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WO 2016/183486 Al 17 November 2016 (17.11.2016) P O P C T

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WO 2016/183486 Al 17 November 2016 (17.11.2016) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2016/183486 Al 17 November 2016 (17.11.2016) 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 16/032465 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, 13 May 2016 (13.05.2016) KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (25) Filing Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (26) Publication Language: English SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 62/161,053 13 May 2015 (13.05.2015) US (84) Designated States (unless otherwise indicated, for every 62/205,591 14 August 2015 (14.08.2015) US kind of regional protection available): ARIPO (BW, GH, 62/257,458 19 November 2015 (19. 11.2015) US GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 62/307,592 14 March 2016 (14.03.2016) US TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (71) Applicant: AGENUS INC. [US/US]; 3 Forbes Road, Lex DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, ington, MA 0242 1 (US). LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, (72) Inventors: BUELL, Jennifer, Slunula; 17 Hathaway GW, KM, ML, MR, NE, SN, TD, TG). Street, Jamaica Plain, MA 02130 (US). CASTLE, John, Christopher; Rudolf-diesel Strasse 40, 55 13 1 Mainz (DE). Published: STEIN, Robert, Benjamin; 155 Oceana Drive East. Apt — with international search report (Art. 21(3)) 4i, Brooklyn, NY 11253 (US). LEVEY, Daniel, Lewis; 80 Broad Street, Unit 1002, Boston, MA 021 10 (US). — before the expiration of the time limit for amending the claims and to be republished in the event of receipt of (74) Agents: WILKINS, Andrew, T. et al; Lathrop & Gage, amendments (Rule 48.2(h)) LLP, 28 State Street, Boston, MA 02109 (US). — with sequence listing part of description (Rule 5.2(a)) 00 o (54) Title: VACCINES FOR TREATMENT AND PREVENTION OF CANCER (57) Abstract: Provided are compositions useful as therapeutic vaccines (e.g., cancer vaccines), and methods of producing such compositions. The compositions disclosed herein generally employ a stress protein and at least one synthetic peptide, which may be a phosphopeptide or phosphopeptide mimetic, comprising a cancer-specific mutation present in a patient's cancer. VACCINES FOR TREATMENT AND PREVENTION OF CANCER TECHNICAL FIELD The invention relates to the field of cancer biology, and more specifically to the treatment and inhibition of recurrence using anti-cancer vaccines. BACKGROUND Immunotherapies are becoming important tools in the treatment of cancer. One immunotherapy approach involves the use of therapeutic cancer vaccines comprising cancer- specific antigenic peptides that actively educate a patient’s immune system to target and destroy cancer cells. However, the generation of such therapeutic cancer vaccines is limited by the availability of cancer-specific antigenic peptides. Accordingly, there is a need in the art for improved methods of identifying cancer- specific antigenic peptides and for creating effective anti-cancer vaccines comprising these peptides. SUMMARY OF INVENTION The instant disclosure provides compositions useful as therapeutic vaccines (e.g., cancer vaccines), and methods of producing such compositions. The compositions disclosed herein generally employ a stress protein and at least one synthetic antigenic peptide comprising a cancer-specific mutation present in a patient’s cancer. The methods disclosed herein are particularly advantageous in that they allow for the preparation of therapeutic vaccine (e.g., cancer vaccine) compositions using only trace amounts of a subject’s tissue (e.g., single cells or exosomes). In one aspect, the disclosure provides a first composition comprising at least two different complexes of a purified stress protein bound to an antigenic peptide, wherein the complexes each comprise a different antigenic peptide, wherein each one of the different antigenic peptides comprises one or more mutant MHC-binding epitopes (e.g., human MHC- binding epitopes) from a cancer cell, and wherein the composition comprises no more than 20 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) different antigenic peptides that contain only wild-type MHC-binding epitopes (e.g., wild-type human MHC- binding epitopes). In one embodiment, the present invention relates to a first composition comprising at least two different complexes of a purified stress protein bound to an antigenic peptide, wherein the complexes each comprise a different antigenic peptide, wherein each one of the different antigenic peptides comprises one or more mutant MHC-binding epitopes from a cancer cell, and wherein the composition comprises no more than 5 different antigenic peptides that contain only wild-type MHC-binding epitopes. In certain embodiments, the composition comprises no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 different antigenic peptides that contain only wild-type MHC-binding epitopes e.g., wild-type MHC-binding epitopes. In certain embodiments, the composition does not comprise any antigenic peptides that contain only wild-type MHC-binding epitopes. In certain embodiments, the composition comprises no more than 100 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, or 20; e.g., about 20, 25, 30, 40, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100) different antigenic peptides. In certain embodiments, the composition comprises no more than 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 25, 30, 40, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 different antigenic peptides. In certain embodiments, each one of the antigenic peptides binds to an MHC molecule with an IC5 0 of 500 nM or less. In certain embodiments, at least one of the antigenic peptides binds to an MHC I molecule with an IC5 0 of 500 nM or less. In certain embodiments, at least one of the antigenic peptides binds to an MHC II molecule with an IC50 of 1000 nM or less. In certain embodiments, each one of the antigenic peptides binds to an MHC II molecule with an IC5 0 of 1000 nM or less. In certain embodiments, the MHC molecule is a human MHC molecule. In certain embodiments, at least one of the antigenic peptides comprises more than one mutant MHC-binding epitope from a cancer cell. In certain embodiments, each one of the antigenic peptides comprises more than one mutant MHC-binding epitope from a cancer cell. In certain embodiments, at least one of the antigenic peptides is capable of binding to more than one distinct MHC molecule with an IC5 0 of less than 500 nM. In certain embodiments, each one of the antigenic peptides is capable of binding to more than one distinct MHC molecule with an IC5 0 of less than 500 nM. In certain embodiments, at least one of the mutant MHC-binding epitopes is expressed in cancer cells of a subject but not in normal cells of the subject. In certain embodiments, each one of the mutant MHC-binding epitopes is expressed in cancer cells of a single subject but not in normal cells of the subject. In certain embodiments, at least one of the mutant MHC-binding epitopes is expressed at a higher level in cancer cells of a subject relative to normal cells of the subject. In certain embodiments, each one of the mutant MHC- binding epitopes is expressed at a higher level in cancer cells of a subject relative to normal cells of the subject. In certain embodiments, at least one of the mutant MHC-binding epitopes comprises an amino acid mutation or a gene fusion mutation. In certain embodiments, each one of the mutant MHC-binding epitopes comprises an amino acid mutation or a gene fusion mutation. In certain embodiments, the amino acid mutation is an amino acid substitution, deletion or insertion. In certain embodiments, the amino acid mutation is present in a subject’s tumor with an allelic frequency of greater than 0.05. In certain embodiments, at least one of the mutant MHC-binding epitopes comprises a modified amino acid. In certain embodiments, each one of the mutant MHC-binding epitopes comprises a modified amino acid. In certain embodiments, the modified amino acid is a Tyr, Ser, Thr, Arg, Lys, or His that has been phosphorylated on a side chain hydroxyl or amine. In certain embodiments, the modified amino acid is a mimetic of a Tyr, Ser, Thr, Arg, Lys, or His amino acid that has been phosphorylated on a side chain hydroxyl or amine. In certain embodiments, at least one of the mutant MHC-binding epitopes has a median expression level of greater than 1 Reads Per Kilobase of transcript per Million mapped reads (RPKM) across multiple cancers of the same indication.
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