Ovarian neoantigens and use thereof

Abstract

Disclosed herein are methods and compositions for treating ovarian cancer. In some embodiments, the compositions comprise polynucleotides encoding polypeptides that are ovarian cancer neoantigen sequences. Also disclosed herein are methods of treating or preventing ovarian cancer in a subject, the methods comprising administering to the subject a treatment regimen comprising Ad26 vector comprising a polynucleotide encoding ovarian neoantigen sequences and self-replicating RNA molecule comprising a polynucleotide encoding ovarian neoantigen sequences.

Description

OVARIAN NEOANTIGENS AND USE THEREOFCROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Provisional Application No. 63 / 625,451, filed on January 26, 2024, and U.S. Provisional Application No. 63 / 662,602, filed on June 21, 2024, the disclosures of each of which are hereby incorporated by reference in their entireties.SEQUENCE LISTING

[0002] The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. The XML copy, created on November 24, 2024, is named JBI6875WOPCTl_SL.xml and is 197,885 bytes in size.BACKGROUND

[0003] Ovarian cancer is the fifth leading cause of cancer-related deaths among women. A woman's risk of getting ovarian cancer during her lifetime is about 1 in 78. The American Cancer Society estimates that in 2020, there will be about 21,750 new cases of ovarian cancer and 13,940 deaths of ovarian cancer in the United States.

[0004] Ovarian cancer results from the uncontrolled growth of abnormal cells inside, near, or on the outer layer of the ovaries. Surgery to remove the cancerous growth is the most common treatment for ovarian cancer. Surgery procedures may include the total abdominal hysterectomy, bilateral salpingo-oophorectomy, omentectomy, visualization of all peritoneal surfaces, and random peritoneal biopsies plus peritoneal washing. After surgery, adjuvant chemotherapy is mandatory in cases of suboptimal debulking (residual disease of 1 cm or more), advanced stages, or early stages with a high risk of recurrence. From the early 2000s, combination platinum-paclitaxel chemotherapy has been the standard of care in the adjuvant and first-line settings.

[0005] Although the first-line treatment with combination platinum-paclitaxel chemotherapy has been shown to have response rates of over 80% in patients with advanced ovarian cancer, most patients eventually relapse, with a median progression-free survival of 18 months. Resistance to platinum-based chemotherapy is the primary cause of the poor overall survival associated with ovarian cancer. Response rates to second-line agents such as liposomal doxorubicin, gemcitabine or topotecan decrease with each subsequent relapse due to chemoresistance, resulting in a five-year overall survival of 30-40%.

[0006] Therefore, a need remains for therapies against an ovarian cancer, including relapsed, refractory and / or platinum-resistant ovarian cancers.BRIEF SUMMARY

[0007] The disclosure provides a polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0008] The disclosure also provides a polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31.

[0009] The disclosure also provides a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 55, 56, 57, 58, or 59, or a fragment thereof.

[0010] The disclosure also provides a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 84, 85, 86, 87, 88, or 89, or a fragment thereof.

[0011] The disclosure also provides a polynucleotide encoding a polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0012] The disclosure also provides a polynucleotide encoding a polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 25, 26, 27, 28, 29, 30, or 31.

[0013] The disclosure also provides a polynucleotide encoding a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 55, 56, 57, 58, or 59, or a fragment thereof.

[0014] The disclosure also provides a polynucleotide comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80 or 81.

[0015] The disclosure also provides a Ad26 vector comprising any of the polynucleotide of the disclosure.

[0016] In some embodiments, the Ad26 vector of the disclosure comprises: a polynucleotide selected from the group consisting of SEQ ID NO: 60, 61, 62, 63, 64, 65, 71, 72, 73, 74, 75, or 76; a polynucleotide encoding a polypeptide comprising the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51; a polynucleotide encoding a polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31; or a polynucleotide encoding a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 55, 56, 58, 85, 86 or 88 or a fragment thereof.

[0017] The disclosure also provides a self-replicating RNA molecule comprising any of the polynucleotide of the disclosure.

[0018] In some embodiments, the self-replicating RNA molecule of the disclosure:comprises a polynucleotide selected from the group consisting of SEQ ID NO: 66, 67, 68, 69, 70, 77, 78, 79, 80 or 81; comprises a polynucleotide encoding a polypeptide comprising the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51; comprises a polynucleotide encoding a polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31; or comprises a polynucleotide encoding a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 57, 59, 85, 87 or 89 or a fragment thereof.

[0019] The disclosure also provides a pharmaceutical composition comprising any of the polypeptide, any of the polynucleotide or any of the vectors of the disclosure.

[0020] Provided are also methods of inducing an immune response in a subject comprising administering to the subject in need thereof any of the polypeptides, any of the polynucleotides, any of the vectors and any of the pharmaceutical compositions of the disclosure.

[0021] The methods of inducing an immune response comprise administering: a. one or more compositions comprising a Ad26 vector that in turn comprises a nucleotide sequence encoding(i). the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51;(ii). one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31; or(iii). the amino acid sequences selected from the group consisting of SEQ ID NOs 55, 56, 58, 85, 86 or 88 or a fragment thereof; and / or b. one or more compositions comprising a self-replicating RNA molecule that in turn comprises a nucleotide sequence encoding(i). the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51;(ii). one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31; or(iii). the amino acid sequences selected from the group consisting of SEQ ID NOs 54, 57, 59,84, 87 or 89 or a fragment thereof.

[0022] Also provided are methods of treating, preventing, reducing a risk of onset or delaying the onset of ovarian cancer in a subject comprising administering to the subject in need thereof a. one or more compositions comprising a Ad26 vector that in turn comprises a nucleotide sequence encoding(i). the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51;(ii). one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31; or(iii). the amino acid sequences selected from the group consisting of SEQ ID NOs 55, 56, 58,85, 86 or 88 or a fragment thereof; and / or b. one or more compositions comprising a self-replicating RNA molecule that in turn comprises a nucleotide sequence encoding:(i). the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51;(ii). one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31; or(iii). the amino acid sequences selected from the group consisting of SEQ ID NOs 54, 57, 59, 84, 87 or 89 or a fragment thereof; to thereby treat or prevent the cancer.

[0023] The methods of treatment of the disclosure comprise administering a composition comprising the Ad26 virus at week 0 and at about week 3 and administering a composition comprising the self-replicating RNA molecule at about week 9.

[0024] The methods of the disclosure comprise further administering a. a composition comprising the Ad26 virus at about week 15 and at about week 18 and administering a composition comprising the self-replicating RNA molecule at about week 24; b. a composition comprising the self-replicating RNA molecule at about week 15, at about week 18 and at about week 24; or c. a composition comprising the Ad26 virus at about week 15, and the self-replicating RNA molecule at about week 24.

[0025] The methods of the disclosure also comprise administering a composition comprising the self-replicating RNA molecule at week 0, at about week 3, at about week 9, at about week 15, at about week 18 and at about week 24; or administering a composition comprising Ad26 at week 0 and at about week 15 and administering a composition comprising a self-replicating RNA molecule at week 9 and at about week 24.

[0026] The methods of the disclosure comprise further administering a composition comprising a Ad26 virus at about week 36, at about week 48, and at about week 60; or further administering a composition comprising a self-replicating RNA molecule at about week 36, at about week 48, and at about week 60.

[0027] The methods of the disclosure comprise further administering a second therapeutic agent, wherein the second therapeutic agent is an anti-CTLA-4 antibody.BRIEF DESCRIPTION OF THE DRAWINGS

[0028] FIG. 1 shows a cartoon of a gene fusion resulting from a chimeric read-through fusion. Neoantigenic peptide sequences arise at the breakpoint junction.

[0029] FIG. 2 shows a cartoon of gene fusions resulting from chromosomal alteration, such as DNA translocations.

[0030] FIG. 3 shows a cartoon of splice variants with alternative 5’ or 3’ splice sites, retained introns, excluded exons or alternative terminations or insertions.

[0031] FIG. 4 shows the cartoon for approach of identification of splice variants.

[0032] FIG. 5 shows immunogenic responses of neoantigens string IB (OVCA IB), string 2A (OVCA 2A) and string 3A (OVCA 3A) in Ad26. Immunogenicity responses were measured by estimating IFNy in the CD4+ and / or CD8+ T-cell populations. OVCA IB, neoantigen peptide String IB; OVCA 2A, neoantigen peptide String 2A; OVCA 3A, neoantigen peptide String 3 A; SFU, spot-forming units. ELISpot readouts were converted to SFU per 106 splenocyte cells.

[0033] FIG. 6 shows immunogenic responses of neoantigens string 1A (OVCA 1A), string 2A (OVCA 2A), string 2B (OVCA 2B), string 3A (OVCA 3A) and string 3B (OVCA 3B) in self-replicating RNA molecule in mice. Immunogenicity responses were measured by estimating IFNy in the CD4+ and / or CD8+ T-cell populations. OvCa, ovarian cancer; SFC, spot- formingcells. ELISpot readouts were converted to SFC per 106 splenocyte cells, adjusted by subtracting the background (DMSO).

[0034] FIG. 7 shows immune response in mice after administration of the Ad26 vector encoding a neoantigen peptide string followed by administration of the self-replication RNA molecule encoding a neoantigen peptide string. OVCA IB, ovarian cancer neoantigen string IB; OVCA 2A, ovarian cancer neoantigen string 2A; 1A, ovarian cancer neoantigen string 1A; 2B, ovarian cancer neoantigen string 2B.

[0035] FIG. 8 shows Ad26 and saRNA transgene induced CD4 / CD8 T cell responses. Ad26-OvCA = Ad26 vector with ovarian cancer neoantigens; saRNA-OvCa = saRNA with ovarian cancer neoantigens.

[0036] FIG. 9A and FIG. 9B show immune response through week 32 after prime-boost in NHP for group 1 (5 ug) and group 2 (30ug), respectively.DETAILED DESCRIPTION

[0037] The disclosure relates to ovarian cancer neoantigens, polypeptides comprising the ovarian cancer neoantigens, polynucleotides encoding them, vectors, and pharmaceutical compositions, useful for treating a broad population of patients having been diagnosed with various stages of ovarian cancer, such as localized or metastasized ovarian cancer.

[0038] Cancer cells produce neoantigens that result from genomic alterations and aberrant transcriptional programs. Neoantigen burden in patients has been associated with response to immunotherapy. The disclosure is based, at least in part, on the identification of ovarian cancer neoantigens that are common in ovarian cancer patients and hence can be utilized to develop a therapy amenable to treatment of a spectrum of ovarian cancer patients.Definitions

[0039] The disclosed methods may be understood more readily by reference to the following detailed description taken in connection with the accompanying figures, which form a part of this disclosure. It is to be understood that the disclosed methods are not limited to the specific methods described and / or shown herein, and that the terminology used herein is for the purpose of describing particular embodiments by way of example only and is not intended to be limiting of the claimed methods.

[0040] It is to be appreciated that certain features of the disclosed methods which are, for clarity, described herein in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the disclosed methods that are, for brevity, described in the context of a single embodiment, may also be provided separately or in any subcombination.

[0041] Unless specifically stated otherwise, any description as to a possible mechanism or mode of action or reason for improvement is meant to be illustrative only, and the disclosed methods are not to be constrained by the correctness or incorrectness of any such suggested mechanism or mode of action or reason for improvement.

[0042] Various terms relating to aspects of the description are used throughout the specification and claims. Such terms are to be given their ordinary meaning in the art unless otherwise indicated. Other specifically defined terms are to be construed in a manner consistent with the definitions provided herein.

[0043] Where a range of numerical values is recited or established herein, the range includes the endpoints thereof and all the individual integers and fractions within the range, and also includes each of the narrower ranges therein formed by all the various possible combinations of those endpoints and internal integers and fractions to form subgroups of the larger group of values within the stated range to the same extent as if each of those narrower ranges was explicitly recited. Where a range of numerical values is stated herein as being greater than a stated value, the range is nevertheless finite and is bounded on its upper end by a value that is operable within the context of the methods as described herein. Where a range of numerical values is stated herein as being less than a stated value, the range is nevertheless bounded on its lower end by a non-zero value. It is not intended that the scope of the methods be limited to the specific values recited when defining a range. All ranges are inclusive and combinable.

[0044] When values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms another embodiment. Reference to a particular numerical value includes at least that particular value, unless the context clearly dictates otherwise. “About” as used herein when referring to a measurable value is meant to encompass variations that are reasonably close to the specified value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. Unless explicitly stated otherwise within the Examples or elsewhere in the Specification in the context of a particular assay, result or embodiment, “about” means within one standard deviation per the practice in the art, or variations of ± 10% orless, variations of ± 5% or less, variations of ± 1% or less, variations of ± 0.5% or less, or variations of ± 0.1% or less from the specified value.

[0045] As used herein, the singular forms “a,” “an,” and “the” include the plural.

[0046] The term “comprising” is intended to include examples encompassed by the terms “consisting essentially of’ and “consisting of’; similarly, the term “consisting essentially of’ is intended to include examples encompassed by the term “consisting of.”

[0047] ‘ ‘Administered with” means that two or more therapeutics (such as a virus and an antibody) can be administered to a subject together in a mixture, concurrently as single agents, or sequentially as single agents in any order.

[0048] “Immunogenic fragment” refers to a polypeptide that is recognized by cytotoxic T lymphocytes, helper T lymphocytes or B cells when the fragment is in complex with MHC class I or MHC class II molecules.

[0049] The term “isolated” refers to a homogenous population of molecules (such as synthetic polynucleotides or polypeptides) which have been substantially separated and / or purified away from other components of the system the molecules are produced in, such as a recombinant cell, as well as a protein that has been subjected to at least one purification or isolation step.

[0050] The term “self-replicating RNA”, “self-replicating RNA molecule”, “self- amplifying RNA or “saRNA” are used interchangeably and refer to RNA molecule which contains all of the genetic information required for directing its own amplification or self- replicating within a permissive cell. To direct its own replication, the RNA molecule: 1) encodes polymerase, replicase, or other proteins which may interact with viral or host cell-derived proteins, nucleic acids or ribonucleoproteins to catalyze the RNA amplification process; and 2) contains cis-acting RNA sequences required for replication and transcription of the saRNA- encoded RNA. Self-replicating RNA molecule is typically derived from the genomes of positive strand RNA viruses and can be used as a basis of introducing foreign sequences to host cells by replacing viral sequences encoding structural or non-structural genes or inserting the foreign sequences 5’ or 3’ of the sequences encoding the structural or non-structural genes. Foreign sequences may be introduced into the subgenomic regions of alphaviruses. Self-replicating RNAmolecule may be packaged into recombinant virus particles, such as recombinant alphavirus particles or alternatively delivered to the host using lipid nanoparticles (LNP).

[0051] “Subject” includes any human or nonhuman animal. Nonhuman animal includes all vertebrates, e.g., mammals and non-mammals, such as nonhuman primates, sheep, dogs, cats, horses, cows, chickens, amphibians, reptiles, etc. The terms “subject” and “patient” can be used interchangeably herein.

[0052] “ Treat,” “treatment,” and like terms refer to both therapeutic treatment and prophylactic or preventative measures, and includes reducing the severity and / or frequency of symptoms of a myeloproliferative disease, a cancer, or a cardiovascular disease, eliminating symptoms and / or the underlying cause of the symptoms of a myeloproliferative disease, a cancer, or a cardiovascular disease, reducing the frequency or likelihood of symptoms of a myeloproliferative disease, a cancer, or a cardiovascular disease and / or their underlying cause, and improving or remediating damage caused, directly or indirectly, by a myeloproliferative disease, a cancer, or a cardiovascular disease. Treatment also includes prolonging survival as compared to the expected survival of a subject not receiving treatment. Subjects to be treated include those that have a myeloproliferative disease, a cancer, or a cardiovascular disease as well as those prone to have, or those in which, a myeloproliferative disease, a cancer, or a cardiovascular disease is to be prevented.Polypeptides

[0053] Disclosed herein are polypeptides comprising ovarian cancer neoantigen sequences that may elicit an immune response in a subject.

[0054] In some embodiments, the disclosure provides an isolated polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 and 51.

[0055] In some embodiments, the disclosure provides a polypeptide comprising two or more amino acid sequences selected from SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50 and 51, wherein the amino acid sequences are connected to each other in any order.

[0056] In some embodiments, the disclosure provides an isolated polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31.

[0057] In some embodiments, the disclosure provides an isolated polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO:25.

[0058] In some embodiments, the disclosure provides an isolated polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO:26.

[0059] In some embodiments, the disclosure provides an isolated polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO:27.

[0060] In some embodiments, the disclosure provides an isolated polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO:28.

[0061] In some embodiments, the disclosure provides an isolated polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38,39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO29.

[0062] In some embodiments, the disclosure provides an isolated polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO 30.

[0063] In some embodiments, the disclosure provides an isolated polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO 31.

[0064] The 51 amino acid sequences of the disclosure are neoantigens that were identified as particular useful in generating an immune response based on expression profile, prevalence and in vitro immunogenicity.

[0065] In some embodiments, the 51 neoantigen amino acid sequences of the disclosure are immunogenic fragments.

[0066] Immunogenic fragments in general are peptides that activate T cells, for example those that induce cytotoxic T cells when presented on MHC. Methods for assessing activation of T cells and / or induction of cytotoxic T lymphocytes are well known. In an exemplary assay, PBMCs isolated from an ovarian cancer patient are cultured in vitro in the presence of a neoantigen, a peptide comprising neoantigens or fragments thereof and IL-25. The cultures may be replenished periodically with IL- 15 and IL-2 and cultured for an additional 12 days. On day 12, the cultures are re-stimulated with the test neoantigen or fragments thereof and the following day, T cell activation may be assessed by measuring a percentage of IFNy+TNFa+ CD8+ cells when compared to a control culture.

[0067] In some embodiments, the 51 neoantigen amino acid sequences of the disclosure are connected to each other head to tail.

[0068] In some embodiments, the neoantigen amino acid sequences are connected to each other in any order. The amino acid sequences of the 51 neoantigens may be assembled inany order, and the order of the neoantigen amino acid sequences may differ between the various delivery options.

[0069] In some embodiments, the neoantigen amino acid sequences are connected to each other in any order, without a linker.

[0070] In some embodiments, the neoantigen amino acid sequences are separated by a linker.

[0071] Exemplary linker sequences include AAY, RR, DPP, HHAA, HHA, HHL, RKSYL, RKSY, SSL, or REKR. In some embodiments, the linkers may comprise a protease cleavage site such that the polypeptides may be cleaved in vivo in a subject into peptide fragments comprising neoantigen sequence.

[0072] In some embodiments, the polypeptide comprises one or more reverse peptide bonds, D-isomers of amino acids, chemical modifications, or any combination thereof.

[0073] In some embodiments, the 51 neoantigen amino acid sequences were assembled head to tail in a specific order. In general, assembly of the neoantigen amino acid sequences into a particular order may be based on generating a minimum number of junctional epitopes utilizing known algorithms.

[0074] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 55, 56, 57, 58, or 59, or a fragment thereof.

[0075] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 54 or a fragment thereof.

[0076] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 55, or a fragment thereof.

[0077] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 56, or a fragment thereof.

[0078] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 57, or a fragment thereof.

[0079] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 58, or a fragment thereof.

[0080] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 59, or a fragment thereof.

[0081] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 54 or a fragment thereof; or having at least 90% sequence identity to SEQ ID NO: 54.

[0082] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 55 or having at least 90% sequence identity to SEQ ID NO:55.

[0083] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 56 or having at least 90% sequence identity to SEQ ID NO:56.

[0084] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 57 or having at least 90% sequence identity to SEQ ID NO:57.

[0085] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 58 or having at least 90% sequence identity to SEQ ID NO:58.

[0086] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 59 or having at least 90% sequence identity to SEQ ID NO:59.

[0087] In some embodiments, the polypeptides of the disclosure may further comprise a leader sequence or T-cell enhancer sequence (TCE) at the N-terminus. Leader sequences can increase the expression and / or increase immunological response. Exemplary leader sequences include the a chain of the TCR receptor of T2 lymphocytes (HAVT20) (MACPGFLWALVISTC LEFSMA; SEQ ID NO: 52), a ubiquitin signal sequence (Ubiq) (MQIFVKTLTGKTITLEVEP SDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGVR; SEQ ID NO: 82), or a T cell enhancer (TCE) sequence, such as a peptide fragment of length of 28aa from the mandarin fish invariant chain (MGQKEQIHTLQKNSERMSKQLTRSSQAV; SEQ ID NO: 83). It is believed that the leader sequences may help in increasing an immune response to the epitopes disclosed herein.

[0088] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 55, 56, 57, 58, or 59, or a fragment thereof and leader sequence of SEQ ID NO: 52.

[0089] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 55, 56, 57, 58, or 59, or a fragment thereof and leader sequence of SEQ ID NO: 82.

[0090] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 55, 56, 57, 58, or 59, or a fragment thereof and leader sequence of SEQ ID NO: 83.

[0091] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 54 or a fragment thereof and leader sequence of SEQ ID NO: 52.

[0092] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 55 or a fragment thereof and leader sequence of SEQ ID NO: 52.

[0093] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 56 or a fragment thereof and leader sequence of SEQ ID NO: 52.

[0094] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 57 or a fragment thereof and leader sequence of SEQ ID NO: 52.

[0095] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 58 or a fragment thereof and leader sequence of SEQ ID NO: 52.

[0096] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 59 or a fragment thereof and leader sequence of SEQ ID NO: 52.

[0097] In some embodiments, the polypeptide of the disclosure may comprise a leader sequence or T-cell enhancer sequence (TCE) at the N-terminus and further comprise a TAG sequence at the C-terminus of SEQ ID NO: 53 (HHHHHH; SEQ ID NO: 53).

[0098] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 54 or a fragment thereof, a leader sequence of SEQ ID NO: 52 and a TAG sequence of SEQ ID NO: 53.

[0099] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 55 or a fragment thereof, a leader sequence of SEQ ID NO: 52 and a TAG sequence of SEQ ID NO: 53.

[0100] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 56 or a fragment thereof, a leader sequence of SEQ ID NO: 52 and a TAG sequence of SEQ ID NO: 53.

[0101] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 57 or a fragment thereof, a leader sequence of SEQ ID NO: 52 and a TAG sequence of SEQ ID NO: 53.

[0102] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 58 or a fragment thereof, a leader sequence of SEQ ID NO: 52 and a TAG sequence of SEQ ID NO: 53.

[0103] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 59 or a fragment thereof, a leader sequence of SEQ ID NO: 52 and a TAG sequence of SEQ ID NO: 53.

[0104] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 84, 85, 86, 87, 88 or 89, or a fragment thereof.

[0105] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 84 or a fragment thereof.

[0106] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 85, or a fragment thereof.

[0107] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 86, or a fragment thereof.

[0108] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 87, or a fragment thereof.

[0109] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 88, or a fragment thereof.

[0110] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 89, or a fragment thereof.

[0111] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 84 or a fragment thereof; or having at least 90% sequence identity to SEQ ID NO: 84.

[0112] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 85 or having at least 90% sequence identity to SEQ ID NO:85.

[0113] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 86 or having at least 90% sequence identity to SEQ ID NO:86.

[0114] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 87 or having at least 90% sequence identity to SEQ ID NO:87.

[0115] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 88 or having at least 90% sequence identity to SEQ ID NO:88.

[0116] In some embodiments, the disclosure provides a polypeptide comprising the amino acid sequence of SEQ ID NO: 89 or having at least 90% sequence identity to SEQ ID NO:89.

[0117] The polypeptides of the disclosure are useful in generating the recombinant viruses, the cells and the compositions of the disclosure and may be used directly as therapeutic agents by delivering them to a subject having an ovarian cancer using various technologies.Polynucleotides

[0118] The disclosure also provides polynucleotide encoding any of the polypeptide disclosed herein.

[0119] In some embodiments, the disclosure provides a polynucleotide encoding a polypeptide comprising the amino acid sequences selected from the group consisting of SEQ IDNOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0120] In some embodiments, the disclosure provides a polynucleotide encoding two or more polypeptides wherein the polypeptide comprises the amino acid sequences selected from SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51, and wherein the two or more polypeptides are connected in any order.

[0121] In some embodiments, the disclosure provides a polynucleotide encoding one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31.

[0122] In some embodiments, the polynucleotide of the disclosure encodes one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO 25.

[0123] In some embodiments, the polynucleotide of the disclosure encodes one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO 26.

[0124] In some embodiments, the polynucleotide of the disclosure encodes one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO 27.

[0125] In some embodiments, the polynucleotide of the disclosure encodes one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO 28.

[0126] In some embodiments, the polynucleotide of the disclosure encodes one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO 29.

[0127] In some embodiments, the polynucleotide of the disclosure encodes one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO 30.

[0128] In some embodiments, the polynucleotide of the disclosure encodes one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and an amino acid sequence of SEQ ID NO 31.

[0129] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences selected from the group consisting of SEQ ID NO: 54, 55, 56, 57, 58 or 59, or a fragment thereof.

[0130] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 54, or a fragment thereof.

[0131] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 55, or a fragment thereof.

[0132] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 56, or a fragment thereof.

[0133] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 57, or a fragment thereof.

[0134] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 58, or a fragment thereof.

[0135] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 59, or a fragment thereof.

[0136] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 54; or having at least 90% sequence identity to SEQ ID NO: 54.

[0137] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 55; or having at least 90% sequence identity to SEQ ID NO: 55.

[0138] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 56; or having at least 90% sequence identity to SEQ ID NO: 56.

[0139] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 57; or having at least 90% sequence identity to SEQ ID NO: 57.

[0140] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 58; or having at least 90% sequence identity to SEQ ID NO: 58.

[0141] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 59; or having at least 90% sequence identity to SEQ ID NO: 59.

[0142] In some embodiments, the polynucleotide comprises DNA.

[0143] In some embodiments, the polynucleotide comprises RNA.

[0144] In some embodiments, the RNA is mRNA or self-replicating RNA.

[0145] In some embodiments, the polynucleotide further comprises a leader polypeptide, a promoter, an enhancer, a polyadenylation site, a Kozak sequence, a stop codon, or any combination thereof.

[0146] In some embodiments the polynucleotide comprises a sequence encoding for a leader polypeptide sequence or a T-cell enhancer sequence (TCE) of SEQ ID NO: 52, 82 or 83 at the N-terminus and a sequence encoding for a TAG sequence of SEQ ID NO: 53 at the C- terminus.

[0147] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences selected from the group consisting of SEQ ID NO: 84, 85, 86, 87, 88 or 89, or a fragment thereof.

[0148] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 84, or a fragment thereof.

[0149] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 85, or a fragment thereof.

[0150] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 86, or a fragment thereof.

[0151] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 87, or a fragment thereof.

[0152] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 88, or a fragment thereof.

[0153] In some embodiments, the polynucleotide of the disclosure encodes a polypeptide comprising the amino acid sequences of SEQ ID NO: 89, or a fragment thereof.

[0154] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 84; or having at least 90% sequence identity to SEQ ID NO: 84.

[0155] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 85; or having at least 90% sequence identity to SEQ ID NO: 85.

[0156] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 86; or having at least 90% sequence identity to SEQ ID NO: 86.

[0157] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 87; or having at least 90% sequence identity to SEQ ID NO: 87.

[0158] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 88; or having at least 90% sequence identity to SEQ ID NO: 88.

[0159] In some embodiments, the disclosure provides a polynucleotide encoding for a polypeptide comprising the amino acid sequences of SEQ ID NO: 89; or having at least 90% sequence identity to SEQ ID NO: 89.

[0160] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO: 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80 or 81; or a fragment thereof.

[0161] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:60, or a fragment thereof.

[0162] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:61, or a fragment thereof.

[0163] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:62, or a fragment thereof.

[0164] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:63, or a fragment thereof.

[0165] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:64, or a fragment thereof.

[0166] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:65, or a fragment thereof.

[0167] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:66, or a fragment thereof.

[0168] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:67, or a fragment thereof.

[0169] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:68, or a fragment thereof.

[0170] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:69, or a fragment thereof.

[0171] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:70, or a fragment thereof.

[0172] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:71, or a fragment thereof.

[0173] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:72, or a fragment thereof.

[0174] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:, or a fragment thereof.

[0175] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:, or a fragment thereof.

[0176] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:, or a fragment thereof.

[0177] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:, or a fragment thereof.

[0178] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:, or a fragment thereof.

[0179] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:, or a fragment thereof.

[0180] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:, or a fragment thereof.

[0181] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:, or a fragment thereof.

[0182] In some embodiments, the disclosure provides a polynucleotide of SEQ ID NO:, or a fragment thereof.

[0183] In some embodiments, the polynucleotide is selected for the group consisting of: a nucleic acid sequence of SEQ ID NO: 60 or having at least 90% sequence identity to SEQ ID NO: 60; a nucleic acid sequence of SEQ ID NO: 61 or having at least 90% sequence identity to SEQ ID NO: 61; a nucleic acid sequence of SEQ ID NO: 62 or having at least 90% sequence identity to SEQ ID NO: 62; a nucleic acid sequence of SEQ ID NO: 63 or having at least 90% sequence identity to SEQ ID NO: 63; a nucleic acid sequence of SEQ ID NO: 64 or having at least 90% sequence identity to SEQ ID NO: 64;a nucleic acid sequence of SEQ ID NO: 65 or having at least 90% sequence identity toSEQ ID NO: 65; a nucleic acid sequence of SEQ ID NO: 66 or having at least 90% sequence identity toSEQ ID NO: 66; a nucleic acid sequence of SEQ ID NO: 67 or having at least 90% sequence identity toSEQ ID NO: 67; a nucleic acid sequence of SEQ ID NO: 68 or having at least 90% sequence identity toSEQ ID NO: 68; a nucleic acid sequence of SEQ ID NO: 69 or having at least 90% sequence identity toSEQ ID NO: 69; a nucleic acid sequence of SEQ ID NO: 70 or having at least 90% sequence identity toSEQ ID NO: 70; a nucleic acid sequence of SEQ ID NO: 71 or having at least 90% sequence identity toSEQ ID NO: 71; a nucleic acid sequence of SEQ ID NO: 72 or having at least 90% sequence identity toSEQ ID NO: 72; a nucleic acid sequence of SEQ ID NO: 73 or having at least 90% sequence identity toSEQ ID NO: 73; a nucleic acid sequence of SEQ ID NO: 74 or having at least 90% sequence identity toSEQ ID NO: 74; a nucleic acid sequence of SEQ ID NO: 75 or having at least 90% sequence identity toSEQ ID NO: 75; a nucleic acid sequence of SEQ ID NO: 76 or having at least 90% sequence identity toSEQ ID NO: 76; a nucleic acid sequence of SEQ ID NO: 77 or having at least 90% sequence identity toSEQ ID NO: 77; a nucleic acid sequence of SEQ ID NO: 78 or having at least 90% sequence identity toSEQ ID NO: 78; a nucleic acid sequence of SEQ ID NO: 79 or having at least 90% sequence identity toSEQ ID NO: 79;a nucleic acid sequence of SEQ ID NO: 80 or having at least 90% sequence identity to SEQ ID NO: 80; or a nucleic acid sequence of SEQ ID NO: 81 or having at least 90% sequence identity to SEQ ID NO: 81.

[0184] Methods of generating polynucleotides of the disclosure are known in the art and include chemical synthesis, enzymatic synthesis (e.g. in vitro transcription), enzymatic or chemical cleavage of a longer precursor, chemical synthesis of smaller fragments of the polynucleotides followed by ligation of the fragments or known PCR methods. The polynucleotide sequence to be synthesized may be designed with the appropriate codons for the desired amino acid sequence. In general, preferred codons may be selected for the intended host in which the sequence will be used for expression.

[0185] The polynucleotides of the disclosure may be utilized as therapeutics by delivering them to a subject having ovarian cancer using various technologies, including viral vectors as described herein or other delivery technologies as also described herein.Vectors

[0186] The polypeptide or polynucleotides of the disclosure can be delivered to a subject in need utilizing any available delivery vehicles, such as vectors. The disclosure also provides compositions comprising any of the vectors used for delivery of the polypeptides and polynucleotides disclosed herein.

[0187] The disclosure provides vectors comprising any of the polynucleotides disclosed herein. The disclosure also provides vectors comprising a polynucleotide encoding for any of the polypeptides disclosed herein.

[0188] The vector may be a viral vector.

[0189] In some embodiments, the vector is a viral vector comprising any of the polynucleotides of the disclosure. In some embodiments, the vector is a viral vector comprising a polynucleotide encoding any of the polypeptides of the disclosure.

[0190] Viral vectors are derived from naturally occurring virus genomes, which typically are modified to be replication incompetent, e.g. non-replicating. Non-replicating viruses requirethe provision of proteins in trans for replication. Typically, those proteins are stably or transiently expressed in a viral producer cell line, thereby allowing replication of the virus. The viral vectors are, thus, typically infectious and non-replicating. Viral vectors may be adenovirus vectors, adeno-associated virus (AAV) vectors (e.g., AAV type 5 and type 2), Great ape adenovirus vectors (GAd), alphavirus vectors (e.g., Venezuelan equine encephalitis virus (VEE), Sindbis virus (SIN), Semliki forest virus (SFV), and VEE-SIN chimeras), herpes virus vectors (e.g. vectors derived from cytomegaloviruses, like rhesus cytomegalovirus (RhCMV)), arena virus vectors (e.g. lymphocytic choriomeningitis virus (LCMV) vectors), measles virus vectors, pox virus vectors (e.g., vaccinia virus, modified vaccinia virus Ankara (MV A), NYVAC (derived from the Copenhagen strain of vaccinia), and avipox vectors: canarypox (ALVAC) and fowlpox (FPV) vectors), self-replicating RNA vectors, vesicular stomatitis virus vectors, retrovirus vectors, lentivirus vectors, viral like particles, and bacterial spores.

[0191] In some embodiments, the viral vector is derived from adenovirus, poxvirus, alphavirus, adeno-associated virus, retrovirus or a self-replicating RNA molecule.

[0192] In some embodiments, the viral vector is derived from adenovirus.

[0193] In some embodiments, the viral vector is derived from a self-replicating RNA molecule.Adenoviral Vectors

[0194] In some embodiments, the polypeptide or polynucleotides of the disclosure can be delivered to a subject in need utilizing a viral vector derived from an adenovirus or compositions comprising adenoviral vectors.

[0195] Adenovirus vectors may be derived from human adenovirus (Ad) but also from adenoviruses that infect other species, such as bovine adenovirus (e.g. bovine adenovirus 3, BAdV3), a canine adenovirus (e.g. CAdV2), a porcine adenovirus (e.g. PAdV3 or 5), or great apes, such as Chimpanzee (Pan), Gorilla (Gorilla), Orangutan (Pongo), Bonobo (Pan paniscus) and common chimpanzee (Pan troglodytes). Typically, naturally occurring great ape adenoviruses are isolated from stool samples of the respective great ape.

[0196] Human adenovirus vectors may be derived from various adenovirus serotypes, for example from human adenovirus serotypes hAd5, hAd7, hAdl 1, hAd26, hAd34, hAd35, hAd48,hAd49 or hAd50 (the serotypes are also referred to as Ad5, Ad7, Adi 1, Ad26, Ad34, Ad35, Ad48, Ad49 or Ad50).

[0197] Great ape adenovirus (GAd) vectors may be derived from various adenovirus serotypes, for example from great ape adenovirus serotypes GAd20, Gadl9, GAd21, GAd25, GAd26, GAd27, GAd28, GAd29, GAd30, GAd31, ChAd3, ChAd4, ChAd5, ChAd6, ChAd7, ChAd8, ChAd9, ChAdlO, ChAdl l, ChAdl6, ChAdI7, ChAdl9, ChAd20, ChAd22, ChAd24, ChAd26, ChAd30, ChAd31, ChAd37, ChAd38, ChAd44, ChAd55, ChAd63, ChAd73, ChAd82, ChAd83, ChAdl46, ChAdl47, PanAdl, PanAd2, or PanAd3.

[0198] Adenovirus vectors are known in the art. The sequences of most of the human and non-human adenoviruses are known in the art, and for others can be obtained using routine procedures. An exemplary genome sequence of Ad26 is found in GenBank Accession number EFl 53474 and in SEQ ID NO: 1 of Int. Pat. Publ. No. W02007 / 104792. Vectors based on Ad26 are described for example, in Int. Pat. Publ. No. W02007 / 104792. Vectors based on ChAd3, ChAd4, ChAd5, ChAd6, ChAd7, ChAd8, ChAd9, ChAdlO, ChAdl l, ChAdl6, ChAdl7, ChAdl9, ChAd20, ChAd22, ChAd24, ChAd26, ChAd30, ChAd31, ChAd37, ChAd38, ChAd44, ChAd63 and ChAd82 are described in W02005 / 071093. Vectors based on PanAdl, PanAd2, PanAd3, ChAd55, ChAd73, ChAd83, ChAdl46, and ChAdl47 are described in Int. Pat. Publ. No. WO2010 / 086189.

[0199] Adenovirus vectors are engineered to comprise at least one functional deletion or a complete removal of a gene product that is essential for viral replication, such as one or more of the adenoviral regions El, E2 and E4, therefore rendering the adenovirus to be incapable of replication. The deletion of the El region may comprise deletion of EIA, EIB 55K or EIB 2 IK, or any combination thereof. Replication deficient adenoviruses are propagated by providing the proteins encoded by the deleted region(s) in trans by the producer cell by utilizing helper plasmids or engineering the produce cell to express the required proteins. Adenovirus vectors may also have a deletion in the E3 region, which is dispensable for replication, and hence such a deletion does not have to be complemented. The adenovirus vector of the disclosure may comprise a functional deletion or a complete removal of the El region and at least part of the E3 region. The adenovirus vector of the disclosure may further comprise a functional deletion or a complete removal of the E4 region and / or the E2 region. Suitable producer cells that can beutilized are human retina cells immortalized by El, e.g. 911 or PER.C6 cells (see, e.g., U.S. Pat. No. 5,994,128), El -transformed amniocytes (See, e.g., EP 1230354), E 1 -transformed A549 cells (see e.g. Int. Pat. Publ. No. WO1998 / 39411, U.S. Pat. No. 5,891,690). Exemplary vectors that may be used are Ad26 comprising a functional El coding region that is sufficient for viral replication, a deletion in the E3 coding region and a deletion in the E4 coding region, provided that E4 open reading frame 6 / 7 is not deleted (see e.g. U.S. Pat. No. 9,750,801)

[0200] In some embodiments, the adenovirus vector is a human adenovirus (Ad) vector. In some embodiments, the Ad vector is derived from Ad5. In some embodiments, the Ad vector is derived from Adi 1. In some embodiments, the Ad vector is derived from Ad7. In some embodiments, the Ad vector is derived from Ad26. In some embodiments, the Ad vector is derived from Ad34. In some embodiments, the Ad vector is derived from Ad35. In some embodiments, the Ad vector is derived from Ad48. In some embodiments, the Ad vector is derived from Ad49. In some embodiments, the Ad vector is derived from Ad50.

[0201] In some embodiments, the adenovirus vector is a great ape adenovirus (GAd) vector. In some embodiments, the GAd vector is derived from GAd20. In some embodiments, the GAd vector is derived from GAdl9. In some embodiments, the GAd vector is derived from GAd21. In some embodiments, the GAd vector is derived from GAd25. In some embodiments, the GAd vector is derived from GAd26. In some embodiments, the GAd vector is derived from GAd27. In some embodiments, the GAd vector is derived from GAd28. In some embodiments, the GAd vector is derived from GAd29. In some embodiments, the GAd vector is derived from GAd30. In some embodiments, the GAd vector is derived from GAd31. In some embodiments, the GAd vector is derived from ChAd3. In some embodiments, the GAd vector is derived from ChAd4. In some embodiments, the GAd vector is derived from ChAd5. In some embodiments, the GAd vector is derived from ChAd6. In some embodiments, the GAd vector is derived from ChAd7. In some embodiments, the GAd vector is derived from ChAd8. In some embodiments, the GAd vector is derived from ChAd9. In some embodiments, the GAd vector is derived from ChAd9. In some embodiments, the GAd vector is derived from ChAdlO. In some embodiments, the GAd vector is derived from ChAdl 1. In some embodiments, the GAd vector is derived from ChAdl6. In some embodiments, the GAd vector is derived from ChAdl 7. In some embodiments, the GAd vector is derived from ChAdl 9. In some embodiments, the GAd vectoris derived from ChAd20. In some embodiments, the GAd vector is derived from ChAd22. In some embodiments, the GAd vector is derived from ChAd24. In some embodiments, the GAd vector is derived from ChAd26. In some embodiments, the GAd vector is derived from ChAd30. In some embodiments, the GAd vector is derived from ChAd31. In some embodiments, the GAd vector is derived from ChAd32. In some embodiments, the GAd vector is derived from ChAd31. In some embodiments, the GAd vector is derived from ChAd33. In some embodiments, the GAd vector is derived from ChAd37. In some embodiments, the GAd vector is derived from ChAd38. In some embodiments, the GAd vector is derived from ChAd44. In some embodiments, the GAd vector is derived from ChAd55. In some embodiments, the GAd vector is derived from ChAd63. In some embodiments, the GAd vector is derived from ChAd68. In some embodiments, the GAd vector is derived from ChAd73. In some embodiments, the GAd vector is derived from ChAd82. In some embodiments, the GAd vector is derived from ChAd83. GAdl9-21 and GAd25-31 are described in Int. Pat. Publ. No. W02019 / 008111 and represents strains with high immunogenicity and no pre-existing immunity in the general human population. The polynucleotide sequence of GAd20 genome is disclosed in Int. Pat. Publ. No. WO20 19 / 008111.

[0202] The nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88, or 89 may be inserted into a site or region (insertion region) in the vector that does not affect virus viability of the resultant recombinant virus. Such regions can be readily identified by testing segments of virus DNA for regions that allow recombinant formation without seriously affecting virus viability of the recombinant virus. The polynucleotides encoding the amino acid sequence of SEQ ID NO: 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88, or 89 may be inserted into the deleted El region in parallel (transcribed 5' to 3') or anti-parallel (transcribed in a 3' to 5' direction relative to the vector backbone) orientation. Appropriate transcriptional regulatory elements able to direct expression of the polypeptide of the disclosure in the mammalian host cells may be operatively linked to the polypeptide of the disclosure.

[0203] Recombinant adenoviral particles may be prepared and propagated according to any conventional technique in the field of the art using a complementation cell line or a helper virus, which supplies in trans the missing viral genes necessary for viral replication. The celllines 293, PER.C6, El A549 and 911 are commonly used to complement El deletions. The adenoviral particles may be recovered from the culture supernatant but also from the cells after lysis and optionally further purified according to standard techniques (e.g., chromatography, ultracentrifugation, as described in Int. Pat. Publ. No. WO 1996 / 27677, Int. Pat. Publ. No. WO1998 / 00524, Int. Pat. Publ. No. WO1998 / 26048 and Int. Pat. Publ. No. W02000 / 50573). The construction and methods for propagating adenoviral vectors are also described in for example, U.S. Pat. Nos. 5,559,099, 5,837,511, 5,846,782, 5,851,806, 5,994,106, 5,994,128, 5,965,541, 5,981,225, 6,040,174, 6,020,191, and 6,113,913.

[0204] Provided herein is a viral vector comprising a polynucleotide encoding for any of the polypeptide of the disclosure, wherein the vector is derived from hAd26 (also referred to as Ad26).

[0205] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 54 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 54.

[0206] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 55 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 55.

[0207] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 56 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 56.

[0208] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 57 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 57.

[0209] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 58 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 58.

[0210] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 59 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 59.

[0211] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 84 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 84.

[0212] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 85 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 85.

[0213] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 86 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 86.

[0214] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 87 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 87.

[0215] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 88 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 88.

[0216] In some embodiments, the Ad26 vector comprises a polynucleotide encoding a polypeptide of SEQ ID NO: 89 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 89.

[0217] In some embodiments, the Ad26 vector comprises any of the polynucleotides of the disclosure.

[0218] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 60 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 60.

[0219] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 61 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 61.

[0220] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 62 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 62.

[0221] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 63 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 63.

[0222] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 64 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 64.

[0223] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 65 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 65.

[0224] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 71 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 71.

[0225] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 72 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 72.

[0226] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 73 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 73.

[0227] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 74 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 74.

[0228] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 75 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 75.

[0229] In some embodiments, the Ad26 vector comprises a polynucleotide of SEQ ID NO: 76 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 76.Self-replicating RNA Molecules

[0230] In some embodiments, the polypeptide or polynucleotides of the disclosure can be delivered to a subject in need utilizing a self-replicating RNA molecule or compositions comprising self-replicating RNA molecule.

[0231] Self-replicating RNA may be derived from alphavirus. Alphaviruses may belong to the VEEV / EEEV group, or the SF group, or the SIN group. Non-limiting examples of SF group alphaviruses include Semliki Forest virus, O'Nyong-Nyong virus, Ross River virus, Middelburg virus, Chikungunya virus, Barmah Forest virus, Getah virus, Mayaro virus, Sagiyama virus, Bebaru virus, and Una virus. Non-limiting examples of SIN group alphaviruses include Sindbis virus, Girdwood S. A. virus, South African Arbovirus No. 86, Ockelbo virus, Aura virus, Babanki virus, Whataroa virus, and Kyzylagach virus. Non-limiting examples of VEEV / EEEV group alphaviruses include Eastern equine encephalitis virus (EEEV), Venezuelan equine encephalitis virus (VEEV), Everglades virus (EVEV), Mucambo virus (MUCV), Pixuna virus (PIXV), Middleburg virus (MIDV), Chikungunya virus (CHIKV), O'Nyong-Nyong virus (ONNV), Ross River virus (RRV), Barmah Forest virus (BF), Getah virus (GET), Sagiyama virus (SAGV), Bebaru virus (BEBV), Mayaro virus (MAYV), and Una virus (UNAV).

[0232] The self-replicating RNA molecules can be derived from alphavirus genomes, meaning that they have some of the structural characteristics of alphavirus genomes, or similar to them. The self-replicating RNA molecules can be derived from modified alphavirus genomes.

[0233] Self-replicating RNA molecules may be derived from Eastern equine encephalitis virus (EEEV), Venezuelan equine encephalitis virus (VEEV), Everglades virus (EVEV), Mucambo virus (MUCV), Semliki forest virus (SFV), Pixuna virus (PIXV), Middleburg virus (MIDV), Chikungunya virus (CHIKV), O'Nyong-Nyong virus (ONNV), Ross River virus (RRV), Barmah Forest virus (BF), Getah virus (GET), Sagiyama virus (SAGV), Bebaru virus (BEBV), Mayaro virus (MAYV), Una virus (UNAV), Sindbis virus (SINV), Aura virus (AURAV), Whataroa virus (WHAV), Babanki virus (BABV), Kyzylagach virus (KYZV), Western equine encephalitis virus (WEEV), Highland J virus (HJV), Fort Morgan virus (FMV), Ndumu (NDUV), and Buggy Creek virus. Virulent and avirulent alphavirus strains are both suitable. In some embodiments, the alphavirus RNA saRNA is of a Sindbis virus (SIN), aSemliki Forest virus (SFV), a Ross River virus (RRV), a Venezuelan equine encephalitis virus (VEEV), or an Eastern equine encephalitis virus (EEEV).

[0234] In some embodiments, the alphavirus-derived self-replicating RNA molecule is a Venezuelan equine encephalitis virus (VEEV).

[0235] The self-replicating RNA molecules can contain RNA sequences from (or amino acid sequences encoded by) a wild-type New World or Old World alphavirus genome. Any of the self-replicating RNA molecules disclosed herein can contain RNA sequences “derived from” or “based on” wild type alphavirus genome sequences, meaning that they have at least 60% or at least 65% or at least 68% or at least 70% or at least 80% or at least 85% or at least 90% or at least 95% or at least 97% or at least 98% or at least 99% or 100% or 80-99% or 90-100% or 95- 99% or 95-100% or 97-99% or 98-99% sequence identity with an RNA sequence (which can be a corresponding RNA sequence) from a wild type RNA alphavirus genome, which can be a New World or Old World alphavirus genome.

[0236] Self-replicating RNA molecules contain all of the genetic information required for directing their own amplification or self-replication within a permissive cell. To direct their own replication, self-replicating RNA molecules encode polymerase, replicase, or other proteins which may interact with viral or host cell-derived proteins, nucleic acids or ribonucleoproteins to catalyze the RNA amplification process; and contain cis-acting RNA sequences required for replication and transcription of the saRNA-encoded RNA. Thus, RNA replication leads to the production of multiple daughter RNAs. These daughter RNAs, as well as collinear subgenomic transcripts, can be translated to provide in situ expression of a gene of interest, or can be transcribed to provide further transcripts with the same sense as the delivered RNA which are translated to provide in situ expression of the gene of interest.

[0237] There are two open reading frames (ORF's) in the genome of alphaviruses, non- structural (ns) and structural genes. The ns ORF encodes proteins (nsPl-nsP4) necessary for transcription and replication of viral RNA and are produced as a polyprotein and are the virus replication machinery. The structural ORF encodes three structural proteins: the core nucleocapsid protein C, and the envelope proteins P62 and El that associate as a heterodimer. The four ns protein genes are encoded by genes in the 5' two-thirds of the genome, while thethree structural proteins are translated from a subgenomic mRNA colinear with the 3' one-third of the genome.

[0238] Self-replicating RNA molecules can be used as basis of introducing foreign sequences to host cells by replacing viral sequences encoding structural genes or inserting the foreign sequences 5’ or 3’ of the sequences encoding the structural genes. They can be engineered to replace the viral structural genes downstream of the replicase, which are under control of a subgenomic promoter, by genes of interest (GOI), e.g. the polynucleotide encoding for the polypeptide of the disclosure. Upon transfection, the replicase which is translated immediately, interacts with the 5' and 3' termini of the genomic RNA, and synthesizes complementary genomic RNA copies. Those act as templates for the synthesis of novel positive- stranded, capped, and poly-adenylated genomic copies, and subgenomic transcripts. Amplification eventually can lead to very high RNA copy numbers of up to 2 x 105 copies per cell. The result is a uniform and / or enhanced expression of a GOI (e.g. the polynucleotide encoding for the polypeptide of the disclosure).

[0239] The nucleotide sequences encoding the amino acid sequence of SEQ ID NO: 54, 57 or 59 of the disclosure may be inserted into the deleted viral structural gene downstream of the replicase, and under control of the subgenomic promoter. In addition, appropriate transcriptional regulatory elements able to direct expression of the polypeptide of the disclosure in the mammalian host cells may be operatively linked to the polypeptide of the disclosure.

[0240] Provided herein is a self-replicating RNA molecule comprising a polynucleotide encoding for any of the polypeptide of the disclosure.

[0241] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 54 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 54.

[0242] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 55 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 55.

[0243] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 56 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 56.

[0244] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 57 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 57.

[0245] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 58 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 58.

[0246] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 59 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 59.

[0247] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 84 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 84.

[0248] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 85 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 85.

[0249] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 86 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 86.

[0250] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 87 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 87.

[0251] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 88 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 88.

[0252] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding for a polypeptide of SEQ ID NO: 89 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 89.

[0253] In some embodiments, the self-replicating RNA molecule comprises any of the polynucleotides of the disclosure.

[0254] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence derived from a polynucleotide of SEQ ID NO: 66 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 66.

[0255] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence derived from a polynucleotide of SEQ ID NO: 67 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 67.

[0256] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence derived from a polynucleotide of SEQ ID NO: 68 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 68.

[0257] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence derived from a polynucleotide of SEQ ID NO: 69 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 69.

[0258] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence derived from a polynucleotide of SEQ ID NO: 70 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 70.

[0259] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence derived from a polynucleotide of SEQ ID NO: 77 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 77.

[0260] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence derived from a polynucleotide of SEQ ID NO: 78 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 78.

[0261] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence derived from a polynucleotide of SEQ ID NO: 79 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 79.

[0262] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence derived from a polynucleotide of SEQ ID NO: 80 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 80.

[0263] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence derived from a polynucleotide of SEQ ID NO: 81 or having at least 90% sequence identity, or at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 81.

[0264] Any of the above self-replicating RNA molecules can further comprise one or more of the following: one or more nonstructural genes nsPl, nsP2, nsP3 and nsP4; at least one of a DLP motif, a 5’ UTR, a 3’UTR and a Poly A; and a subgenomic promoter.In some embodiments, for example, the self-replicating RNA molecule can comprise one or more of the following: one or more nonstructural genes nsPl, nsP2, nsP3 and nsP4; at least one of a DLP motif, a 5’ UTR, a 3’UTR and a Poly A; and a subgenomic promoter; and an RNA encoding for amino acids of SEQ ID NOs: 54, 57, 59, 84, 87, or 89 and operably linked to the subgenomic promoter.

[0265] In some embodiments, the self-replicating RNA molecule comprises an RNA sequence encoding a polypeptide of SEQ ID NO: 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88, or 89; 5’ and 3’ alphavirus untranslated regions; RNA sequences encoding amino acid sequences derived from New World alphavirus VEEV nonstructural proteins nsPl, nsP2, nsP3 and nsP4; a sub-genomic promoter that is operably linked to and regulates translation of the RNA sequence encoding the protein; a 5’ cap and a 3’ poly- A tail; positive sense, single-stranded RNA; a DLP from Sindbis virus upstream of the non-structural protein l(nsPl); a 2A ribosome skipping element; and a nspl nucleotide repeat downstream of the 5 ’-UTR and upstream of the DLP.

[0266] In some embodiments, the self-replicating RNA molecules may be at least 1 kb or at least 2 kb or at least 3 kb or at least 4 kb or at least 5 kb or at least 6 kb or at least 7 kb or at least 8 kb or at least 10 kb or at least 12 kb or at least 15 kb or at least 17 kb or at least 19 kb or at least 20 kb in size, or can be 100 bp-8 kb or 500 bp-8 kb or 500 bp-7 kb or 1-7 kb or 1-8 kb or 2-15 kb or 2-20 kb or 5-15 kb or 5-20 kb or 7-15 kb or 7-18 kb or 7-20 kb in size.Composition

[0267] The disclosure also provides compositions comprising any of the polynucleotides, any of the polypeptides, and any of the vectors disclosed herein.

[0268] The compositions of the disclosure may be formulated into a pharmaceutical composition comprising the composition and a pharmaceutically acceptable excipient. "Pharmaceutically acceptable" refers to the excipient that at the dosages and concentrations employed, will not cause unwanted or harmful effects in the subjects to which they are administered and include carrier, buffers, stabilizers or other materials well known to those skilled in the art. The precise nature of the carrier or other material may depend on the route of administration, e.g., intramuscular, subcutaneous, oral, intravenous, cutaneous, intramucosal (e.g., gut), intranasal or intraperitoneal routes. Liquid carriers such as water, petroleum, animal or vegetable oils, mineral oil or synthetic oil may be included. Physiological saline solution, dextrose or other saccharide solution or glycols such as ethylene glycol, propylene glycol or polyethylene glycol may be included. Suitable formulations known in the art, for the storage and for pharmaceutical administration of purified pharmaceutical preparations may be used in the composition of the disclosure.

[0269] The composition may comprise one or more adjuvants.

[0270] In some embodiments, the compositions of the disclosure comprise nanoparticles.

[0271] Any of the polynucleotides or polypeptides of the disclosure may be attached to or in contact with nanoparticles for delivery to a subject. Delivery of any of the polynucleotides or polypeptides of the disclosure using nanoparticles may eliminate the need to include a virus or an adjuvant in the composition.

[0272] Nanoparticles are typically from about 1 nm to about 100 nm in diameter, such as about 20 nm to about 40 nm. Nanoparticles with a mean diameter of 20 to 40 nm may facilitate uptake of the nanoparticle to the cytosol (see. e.g. WO2019 / 135086). Exemplary nanoparticles are polymeric nanoparticles, inorganic nanoparticles, liposomes, lipid nanoparticles (LNP), an immune stimulating complex (ISCOM), a virus-like particle (VLP), or a self-assembling protein. The nanoparticles may be calcium phosphate nanoparticles, silicon nanoparticles or gold nanoparticles. The polymeric nanoparticles may comprise one or more synthetic polymers, such as poly(d,l-lactide-co-glycolide) (PLG), poly(d,l-lactic-coglycolic acid) (PLGA), poly(g- glutamic acid) (g-PGA)m poly(ethylene glycol) (PEG), or polystyrene or one or more natural polymers such as a polysaccharide, for example pullulan, alginate, inulin, and chitosan.

[0273] Nanoparticles may contain immune danger signals that help to effectively induce an immune response to the peptides. The nanoparticles may induce dendritic cell (DC) activation and maturation, required for a robust immune response. The nanoparticles may contain non-self components that improve uptake of the nanoparticles and thus the peptides by cells, such as antigen presenting cells.

[0274] In some embodiments, the self-replicating RNA molecules and / or compositions comprising the self-replicating RNA molecules encoding any of the polypeptides of the disclosure may be encapsulated using liposomes, lipoplex and / or lipid nanoparticles.

[0275] Liposomes are artificially prepared vesicles which can primarily be composed of a lipid bilayer and can be used as a delivery vehicle for the administration of polynucleotides and self-replicating RNA molecules. Liposomes can be of different sizes such as, but not limited to, a multilamellar vesicle (MLV) which can be hundreds of nanometers in diameter and can contain a series of concentric bilayers separated by narrow aqueous compartments, a small unicellular vesicle (SUV) which can be smaller than 50 nm in diameter, and a large unilamellar vesicle (LUV) which can be between 50 and 500 nm in diameter. Liposome design can include, but is not limited to, opsonins or ligands in order to improve the attachment of liposomes to unhealthy tissue or to activate events such as, but not limited to, endocytosis. Liposomes can contain a low or a high pH in order to improve the delivery of the polynucleotides and self-replicating RNA molecules disclosed herein.

[0276] The formation of liposomes can depend on the physicochemical characteristics such as, but not limited to, the pharmaceutical formulation entrapped and the liposomal ingredients, the nature of the medium in which the lipid vesicles are dispersed, the effective concentration of the entrapped substance and its potential toxicity, any additional processes involved during the application and / or delivery of the vesicles, the optimization size, polydispersity and the shelf-life of the vesicles for the intended application, and the batch-to- batch reproducibility and possibility of large-scale production of safe and efficient liposomal products.

[0277] In some embodiments, the self-replicating RNA molecule is encapsulated in, bound to or adsorbed on a liposome, a lipoplex, a lipid nanoparticle, or combinations thereof, preferably the self-replicating RNA molecule is encapsulated in a lipid nanoparticle.

[0278] Lipid nanoparticles (LNPs) are similar to liposomes but have slightly different function and composition. LNPs are designed toward encapsulating polynucleotides, such as DNA, mRNA, siRNA and sRNA. Traditional liposomes contain an aqueous core surrounded by one or more lipid bilayers. LNPs may assume a micelle-like structure, encapsulating polynucleotides in a non-aqueous core. LNPs typically contain a cationic lipid, a non-cationic lipid, and a lipid that prevents aggregation of the particle (e.g., a PEG-lipid conjugate). LNPs are useful for systemic applications, as they exhibit extended circulation lifetimes following intravenous (i.e.) injection and accumulate at distal sites (e.g., sites physically separated from the administration site). The LNPs may have a mean diameter of about 50 nm to about 150 nm, such as about 60 nm to about 130 nm, or about 70 nm to about 110 nm, or about 70 nm to about 90 nm, and are substantially nontoxic. Preparation of polynucleotide loaded LNPs are disclosed in, e.g., U.S. Patent Nos. 5,976,567; 5,981,501; 6,534,484; 6,586,410; 6,815,432; and PCT Publication No. WO 96 / 40964. Polynucleotide containing LNPs are described for example in W02019 / 191780.

[0279] Components of the lipid nanoparticle can be combined in a core-shell, hybrid, and / or layer-by-layer architecture, to allow for fine-tuning of the nanoparticle so that delivery of the molecules and / or compositions of the disclosure can be enhanced.

[0280] The lipid particles may encapsulate at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more self-replicating RNA molecules that encode for one or more polypeptides.

[0281] In some embodiments, the self-replicating RNA molecule encoding the any of the polypeptides of the disclosure can be fully encapsulated within the lipid portion of the particle, thereby protecting the RNA from nuclease degradation. “Fully encapsulated” means that the RNA is not significantly degraded after exposure to serum or a nuclease assay that would significantly degrade free RNA. When fully encapsulated, preferably less than 25% of the nucleic acid in the particle is degraded in a treatment that would normally degrade 100% of free nucleic acid, more preferably less than 10%, and most preferably less than 5% of the nucleic acid in the particle is degraded. “Fully encapsulated” also means that the nucleic acid-lipid particles do not rapidly decompose into their component parts upon in vivo administration.Method of Treatment

[0282] The disclosure also provides methods for inducing an immune response in a subject comprising administering the various compositions of the disclosure that can be used to introduce the ovarian cancer neoantigens of the disclosure into the subject, e.g. the polynucleotides, the polypeptides, the vectors, and the recombinant viruses of the disclosure.

[0283] In some embodiments, the immune response is specific against one or more of the polypeptides selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 or 51 or a combination thereof.

[0284] In some embodiments, the immune response is specific against the amino acid sequences selected from the group consisting of SEQ ID NOs: 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88, and 89 or a fragment thereof.

[0285] In some embodiments, the cellular immune response is activation of neoantigen- specific CD8+ T cells, CD4+ T cells, or CD8+ T cells and CD4+ T cells, wherein activation is assessed by increased production of TNFa, IFNy, or TNFa and IFNy by CD8+ T cells, CD4+ T cells, or CD8+ T cells and CD4+ T cells.

[0286] In some embodiments, the method of inducing an immune response comprises administering to the subject in need thereof a composition comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0287] In some embodiments, the method of inducing an immune response comprises administering to the subject in need thereof a composition comprising a polynucleotide encoding a polypeptide that comprises one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31.

[0288] In some embodiments, the method of inducing an immune response comprises administering to the subject in need thereof a composition comprising a polynucleotide encodinga polypeptide that comprises the amino acid sequences selected from the group consisting of SEQ ID NOs: 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88 or 89or a fragment thereof

[0289] In some embodiments, the methods of inducing an immune response disclosed herein comprise administering to the subject in need thereof a composition comprising a polynucleotide selected from the group consisting of SEQ ID NO: 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80 or 81 or a fragment thereof

[0290] In any of the methods disclosed herein, the composition that is administered to a subject may comprise a vector selected from an adenovirus vector, an alphaviral vector, a poxvirus vector, an adeno-associated virus vector, a retrovirus vector, a self-replicating RNA molecule, and a combination thereof.

[0291] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition, wherein the composition comprises a Ad26 vector, a self-replicating RNA molecule, a GAd20 vector, a MVA vector, or combinations thereof.

[0292] In some embodiments, the method of inducing an immune response comprises administering a composition comprising a GAd20 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0293] In some embodiments, the method of inducing an immune response comprises administering a composition comprising a MVA vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0294] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0295] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31.

[0296] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from the group consisting of SEQ ID NOs: 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88, or 89, or a fragment thereof.

[0297] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 54 or a fragment thereof.

[0298] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 55 or a fragment thereof.

[0299] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 56 or a fragment thereof.

[0300] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 57 or a fragment thereof.

[0301] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotideencoding a polypeptide that comprises the amino acid sequences of SEQ ID NO: 58 or a fragment thereof.

[0302] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 59 or a fragment thereof.

[0303] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 84 or a fragment thereof.

[0304] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 85 or a fragment thereof.

[0305] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 86 or a fragment thereof.

[0306] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 87 or a fragment thereof.

[0307] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 88 or a fragment thereof.

[0308] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 89 or a fragment thereof.

[0309] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide selected from the group consisting of SEQ ID NOs: 60, 61, 62, 63, 64, 65, 71, 72, 73, 74, 75 or 76; or a fragment thereof.

[0310] In some embodiments, the method of treatment comprises administering a composition comprising a self-replicating RNA molecule.

[0311] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0312] In some embodiments, the method of inducing an immune response comprises administering to the subject in need thereof a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31.

[0313] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from SEQ ID NOs: 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88, or 89; or a fragment thereof.

[0314] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 54 or a fragment thereof.

[0315] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprisinga polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 55 or a fragment thereof.

[0316] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 56 or a fragment thereof.

[0317] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 57 or a fragment thereof.

[0318] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 58 or a fragment thereof.

[0319] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 59 or a fragment thereof.

[0320] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 84 or a fragment thereof.

[0321] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 85 or a fragment thereof.

[0322] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 86 or a fragment thereof.

[0323] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 87 or a fragment thereof.

[0324] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 88 or a fragment thereof.

[0325] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence selected from SEQ ID NO: 89 or a fragment thereof.

[0326] In some embodiments, the method of inducing an immune response comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising an RNA sequence derived from a polynucleotide selected from the group consisting of SEQ ID NOs: 66, 67, 68, 69, 70, 77, 78, 79, 80 or 81; or a fragment thereof.

[0327] In some embodiments, the self-replicating RNA molecule used in the methods of generating an immune response described above may be encapsulated in a lipid nanoparticle.

[0328] Provided herein are methods for treating ovarian cancer in a subject with the compositions disclosed herein. The methods of treatment provided herein comprise administering a composition comprising any of the polynucleotides, polypeptides, vectors, and recombinant viruses of the disclosure.

[0329] The methods for treating ovarian cancer comprise administering to a subject the various compositions of the disclosure and thereby introducing the ovarian cancer neoantigens of the disclosure into the subject, e.g. the polynucleotides, the polypeptides, the vectors, the recombinant viruses and compositions of the disclosure.

[0330] “ Ovarian cancer” is meant to include all types of cancerous growths within the ovary or oncogenic processes, metastatic tissues or malignantly transformed cells, tissues, or organs, irrespective of histopathology type or stage of invasiveness.

[0331] In some embodiments, the ovarian cancer is High-Grade Serous Carcinoma, Low- Grade Serous Carcinoma, mucinous ovarian cancer, endometrioid ovarian cancer, or clear-cell carcinoma.

[0332] In some embodiments, the ovarian cancer is selected from epithelial ovarian cancer, germ cell ovarian cancer, stromal cell ovarian cancer, small cell ovarian cancer, primary peritoneal cancer, fallopian tube carcinoma, relapsed or refractory ovarian cancer, platinum- resistant ovarian cancer, or a combination thereof.

[0333] In some embodiments, the ovarian cancer is stage 1 ovarian cancer, stage 2 ovarian cancer, stage 3 ovarian cancer, and stage 4 ovarian cancer.

[0334] In some embodiments, the ovarian cancer is a metastatic ovarian cancer. In some embodiments, the ovarian cancer has metastasized to pelvis, fallopian tubes, bladder, rectum, uterus, lining of the abdomen, abdomen, lymph nodes, liver, lungs, spleen, skin, brain, or bone, or any combination thereof.

[0335] In some embodiments, the ovarian cancer is an adenocarcinoma.

[0336] In some embodiments, the ovarian cancer is high grade serous ovarian cancer.

[0337] In some embodiments, the ovarian cancer is primary peritoneal cancer.

[0338] In some embodiments, the ovarian cancer is fallopian tube carcinoma.

[0339] In some embodiments, the ovarian cancer is an epithelial ovarian cancer.

[0340] In some embodiments, the ovarian cancer is a relapsed or a refractory ovarian cancer.

[0341] In some embodiments, the ovarian cancer is a platinum-resistant ovarian cancer.

[0342] In some embodiments, the ovarian cancer is stage 1 ovarian cancer. In some embodiments, the ovarian cancer is stage 2 ovarian cancer. In some embodiments, the ovarian cancer is stage 3 ovarian cancer. In some embodiments, the ovarian cancer is stage 4 ovarian cancer.

[0343] In some embodiments, the ovarian cancer is sensitive to chemotherapy.

[0344] In some embodiments, the ovarian cancer is insensitive to chemotherapy.

[0345] In some embodiments, the subject is treatment naive.

[0346] In some embodiments, the subject has received surgery.

[0347] In some embodiments, the subject has an elevated level of the cancer antigen 125 (CA 125). CA 125 is elevated in a subject when the level is typically about >35 U / mL. CA 125 levels may also be compared to post-surgery levels.

[0348] In some embodiments, the ovarian cancer neoantigens identified herein are expressed at least about 1% or more, about 2% or more, about 3% or more, about 4% or more, about 5% or more, about 6% or more, about 7% or more, about 8% or more, about 9% or more, about 10% or more, about 11% or more, about 12% or more, about 13% or more, about 14% or more, about 15% or more, about 16% or more about 17% or more, about 18% or more, about 19% or more, about 20% or more, about 21% or more, about 22% or more, about 23% or more, about24% or more, about 25% or more, about 26% or more, about 27% or more, about 28% or more, about 29% or more, about 30% or more, about 35% or more, about 40% or more, about 45% or more, about 50% or more, about 55% or more, about 60% or more, about 65% or more or about 70% or more higher in a population of subjects having the ovarian cancer when compared to subjects not having ovarian cancer.

[0349] In some embodiments, the method of treating ovarian cancer comprises administering to the subject in need thereof a composition comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0350] In some embodiments, the method of treating ovarian cancer comprises administering to the subject in need thereof a composition comprising a polynucleotide encoding a polypeptide that comprises one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31.

[0351] In some embodiments, the method of treating ovarian cancer comprises administering to the subject in need thereof a composition comprising a polynucleotide encoding for a polypeptide that comprises the amino acid sequences selected from the group consisting of SEQ ID NOs: 54, 55, 56, 57, 58, 59, 84, 85, 86, 86, or 89 or a fragment thereof.

[0352] In some embodiments, the methods disclosed herein comprise administering to the subject in need thereof a composition comprising a polynucleotide selected from the group consisting of SEQ ID NO: 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80 or 81 or a fragment thereof.

[0353] In any of the methods disclosed herein, the composition that is administered to a subject may comprise a vector selected from an adenovirus vector, an alphaviral vector, a poxvirus vector, an adeno-associated virus vector, a retrovirus vector, a self-replicating RNA molecule, and a combination thereof.

[0354] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition, wherein the composition comprises a Ad26 vector, a self-replicating RNA molecule, a GAd20 vector, a MVA vector, or combinations thereof.

[0355] In some embodiments, the method of treating ovarian cancer comprises administering a composition comprising a GAd20 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0356] In some embodiments, the method of treating ovarian cancer comprises administering a composition comprising a MVA vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0357] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0358] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotideencoding a polypeptide that comprises one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31.

[0359] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from the group consisting of SEQ ID NOs: 54, 55, 56, 57, 58, 59, 84, 85, 86, 86, 88 or 89, or a fragment thereof.

[0360] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 54 or a fragment thereof.

[0361] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 55 or a fragment thereof.

[0362] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 56 or a fragment thereof.

[0363] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 57 or a fragment thereof.

[0364] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 58 or a fragment thereof.

[0365] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 59 or a fragment thereof.

[0366] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 84 or a fragment thereof.

[0367] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 85 or a fragment thereof.

[0368] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 86 or a fragment thereof.

[0369] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 87 or a fragment thereof.

[0370] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 88 or a fragment thereof.

[0371] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO: 89 or a fragment thereof.

[0372] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising an Ad26 vector comprising a polynucleotide of SEQ ID NOs: 60, 61, 62, 63, 64, 65, 71, 72, 73, 74, 75 or 76; or a fragment thereof

[0373] In some embodiments, the method of treating ovarian cancer comprises administering a composition comprising a self-replicating RNA molecule.

[0374] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0375] In some embodiments, the method of treating ovarian cancer comprises administering to the subject in need thereof a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31.

[0376] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequences selected from SEQ ID NOs: 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88, or 89; or a fragment thereof.

[0377] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:54 or a fragment thereof.

[0378] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:55 or a fragment thereof.

[0379] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:56 or a fragment thereof.

[0380] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:57 or a fragment thereof.

[0381] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:58 or a fragment thereof.

[0382] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:59 or a fragment thereof.

[0383] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:84 or a fragment thereof.

[0384] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:85 or a fragment thereof.

[0385] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:86 or a fragment thereof.

[0386] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprisinga polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:87 or a fragment thereof.

[0387] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:88 or a fragment thereof.

[0388] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide that comprises the amino acid sequence of SEQ ID NO:89 or a fragment thereof.

[0389] In some embodiments, the method of treating ovarian cancer comprises administering to a subject a composition comprising a self-replicating RNA molecule comprising an RNA sequence derived from a polynucleotide selected from the group consisting of SEQ ID NOs: 66, 67, 68, 69, 70, 77, 78, 79, 80 or 81; or a fragment thereof.

[0390] In some embodiments, the self-replicating RNA molecule used in the method of treating ovarian cancer described above may be encapsulated in a lipid nanoparticle.Treatment Regimens

[0391] Any of the above methods can comprise one or more administrations of the compositions provided in the disclosure. For example, the methods of inducing an immune response or of treating ovarian cancer in a subject may comprises a first administration followed by a second administration, with a time period between the two administrations.

[0392] In some embodiments, the first administration and the second administration may comprise the same or different compositions. For example, the first administration may comprise a composition comprising an Ad26 vector or a self-replicating RNA molecule comprising a nucleotide encoding a polypeptide comprising the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

[0393] In some embodiments, the second administration may comprise a composition comprising an Ad26 vector or a self-replicating RNA molecule comprising a nucleotide encoding for a polypeptide comprising the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 and 51.

[0394] In some embodiments, the first administration may comprise a composition comprising a Ad26 vector or self-replicating RNA molecule comprising a nucleotide encoding for polypeptides comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88 or 89 or a fragment thereof. In some embodiments, the second administration may comprise a composition comprising a Ad26 vector, or a self-replicating RNA molecule comprising a nucleotide encoding for polypeptides comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88 or 89 or a fragment thereof.

[0395] In some embodiments, the first administration comprises a composition comprising a Ad26 vector comprising a nucleotide encoding for polypeptides comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 55, 56, 58, 85, 86 or 88 or a fragment thereof and the second administration comprises a composition comprising a self- replicating RNA molecule comprising a nucleotide encoding for polypeptides comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 57,59, 84, 87 or 89 or a fragment thereof.

[0396] In some embodiments, the first administration comprises a composition comprising a self-replicating RNA molecule comprising a nucleotide encoding for polypeptides comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 57, 59, 84, 87 or 89 or a fragment thereof and the second administration comprises a Ad26 vector comprising a nucleotide encoding for polypeptides comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 55, 56, 58, 85, 86 or 88 or a fragment thereof.

[0397] In some embodiments, the first administration may comprise a composition comprising a Ad26 vector, or a self-replicating RNA molecule comprising a polynucleotide selected from the group consisting of SEQ ID NO: 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,72, 73, 74, 75, 76, 77, 78, 79, 80 and 81, or a fragment thereof. In some embodiments, the second administration may comprise a composition comprising a Ad26 vector, or a self- replicating RNA molecule comprising a polynucleotide selected from the group consisting of SEQ ID NO: 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80 and 81, or a fragment thereof.

[0398] In some embodiments, the first administration comprises a composition comprising a Ad26 vector comprising a polynucleotide selected from the group consisting of SEQ ID NO: 60, 61, 62, 63, 64, 65, 71, 72, 73, 74, 75, or 76, or a fragment thereof and the second administration comprises a composition comprising a self-replicating RNA molecule comprising a polynucleotide selected from the group consisting of SEQ ID NO: 66, 67, 68, 69, 70, 77, 78, 79, 80 or 81, or a fragment thereof.

[0399] In some embodiments, the first administration comprises a composition comprising a self-replicating RNA molecule comprising a polynucleotide selected from the group consisting of SEQ ID NO: 66, 67, 68, 69, 70, 77, 78, 79, 80 or 81, or a fragment thereof and the second administration comprises a composition comprising a Ad26 vector comprising a polynucleotide selected from the group consisting of SEQ ID NO: 60, 61, 62, 63, 64, 65, 71, 72,73, 74, 75, or 76, or a fragment thereof.

[0400] The methods can further comprise administering one or more compositions comprising the Ad26 vector, or one or more compositions comprising the self-replicating RNA molecule. In some embodiments, the methods can further comprise administering the treatment regimen two or more times. After the initial treatment regimen, for example, the methods can comprise administering two compositions comprising the Ad26 vector and one composition comprising the self-replicating RNA molecule. In some embodiments, the methods can further comprise administering one composition comprising the Ad26 vector and one composition comprising the self-replicating RNA molecule. In some embodiments, the methods can further comprise administering one or more compositions comprising the Ad26 vector. The methods can further comprise, for example, administering three compositions comprising the Ad26 vector. The methods can further comprise, for example, administering two compositions comprising the self-replication RNA molecule. The methods can further comprise, for example, administering three compositions comprising the self-replication RNA molecule.

[0401] Suitable amounts of the Ad26 vector that can be administered comprise about 1 x 108viral particles (VP) to about 1 x 1013VP of the Ad26 vector.

[0402] Suitable amounts self-replicating RNA molecule that can be administered comprise about 1 microgram to about 100 micrograms.

[0403] The methods can comprise administering a composition comprising the Ad26 vector at week 0 and at about week 3 and administering a composition comprising the self- replicating RNA molecule at about week 9, and:- Administering a composition comprising the Ad26 vector at about week 15 and about week 18 and administering a composition comprising the self-replicating RNA molecule at about week 24; or-Administering a composition comprising the self-replicating RNA molecule at about week 15, about week 18 and about week 24; or-Administering a composition comprising the Ad26 vector at about week 15, and the self- replicating RNA molecule at about week 24.

[0404] The methods can comprise administering a composition comprising the self- replicating RNA molecule at week 0, at about week 3, at about week 9, at about week 15, at about week 18 and at about week 24.

[0405] The methods can comprise administering a composition comprising Ad26 vector at week 0 and at about week 15 and administering a composition comprising a self-replicating RNA molecule at week 9 and at about week 24.

[0406] In some embodiments, the methods further comprise administering a composition comprising a Ad26 vector at about week 36, about week 48, and about week 60.

[0407] In some embodiments, the methods further comprise administering a composition comprising a self-replicating RNA at about week 36, about week 48, and about week 60.

[0408] The disclosed methods can comprise the exemplary administration schedules provided in Table 1 below:Table 1. Exemplary administration schedules

[0409] The methods can comprise administering a composition comprising the Ad26 vector that in turn comprises a polynucleotide encoding an amino acid sequence selected from SEQ ID NOs: 55, 56, 58, 85, 86 and 88 at week 0 and at about week 3 and administering a composition comprising the self-replicating RNA molecule that in turn comprises a polynucleotide encoding an amino acid sequence selected from SEQ ID NOs: 54, 57, 59, 84, 87 and 89 at about week 9, and:Administering a composition comprising the Ad26 vector comprising a polynucleotide encoding an amino acid sequence selected from SEQ ID NOs: 55, 56, 58, 85, 86 and 88 at about week 15 and about week 18 and administering a composition comprising the self- replicating RNA molecule comprising a polynucleotide encoding an amino acid sequence selected from SEQ ID NOs: 54, 57, 59, 84, 87 and 89 at about week 24; orAdministering a composition comprising the self-replicating RNA molecule comprising a polynucleotide encoding an amino acid sequence selected from SEQ ID NOs: 54, 57, 59, 84, 87 and 89 at about week 15, about week 18 and about week 24; orAdministering a composition comprising the Ad26 vector comprising a polynucleotide encoding an amino acid sequence selected from SEQ ID NOs: 55, 56, 58, 85, 86 and 88 at about week 15, and the self-replicating RNA molecule comprising a polynucleotide encoding an amino acid sequence selected from SEQ ID NOs: 54, 57, 59, 84, 87 and 89 at about week 24.

[0410] The methods can comprise administering a composition comprising the self- replicating RNA molecule comprising a polynucleotide encoding an amino acid sequence selected from SEQ ID NOs: 54, 57, 59, 84, 87 and 89 at week 0, at about week 3, at about week 9, at about week 15, at about week 18 and at about week 24.

[0411] The methods can comprise administering a composition comprising Ad26 vector comprising a polynucleotide encoding an amino acid sequence selected from SEQ ID NOs: 55, 56, 58, 85, 86 and 88 at week 0 and at about week 15 and administering a composition comprising a self-replicating RNA molecule at week 9 and at about week 24.

[0412] In some embodiments, the methods further comprise administering a composition comprising a Ad26 vector comprising a polynucleotide encoding an amino acid sequence selected from SEQ ID NOs: 55, 56, 58, 85, 86 and 88 at about week 36, about week 48, and about week 60.

[0413] In some embodiments, the methods further comprise administering a composition comprising a self-replicating RNA molecule comprising a polynucleotide encoding an amino acid sequence selected from SEQ ID NOs: 54, 57, 59, 84, 87 and 89 at about week 36, about week 48, and about week 60.

[0414] Any of the above methods can further comprise administering a second therapeutic agent. In some embodiments, the second therapeutic is an immunostimulating agent, a chemotherapeutic agent, an antibiotic, a checkpoint inhibitor, or a cellular therapy.

[0415] ‘ ‘Administered with” means that two or more therapeutics (such as a virus and an antibody) can be administered to a subject together in a mixture, concurrently as single agents, or sequentially as single agents in any order.

[0416] In some embodiments, the second therapeutic is selected from CTLA-4 antibody, CTLA4 ligand, a PD-1 axis inhibitor, or PD-L1 axis inhibitor. The second therapeutic agent may be administered in combination with Ad26 vector or self-replicating RNA molecule or both.

[0417] Any of the above methods can further comprise administering an anti-CTLA4 antibody. The anti-CTLA4 antibody can be administered with the composition comprising the Ad26 vector, with the composition comprising the self-replicating RNA molecule, or both. The anti-CTLA4 antibody can be administered with each administration of the composition comprising the Ad26 vector, with each administration of the composition comprising the self-replicating RNA molecule, or both. Suitable amounts of the anti-CTLA4 antibody comprise about 0.5 mg / kg to about 5 mg / kg. Any antagonistic anti-CTLA4 antibody can be used in the disclosed methods. Suitable anti-CTLA4 antibodies for use in the disclosed methods include, without limitation, human anti-CTLA4 antibodies, mouse anti-CTLA4 antibodies, mammalian anti-CTLA4 antibodies, humanized anti-CTLA4 antibodies, monoclonal anti-CTLA4 antibodies, polyclonal anti-CTLA4 antibodies, and chimeric anti-CTLA4 antibodies. Non-limiting examples of anti-CTLA4 antibodies include Ipilimumab and tremelimumab.

[0418] Any of the above methods can further comprise administering an anti-PD-1 antibody. The anti-PD-1 antibody can be administered with the composition comprising the Ad26 vector, with the composition comprising the self-replicating RNA molecule, or both. The anti-PD-1 antibody can be administered with each administration of the composition comprising the Ad26 vector, with each administration of the composition comprising the self-replicating RNA molecule, or both. Suitable amounts of the anti-PD-1 antibody comprise about 0.5 mg / kg to about 5 mg / kg. Any antagonistic anti-PD-1 antibody can be used in the disclosed methods. Suitable anti-PD-1 antibodies for use in the disclosed methods include, without limitation, human anti-PD-1 antibodies, mouse anti-PD-1 antibodies, mammalian anti-PD-1 antibodies, humanized anti-PD-1 antibodies, monoclonal anti-PD-1 antibodies, polyclonal anti-PD-1 antibodies, and chimeric anti-PD-1 antibodies. Non-limiting examples of anti-PD-1 antibodies include cetrelimab, pembrolizumab, nivolumab, sintilimab, cemiplimab, toripalimab, camrelizumab, tislelizumab, dostralimab, spartalizumab, prolgolimab, balstilimab, budigalimab, sasanlimab, avelumab, atezolizumab, durvalumab, envafolimab, and iodapolimab.EXAMPLES

[0419] The following examples are provided to further describe some of the embodiments disclosed herein. The examples are intended to illustrate, not to limit, the disclosed embodiments.Example 1: Identification of neoantigens by bioinformatics

[0420] A computational framework was developed to analyze various cancer RNA-seq datasets by bioinformatics means to identify common cancer neoantigens resulting from genefusion events that resulted in generation of novel peptide sequences, intron retention, alternatively spliced variants, aberrant expression of developmentally silenced genes or point mutations.

[0421] The datasets queried were:The Genotype-Tissue Expression (GTEx) Consortium. This dataset encompasses 6137 RNA-seq datasets from 49 normal tissues and was used to annotate RNA features in normal tissues and assess frequency of potential ovarian cancer neoantigen candidates in normal tissue.Immune cell-type specific RNA-seq dataset. This internal study comprised of 110 RNA- seq datasets obtained from 20 immune cell-types (T cells, B cells, NK cells and Myeloid cell-types) derived from five healthy donors.TCGA Ovarian Cancer. This study comprised of 330 RNA-seq datasets obtained from treatment naive patients with localized ovarian cancer.Internal Ovarian Cancer study. This study comprised of 306 RNA-seq datasets obtained from patients with localized ovarian cancer.

[0422] Quality control (QC) of raw data was conducted prior to analysis. Sequencing reads were first trimmed to remove Illumina’s adapter sequences and reads mapping to human tRNA and rRNA were removed from downstream analysis. Reads were also trimmed of low- quality base calls (<10 Phred quality score; indicating a base with a l in 10 probability of being incorrect) at either ends. Trimmed reads with less than 25 base pairs (bp) were removed from the datasets. Additionally, following QC steps were considered to remove poor quality reads: remove reads having maximal base quality score less than 15, remove reads with average base quality score less than 10, remove reads having polyATCG rate >80%, remove RNA sequences in which one of the two reads failed.

[0423] Reads were later mapped to Human Genome Build 38 using Array Studio (www omicsoft com / array-studio / ) platform. NCBI’s Refseq gene model (release date June 6, 2017) was used to map reads to known exonic regions of human genome.Identification of gene fusion events

[0424] FusionMap algorithm was used to identify gene fusion events in the cancer datasets described above. See Ge H et al., Bioinformatics. 2011; 27(14): 1922-8., which is incorporated herein by reference in its entirety for all purposes. FusionMap detected fusion junctions based on reads that contained the fusion position in the middle region of the sequencing reads. This was followed by searching possible fusion junction positions from the consensus of seed reads. FusionMap build the reference index based on the pseudo fusion library and aligned unmapped potential fusion reads to this pseudo reference. Reads mapped during this step were considered as rescue reads.

[0425] This algorithm identified both chimeric read-through fusions as shown in FIG. 1 and gene fusion events resulting from chromosomal translocations as shown in FIG. 2. A gene fusion event was called in a RNA-seq dataset when following criteria were met: at least two seed reads with different mapping position in the genome, at least four seed and rescued reads supporting the fusion junction and at least one junction spanning read pair. Gene fusion events coming from gene pairs that shared high sequence similarity (orthologs and protein families) were ignored from downstream analysis.

[0426] Shared neoantigens originating from gene fusion events were identified using following criteria: the incidence of gene fusion event in a disease cohort should be greater than 5% (10% for internal ovarian cancer dataset), the occurrence of the gene fusion event were to be less than 1% in the entire GTEx dataset using a lenient criteria (at least 2 seed reads and one junction spanning read) and the occurrence of the gene fusion event were to be <= 2 RNA-seq datasets derived from normal immune cell-types. The open reading frame from Gene A (FIG. 1 and 2) was used to obtain protein sequence originating from the identified novel junction.Identification of splice variants

[0427] A custom bioinformatics process was developed to analyze paired-end RNA-seq data to identify potential neoantigens arising from alternative splicing events. Utilizing the developed process, splice variants with alternative 5’ or 3’ splice sites, retained introns, excluded exons, alternative terminations or insertion(s) of novel cassettes as shown in FIG. 3 were identified. The process identified splice variants that were not present in the NCBI’s RefSeqgene model through two main functionalities: 1) Identification of novel junctions based on sequencing reads with alignment gaps > 5 base pair and > 15 base pair aligned on each side of the gap, henceforth referred to as split-mapped reads. For each RNA-seq dataset, novel junctions were called if they were supported by at least 5 split-mapped reads and one mate pair of junction-spanning reads 2) Identification of islands of aligned reads, henceforth referred to as coverage islands. FIG. 4 shows the cartoon of the approach.

[0428] In order to assess the signal to noise ratio in each sample, where genomic DNA and pre-mRNA are potential contributors to noise, two parameters were computed from a set of 200 highly expressed housekeeping genes:. Intron depth of coverage (IDC): 90th percentile depth of coverage for all housekeeping intronic bases. If the coverage of a particular region fell below this value, the first base where this occurred was defined as a coverage island boundary.. Intron / exon coverage ratio (IECR): 90th percentile of the ratio between median intron coverage and median coverage of the nearest upstream exon of all housekeeping gene introns.

[0429] The following criteria was used to classify the various splice variants:. Alternative 375’ splice site identification:Novel splice site boundary was defined by split-mapped readsIntronic region resulting from using the splice site (if applicable) exceeded IECR and entire region exceeded IDC. Novel cassette identification:Two novel splice sites in an intronic region defined by split-mapped reads Region between the two splice sites exceeded IECR and entire region exceeded IDC. Intron retention identification:Intronic region exceeded IECR and entire region exceeded IDC. At least 5 reads spanned both intron-exon boundaries, with at least 15 bp aligned on each side of the boundaries. Alternative termination identification:3 ’ boundary defined as the edge of a coverage island that did not fall within 60 bp of the 3 ’ end of a canonical exonAny intronic regions between 5’ end of a canonical exon and the 3’ boundary exceeded IECR and entire region exceeded IDC. Exon exclusion identification:Novel junction defined by split- mapped reads where one or more canonical exons were skipped

[0430] Shared neoantigens originating from aberrant splicing events were identified using following criteria: the incidence of a splicing event in a disease cohort were to be greater than 5% (10% for internal ovarian cancer dataset), the occurrence of the splicing event were to be less than 1% in the entire GTEx dataset using a lenient criteria (at least 2 split- mapped reads) and the splicing event were to be present in < 2 RNA-seq datasets derived from normal immune cell-types. For exon exclusion, novel cassette, and alternative 375’ splice sites, events were to have a median split- mapped read counts per million mapped reads (CPM) > 0.05 and a median percent spliced-in (PSI) > 0.1, calculated using the formula below: inclusion readsPSI = - inclusion + exclusion reads

[0431] Events with median value of 0.05 > PSI > 0.1 were selected if the aberrantly spliced gene was found to be 2-fold upregulated in disease cohort versus healthy tissue differential gene expression analysis. For alternative termination and retained introns, events were to have a median number of split-mapped CPM > 0.1 and a median PSI > 0.5. Neoantigens originating from genes MUC16 and NR2F2 were included regardless of median split-mapped CPM and PSI values.Isoform prediction and translation

[0432] In order to assemble isoforms containing the alternatively spliced neoantigens, canonical exons neighboring the novel spliced features were identified using the split-mapped reads. The most highly expressed isoform that could potentially contain the predicted neoepitope was chosen for translation into the corresponding protein by choice of the appropriate openreading frame. The neoantigen portion of the protein sequence was extracted and concatenated with an additional 8 amino acid residues upstream of the first altered amino acid. This protein sequence was then used for subsequent validation studies.Identification of DNA mutation and frameshift based neoantigens

[0433] Datasets generated by The Cancer Genome Atlas (TCGA) consortium containing exome sequencing data from patients with Ovarian Cancer were examined. See Berger A. C. et. Al. Cancer Cell 2018, 33(4) 690-705, which is incorporated herein by reference in its entirety for all purposes. Mutation calls published by the consortia that generated this dataset were downloaded, and gene mutations that were present in > 10% of the patient population or in genes known to be critical drivers of cancer were identified. For each single point mutation chosen, a 17 mer peptide with the mutated amino acid at its center was identified for further validation studies.

[0434] 51 neoantigen peptides were identified using the methods described above and are described in Tables 2-6.

[0435] Table 2 shows gene origin and amino acid sequence of identified neoantigens that arose from gene fusion (FUS) events. In Table 2, bolded letters indicate canonical amino acids from gene 1. Italic letters indicate canonical amino acids from gene 2 for in-frame gene fusion events. Unbolded letters indicate novel amino acid sequences generated from out-of-frame gene fusion events. Table 3 lists long-form names for the genes fused to form each gene fusion.Table 2.Table 3.

[0436] Table 4 shows gene origin and amino acid sequences of identified neoantigens that arose from alternative splicing (AS) events. Bolded letters represent sequences from the wild-type protein while regular letters represent mutant sequences resulted from alternative splicing events. Table 5 shows long-form names for each gene and the genomic coordinates of the alternative splicing events.Table 4.Table 5.

[0437] Table 6 shows gene origin, full gene name, mutation and amino acid sequence of identified neoantigens that arose from point mutations events (M). Point mutations are indicated with bolded letters. Point mutations are indicated with bolded letters and the codons for the mutated residues are underlined.Table 6.Example 2. Generation of neoantigen sequences comprising the 51 neoantigensGeneration of the layouts

[0438] The 51 neoantigen amino acidic sequences were joined head to tail without any linker. The order of the neoantigens sequences was determined according to a strategy that minimized the formation of predicted junctional epitopes that may be generated by the juxtaposition of two adjacent neoantigen peptides.

[0439] To this purpose, custom tools were developed to split the 51 neoantigens into 4 smaller lists (sublists) of similar cumulative length and to generate, for each sublist, 2 million scrambled layouts of the synthetic gene with a different neoantigen order. The tool proceeded iteratively. At each loop a scrambled layout was generated and compared to the layouts alreadygenerated. If the number of predicted junctional epitopes in the new layout was lower than the number of the previously best layout, the new layout was considered as the best. Each scrambled layout was analyzed estimating the number of potential junctional epitopes predicted to bind one out of a subset of 9 class I HLA haplotypes with an IC50 <=1500nM (considering only 9mer epitopes predicted by the IEDB recommended method included in the IEDB 2. 17 software). The 9 class I HLA haplotypes cumulatively cover 82% of the world population as estimated by analyzing haplotypes annotated for subjects in the 1000 genomes project. Scrambled layouts with neoantigens that formed predicted junctional epitopes with the N-terminal T-cell enhancer or the C-terminal TAG sequence were excluded. As an additional constraint, in each layout, junctions that contained a 9mer peptide that matched a protein annotated in the human wildtype proteome were also excluded.

[0440] The best layouts obtained after scrambling 2 million times each of the 4 sublists were then joined to generate an overall layout comprising all 51 neoantigens. Out of all possible combinations of the best 4 layouts the one with the minimal number of predicted epitopes formed by the newly formed junctions was selected.

[0441] The whole procedure described was applied two times independently to generate artificial genes to be encoded alternatively by the Ad26 vector or the self-replicating RNA molecule. For the self-replication RNA molecule, the scrambled layouts were designed with additional constraints to avoid the junctions with predicted junctional epitopes that were already present in the layout selected for the Adenoviral transgene.

[0442] The polypeptide sequences or transgenes comprising the 51 neoantigens in optimized order (or layout) are herein referred to as “strings”. Six optimized layouts (or strings) of the neoantigens peptides were generated using the procedure described above. The order (or layout) of the neoantigens peptides in each string is described below. Numbers listed correspond to the SEQ ID NOs of each individual neoantigen peptides:String 1A (OVCA 1A)51116|44|29|27|42|38| 10|6|40| 5|4|45|9|24|20|37| 1130|3|7| 8|28| 50| 13| 18| 12| 19|43148|2|41132|31122|36| 35|39|23|25|34|11114|26|47|46| 17| 15|21149|33String IB (OVCA IB)11127|43|7|40|25|3142|49|32|46|38| 15| 19|2|21148|45| 17| 10|28|31137|4| 18|22|29| 14|47|9| 16|34|36|44| 50|6|51|8|20|13|26|39|41|5| l|35|30|12|33|24|23String 2A (OVCA 2A) l|41|44|50|6|47|28|31|22|36|23|24|20|37|30| 12|33|38| 10|39|21|32|46|14|26|42|15|25|34|l 1|27|45| 17| 35|48|9| 16|40| 5|4| 51119|43|7| 8|3|2| 18|49|29| 13String 2B (OVCA 2B)12| 19|47|31|37|2|l |21|48|27|30|3|42|41|5|34|38| 15|6|40|7|29| 14| 10|28|50|23|16|36|44|43| l l|9|24|35| 25| 18|22|26|39|46| 17|51|8|20| 13|4|45|33|49|32String 3A (OVCA 3A)46|6|40|5|18|12|20|l 1114|26| 10|45| 17| 15| 19|34|36|49|33|38|47|28|31122|29|27|30|3|42| 1314|37| 1123|2 5|2|21|48|35|39|8|9|24|51| 16|44|50|41|32|7|43String 3B (OVCA 3B)36|44|46| 17| 10|6|43|9|21135|25|3| 5| 1133|24|20|29| 13| 18|22|23| 16|40|26| 51119|47|34| 11138| 15|45|30| 1 2|31|37|4|48|27|42|49|32|28|50| 14|39|7|8|2|41

[0443] The amino acid sequences of the 6 neoantigen peptides strings comprising the 51 neoantigen peptides in a specific order are shown in Table 7.Table 7. Amino Acid sequences of the neoantigen strings (without the leader sequence and Tag)Insertion of T-cell enhancer and TAG sequences

[0444] A small peptide fragment of 21 amino acid long from the a chain of the TCR receptor of T2 lymphocytes (HAVT20) (MACPGFLWALVISTCLEFSMA; SEQ ID NO: 52) was placed at the N-terminus of each transgene encoding the 51 neoantigens. A small segment of 6 amino acids (TAG sequence; seq: HHHHHH; SEQ ID NO: 53) was added at the C-terminus of the transgene for the purpose of monitoring the expression of the encoded transgene.

[0445] The amino acid sequences of the 6 neoantigen peptides strings comprising the 51 neoantigen peptides, the T-cell enhancer HAVT20 at the N-terminus and the Tag sequence at the C-terminus are shown in Table 8.Table 8. Amino Acid sequences of the neoantigen strings (with the leader sequence and Tag)Conversion into nucleotide sequence and codon optimization

[0446] The amino acid sequence of the neoantigen strings comprising the 51 neoantigens, the HAVT20 and TAG sequence were converted into nucleotide sequences and codon optimized for expression into Ad26 vector or self-replicating RNA molecule.

[0447] The nucleotide sequences of the optimized layouts for Ad26 that omit the HAVT20 and the TAG are shown in Table 9. The nucleotide sequences of the optimized layouts for self-replicating RNA molecule that omit the HAVT20 and the TAG are shown in Table 10.

[0448] The nucleotide sequences of the optimized layouts for Ad26 that include the HAVT20 and the TAG are shown in Table 11. The nucleotide sequences of the optimized layouts for self-replicating RNA that include the HAVT20 and the TAG are shown in Table 12.Table 9. Nucleotide sequences of the optimized neoantigen strings for Ad26 without theHAVT20 and without the TAGTable 10. The nucleotide sequences of the optimized layouts for the self-replicating RNA molecule without the HAVT20 and the TAGTable 11. Nucleotide sequences of the optimized neoantigen strings for Ad26 including theHAVT20 and the TAGTable 12. Nucleotide sequences of the optimized layouts for self-replicating RNA molecule including the HAVT20 and the TAG

[0449] The optimized transgenes were subcloned in a Ad26 vector or a self-replicating RNA molecule.Example 3. Immunogenicity of Ad26 Transgenes in mice

[0450] A mouse immunogenicity study was performed to evaluate the immunogenicity of the neoantigen peptide strings OVCA IB, OVCA 2A, and OVCA 3A expressed in Ad26 vector. Mice were dosed with adenovirus at 5E8 VP / mouse and 1E10 VP / mouse and T-cell responses were assessed by enzyme-linked immunospot assay (ELISpot) after 14 days.

[0451] All three Ad26 vectors encoding ovarian cancer antigens were immunogenic (FIG. 5).Example 4. Immunogenicity of self-replicating RNA Transgenes in mice

[0452] A mouse immunogenicity study was performed to evaluate the immunogenicity of the neoantigen peptide strings OVCA 1A, OVCA 2A, OVCA 2B, OVCA 3A, and OVCA 3B expressed in self-replication RNA molecule. Mice were dosed at 3 ug of the ovarian cancer neoantigen peptide string and T-cell responses (expression of INFy) were assessed by enzyme- linked immunospot assay (ELISpot) after 28 days. All neoantigen peptide strings were able to generate significant ovarian cancer-specific T-cell responses at the 3 ug dose (FIG. 6).Example 5. Immunogenicity of string pairs in mice

[0453] The goal of this study was to evaluate the ability of self-replicating transgene to boost the Ad26 transgene induced T cell response. Balb / c mice were primed with adenovirus (5E8 VP / mouse) expresing neoantigen peptide string IB (OVCA IB) or 2A (OVCA 2A) at week 0 and boosted with 3 ug of self-replicating RNA molecule expressing neoantigen peptide string 1A (OVCA 1 A) or 2B (OVCA 2B) at week 3. T-cell responses were assessed by enzyme-linked immunospot assay (ELISpot) with INF-y as the primary read. The prime-boost schedule used is summarized in Table 13.Table 13.

[0454] Administration of Ad26 followed by self-replicating RNA generated a stronger antigen response compared to Ad26 alone (FIG. 7). There was no significant difference seen between the neoantigen peptide 1B / 1 A string pairs and the 2A / 2B string pairs in mice.Example 6. Ovarian neoantigen in vitro immunogenicity

[0455] The aim of the study was to test the capacity of human antigen-presenting cells (APC) to process and present peptides corresponding to the ovarian cancer neoantigens and to mount T cell responses. Due to the number of ovarian neoantigens in the vectors, most of the neoantigens were assessed in a larger pool of peptides. The full pool contained overlapping peptides for the entire ovarian neoantigen sequence excluding the neoantigen junctional epitopes. The peptides in the full pool were split into 4 sub-pools and assessed following transduction of APCs with Ad26 and self-replicating RNA expressing transgene. Flow cytometry was used to examine T cell markers (ie, CD4, CD8, CD3) and markers of activated T cells (ie, IFN y, TNF a) following coculture of transgene-transduced APCs with autologous T cells. Increased IFNy and TNFa staining after overnight stimulation of peptides on Day 12 indicated expansion of ovarian- neoantigen-specific T cells. The results consistently indicated that ovarian-neoantigen-specific immunogenic epitopes were expressed, processed, and presented from the transgene constructs. Ad26-OvCA neoantigens and saRNA-OvCA neoantigens could drive specific and detectable polyfunctional high-quality T cell responses in both CD8+ (Class I) and CD4+ (Class II) T cells (FIG. 8). The magnitude of response was 81% for Ad26-OvCa neoantigens and 100% for saRNA-OvCa neoantigens and confirmed immunoreactivity of Ad26-OvCa neoantigen and saRNA-OvCa neoantigen across a wide range of donors with unrestricted HLA types.Example 7. Immunogenicity of string pairs in Non-Human Primates

[0456] The goal of this study was to evaluate the ability of a neoantigen peptide string encoded in the self-replicating RNA molecule to boost the immune response in cynomolgus macaques, generated by priming with a neoantigen string encoded in the Ad26 vector in combination with aCTLA4. The prime-boost schedule used is described in Table 14. Ipilimumab (an aCTLA4 IV inhibitor) was given at 3 mg / kg at each injection.Table 14.

[0457] Administration of Ad26 followed by self-replicating RNA generated a strong antigen response through week 32 at both 5 and 30 ug self-replication RNA (FIG. 9A and FIG. 9B). Following 2 cycles of vaccination all animals demonstrated antigen specific OvCa T cell responses with a mean of >500 spot-forming units (SFU) per 106 PBMCs.

Claims

Claims1. A polypeptide comprising the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51.

2. A polypeptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31.

3. The polypeptide of claim 1 and 2, wherein the amino acid sequences are connected to each other in any order.

4. The polypeptide of any one of claims 1-3, wherein the amino acid sequences are connected to each other without a linker.

5. The polypeptide of any one of claims 1-4, wherein the polypeptide comprises one or more reverse peptide bonds, D-isomers of amino acids, chemical modifications, or any combination thereof.

6. The polypeptide of any one of claims 1-5, wherein the polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: 54, 55, 56, 57, 58, or 59, or a fragment thereof.

7. The polypeptide of any one of claims 1-6, wherein the polypeptide comprises a. an amino acid sequence of SEQ ID NO: 54 or having at least 90% sequence identity to SEQ ID NO: 54;b. an amino acid sequence of SEQ ID NO: 55 or having at least 90% sequence identity to SEQ ID NO: 55; c. an amino acid sequence of SEQ ID NO: 56 or having at least 90% sequence identity to SEQ ID NO: 56; d. an amino acid sequence of SEQ ID NO: 57 or having at least 90% sequence identity to SEQ ID NO: 57; e. an amino acid sequence of SEQ ID NO: 58 or having at least 90% sequence identity to SEQ ID NO: 58; or f. an amino acid sequence of SEQ ID NO: 59 or having at least 90% sequence identity to SEQ ID NO: 59.

8. The polypeptide of any one of claims 1-7, wherein the polypeptide further comprises a leader sequence of SEQ ID NO: 52.

9. The polypeptide of any one of claims 1-8, wherein the polypeptide further comprises a histidine tag of SEQ ID NO: 53.

10. The polypeptide of any one of claims 1-9, wherein the polypeptide comprises a. an amino acid sequence of SEQ ID NO: 84 or having at least 90% sequence identity to SEQ ID NO: 84; b. an amino acid sequence of SEQ ID NO: 85 or having at least 90% sequence identity to SEQ ID NO: 85; c. an amino acid sequence of SEQ ID NO: 86 or having at least 90% sequence identity to SEQ ID NO: 86; d. an amino acid sequence of SEQ ID NO: 87 or having at least 90% sequence identity to SEQ ID NO: 87; e. an amino acid sequence of SEQ ID NO: 88 or having at least 90% sequence identity to SEQ ID NO: 88; or f. an amino acid sequence of SEQ ID NO: 89 or having at least 90% sequence identity to SEQ ID NO: 89.

11. A polynucleotide encoding the polypeptide of any one of claims 1-10.

12. The polynucleotide of claim 11, wherein the polynucleotide encodes a polypeptide comprising a. one or more amino acid sequences selected from the group consisting of SEQ ID NOs:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51; or b. one or more amino acid sequences selected from the group consisting of SEQ ID NOs:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36,37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31.

13. The polynucleotide of claims 11-12, wherein the polynucleotide encodes a polypeptide comprising the amino acid sequences selected from the group consisting of SEQ ID NO: 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88, or 89 or a fragment thereof.

14. The polynucleotide of any one of claims 11-13, wherein the polynucleotide comprises: a nucleic acid sequence of SEQ ID NO: 60 or having at least 90% sequence identity to SEQ ID NO: 60; a nucleic acid sequence of SEQ ID NO: 61 or having at least 90% sequence identity to SEQ ID NO: 61; a nucleic acid sequence of SEQ ID NO: 62 or having at least 90% sequence identity to SEQ ID NO: 62; a nucleic acid sequence of SEQ ID NO: 63 or having at least 90% sequence identity to SEQ ID NO: 63; a nucleic acid sequence of SEQ ID NO: 64 or having at least 90% sequence identity to SEQ ID NO: 64;a nucleic acid sequence of SEQ ID NO: 65 or having at least 90% sequence identity to SEQ ID NO: 65; a nucleic acid sequence of SEQ ID NO: 66 or having at least 90% sequence identity to SEQ ID NO: 66; a nucleic acid sequence of SEQ ID NO: 67 or having at least 90% sequence identity to SEQ ID NO: 67; a nucleic acid sequence of SEQ ID NO: 68 or having at least 90% sequence identity to SEQ ID NO: 68; a nucleic acid sequence of SEQ ID NO: 69 or having at least 90% sequence identity to SEQ ID NO: 69; a nucleic acid sequence of SEQ ID NO: 70 or having at least 90% sequence identity to SEQ ID NO: 70; a nucleic acid sequence of SEQ ID NO: 71 or having at least 90% sequence identity to SEQ ID NO: 71; a nucleic acid sequence of SEQ ID NO: 72 or having at least 90% sequence identity to SEQ ID NO: 72; a nucleic acid sequence of SEQ ID NO: 73 or having at least 90% sequence identity to SEQ ID NO: 73; a nucleic acid sequence of SEQ ID NO: 74 or having at least 90% sequence identity to SEQ ID NO: 74; a nucleic acid sequence of SEQ ID NO: 75 or having at least 90% sequence identity to SEQ ID NO: 75; a nucleic acid sequence of SEQ ID NO: 76 or having at least 90% sequence identity to SEQ ID NO: 76; a nucleic acid sequence of SEQ ID NO: 77 or having at least 90% sequence identity to SEQ ID NO: 77: a nucleic acid sequence of SEQ ID NO: 78 or having at least 90% sequence identity to SEQ ID NO: 78; a nucleic acid sequence of SEQ ID NO: 79 or having at least 90% sequence identity to SEQ ID NO: 79;a nucleic acid sequence of SEQ ID NO: 80 or having at least 90% sequence identity toSEQ ID NO: 80; and a nucleic acid sequence of SEQ ID NO: 81 or having at least 90% sequence identity to SEQ ID NO: 81.

15. The polynucleotide of any one of claims 11-14, wherein the polynucleotide comprises DNA or RNA.

16. The polynucleotide of claim 15, wherein the RNA is mRNA.

17. A vector comprising the polynucleotide of any one of claims 11-16.

18. The vector of claim 17, wherein the vector is selected from an adenovirus vector, a poxvirus vector, adeno-associated virus vector, a retrovirus vector, a self-replicating RNA molecule, and a combination thereof.

19. The vector of claim 18, wherein the vector is the adenovirus vector comprising a polynucleotide encoding any one of the polypeptides of any one of claims 1-10.

20. The vector of claim 19, wherein the adenovirus vector is the Ad26 vector comprising a polynucleotide encoding a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 55, 56, 58, 85, 86, or 88 or a fragment thereof.

21. The vector of claim 19, wherein the vector is the Ad26 vector comprising a polynucleotide selected from the group consisting of SEQ ID NO: 60, 61, 62, 63, 64, 65, 71, 72, 73, 74, 75 or 76 or a fragment thereof.

22. The vector of claim 21, wherein the Ad26 vector comprises a polynucleotide of SEQ ID NO: 60 or having at least a 90% sequence identity to SEQ ID NO: 60.

23. The vector of claim 21, wherein the Ad26 vector comprises a polynucleotide of SEQ ID NO:61 or having at least a 90% sequence identity to SEQ ID NO: 61.

24. The vector of claim 21, wherein the Ad26 vector comprises a polynucleotide of SEQ ID NO:62 or having at least a 90% sequence identity to SEQ ID NO: 62.

25. The vector of claim 21, wherein the Ad26 vector comprises a polynucleotide of SEQ ID NO:63 or having at least a 90% sequence identity to SEQ ID NO: 63.

26. The vector of claim 21, wherein the Ad26 vector comprises a polynucleotide of SEQ ID NO:64 or having at least a 90% sequence identity to SEQ ID NO: 64.

27. The vector of claim 21, wherein the Ad26 vector comprises a polynucleotide of SEQ ID NO:65 or having at least a 90% sequence identity to SEQ ID NO: 65.

28. The vector of claim 21, wherein the vector is the Ad26 vector comprises a polynucleotide of SEQ ID NO: 71 or having at least a 90% sequence identity to SEQ ID NO: 71.

29. The vector of claim 21, wherein the vector is the Ad26 vector comprises a polynucleotide of SEQ ID NO: 72 or having at least a 90% sequence identity to SEQ ID NO: 72.

30. The vector of claim 21, wherein the vector is the Ad26 vector comprises a polynucleotide of SEQ ID NO: 73 or having at least a 90% sequence identity to SEQ ID NO: 73.

31. The vector of claim 21, wherein the vector is the Ad26 vector comprises a polynucleotide of SEQ ID NO: 74 or having at least a 90% sequence identity to SEQ ID NO: 74.

32. The vector of claim 21, wherein the vector is the Ad26 vector comprises a polynucleotide of SEQ ID NO: 75 or having at least a 90% sequence identity to SEQ ID NO: 75.

33. The vector of claim 21, wherein the vector is the Ad26 vector comprises a polynucleotide of SEQ ID NO: 76 or having at least a 90% sequence identity to SEQ ID NO: 76.

34. The vector of claim 18, wherein the vector is the self-replicating RNA molecule comprising a polynucleotide encoding any one of the polypeptides of any one of claims 1-10.

35. The vector of claim 34, wherein the vector is the self-replicating RNA molecule comprising a polynucleotide encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 54, 57, 59, 84, 87 or 89 or a fragment thereof.

36. The vector of claim 34, wherein the self-replicating RNA molecule comprises a polynucleotide of SEQ ID NO: 66, 67, 68, 69, 70, 77, 78, 79, 80 or 81 or a fragment thereof.

37. The vector of claim 36, wherein the self-replicating RNA molecule comprises a polynucleotide of SEQ ID NO: 66 or having at least a 90% sequence identity to SEQ ID NO: 66.

38. The vector of claim 36, wherein the self-replicating RNA molecule comprises a polynucleotide of SEQ ID NO: 67 or having at least a 90% sequence identity to SEQ ID NO: 67.

39. The vector of claim 36, wherein the self-replicating RNA molecule comprises a polynucleotide of SEQ ID NO: 68 or having at least a 90% sequence identity to SEQ ID NO: 68.

40. The vector of claim 36, wherein the self-replicating RNA molecule comprises a polynucleotide of SEQ ID NO: 69 or having at least a 90% sequence identity to SEQ ID NO: 69.

41. The vector of claim 36, wherein the self-replicating RNA molecule comprises a polynucleotide of SEQ ID NO: 70 or having at least a 90% sequence identity to SEQ ID NO: 70.

42. The vector of claim 36, wherein the self-replicating RNA molecule comprises a polynucleotide of SEQ ID NO: 77 or having at least a 90% sequence identity to SEQ ID NO: 77.

43. The vector of claim 36, wherein the self-replicating RNA molecule comprises a polynucleotide of SEQ ID NO: 78 or having at least a 90% sequence identity to SEQ ID NO: 78.

44. The vector of claim 36, wherein the self-replicating RNA molecule comprises a polynucleotide of SEQ ID NO: 79 or having at least a 90% sequence identity to SEQ ID NO: 79.

45. The vector of claim 36, wherein the self-replicating RNA molecule comprises a polynucleotide of SEQ ID NO: 80 or having at least a 90% sequence identity to SEQ ID NO: 80.

46. The vector of claim 36, wherein the self-replicating RNA molecule comprises a polynucleotide of SEQ ID NO: 81 or having at least a 90% sequence identity to SEQ ID NO: 81.

47. A pharmaceutical composition comprising a polypeptide of any one of claims 1-10, a polynucleotide of any one of claims 11-16, or a vector of any one of claims 17-46.

48. A method of inducing an immune response in a subject comprising administering to the subject in need thereof a pharmaceutical composition of claim 47.

49. The method of claim 48, wherein the method comprises administering a. one or more compositions comprising a Ad26 vector that comprises a nucleotide sequence encoding i. one or more amino acid sequences selected from the group consisting of SEQ ID NOs:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51; ii. one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more aminoacid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31 ; or iii. the amino acid sequences selected from the group consisting of SEQ ID NOs 54, 55, 56, 57, 58, 59, 84, 85, 86, 87, 88, or 89 or a fragment thereof; and / or b. one or more compositions comprising a self-replicating RNA molecule that comprises a nucleotide sequence encoding i. one or more amino acid sequences selected from the group consisting of SEQ ID NOs:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51; ii. one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31 ; or iii. the amino acid sequences selected from the group consisting of SEQ ID NOs 54, 55, 56, 57, 58, 59, 94, 85, 86, 87, 88 or 89 or a fragment thereof.

50. The method of any one of claims 48-49, wherein the method comprises administering a. one or more compositions comprising a Ad26 vector that comprises a nucleotide sequence encoding an amino acid sequence of SEQ ID NO: 85 and one or more compositions comprising a self-replicating RNA molecule that comprises a nucleotide sequence encoding an amino acid sequence of SEQ ID NO: 84; b. one or more compositions comprising a Ad26 vector that comprises a nucleotide sequence encoding an amino acid sequence of SEQ ID NO: 86 and one or more compositions comprising a self-replicating RNA molecule that comprises a nucleotide sequence encoding an amino acid sequence of SEQ ID NO: 87; or c. one or more compositions comprising a Ad26 vector that comprises a nucleotide sequence encoding an amino acid sequence of SEQ ID NO: 88 and one or more compositionscomprising a self-replicating RNA molecule that comprises a nucleotide sequence encoding an amino acid sequence of SEQ ID NO: 89.

51. The method of any one of claims 48-50, wherein the immune response is activation of specific CD8+T cells, CD4+T cells, or CD4+T cells and CD8+T cells, wherein activation is assessed by increased production of TNFa, IFNy, or IFNy and TNFa by CD8+T cells, CD4+T cells, or CD4+T cells and CD8+T cells and wherein the immune response is specific against one or more of the polypeptides selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51 or a combination thereof.

52. A method of treating ovarian cancer in a subject comprising administering to the subject in need thereof a pharmaceutical composition of claim 47.

53. The method of claim 52, wherein the ovarian cancer is a relapsed ovarian cancer, a refractory ovarian cancer, a metastatic ovarian cancer or a platinum-resistant ovarian cancer, or any combination thereof.

54. The method of any one of claims 52-53, wherein the ovarian cancer is High-Grade Serous Carcinoma, Low-Grade Serous Carcinoma, mucinous ovarian cancer, endometrioid ovarian cancer, clear-cell carcinoma, epithelial ovarian cancer, germ cell ovarian cancer, stromal cell ovarian cancer, small cell ovarian cancer, primary peritoneal cancer, or fallopian tube carcinoma.

55. The method of any one of claims 52-54, wherein the method comprises administering a. one or more compositions comprising a Ad26 vector that in turn comprises a nucleotide sequence encoding i. the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51;ii. one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31 ; or iii. the amino acid sequences selected from the group consisting of SEQ ID NOs 55, 56,58, 85, 86 or 88 or a fragment thereof; and / or b. one or more compositions comprising a self-replicating RNA molecule that in turn comprises a nucleotide sequence encoding i. the amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 and 51; ii. one or more amino acid sequences selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or 51, and one or more amino acid sequences selected from the group consisting of SEQ ID NOs 25, 26, 27, 28, 29, 30, or 31 ; or iii. the amino acid sequences selected from the group consisting of SEQ ID NOs 54, 57,59, 84, 87 or 89 or a fragment thereof.

56. The method of any one of claims 52-55, wherein the method comprises administering one or more compositions comprising a Ad26 vector comprising a nucleotide sequence encoding an amino acid sequence selected from SEQ ID NO: 55, 56, 58, 85, 86 or 88 and one or more compositions comprising a self-replicating RNA molecule that in turn comprises a nucleotide sequence encoding an amino acid sequence selected from SEQ ID NO: 54, 57, 59, 84, 87 or 89.

57. The method of any one of claims 52-56, wherein the method comprises administering one or more compositions comprising a Ad26 vector that comprises a nucleotide sequence selected from SEQ ID NOs: 71, 72, 73, 74, 75, and 76 and one or more compositions comprising a self-replicating RNA molecule that comprises a nucleotide sequence selected from SEQ ID NOs: 77, 78, 79, 80, and 81.

58. The method of any one of claims 48-57, comprising administering a composition comprising the Ad26 virus at week 0 and at about week 3 and administering a composition comprising the self-replicating RNA molecule at about week 9.

59. The method of claim 58, wherein the Ad26 virus administered at week 0 and at about week 3 comprises a polynucleotide encoding the amino acid sequence selected from SEQ ID NO: 55, 56, 58, 85, 86, or 88 and wherein the self-replicating RNA molecule administered at week 9 comprises a polynucleotide encoding the amino acid sequence selected from SEQ ID NO: 54, 57,59. 84, 87 or 89.

60. The method of claim 59, comprising further administering a. a composition comprising the Ad26 virus at about week 15 and at about week 18 and administering a composition comprising the self-replicating RNA molecule at about week 24; b. a composition comprising the self-replicating RNA molecule at about week 15, at about week 18 and at about week 24; or c. a composition comprising the Ad26 virus at about week 15, and the self-replicating RNA molecule at about week 24.

61. The method of any one of claims 48-57, comprising a. administering a composition comprising the self-replicating RNA molecule at week 0, at about week 3, at about week 9, at about week 15, at about week 18 and at about week 24; or b. administering a composition comprising Ad26 at week 0 and at about week 15 and administering a composition comprising a self-replicating RNA molecule at week 9 and at about week 24.

62. The method of claim 61, wherein the self-replicating RNA molecule comprises a polynucleotide encoding the amino acid sequence selected from SEQ ID NO: 54, 57, 59, 84, 87and 89 and the Ad26 virus comprises a polynucleotide encoding the amino acid sequence selected from SEQ ID NO: 55, 56, 58, 85, 86 and 88.

63. The method of any one of claims 48-62, comprising further administering a a. a composition comprising a Ad26 virus at about week 36, at about week 48, and at about week 60; or b. a composition comprising a self-replicating RNA molecule at about week 36, at about week 48, and at about week 60.

64. The method of claims 63, wherein the Ad26 virus administered at about week 36, at about week 48, and at about week 60 comprises a polynucleotide encoding an amino acid sequence selected from SEQ ID NO: 55, 56, 58, 85, 86 and 88; and wherein the self-replicating RNA molecule administered at about week 36, at about week 48, and at about week 60 comprises a polynucleotide encoding an amino acid sequence selected from SEQ ID NO: 54, 57, 59, 84, 87 and 89.

65. The method of any one of claims 48-64 further comprising administering a second therapeutic agent.

66. The method of claim 65, wherein the second therapeutic agent is a surgery, a chemotherapy, radiation, a checkpoint inhibitor, a targeted therapy, or any combination thereof.

67. The method of claim 66, wherein the second therapeutic agent is an anti-CTLA-4 antibody68. The method of claim 67, wherein the subject is treatment naive.

69. The method of claim 68, wherein the subject has received surgery.

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