemotherapy, surgery, or a combination thereof. 
     
     
         25 . A method of identifying a cancer patient as a candidate for immunotherapy comprising
 sequencing at least a portion of the cancer patient's RNA or DNA in both a healthy tissue and a cancer tissue, to produce a healthy tissue RNA or DNA sequence and a cancer tissue RNA or DNA sequence,   comparing the healthy tissue RNA or DNA sequence and the cancer tissue RNA or DNA sequence and identifying differences between the healthy tissue RNA or DNA sequence and the cancer tissue RNA or DNA sequence to produce a difference DNA marker set,   analyzing the difference DNA marker set to produce a tumor-specific epitope set, wherein the tumor-specific epitope set comprises one or more tumor-specific epitopes,   quantifying the percentage of non-synonymous single nucleotide variants in the tumor-specific epitope set, and   identifying the cancer patient as a candidate for immunotherapy when less than 65% of the single nucleotide variants in the tumor-specific epitope set are non-synonymous single nucleotide variants.   
     
     
         26 . The method of  claim 25 , further comprising providing a numerical score called the Differential Agretopic Index for each epitope in the tumor-specific epitope set, wherein the Differential Agretopic Index is calculated by subtracting a score for a normal epitope from a score for the tumor-specific epitope as described herein.