WO 2014/168874 A2 16 October 2014 (16.10.2014) P O P C T
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(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2014/168874 A2 16 October 2014 (16.10.2014) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every A61K 39/00 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (21) International Application Number: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, PCT/US20 14/033 185 DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 7 April 2014 (07.04.2014) KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (25) Filing Language: English OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (26) Publication Language: English SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, (30) Priority Data: ZW. 61/809,406 7 April 2013 (07.04.2013) 61/869,721 25 August 2013 (25.08.2013) (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (71) Applicants: THE BROAD INSTITUTE, INC. [US/US]; GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, 7 Cambridge Center, Room 7034, Cambridge, MA 02142 UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, (US). DANA-FARBER CANCER INSTITUTE, INC. TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, [US/US]; 450 Brookline Avenue, Boston, MA 02215 (US). EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, THE GENERAL HOSPITAL CORPORATION MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, [US/US]; 55 Fruit Street, Boston, MA 021 14 (US). TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). (72) Inventors: HACOHEN, Nir; 117 Mason Terrace, Brook line, MA 02446 (US). WU, Catherine, J.; 117 Mason Ter Published: race, Brookline, MA 02446 (US). FRITSCH, Edward, F.; — without international search report and to be republished 74 Minot Road, Concord, MA 01742 (US). upon receipt of that report (Rule 48.2(g)) (74) Agents: CORLESS, Peter, F. et al; Edwards Wildman Palmer LLP, P.O. Box 55874, Boston, MA 02205 (US). (54) Title: COMPOSITIONS AND METHODS FOR PERSONALIZED NEOPLASIA VACCINES < 00 00 FIG. 1 (57) Abstract: The invention provides a method of making a personalized neoplasia vaccine for a subject diagnosed as having a neo o plasia, which includes identifying a plurality of mutations in the neoplasia, analyzing the plurality of mutations to identify a subset of at least five neo-antigenic mutations predicted to encode neo-antigenic peptides, the neo-antigenic mutations selected from the group consisting of missense mutations, neoORF mutations, and any combination thereof, and producing, based on the identified subset, a personalized neoplasia vaccine. COMPOSITIONS AND METHODS FOR PERSONALIZED NEOPLASIA VACCINES STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH This work was supported by the following grants from the National Institutes of Health, Grant No's: NIH/NCI-1R01CA155010-02 and NHLBI-5R01HL103532-03. The government has certain rights in the invention. RELATED APPLICATIONS This application claims the benefit of and priority to U.S. Provisional Patent Application No. 61/809,406, filed April 7, 2013 and U.S. Provisional Patent Application No. 61/869,721, filed August 25, 2013, the contents of which are incorporated herein by reference. FIELD OF THE INVENTION The present invention relates to personalized strategies for the treatment of neoplasia. More particularly, the present invention relates to the identification and use of a patient specific pool of tumor specific neo-antigens in a personalized tumor vaccine for treatment of the subject. BACKGROUND Approximately 1.6 million Americans are diagnosed with neoplasia every year, and approximately 580,000 people in the United States are expected to die of the disease in 2013. Over the past few decades there been significant improvements in the detection, diagnosis, and treatment of neoplasia, which have significantly increased the survival rate for many types of neoplasia. However, only about 60% of people diagnosed with neoplasia are still alive 5 years after the onset of treatment, which makes neoplasia the second leading cause of death in the United States. Currently, there are a number of different existing cancer therapies, including ablation techniques (e.g., surgical procedures, cryogenic/heat treatment, ultrasound, radiofrequency, and radiation) and chemical techniques (e.g., pharmaceutical agents, cytotoxic/chemotherapeutic agents, monoclonal antibodies, and various combinations thereof). Unfortunately, such therapies are frequently associated with serious risk, toxic side effects, and extremely high costs, as well as uncertain efficacy. There is a growing interest in cancer therapies that seek to target cancerous cells with a patient's own immune system (e.g., cancer vaccines) because such therapies may mitigate/eliminate some of the above-described disadvantages. Cancer vaccines are typically composed of tumor antigens and immunostimulatory molecules (e.g., cytokines or TLR ligands) that work together to induce antigen-specific cytotoxic T cells that target and destroy tumor cells. Current cancer vaccines typically contain shared tumor antigens, which are native proteins (i.e. - proteins encoded by the DNA of all the normal cells in the individual) that are selectively expressed or over-expressed in tumors found in many individuals. While such shared tumor antigens are useful in identifying particular types of tumors, they are not ideal as immunogens for targeting a T-cell response to a particular tumor type because they are subject to the immune dampening effects of self-tolerance. Accordingly, there is a need for methods of identifying more effective tumor antigens that may be used for neoplasia vaccines. SUMMARY OF THE INVENTION The present invention relates to a strategy for the personalized treatment of neoplasia, and more particularly to the identification and use of a personalized cancer vaccine consisting essentially of a pool of tumor-specific and patient-specific neo-antigens for the treatment of tumors in a subject. As described below, the present invention is based, at least in part, on the discovery that whole genome/exome sequencing may be used to identify all, or nearly all, mutated neo-antigens that are uniquely present in a neoplasia/tumor of an individual patient, and that this collection of mutated neo-antigens may be analyzed to identify a specific, optimized subset of neo-antigens for use as a personalized neoplasia vaccine for treatment of the patient's neoplasia/tumor. In one aspect, the invention provides a method of making a personalized neoplasia vaccine for a subject diagnosed as having a neoplasia, which includes identifying a plurality of mutations in the neoplasia, analyzing the plurality of mutations to identify a subset of at least five neo-antigenic mutations predicted to encode neo-antigenic peptides, the neo-antigenic mutations selected from the group consisting of missense mutations, neoORF mutations, and any combination thereof, and producing, based on the identified subset, a personalized neoplasia vaccine. In an embodiment, the invention provides that the identifying step further includes sequencing the genome, transcriptome, or proteome of the neoplasia. In another embodiment, the analyzing step may further include determining one or more characteristics associated with the subset of at least five neo-antigenic mutations predicted to encode neo-antigenic peptides, the characteristics selected from the group consisting of molecular weight, cysteine content, hydrophilicity, hydrophobicity, charge, and binding affinity; and ranking, based on the determined characteristics, each of the neo-antigenic mutations within the identified subset of at least five neo-antigenic mutations. In an embodiment, the top 5-30 ranked neo-antigenic mutations are included in the personalized neoplasia vaccine. In another embodiment, the neo-antigenic mutations are ranked according to the order shown in FIG. 8. In one embodiment, the personalized neoplasia vaccine comprises at least about 20 neo- antigenic peptides corresponding to the neo-antigenic mutations. In another embodiment, the personalized neoplasia vaccine comprises one or more DNA molecules capable of expressing at least about 20 neo-antigenic peptides corresponding to the neo-antigenic mutations. In another embodiment, the personalized neoplasia vaccine comprises one or more RNA molecules capable of expressing at least 20 neo-antigenic peptides corresponding to the neo-antigenic mutations. In embodiments, the personalized neoplasia vaccine comprises neoORF mutations predicted to encode a neoORF polypeptide having a Kd of < 500 nM. In another embodiment, the personalized neoplasia vaccine comprises missense mutations predicted to encode a polypeptide having a Kd of < 150 nM, wherein the native cognate protein has a Kd of > 1000 nM or < 150 nM. In another embodiment, the at least about 20 neo-antigenic peptides range from about 5 to about 50 amino acids in length. In another embodiment, the at least about 20 neo-antigenic peptides range from about 15 to about 35 amino acids in length. In another embodiment, the at least about 20 neo-antigenic peptides range from about 18 to about 30 amino acids in length. In another embodiment, the at least about 20 neo-antigenic peptides range from about 6 to about 15 amino acids in length. In yet another embodiment, the at least about 20 neo-antigenic peptides are 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 amino acids in length. In one embodiment, the personalized neoplasia vaccine further includes an adjuvant.