HPV immunotherapy

Abstract

To provide compositions and methods related to the treatment of an HPV infection and / or cancer in a subject.SOLUTION: Provided are compositions and methods related to development of HPV-specific prophylactic and / or therapeutic immunotherapy based on T cell epitopes that are recognized by cytotoxic T lymphocytes and can be employed in the prevention and / or treatment of HPV infection, and / or cancer, and / or precancerous lesions.SELECTED DRAWING: None

Description

[Technical Field]

[0001] Related Applications This application claims the benefit of priority to U.S. Provisional Patent Application No. 62 / 621,279, filed January 24, 2018, which is incorporated herein by reference in its entirety. [Background technology]

[0002] Human papillomavirus (HPV) is a family of viruses containing over 150 types. Selective infection of the skin or mucous membranes is a classic feature of HPV, and its replication is closely associated with the maturation of cells in these membranes. The most common HPV types are low-risk HPV-6 and HPV-11, which cause 90% of genital warts and a disease known as recurrent respiratory papillomatosis, in which tumors grow in the respiratory tract. HPV-16 and HPV-18 account for the majority of cancers of the cervix, anus, vagina, vulva, penis, base of tongue, larynx, and tonsils. HPV plays a role in the development of nonmelanoma skin cancers (NMSC), including cutaneous squamous cell carcinoma (SCC), in patients with chronic lymphocytic leukemia (CLL) and blood and bone marrow transplant (BMT). A recent U.S. population-based study conducted by the Center for Disease Control indicates that 66% of cervical cancers, 55% of vaginal cancers, 79% of anal cancers, and 62% of oropharyngeal cancers can be attributed to HPV types 16 or 18. Globally, HPV infection accounts for an estimated 530,000 cervical cancer cases (approximately 270,000 deaths) annually, with the majority (86% of cases and 88% of deaths) occurring in developing countries. In total, HPV accounts for 5.2% of the global burden of cancer. Each year in the United States, an estimated 26,000 new cancers can be attributed to HPV, approximately 17,000 in women and 9,000 in men. Summary of the Invention [Problem to be solved by the invention]

[0003] Standard treatment options for HPV-associated lesions include cryotherapy (i.e., using extremely low temperatures to destroy tissue), chemical cauterization (i.e., using chemicals to destroy tissue), and physical removal by laser or surgical excision. However, surgery alone is not highly effective for precancerous lesions, as more than 20-30% of cases recur, both at previously treated sites due to failure of surgery to remove HPV and at new sites due to new infection. When this occurs, radiation therapy and chemotherapy are then used with relative success, but approximately 50% of patients with HPV-associated cancer still die from the disease. Clearly, novel treatment strategies to control the burden of HPV-associated cancer are urgently needed. [Means for solving the problem]

[0004] Provided herein are compositions and methods for the development of HPV-specific prophylactic and / or therapeutic immunotherapies based on T-cell epitopes (e.g., HPV epitopes listed in Table 1) that are recognized by cytotoxic T lymphocytes (CTLs) and can be used in the prevention and / or treatment of HPV infection, and / or cancer (e.g., cancers that express the HPV antigens provided herein), and / or precancerous lesions.

[0005] In some embodiments, the compositions described herein may be administered conjointly with chemical and / or non-chemical methods of treating HPV-infected lesions and / or HPV-associated tumors. In certain embodiments, the compositions described herein may be administered conjointly with thermal ablation, cryotherapy, surgical excision, chemical ablation, cauterization, or any combination thereof.

[0006] In some embodiments, the compositions described herein may be administered in combination with an antiviral agent that inhibits HPV replication. In certain embodiments, the compositions described herein may be administered in combination with podofilox, imiquimod, sinecatechins, podophyllin resin, trichloroacetic acid, bichloracetic acid, or any combination thereof. In certain aspects, provided herein are compositions (e.g., therapeutic and / or prophylactic compositions, e.g., vaccine compositions) comprising a polypeptide comprising one or more HPV epitopes described herein (e.g., HPV epitopes listed in Table 1) and / or a nucleic acid encoding such a polypeptide, as well as methods of treating and / or preventing HPV infection, cancer, and / or precancerous lesions by administering such compositions to a subject. In some embodiments, the HPV epitope is derived from HPV E1, E2, E4, E5, E6, and / or E7. In some embodiments, the HPV is type 16 or 18. For example, suitable HPV epitopes may be derived from HPV16-E2, HPV18-E6, and / or HPV18-E5, e.g., HPV epitopes listed in Table 1. In some embodiments, the polypeptide is not a full-length HPV protein. In some embodiments, the polypeptide contains no more than 5, 10, 15, or 20 consecutive amino acids of a full-length HPV protein. In some embodiments, the polypeptide consists essentially of a plurality of HPV epitopes described herein. In some embodiments, the polypeptide consists of an HPV epitope described herein. In some embodiments, the polypeptide is no more than 15, 20, 25, 30, 35, or 40 amino acids in length. In some embodiments, the composition further comprises an adjuvant.

[0007] In some aspects, provided herein are methods of treating and / or preventing cancer and / or precancerous lesions in a subject, e.g., by administering to the subject one or more vaccine compositions described herein. In some such embodiments, the one or more vaccine compositions comprise one or more HPV epitopes listed in Table 1. The vaccine composition may further comprise an adjuvant. In certain preferred embodiments, the method of treating and / or preventing cancer and / or precancerous lesions in a subject comprises administering to the subject one or more peptides described herein, e.g., immunostimulatory peptides comprising one or more epitopes listed in Table 1.

[0008] In some aspects, provided herein are methods of treating and / or preventing HPV infection in a subject, e.g., by administering to the subject one or more vaccine compositions described herein. In some such embodiments, the one or more vaccine compositions comprise one or more HPV epitopes listed in Table 1. The vaccine composition may further comprise an adjuvant. In some embodiments, the method of treating and / or preventing HPV infection in a subject comprises administering to the subject one or more peptides described herein, e.g., immunostimulatory peptides comprising one or more epitopes listed in Table 1.

[0009] In some embodiments, provided herein are methods for generating, activating, and / or inducing proliferation of CTLs that recognize one or more HPV epitopes described herein, e.g., by incubating a sample containing CTLs (i.e., a peripheral blood mononuclear cell, PBMC sample) with antigen-presenting cells (APCs) that present one or more HPV epitopes described herein (e.g., APCs that present peptides comprising an HPV epitope described herein on class I MHC complexes). In some embodiments, the APCs are autologous to the subject from which the CTLs were obtained. In some embodiments, the APCs are not autologous to the subject from which the CTLs were obtained. In some embodiments, the APCs are B cells, antigen-presenting T cells, dendritic cells, or artificial antigen-presenting cells (e.g., aK562 cells). In some embodiments, the antigen-presenting cells (e.g., aK562 cells) express CD80, CD83, 41BB-L, and / or CD86.

[0010] In some aspects, provided herein are compositions (e.g., prophylactic and / or therapeutic compositions) comprising CTLs that recognize one or more HPV epitopes described herein (i.e., CTLs that express a T cell receptor (TCR) that binds to a peptide comprising an HPV epitope described herein presented on a class I MHC complex), and methods of treating and / or preventing HPV infection and / or cancer and / or precancerous lesions by administering such compositions to a subject. For example, in some embodiments, provided herein are methods of treating and / or preventing cancer, precancerous lesions, and / or HPV infection in a subject, comprising administering to the subject a composition comprising CTLs that recognize one or more HPV epitopes described herein. In some embodiments, the CTLs are not autologous to the subject. In some embodiments, the T cells are autologous to the subject. In some embodiments, the CTLs are stored in a cell bank before being administered to the subject. In some embodiments, the method further comprises generating, activating, and / or inducing proliferation of the CTLs using the methods described herein. In some embodiments, provided herein are T cells (e.g., CTLs) that express a T cell receptor (TCR) that binds to a peptide listed in Table 1 presented on the major histocompatibility complex (MHC).

[0011] In some embodiments, provided herein are APCs that present one or more peptides (including polyepitopes) comprising one or more HPV epitopes described herein (e.g., APCs that present one or more HPV epitopes on class I MHC). In certain aspects, provided herein are methods of generating APCs that present one or more HPV epitopes described herein, the methods comprising contacting APCs with peptides comprising an HPV epitope described herein and / or nucleic acids encoding an HPV epitope described herein. In some embodiments, the APCs are not autologous to the subject from which the CTLs were obtained. In some embodiments, the APCs are B cells, antigen-presenting T cells, dendritic cells, or artificial antigen-presenting cells (e.g., aK562 cells). In some aspects, the antigen-presenting cells (e.g., aK562 cells) express CD80, CD83, 41BB-L, and / or CD86. In some embodiments, provided herein are methods for treating or preventing cancer, precancerous lesions, and / or HPV infection in a subject, the methods comprising administering to the subject an APC described herein.

[0012] In certain aspects, provided herein are antigen-binding molecules (e.g., antibodies, antibody fragments, TCRs, chimeric antigen receptors (CARs)) that specifically bind to the HPV epitopes described herein. In some embodiments, the antigen-binding molecule is an antibody or an antigen-binding fragment thereof. In some embodiments, the antibody is a chimeric antibody, a humanized antibody, or a fully human antibody. In some embodiments, the antibody or antigen-binding fragment thereof is a full-length immunoglobulin molecule, scFv, Fab fragment, Fab' fragment, F(ab')2 fragment, Fv, camelid Fv, a disulfide-linked Fv, or a designed ankyrin repeat protein (DARPin). In some embodiments, the antibody specifically binds to an epitope provided herein within about 10 -7 M, 10 -8M or 10 -9 The antigen-binding molecule binds to the target antigen with a dissociation constant of M or less. In some embodiments, the antigen-binding molecule is conjugated to a drug (e.g., as part of an antibody-drug conjugate). In some embodiments, the antigen-binding molecule is linked to a cytotoxic agent (e.g., MMAE, DM-1, maytansinoid, doxorubicin derivative, auristatin, calcheamicin, CC-1065, aduocarmycin, or an anthracycline). In some embodiments, the antigen-binding molecule is linked to an antiviral drug (e.g., ganciclovir, valganciclovir, foscarnet, cidofovir, acyclovir, fomivirsen, maribavir, BAY 38-4766, or GW275175X). In some embodiments, provided herein are methods for treating cancer, precancerous lesions, and / or HPV infection in a subject, the methods comprising administering to the subject an antigen-binding molecule disclosed herein.

[0013] In some embodiments, the present invention provides a nucleic acid comprising a sequence encoding one or more peptides provided herein.In some embodiments, the sequence encoding one or more peptides provided herein is operably linked to one or more regulatory sequences.In some embodiments, the nucleic acid is an expression vector.In some embodiments, the nucleic acid is an adenovirus vector.

[0014] In some aspects, provided herein are pharmaceutical compositions comprising the HPV peptides, CTLs, APCs, nucleic acids, and / or antigen-binding molecules described herein and a pharmaceutically acceptable carrier. In some embodiments, provided herein are methods for treating and / or preventing HPV infection and / or cancer and / or precancerous lesions in a subject by administering the pharmaceutical compositions provided herein.

[0015] In some aspects, provided herein are methods for identifying a subject suitable for a method of treatment provided herein (e.g., administration of a CTL, APC, polypeptide, composition, antibody, or nucleic acid described herein), the method comprising isolating a sample (e.g., a blood or tumor sample) from the subject and detecting the presence of an HPV epitope provided herein or a nucleic acid encoding an HPV epitope provided herein in the sample (e.g., the blood or tumor sample). In some embodiments, the HPV epitope provided herein is detected by contacting the sample with an antigen-binding molecule provided herein. In some embodiments, a subject identified as suitable for a method of treatment provided herein is treated using the method of treatment. The present invention also relates to the following: [Item 1] An isolated peptide consisting of a cytotoxic T cell epitope having an amino acid sequence selected from the cytotoxic T cell epitope amino acid sequences set forth in SEQ ID NOs: 1 to 24. [Item 2] An isolated polyepitope peptide comprising multiple T cell epitope amino acid sequences selected from the T cell epitope amino acid sequences listed in Table 1. [Item 3] 3. The isolated polyepitope peptide according to item 2, comprising an amino acid sequence set forth in any one of SEQ ID NOs: 34, 36, and 38. [Item 4] An isolated nucleic acid comprising a nucleotide sequence encoding a peptide consisting of a cytotoxic T cell epitope having an amino acid sequence selected from SEQ ID NOs: 1 to 24. [Item 5] 5. The nucleic acid according to item 4, which is an expression vector. [Item 6] 6. The nucleic acid of item 5, wherein the expression vector is a viral vector. [Item 7] 7. The nucleic acid of item 6, wherein the viral vector is an adenovirus-based expression vector. [Item 8] 8. A vaccine composition comprising the peptide according to any one of items 1 to 3 or the nucleic acid according to any one of items 4 to 7. [Item 9] 9. The vaccine composition according to item 8, comprising a peptide and an adjuvant. [Item 10] An isolated polypeptide comprising a plurality of isolated HPV CTL epitopes having an amino acid sequence selected from the HPV CTL amino acid sequences set forth in SEQ ID NOs: 1-24. [Item 11] 10. The isolated polypeptide according to item 9, comprising the amino acid sequence set forth in any one of SEQ ID NOs: 34 and 38. [Item 12] A method for preparing a composition for use in inducing CTLs in a subject, the method comprising mixing at least one peptide consisting essentially of an amino acid sequence set forth in Table 1 with a pharmaceutically acceptable carrier, diluent or excipient. [Item 13] A method of treating cancer in a subject, comprising administering to the subject a pharmaceutical composition comprising cytotoxic T cells (CTLs) comprising a T cell receptor (TCR) that specifically binds to one or more HPV epitope peptides bound to an HLA class I or HLA class II molecule comprising one or more epitope peptides listed in Table 1 presented on class I MHC. [Item 14] A method of treating a precancerous condition in a subject, comprising administering to the subject a pharmaceutical composition comprising cytotoxic T cells (CTLs) comprising a T cell receptor (TCR) that specifically binds to one or more HPV epitope peptides bound to an HLA class I or HLA class II molecule that comprises one or more epitope peptides listed in Table 1 presented on class I MHC. [Item 15] A method for treating a human papillomavirus (HPV) infection in a subject, comprising administering to the subject a pharmaceutical composition comprising cytotoxic T cells (CTLs) comprising a T cell receptor (TCR) that specifically binds to one or more HPV epitope peptides bound to an HLA class I or HLA class II molecule comprising one or more epitope peptides listed in Table 1 presented on class I MHC. [Item 16] 16. The method of any one of items 13 to 15, wherein the CTLs are autologous to the subject. [Item 17] 16. The method of any one of items 13 to 15, wherein the CTLs are not autologous to the subject. [Item 18] 18. The method according to item 17, wherein the CTLs are obtained from a library or bank of CTLs. [Item 19] A method for inducing proliferation of HPV-specific cytotoxic T cells (CTLs), comprising incubating a sample containing CTLs with antigen-presenting cells (APCs) that present one or more HPV peptides comprising one or more epitopes listed in Table 1, thereby inducing proliferation of peptide-specific CTLs in the sample. [Item 20] 20. The method of item 19, wherein the sample further comprises one or more cytokines. [Item 21] 21. The method of item 19 or 20, wherein the APC is a B cell. [Item 22] 21. The method of item 19 or 20, wherein the APC is an antigen-presenting T cell. [Item 23] 21. The method according to item 19 or 20, wherein the APC is a dendritic cell. [Item 24] 22. The method of item 20 or 21, wherein the APCs are aK562 cells. [Item 25] 24. The method of any one of items 19 to 23, wherein the sample comprises peripheral blood mononuclear cells (PBMCs). [Item 26] 26. The method of any one of items 19 to 25, wherein the HPV peptide is 20 amino acids or less in length. [Item 27] 27. The method of item 26, wherein the HPV peptide is 15 amino acids or less in length. [Item 28] 27. The method of item 26, wherein the HPV peptide is 10 amino acids or less in length. [Item 29] 26. The method of any one of items 19 to 25, wherein the HPV peptide is an HPV16-E1 antigen. [Item 30] 30. The method according to item 29, wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 5 to 8 and 20. [Item 31] 26. The method of any one of items 19 to 25, wherein the HPV peptide is an HPV16-E2 antigen. [Item 32] 32. The method of claim 31, wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 1, 9, 10, 26, and 27. [Item 33] 26. The method of any one of items 19 to 25, wherein the HPV peptide is HPV16-E4 antigen. [Item 34] 34. The method of claim 33, wherein the HPV peptide comprises the sequence WPTTPPRPI (SEQ ID NO: 11). [Item 35] 26. The method of any one of items 19 to 25, wherein the HPV peptide is HPV18-E6 antigen. [Item 36] 36. The method of item 35, wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 2, 20, and 21. [Item 37] 26. The method of any one of items 19 to 25, wherein the HPV peptide is HPV18-E5 antigen. [Item 38] 38. The method of item 37, wherein the HPV peptide comprises the sequence SPATAFTVY (SEQ ID NO: 3). [Item 39] 26. The method of any one of items 19 to 25, wherein the HPV peptide is an HPV16-E5 antigen. [Item 40] 40. The method of claim 39, wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 4 and 12. [Item 41] 26. The method of any one of items 19 to 25, wherein the HPV peptide is HPV16-E6 antigen. [Item 42] Item 42. The method according to Item 41, wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 13 to 19 and 28 to 30. [Item 43] 26. The method of any one of items 19 to 25, wherein the HPV peptide is an HPV16-E7 antigen. [Item 44] 44. The method of item 43, wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 22, 23, and 24. [Item 45] A peptide comprising an amino acid sequence listed in Table 1, wherein the peptide does not contain more than 30 consecutive amino acids of an HPV protein. [Item 46] 46. ​​The peptide according to item 45, wherein the amino acid sequence listed in Table 1 is LQDVSLEVYL, TVLELTEVFEF, SPATAFTVY or SAFRCFIVY. [Item 47] 47. The peptide according to item 45 or 46, comprising two or more sequences listed in Table 1. [Item 48] 48. A vaccine composition comprising the peptide according to any one of items 45 to 47. [Item 49] 49. The vaccine composition of item 48, further comprising an adjuvant. [Item 50] 50. A method for treating and / or preventing cancer in a subject, comprising administering to the subject one or more vaccine compositions according to items 48 or 49. [Item 51] 50. A method for treating and / or preventing a precancerous condition in a subject, comprising administering to the subject one or more vaccine compositions according to items 48 or 49. [Item 52] 50. A method for treating and / or preventing HPV infection in a subject, comprising administering to the subject one or more vaccine compositions according to items 48 or 49. [Item 53] 48. A method for treating and / or preventing cancer in a subject, comprising administering to the subject one or more peptides according to any one of items 45 to 47. [Item 54] 48. A method for treating and / or preventing a precancerous condition in a subject, comprising administering to the subject one or more peptides according to any one of items 45 to 47. [Item 55] 48. A method for treating and / or preventing HPV infection in a subject, comprising administering to the subject one or more peptides according to any one of items 45 to 47. [Item 56] 48. An antigen-presenting cell (APC) comprising the peptide of any one of items 45 to 47, presented on class I MHC. [Item 57] 57. The APC according to item 56, which is an antigen-presenting T cell. [Item 58] 57. The APC according to item 56, which is a dendritic cell. [Item 59] 57. The APC according to item 56, which is a B cell. [Item 60] 57. The APC of item 56, which is an artificial APC. [Item 61] 57. The APC of item 56, wherein the artificial APC is an aK562 cell. [Item 62] 48. A method for generating antigen-presenting cells (APCs) that present one or more HPV peptides, comprising incubating antigen-presenting cells with one or more peptides according to any one of items 45 to 47, or one or more nucleic acids encoding one or more peptides according to any one of items 45 to 47. [Item 63] 63. The method of item 62, wherein the APC is an antigen-presenting T cell. [Item 64] Item 63. The method of item 62, wherein the APC is a dendritic cell. [Item 65] 63. The method of item 62, wherein the APC is a B cell. [Item 66] 63. The method of item 62, wherein the APC is an artificial APC. [Item 67] 63. The method of item 62, wherein the artificial APC is aK562 cell. [Item 68] 62. A method for treating or preventing cancer in a subject, the method comprising administering to the subject the APC of any one of items 56 to 61. [Item 69] 69. The method of item 68, wherein the APCs are autologous to the subject. [Item 70] 69. The method of item 68, wherein the APCs are not autologous to the subject. [Item 71] 62. A method for treating or preventing a precancerous condition in a subject, the method comprising administering to the subject the APC of any one of items 56 to 61. [Item 72] 72. The method of item 71, wherein the APCs are autologous to the subject. [Item 73] 72. The method of item 71, wherein the APCs are not autologous to the subject. [Item 74] 62. A method for treating or preventing HPV infection in a subject, comprising administering to the subject the APC of any one of items 56 to 61. [Item 75] 75. The method of item 74, wherein the APCs are autologous to the subject. [Item 76] 75. The method of item 74, wherein the APCs are not autologous to the subject. [Item 77] 48. A nucleic acid encoding the peptide according to any one of items 45 to 47. [Item 78] 78. The nucleic acid of item 77, which is an expression vector. [Item 79] 79. The nucleic acid of item 78, wherein the expression vector is a viral vector. [Item 80] 80. The nucleic acid of item 79, wherein the viral vector is an adenovirus-based expression vector. [Item 81] 81. A vaccine composition comprising the nucleic acid of any one of items 77 to 80. [Item 82] 82. A method for treating and / or preventing cancer in a subject, comprising administering to the subject the vaccine composition of item 81. [Item 83] 82. A method for treating and / or preventing a precancerous condition in a subject, comprising administering to the subject the vaccine composition of item 81. [Item 84] 82. A method for treating or preventing HPV infection in a subject, comprising administering to the subject the vaccine composition of item 81. [Item 85] An antibody or antigen-binding fragment thereof that binds to an HPV epitope listed in Table 1. [Item 86] full-length immunoglobulin molecules, scFv, Fab fragments, Fab' fragment, F(ab')2, Fv, camel antibodies, Disulfide-linked Fv, Designed Ankyrin Repeat Protein (DARPin) 86. The antibody or antigen-binding fragment thereof according to Item 85, [Item 87] 87. A method of treating cancer in a subject, comprising administering to the subject the antibody or antigen-binding fragment thereof of item 85 or 86. [Item 88] 87. A method for treating a precancerous condition in a subject, comprising administering to the subject the antibody or antigen-binding fragment thereof of item 85 or 86. [Item 89] 87. A method of treating an HPV infection in a subject, comprising administering to the subject the antibody or antigen-binding fragment thereof of item 85 or 86. [Item 90] A T cell expressing a T cell receptor (TCR) that binds to one or more peptides containing one or more epitopes listed in Table 1 presented on the major histocompatibility complex (MHC). [Item 91] 91. The T cell of item 90, which is a cytotoxic T cell (CTL). [Brief explanation of the drawings]

[0016] [Figure 1] 1 shows the total T cell response to HPV16 antigen in HNC patients. [Figure 2] 1 shows the total T cell response to HPV18 antigens in HNC patients. [Figure 3] 1 is a flow chart showing the epitope mapping process described herein. [Figure 4] A representative workflow strategy for identifying HPV epitope sequences is shown. [Figure 5] Illustrates the fine mapping process that identified the HPV18-E6 CD8+ T cell epitope TVLELTEVFEFA. [Figure 6] Illustrates the CD4+ T cell epitope fine mapping process of the HPV16-E6 pool that identified the epitope KQRFHNIRGRWTGRC. [Figure 7A]Figure 1 shows a schematic design of the HPV polyepitope protein construct encoding a CD8+ T cell polyepitope, a CD4+ T cell polyepitope, and a CD8IRESCD4 polyepitope. Each of the T cell epitope sequences (selected from Table 1) is shown in alternating bold and underlined italic letters. The HPV CD4+ T cell polyepitope contains an ER (endoplasmic reticulum) signal sequence at the amino terminus and a lysosomal signal sequence at the carboxy terminus (B). For generation of the CD8+ and CD4+ T cell polyepitope constructs, both polyepitope sequences were separated by an internal ribosome entry site (IRES) sequence derived from encephalomyocarditis virus (C, amino acid sequence of the translated peptide; and D, nucleic acid sequence encoding the CD8IRESCD4 polyepitope polypeptide, where the CD8 sequence is shown in bold, the IRES sequence is underlined, and the CD4 sequence is italicized). DNA sequences encoding CD8+, CD4+, and CD8+ and CD4+ T cell polyepitopes were obtained from Atum Bio in the pJ201 vector. [Figure 7B] This is a continuation of Figure 7A. [Figure 7C] This is a continuation of Figure 7B. [Figure 7D] This is a continuation of Figure 7C. [Figure 8] Figure 1 shows an outline of the cloning of HPV polyepitope protein constructs encoding the CD8+ T cell polyepitope, CD4+ T cell polyepitope, and CD8IRESCD4 T cell polyepitope into the Ad5F35 vector. DNA sequences encoding the HPV CD8+, CD4+, or CD8IRESCD4 T cell polyepitope were cloned into the pShuttle2 vector using the restriction sites indicated in the figure and then subcloned into the Ad5F35 expression vector. Recombinant Ad5F35 viruses expressing the HPV CD8+, CD4+, or CD8IRESCD4 T cell polyepitope were generated by infecting HEK293 cells with the Ad5F35 vector. Recombinant adenoviruses were recovered from transfected HEK293 cells by repeated freeze-thaw cycles. [Figure 9]PCR confirmation of the master stocks of AdHPVCD8, AdHPVCD4, and AdCD8IRESCD4 polyepitope recombinant viruses is shown. HEK293 cells were infected with recombinant adenoviruses encoding HPV CD8+, CD4+, or CD8IRESCD4 polyepitopes. Genomic DNA was isolated and subjected to PCR. DNA from uninfected HEK293 cells or adenoviral vectors encoding the CD8+, CD4+, or CD8IRESCD4 polyepitopes was used as negative and positive controls, respectively. [Figure 10] Figure 1 shows a FACS plot of AdHPVCD8 polyepitope presentation by JuSt fibroblasts. JuSt fibroblasts were activated with IFN-γ 24 hours before the assay and then pulsed with AdHPVCD8 poly recombinant virus for 1 hour. Cells were then washed, incubated overnight, and then exposed to HPV-specific CD8+ T cells specific for various HLA-restricted (HLA A02:01 and HLA A01:01) epitopes derived from various HPV antigens (HPV16-E2, HPV18-E6, HPV16-E6). FACS analysis shows IFN-γ expression by HPV-specific CD8+ T cells after coculture with JuSt fibroblasts pulsed with AdHPVCD8 poly or HPV pepmix (positive control). [Figure 11] Figure 1 shows the proliferation of HPV-specific CD8+ T cells from an HPV HNC patient. PBMCs (5 x 106) were stimulated with HPV AdCD8 polyrecombinant virus and cultured for 14 days in the presence of IL-2. The frequency of HPV-specific CD8+ T cells was determined by measuring IFN-γ secretion in response to stimulation with an HPV-specific pepmix. The stacked bar graph and representative FACS plot show the percentage of HPV-specific CD8+ T cells expressing IFN-γ. [Figure 12]Figure 1 shows the proliferation of HPV-specific CD4+ and CD8+ T cells from an HPV HNC patient. PBMCs (5 x 106) were stimulated with HPV AdCD4 polyrecombinant virus and cultured for 14 days in the presence of IL-2. In the same experiment, PBMCs were stimulated with HPV pepmix as a control. The frequencies of HPV-specific CD4+ and CD8+ T cells were determined by measuring IFN-γ secretion in response to stimulation with the HPV-specific pepmix. [Figure 13-1] Figure 1 shows the proliferation of HPV-specific CD8+ and CD4+ T cells from an HPV HNC patient. PBMCs (5 x 106) from an HPV HNC patient were stimulated with HPV AdCD8IRESCD4 poly recombinant virus and cultured for 14 days in the presence of IL-2. In the same experiment, PBMCs stimulated with HPV AdCD8 poly and AdCD4 poly were also included as controls. The frequencies of HPV-specific CD4+ (panels A and B) and CD8+ (panels C and D) T cells were determined by measuring IFN-γ secretion in response to stimulation with an HPV-specific pepmix. Bar graphs and representative FACS plots show the percentage of HPV-specific CD8+ T cells expressing IFN-γ. [Figure 13-2] This is a continuation of Figure 13-1. DETAILED DESCRIPTION OF THE INVENTION

[0017] Summary While the innate immune response plays an important role in controlling primary HPV infection, long-term protection relies on the adaptive immune response, including humoral and cell-mediated immunity. In immunocompetent individuals, the majority of HPV infections are cleared within two years of primary infection. CD4 + and CD8 + T cell infiltration is frequently observed in spontaneously regressing lesions.

[0018] Several immunotherapeutic strategies have been tested for the treatment of HPV-associated diseases. While HPV prophylactic vaccines are based on the L1 protein, this viral antigen is not critical for the treatment of HPV-associated diseases. This protein is expressed only in the late stages of HPV replication, particularly in terminally differentiated keratinocytes. In contrast, other proteins associated with the HPV replication cycle, namely E1, E2, E6, and E7, have been identified as important targets for immunotherapeutic strategies. This is primarily because the expression of all of these proteins is maintained throughout multiple stages of infection. While much of the design of immunotherapeutic strategies focuses on the E6 and E7 antigens, it is important to understand that E1 and E2 proteins are involved in HPV DNA replication, and therefore, their expression is maintained throughout multiple stages of infection. This highlights the importance of these proteins as potential targets for immunotherapy aimed at sustained elimination of HPV-infected cells, regardless of the stage of pathogenesis. Indeed, previous studies using animal models (dogs and rabbits) have shown that immunization with DNA vaccines encoding codon-optimized E1 or E2 genes results in complete regression of papillomas. The primary method of protection in these animal models is mediated by the induction of effective T cell responses to E1 and E2 antigens. Further clinical trials using a modified vaccinia Ankara vector encoding E2 in human subjects with HPV-induced cervical lesions (C1N1-C1N3) demonstrated complete clearance of cervical lesions, with regression from C1N3 to C1N1, and a significant reduction in HPV viral load. Again, the induction of E2-specific T cell immunity strongly correlated with clinical response. The development of anti-vector antibodies resulted in a poor response to booster immunizations, and some patients experienced recurrence of lesions after completion of the trial. Furthermore, this treatment requires direct injection of the vector into uterine tissue to be effective, thus limiting its widespread use in the general population.

[0019] A retrospective clinical trial was conducted on patients with high-grade cervical intraepithelial neoplasia who showed regression until the lesion was removed and subsequently showed a decrease in HPV viral load. + T cell epitopes were identified in these patients, and immune profiling of their peripheral blood mononuclear cells revealed that HPV E7-specific T cells exhibited a Th1 bias characterized by IFN-γ and TNF expression. Indeed, ex vivo analysis of patients showing resolution of HPV-induced pathology without disease recurrence after intervention revealed that potent T cell responses were directed against E6 and E7 proteins. In contrast, T cells from patients diagnosed with disease recurrence did not display this antigen-specific profile. Reconstitution of stable T cell immunity against E6 and E7 antigens may help provide long-term protection from disease recurrence.

[0020] Provided herein are compositions and methods relating to HPV epitopes (e.g., HPV epitopes listed in Table 1) that are recognized by cytotoxic T lymphocytes (CTLs) and are useful for preventing and / or treating HPV infection and / or cancer and / or precancerous lesions. In certain aspects, provided herein are compositions (e.g., prophylactic and / or therapeutic compositions such as vaccine compositions) containing polypeptides comprising one or more HPV epitopes described herein (e.g., HPV epitopes listed in Table 1), nucleic acids encoding such polypeptides, CTLs that recognize such peptides, APCs that present such peptides, and / or antigen-binding molecules that specifically bind to such peptides, as well as methods for treating and / or preventing HPV infection and / or cancer and / or precancerous lesions by administering such compositions to a subject. In some embodiments, provided herein are methods for identifying a subject suitable for treatment according to the methods provided herein.

[0021] definition For convenience, certain terms employed in the specification, examples, and appended claims are collected here.

[0022] The articles "a" and "an" are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, "an element" means one element or more than one element.

[0023] As used herein, the term "administer" means providing a pharmaceutical agent or composition to a subject, and includes, but is not limited to, administration by a medical professional and self-administration. Such agents may include, for example, the peptides described herein, the antigen-presenting cells provided herein, and / or the CTLs provided herein.

[0024] The term "amino acid" is intended to encompass all molecules, natural or synthetic, that contain both an amino functionality (amino functionality) and an acid functionality (acid functionality) and that can be included in a polymer of natural amino acids. Exemplary amino acids include natural amino acids, their analogs, derivatives and congeners, amino acid analogs with variant side chains, and all stereoisomers of any of the above.

[0025] As used herein, the term "antibody" can refer to both intact antibodies and antigen-binding fragments thereof. An intact antibody is a glycoprotein comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds. Each heavy chain contains a heavy chain variable region (herein referred to as V H Each light chain comprises a light chain variable region (abbreviated herein as V) and a heavy chain constant region. L V H and V LThese regions can be further subdivided into hypervariable regions, called complementarity-determining regions (CDRs), flanked by more conserved regions, called framework regions (FRs). The variable regions of the heavy and light chains contain binding domains that interact with antigens. The constant regions of the antibody may mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component of the classical complement system (Clq). The term "antibody" includes, for example, monoclonal antibodies, polyclonal antibodies, chimeric antibodies, humanized antibodies, human antibodies, multispecific antibodies (e.g., bispecific antibodies), single-chain antibodies, and antigen-binding antibody fragments.

[0026] As used herein, the terms "antigen-binding fragment" and "antigen-binding portion" of an antibody refer to one or more fragments of an antibody that retain the ability to bind to an antigen. Examples of binding fragments encompassed by the term "antigen-binding fragment" of an antibody include Fab, Fab', F(ab')2, Fv, scFv, disulfide-linked Fv, Fd, diabodies, single-chain antibodies, camelid antibodies, isolated CDRH3, designed ankyrin repeat proteins (DARPins), and other antibody fragments that retain at least a portion of the variable region of an intact antibody. These antibody fragments can be obtained using conventional recombinant and / or enzymatic techniques and can be screened for antigen binding in the same way as intact antibodies.

[0027] The terms "bind" or "interact" refer to an association, which can be a stable association between two molecules, e.g., between a peptide and a binding partner or substance (e.g., a small molecule), e.g., through electrostatic, hydrophobic, ionic, and / or hydrogen-bonding interactions under physiological conditions.

[0028] The terms "biological sample," "tissue sample," or simply "sample" each refer to a collection of cells obtained from a subject's tissue. The source of a tissue sample can be solid tissue, such as from a fresh, frozen, and / or preserved organ, tissue sample, biopsy, or aspirate, blood or any blood component, serum, blood, bodily fluids, such as spinal fluid, amniotic fluid, peritoneal fluid, or interstitial fluid, urine, saliva, feces, tears, or cells from any point in a subject's pregnancy or development.

[0029] As used herein, the term "cancer" includes, but is not limited to, solid tumors and blood-borne tumors. The term cancer includes diseases of the skin, tissues, organs, bone, cartilage, blood, and blood vessels, including those of the cervix, anus, vagina, vulva, penis, base of tongue, larynx, and tonsils. The term "cancer" further encompasses primary and metastatic cancers.

[0030] The term "precancerous lesion" or "precancerous condition" refers to atypical cells and / or tissues that are associated with an increased risk of cancer. The term "precancerous lesion" can refer, for example, to in situ dysplasia, benign neoplasia, or cancer.

[0031] The term "epitope" refers to a protein determinant capable of specific binding to an antibody. Epitopes usually consist of chemically active surface groups of molecules, such as amino acids or sugar side chains. A particular epitope can be defined by a specific sequence of amino acids to which a T-cell receptor or an antibody can bind.

[0032] The term "isolated nucleic acid" refers to a polynucleotide of natural or synthetic origin, or any combination thereof, that (1) is not associated with a cell in which the "isolated nucleic acid" is found in nature, and / or (2) is operably linked to a polynucleotide with which it is not naturally linked.

[0033] The term "isolated polypeptide" refers, in certain embodiments, to a polypeptide prepared from recombinant DNA or RNA, or of synthetic origin, or any combination thereof, that (1) is not associated with proteins with which it is normally found in nature, (2) is isolated from the cell in which it normally resides, (3) is isolated free from other proteins from the same cellular source, (4) is expressed by cells from a different species, or (5) is not naturally occurring.

[0034] As used herein, the term "pharmaceutically acceptable" refers to agents, compounds, materials, compositions, and / or dosage forms that are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit / risk ratio.

[0035] As used herein, the term "pharmaceutically acceptable carrier" means a pharmaceutically acceptable material, composition, or vehicle, such as a liquid or solid filler, diluent, excipient, or material encapsulating a solvent, that is involved in carrying or transporting from one organ or part of the body to another. Each carrier must be "acceptable" in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient. Some examples of materials that can serve as pharmaceutically acceptable carriers include: (1) sugars, such as lactose, glucose, and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose and its derivatives, such as sodium carboxymethylcellulose, ethylcellulose, and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipients, such as cocoa butter and suppository wax; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil, and soybean oil; (10) glycols; For example, propylene glycol, (11) polyols, such as glycerin, sorbitol, mannitol, and polyethylene glycol, (12) esters, such as ethyl oleate and ethyl laurate, (13) agar, (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide, (15) alginic acid, (16) pyrogen-free water, (17) isotonic saline, (18) Ringer's solution, (19) ethyl alcohol, (20) pH buffered solutions, (21) polyesters, polycarbonates, and / or polyanhydrides, and (22) other non-toxic compatible substances used in pharmaceutical formulations.

[0036] The terms "polynucleotide" and "nucleic acid" are used interchangeably. They refer to a polymeric form of nucleotides of any length, whether deoxyribonucleotides, ribonucleotides, or their analogs. Polynucleotides may have any three-dimensional structure and may perform any function. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci determined by linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. Polynucleotides may contain modified nucleotides, such as methylated nucleotides and nucleotide analogs. Modifications to the nucleotide structure, if present, may be imparted before or after assembly of the polymer. Polynucleotides may be further modified, such as by conjugation with a labeling component. In all nucleic acid sequences provided herein, U nucleotides are interchangeable with T nucleotides.

[0037] As used herein, a therapeutic agent that "prevents" a condition refers to a compound that, when administered to a statistical sample prior to the onset of the disorder or condition, reduces the occurrence of the disorder or condition in the treated sample compared to an untreated control sample, or delays the onset of or reduces the severity of one or more symptoms of the disorder or condition compared to an untreated control sample.

[0038] As used herein, "specific binding" refers to the ability of an antibody to bind to a predetermined antigen or a peptide to bind to its predetermined binding partner. Typically, an antibody or peptide binds to a specific antigen within about 10 -7 K below M Dand with an affinity (K) that is at least 10-fold less, at least 100-fold less, or at least 1000-fold less than the affinity for binding to a nonspecific and unrelated antigen / binding partner (e.g., BSA, casein). D The target antigen / binding partner binds to the target antigen / binding partner via the ATP-binding domain (e.g., as represented by

[0039] As used herein, the term "subject" means a human or non-human animal selected for treatment or therapy.

[0040] As used herein, the terms "therapeutically effective amount" and "effective amount" mean an amount of an agent effective to produce a desired prophylactic and / or therapeutic effect in at least a subpopulation of cells in a subject, at a reasonable benefit / risk ratio applicable to any medical treatment.

[0041] "Treating" a disease in a subject or a subject with a disease refers to administering a medical treatment to the subject, e.g., administering a drug, to reduce or prevent at least one symptom of the disease from worsening.

[0042] The term "vector" refers to a means by which nucleic acids can be propagated (propagated) and / or transferred between organisms, cells, or cellular components. Vectors include plasmids, viruses, bacteriophages, proviruses, phagemids, transposons, and artificial chromosomes, which may or may not replicate autonomously, or which may integrate into a host cell chromosome.

[0043] peptide Provided herein are peptides comprising HPV epitopes that are recognized by cytotoxic T lymphocytes (CTLs) and are useful for the prevention and / or treatment of HPV infection and / or cancer (e.g., cancers that express the HPV epitopes provided herein) and / or precancerous lesions. In certain embodiments, the HPV epitopes are those listed in Table 1.

[0044] [Table 1] JPEG2025131713000002.jpg61155

[0045] In some embodiments, the peptides provided herein are full-length HPV proteins. In some embodiments, the peptides provided herein comprise less than 100, 90, 80, 70, 60, 50, 40, 30, 25, 20, 15, or 10 consecutive amino acids of an HPV viral protein. In some embodiments, the peptides provided herein comprise two or more HPV epitopes listed in Table 1. For example, in some embodiments, the peptides provided herein comprise two or more HPV epitopes listed in Table 1 connected by a polypeptide linker. In some embodiments, the peptides provided herein comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 of the epitopes listed in Table 1.

[0046] In some embodiments, the peptides provided herein consist of an epitope listed in Table 1. In some embodiments, the peptides provided herein consist essentially of an epitope listed in Table 1. In some embodiments, the peptides provided herein comprise no more than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid(s) in addition to an epitope listed in Table 1.

[0047] In some embodiments, the sequence of the peptide comprises an EPV viral protein sequence except for one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) conservative sequence modifications. As used herein, the term "conservative sequence modifications" is intended to refer to amino acid modifications that do not significantly affect or alter the interaction between a TCR and a peptide containing the amino acid sequence presented on an MHC. Such conservative modifications include amino acid substitutions, additions (e.g., addition of an amino acid to the N- or C-terminus of the peptide), and deletions (e.g., deletion of an amino acid from the N- or C-terminus of the peptide). A conservative amino acid substitution is one in which an amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine, tryptophan), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine), beta-branched side chains (e.g., threonine, valine, isoleucine), and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, one or more amino acid residues in the peptides described herein can be substituted with other amino acid residues from the same side chain family, and the altered peptides can be tested for retention of TCR binding using methods known in the art. Modifications can be introduced into antibodies by standard techniques known in the art, such as site-directed mutagenesis and PCR-mediated mutagenesis.

[0048] To determine the percent identity of two amino acid sequences or two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced into one or both of the first and second amino acid or nucleic acid sequences for optimal alignment, and non-identical sequences can be ignored for comparison purposes). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, the molecules are identical at that position. The percent identity between two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps that need to be introduced for optimal alignment of the two sequences and the length of each gap.

[0049] Chimeric or fusion proteins are also provided herein. As used herein, a "chimeric protein" or "fusion protein" includes a peptide provided herein (e.g., one comprising an epitope listed in Table 1) linked to a separate peptide to which it is not naturally linked. For example, the separate peptide can be fused directly to the N-terminus or C-terminus of the peptide via a peptide bond or indirectly via a chemical linker. In some embodiments, a peptide provided herein is linked to a polypeptide comprising another HPV epitope. In some embodiments, a peptide provided herein is linked to a peptide comprising an epitope from another viral disease and / or infectious disease. In some embodiments, a peptide provided herein is linked to a peptide encoding a cancer-associated epitope.

[0050] The chimeric or fusion peptides provided herein can be produced by standard recombinant DNA techniques. For example, DNA fragments encoding different peptide sequences can be ligated in-frame according to conventional techniques, e.g., by using blunt or staggered ends for ligation, restriction enzyme digestion to provide appropriate ends, filling in sticky ends as needed, alkaline phosphatase treatment to avoid undesired ligations, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques, including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be performed using anchor primers that generate complementary overhangs between two consecutive gene fragments, followed by annealing and reamplified to generate a chimeric gene sequence (see, e.g., Current Protocols in Molecular Biology, Ausubel et al., eds., John Wiley & Sons, 1992). Furthermore, numerous expression vectors already encoding fusion moieties are commercially available.

[0051] In some aspects, provided herein are cells that present a peptide described herein (e.g., a peptide comprising an epitope listed in Table 1). In some embodiments, the cell is a mammalian cell. In some embodiments, the cell is an antigen-presenting cell (APC) (e.g., an antigen-presenting T cell, a dendritic cell, a B cell, a macrophage, or an artificial antigen-presenting cell, such as aK562 cell). Cells that present a peptide described herein can be produced by standard techniques known in the art. For example, the cells can be pulsed to promote peptide uptake. In some embodiments, the cells are transfected with a nucleic acid encoding a peptide provided herein. In some aspects, provided herein are methods of producing antigen-presenting cells (APCs), comprising pulsing the cells with a peptide described herein. Illustrative examples of producing antigen-presenting cells can be found in WO2013088114, which is incorporated herein in its entirety.

[0052] The peptides provided herein can be isolated from cells or tissue sources by an appropriate purification scheme using standard protein purification techniques, can be produced by recombinant DNA technology, and / or can be chemically synthesized using standard peptide synthesis techniques. The peptides described herein can be produced in prokaryotic or eukaryotic host cells by expression of nucleotides encoding the peptide(s) of the invention. Alternatively, such peptides can be synthesized by chemical methods. Methods for expression of heterologous peptides in recombinant hosts, chemical synthesis of peptides, and in vitro translation are well known in the art and can be found in further publications such as Maniatis et al., Molecular Cloning: A Laboratory Manual (1989), 2nd ed., Cold Spring Harbor, NY; Berger and Kimmel, Methods in Enzymology, Vol. 152, Guide to Molecular Cloning Techniques (1987), Academic Press, Inc., San Diego, Calif.; Merrifield, J. (1969) J. Am. Chem. Soc. 91:501; Chaiken IM (1981) CRC Crit. Rev. Biochem. 11:255; Kaiser et al. (1989) Science 243:187; Merrifield, B. (1986) Science 232:342; Kent, SBH (1988) Annu. Rev. Biochem. 57:957, and Offord, RE (1980) Semisynthetic Proteins, Wiley Publishing.

[0053] nucleic acid molecule The present specification provides nucleic acid molecules encoding the peptides described herein.In some embodiments, the present specification provides a method for treating cancer, precancerous lesions, or HPV by administering the nucleic acid disclosed herein to a subject.The nucleic acid can be present, for example, in whole cells, in cell lysates, or in a partially purified or substantially pure form.

[0054] In some embodiments, provided herein are vectors (e.g., viral vectors, e.g., adenovirus-based expression vectors, etc.) comprising the nucleic acid molecules described herein. As used herein, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid," which refers to a circular double-stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, in which additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication, episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) can be integrated into the genome of a host cell upon introduction into the host cell, thereby replicating along with the host genome. Additionally, certain vectors are capable of directing the expression of genes. Such vectors are referred to herein as "recombinant expression vectors" (or simply "expression vectors"). In some embodiments, provided herein are nucleic acids operably linked to one or more regulatory sequences (e.g., promoters) in an expression vector. In some embodiments, the cell transcribes the nucleic acid provided herein, thereby expressing the antibody, antigen-binding fragment thereof, or peptide described herein. The nucleic acid molecule can be integrated into the genome of the cell, or it can be extrachromosomal.

[0055] In some embodiments, the nucleic acids provided herein are part of a vaccine. In some embodiments, the vaccine is delivered to a subject by a vector, such as, but not limited to, a bacterial vector and / or a viral vector. Examples of bacterial vectors include, but are not limited to, Mycobacterium bovis (BCG), Salmonella Typhimurium ssp., Salmonella Typhi ssp., Clostridium sp. spores, Escherichia coli Nissle 1917, Escherichia coli K-12 / LLO, Listeria monocytogenes, and Shigella flexneri. Examples of viral vectors include, but are not limited to, vaccinia, adenovirus, RNA viruses (replicons), and replication-deficient viruses such as avipox, fowlpox, canarypox, MVA, and adenovirus.

[0056] In some embodiments, provided herein are cells containing a nucleic acid described herein (e.g., a nucleic acid encoding an antibody, antigen-binding fragment thereof, or peptide described herein). The cell can be, for example, prokaryotic, eukaryotic, mammalian, avian, murine, and / or human. In some embodiments, the cell is a mammalian cell. In some embodiments, the cell is an APC (e.g., an antigen-presenting T cell, a dendritic cell, a B cell, or an aK562 cell). In the methods, the nucleic acid described herein can be administered to the cell as a nucleic acid without a delivery vehicle, in combination with a delivery reagent. In some embodiments, any nucleic acid delivery method known in the art can be used in the methods described herein. Suitable delivery reagents include, but are not limited to, Mirus Transit TKO lipophilic reagent, lipofectin, lipofectamine, cellfectin, polycations (e.g., polylysine), atelocollagen, nanoplexes, and liposomes. In some embodiments of the methods described herein, liposomes are used to deliver the nucleic acid to a cell or a subject. Liposomes suitable for use in the methods described herein can be formed from standard vesicle-forming lipids, which generally include neutral or negatively charged phospholipids and sterols, such as cholesterol.The selection of lipids is generally guided by factors such as the desired liposome size and the half-life of the liposomes in the bloodstream.Various methods for preparing liposomes are known, and are described, for example, in Szoka et al. (1980), Ann. Rev. Biophys. Bioeng. 9:467, and U.S. Patent Nos. 4,235,871, 4,501,728, 4,837,028 and 5,019,369, the entire disclosures of which are incorporated herein by reference.

[0057] antibody In some aspects, the compositions and methods provided herein relate to antibodies and antigen-binding fragments thereof that specifically bind to proteins expressed on the plasma membrane of HPV-infected cells, cancer cells, or precancerous lesions (e.g., proteins comprising an epitope listed in Table 1). In some embodiments, the antibody binds to a specific epitope of one of the peptides provided herein. In some embodiments, the antibody binds to an HPV protein comprising an epitope having an amino acid sequence in Table 1 (wherein the HPV protein is not a full-length HPV protein). In some embodiments, the epitope is an extracellular epitope. In some embodiments, the epitope is an epitope listed in Table 1. In some embodiments, the HPV epitope is derived from HPV E1, E2, E4, E5, E6, and / or E7. In some embodiments, the HPV is type 16 or 18. In some embodiments, the antibody can be polyclonal or monoclonal, and can be, for example, murine, chimeric, humanized, or fully human. In some embodiments, the antibody is a full-length immunoglobulin molecule, an scFv, a Fab fragment, a Fab' fragment, a F(ab')2 fragment, an Fv, a camelid antibody, a disulfide-linked Fv, or a designed ankyrin repeat protein (DARPin).

[0058] Polyclonal antibodies can be prepared by immunizing a suitable subject (e.g., a mouse) with a peptide immunogen (e.g., an amino acid sequence listed in Table 1). In some embodiments, the peptide immunogen comprises an extracellular epitope of a target protein provided herein. Peptide antibody titers in immunized subjects can be monitored over time by standard techniques, such as enzyme-linked immunosorbent assay (ELISA) using immobilized peptide. If desired, antibodies against the antigen can be isolated from the mammal (e.g., from the blood) and further purified by well-known techniques, such as protein A chromatography, to obtain an IgG fraction.

[0059] At an appropriate time after immunization, e.g., when antibody titers are highest, antibody-producing cells are obtained from the subject and used to generate antibodies using standard techniques, such as the hybridoma technique first described by Kohler and Milstein (1975) Nature 256:495-497 (see also Brown et al. (1981) J. Immunol. 127:539-46; Brown et al. (1980) J. Biol. Chem. 255:4980-83; Yeh et al. (1976) Proc. Natl. Acad. Sci. 76:2927-31; and Yeh et al. (1982) Int. J. Cancer 29:269-75), the human B cell hybridoma technique (Kozbor et al. (1983) Immunol. Today 4:72), the EBV-hybridoma technique (Cole et al. (1985) Monoclonal antibodies can be prepared using hybridoma technology (Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma technology. Techniques for producing monoclonal antibody hybridomas are well known (see generally Kenneth, RH Monoclonal Antibodies: A New Dimension In Biological Analyses, Plenum Publishing Corp., New York, New York (1980); Lerner, EA (1981) Yale J. Biol. Med. 54:387-402; Gefter, ML et al. (1977) Somatic Cell Genet. 3:231-36). Briefly, an immortal cell line (typically a myeloma) is fused with lymphocytes (typically splenocytes) from a mammal immunized with an immunogen as described above, and the resulting hybridoma cell culture supernatant is screened to identify hybridomas that produce monoclonal antibodies that bind, preferably specifically, to the peptide antigen.

[0060] As an alternative to preparing monoclonal antibody-secreting hybridomas, monoclonal antibodies that bind to a target protein described herein can be obtained by screening a recombinant combinatorial immunoglobulin library with an appropriate peptide (e.g., a peptide containing an epitope in Table 1), thereby isolating immunoglobulin library members that bind to the peptide.

[0061] Furthermore, recombinant antibodies, such as chimeric or humanized monoclonal antibodies, specific for the target proteins provided herein and / or extracellular epitopes of the target proteins provided herein can be produced using standard recombinant DNA techniques. Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, e.g., U.S. Pat. No. 4,816,567, U.S. Pat. No. 5,565,332; Better et al. (1988) Science 240:1041-1043; Liu et al. (1987) Proc. Natl. Acad. Sci. USA 84:3439-3443; Liu et al. (1987) J. Immunol. 139:3521-3526; Sun et al. (1987) Proc. Natl. Acad. Sci. 84:214-218; Nishimura et al. (1987) Cancer Res. 47:999-1005; Wood et al. (1985) Nature 314:446-449; and Shaw et al. (1988) J. Immunol. Natl. Cancer Inst. 80:1553-1559); Morrison, SL (1985) Science 229:1202-1207; Oi et al. (1986) Biotechniques 4:214; Winter U.S. Patent No. 5,225,539; Jones et al. (1986) Nature 321:552-525; Verhoeyan et al. (1988) Science 239:1534; and Beidler et al. (1988) J. Immunol. 141:4053-4060.

[0062] Human monoclonal antibodies specific for the target proteins provided herein and / or extracellular epitopes provided herein can be generated using transgenic or transchromosomic mice carrying parts of the human immune system rather than the mouse system, for example, the "HuMAb mouse" (Lonberg, N. et al. (1994) Nature 368(6474): 856-859), which contain human immunoglobulin gene minilocuses encoding unrearranged human heavy (μ and γ) and κ light chain immunoglobulin sequences, along with targeted mutations that inactivate the endogenous μ and κ chain loci. Thus, these mice exhibit reduced expression of mouse IgM or κ, and in response to immunization, the introduced human heavy and light chain transgenes undergo class switching and somatic mutation to generate high-affinity human IgGκ monoclonal antibodies (Lonberg, N. et al. (1994), supra; reviewed in Lonberg, N. (1994) Handbook of Experimental Pharmacology 113:49 101; Lonberg, N. and Huszar, D. (1995) Intern. Rev. Immunol. Vol. 13: 65 93, and Harding, F. and Lonberg, N. (1995) Ann. N. Y Acad. Sci 764:536 546).HuMAb mouse preparation was performed by Taylor, L. et al. (1992) Nucleic Acids Research 20:6287 6295; Chen, J. et al. (1993) International Immunology 5: 647 656; Tuaillon et al. (1993) Proc. Natl. Acad. Sci USA 90:3720 3724; Choi et al. (1993) Nature Genetics 4:117 123; Chen, J. et al. (1993) EMBO J. 12: 821 830; Tuaillon et al. (1994) J. Immunol. 152:2912 2920; Lonberg et al., (1994) Nature 368(6474): 856 859; Lonberg, N. (1994) Handbook of Experimental Pharmacology 113:49 101; Taylor, L. et al. (1994) International Immunology 6: 579 591; Lonberg, N. and Huszar, D. (1995) Intern. Rev. Immunol. Vol. 13: 65 93; Harding, F. and Lonberg, N. (1995) Ann. NY Acad. Sci 764:536 546; Fishwild, D. et al. (1996) Nature Biotechnology 14: 845 851. See also U.S. Patent Nos. 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,789,650; 5,877,397; 5,661,016; 5,814,318; 5,874,299; 5,770,429; and 5,545,807.

[0063] In some embodiments, the antibodies provided herein are -6 , 10 -7 , 10 -8or 10 -9 The antibodies can bind to the epitopes listed in Table 1 with a dissociation constant of M or less. Standard assays for assessing the binding ability of antibodies are known in the art and include, for example, ELISA, Western blot, and RIA. The binding kinetics (e.g., binding affinity) of the antibodies can also be assessed by standard assays known in the art, such as Biacore analysis.

[0064] In some embodiments, the antibody is part of an antibody-drug conjugate. An antibody-drug conjugate is a therapeutic molecule comprising an antibody (e.g., an antibody that binds to a protein listed in Table 1) linked to a biologically active agent, such as a cytotoxic agent or an antiviral agent. In some embodiments, the biologically active agent is linked to the antibody via a chemical linker. Such linkers can be based on any stable chemical motif, such as a disulfide, hydrazone, peptide, or thioether. In some embodiments, the linker is a cleavable linker, and the biologically active agent is released from the antibody upon binding of the antibody to the plasma membrane target protein. In some embodiments, the linker is a non-cleavable linker.

[0065] In some embodiments, the antibody-drug conjugate comprises an antibody linked to a cytotoxic agent. In some embodiments, any cytotoxic agent capable of killing HPV-infected cells can be used. In some embodiments, the cytotoxic agent is MMAE, DM-1, a maytansinoid, a doxorubicin derivative, an auristatin, a calcheamicin, CC-1065, aduocarmycin, or an anthracycline.

[0066] In some embodiments, the antibody drug conjugate comprises an antibody linked to an antiviral drug. In some embodiments, any antiviral drug capable of inhibiting HPV replication is used. In some embodiments, the antiviral drug is ganciclovir, valganciclovir, foscarnet, cidofovir, acyclovir, formivirsen, maribavir, BAY 38-4766, or GW275175X. In some embodiments, provided herein is a vaccine comprising the antibody or antibody drug conjugate described herein.

[0067] cell In some aspects, provided herein are antigen-presenting cells (APCs) that express on their surface an MHC that presents one or more peptides comprising an HPV epitope described herein (e.g., an APC that presents one or more HPV epitopes listed in Table 1). In some embodiments, the MHC is a class I MHC. In some embodiments, the MHC is a class II MHC. In some embodiments, the class I MHC has an α chain polypeptide that is HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-g, HLA-K, or HLA-L. In some embodiments, the class II MHC has an α chain polypeptide that is HLA-DMA, HLA-DOA, HLA-DPA, HLA-DQA, or HLA-DRA. In some embodiments, the class II MHC has a β chain polypeptide that is HLA-DMB, HLA-DOB, HLA-DPB, HLA-DQB, or HLA-DRB.

[0068] In some embodiments, the APCs are B cells, antigen-presenting T cells, dendritic cells, or artificial antigen-presenting cells (e.g., aK562 cells). Dendritic cells for use in this process can be prepared by collecting PBMCs from a patient sample and adhering them to plastic. Typically, a monocyte population will adhere, and all other cells can be washed away. The adherent population is then differentiated with IL-4 and GM-CSF to produce monocyte-derived dendritic cells. These cells can be matured by the addition of IL-1β, IL-6, PGE-1, and TNF-α (which upregulates important costimulatory molecules on the surface of dendritic cells), and then transduced with one or more of the peptides provided herein.

[0069] In some embodiments, the APCs are artificial antigen-presenting cells, such as aK562 cells. In some embodiments, the artificial antigen-presenting cells are engineered to express CD80, CD83, 41BB-L, and / or CD86. Examples of artificial antigen-presenting cells, such as aK562 cells, are described in U.S. Patent Application Publication No. 2003 / 0147869, which is incorporated herein by reference.

[0070] In certain aspects, provided herein are methods for generating APCs that present one or more HPV epitopes described herein, comprising contacting the APCs with peptides comprising an HPV epitope described herein and / or nucleic acids encoding an HPV epitope described herein. In some embodiments, the APCs are irradiated.

[0071] In certain aspects, provided herein are T cells (e.g., CD4 T cells and / or CD8 T cells) that express a TCR (e.g., an αβ TCR or a γδ TCR) that recognizes a peptide described herein presented on MHC (a peptide comprising an HPV epitope listed in Table 1). In some embodiments, the T cells are CD8 T cells (CTLs) that express a TCR that recognizes a peptide described herein presented on class I MHC. In some embodiments, the T cells are CD4 T cells (helper T cells) that recognize a peptide described herein presented on class II MHC.

[0072] In some aspects, provided herein are methods for generating, activating, and / or inducing the proliferation of T cells (e.g., CTLs) that recognize one or more HPV epitopes described herein. In some embodiments, a sample containing CTLs (i.e., a PBMC sample) is incubated in culture with an APC provided herein (e.g., an APC that presents a peptide comprising an HPV epitope described herein on a class I MHC complex). In some embodiments, the APC is autologous to the subject from which the T cells were obtained. In some embodiments, a sample containing T cells is incubated with an APC provided herein more than once. In some embodiments, the T cells are incubated with the APC in the presence of at least one cytokine. In some embodiments, the cytokine is IL-4, IL-7, and / or IL-15. Exemplary methods for inducing proliferation of T cells using APCs are provided, for example, in U.S. Patent Application Publication No. 2015 / 0017723, which is incorporated herein by reference.

[0073] In some aspects, provided herein are compositions (e.g., prophylactic and / or therapeutic compositions) comprising the T cells and / or APCs provided herein. In some embodiments, such compositions are used to treat and / or prevent cancer and / or precancerous lesions and / or HPV infection in a subject by administering an effective amount of the composition to the subject. In some embodiments, the T cells and / or APCs are not autologous to the subject. In some embodiments, the T cells and / or APCs are autologous to the subject. In some embodiments, the T cells and / or APCs are stored in a cell bank before being administered to the subject.

[0074] Pharmaceutical Composition In some aspects, provided herein are compositions (e.g., pharmaceutical compositions such as vaccine compositions) containing a peptide (e.g., comprising an epitope from Table 1), nucleic acid, antibody, CTL, or APC described herein, formulated with a pharmaceutically acceptable carrier, as well as methods of treating cancer, precancerous lesions, or HPV infection using such pharmaceutical compositions. In some embodiments, the composition comprises a combination of multiple (e.g., two or more) agents provided herein.

[0075] In some embodiments, the pharmaceutical composition further comprises an adjuvant. As used herein, the term "adjuvant" broadly refers to a substance that affects the immunological or physiological response in a patient or subject. For example, an adjuvant may increase the presence of an antigen over time or to an area of ​​interest such as a tumor, help antigen-presenting cells absorb antigens, activate macrophages and lymphocytes, and support cytokine production. By altering the immune response, an adjuvant may allow for a lower dose of an immunointeractive agent, thereby increasing the efficacy or safety of a particular dose of the immunointeractive agent. For example, an adjuvant may prevent T-cell depletion, thus increasing the efficacy or safety of a particular immunointeractive agent. Examples of adjuvants include, but are not limited to, immunomodulatory proteins, adjuvant 65, α-GalCer, aluminum phosphate, aluminum hydroxide, calcium phosphate, β-glucan peptides, CpG DNA, GPI-0100, lipid A, lipopolysaccharide, Lipovant, Montanide, N-acetyl-muramyl-L-alanyl-D-isoglutamine, Pam3CSK4, quil A, and trehalose dimycolate.

[0076] Methods of preparing these formulations or compositions include the step of bringing into association an agent described herein with the carriers and, optionally, one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing into association an agent described herein with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product.

[0077] Pharmaceutical compositions of the present invention suitable for parenteral administration comprise one or more of the agents described herein in combination with one or more pharmaceutically acceptable sterile isotonic aqueous or non-aqueous solutions, dispersions, suspensions or emulsions, or sterile powders that can be reconstituted into sterile injectable solutions or dispersions immediately before use, and may also contain sugars, alcohols, antioxidants, buffers, bacteriostats, solutes that render the formulation isotonic with the blood of the intended recipient, or suspending or thickening agents.

[0078] Examples of suitable aqueous and non-aqueous carriers that can be used in the pharmaceutical compositions of the present invention include water, ethanol, polyols (glycerol, propylene glycol, polyethylene glycol, etc.), and suitable mixtures thereof, vegetable oils (olive oil, etc.), and injectable organic esters (ethyl oleate, etc.). Proper fluidity can be maintained, for example, by the use of coating materials such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.

[0079] Regardless of the selected route of administration, the agents of the present invention, which can be used in a suitable hydrated form, and / or the pharmaceutical compositions of the present invention are formulated into pharmaceutically acceptable dosage forms by conventional methods known to those skilled in the art.

[0080] Treatment method The novel treatment methods take advantage of the inventors' knowledge of how the immune system can eliminate virus-infected cells, primarily through cytotoxic T cells (also known as "killer" T cells). These novel therapies include the use of anti-cancer vaccines and intralesional immune system-based therapies, with the idea being that T cells can be activated and then locate and kill HPV-infected cells.

[0081] In certain embodiments, provided herein are methods of treating HPV infection and / or cancer and / or precancerous lesions in a subject, comprising administering to the subject a pharmaceutical composition provided herein.

[0082] In some embodiments, provided herein are methods for treating HPV infection in a subject. In some embodiments, the subject being treated is immunocompromised. For example, in some embodiments, the subject has a T-cell deficiency. In some embodiments, the subject has leukemia, lymphoma, or multiple myeloma. In some embodiments, the subject is infected with HIV and / or has AIDS. In some embodiments, the subject has undergone a tissue, organ, and / or bone marrow transplant. In some embodiments, the subject has been administered an immunosuppressant. In some embodiments, the subject has undergone and / or is undergoing chemotherapy. In some embodiments, the subject has undergone and / or is undergoing radiation therapy.

[0083] In some embodiments, the subject is also administered an antiviral drug that inhibits HPV replication. For example, in some embodiments, the subject is administered podofilox, imiquimod, sinecatechins, podophyllin resin, trichloroacetic acid, or dichloroacetic acid. In some embodiments, the subject is also treated with an intervention that physically affects HPV-infected lesions and / or HPV-associated tumors. For example, in some embodiments, the lesions are treated with surgical excision, chemical cauterization, cryotherapy, or cauterization.

[0084] In some embodiments, the subject has cancer or a precancerous lesion. In some embodiments, the methods described herein can be used to treat any cancerous or precancerous tumor. In some embodiments, the cancer and / or precancerous lesion expresses one or more of the HPV epitopes provided herein (e.g., the HPV epitopes listed in Table 1). In some embodiments, the precancerous lesion comprises abnormal cellular changes and / or precancerous cellular changes. Precancerous lesions that can be treated by the methods and compositions provided herein include, but are not limited to, cervical intraepithelial neoplasia (CIN), squamous intraepithelial lesions (SIL), or warts on the cervix. In some embodiments, the cancer comprises a solid tumor. Cancers that may be treated by the methods and compositions provided herein include, but are not limited to, cancer cells derived from the cervix, anus, vagina, vulva, penis, base of tongue, larynx, tonsils, bladder, blood, bone, bone marrow, brain, breast, colon, esophagus, gastrointestinal tract, gums, head, kidney, liver, lung, nasopharynx, neck, ovary, prostate, skin, non-melanoma skin cancer (NMSC), cutaneous squamous cell carcinoma (SCC), stomach, testis, tongue, or uterus. In addition, the cancer may be of the following histological types, among others, but not limited to: neoplasia, malignant; carcinoma; carcinoma, undifferentiated; giant cell and spindle cell carcinoma, small cell carcinoma, papillary carcinoma, squamous cell carcinoma, lymphoepithelial carcinoma, basal cell carcinoma, pilomatrix carcinoma, transitional cell carcinoma, papillary transitional cell carcinoma, adenocarcinoma, gastrinoma, malignant; cholangiocarcinoma, hepatocellular carcinoma, combined hepatocellular carcinoma and cholangiocarcinoma, trabecular adenocarcinoma, adenoid cystic carcinoma, adenocarcinoma in adenomatous polyps, adenocarcinoma, familial polyposis coli, solid tumors, carcinoid tumors, malignant; bronchioloalveolar adenocarcinoma, papillary adenocarcinoma, chromophobe carcinoma, eosinophilic carcinoma, Eosinophilic adenocarcinoma, basophilic carcinoma, clear cell adenocarcinoma, granular cell carcinoma, follicular adenocarcinoma, papillary adenocarcinoma and follicular adenocarcinoma, non-encapsulated sclerosing carcinoma, adrenocortical carcinoma, endometrioid carcinoma, cutaneous adnexal carcinoma, apocrine adenocarcinoma, sebaceous adenocarcinoma, cerumen adenocarcinoma, mucoepidermoid carcinoma, cystadenocarcinoma, papillary cystadenocarcinoma, papillary serous cystadenocarcinoma, mucinous sac Cystic carcinoma, mucinous adenocarcinoma, signet ring cell carcinoma, invasive ductal carcinoma, medullary carcinoma, lobular carcinoma, inflammatory carcinoma, Paget's disease of the breast, acinar cell carcinoma, adenosquamous carcinoma, adenocarcinoma with squamous metaplasia, malignant thymoma, malignant ovarian stromal tumor, malignant capsular cell tumor, malignant granulosa cell carcinoma, malignant neuroblastoma (malignantroblastoma), Sertoli cell tumor, malignant Leydig cell tumor, malignant lipid cell tumor, malignant paraganglioma, malignant extramammary paraganglioma, pheochromocytoma, hemangiosarcoma, malignant melanoma, amelanotic melanoma, superficial spreading melanoma, malignant melanoma in giant pigmented nevus, epithelioid cell melanoma, malignant blue nevus, sarcoma, fibrosarcoma, malignant fibrous histiocytoma, myxosarcoma, liposarcoma, leiomyosarcoma, rhabdomyosarcoma, embryonal rhabdomyosarcoma, alveolar rhabdomyosarcoma, stromal sarcoma, mixed malignant Tumor, mixed Müllerian tumor, nephroblastoma, hepatoblastoma, carcinosarcoma, malignant mesenchymoma, malignant Brenner tumor, malignant phyllodes tumor, synovial sarcoma, malignant mesothelioma, dysgerminoma, embryonal carcinoma, malignant teratoma, malignant ovarioma, choriocarcinoma, malignant mesonephroma, angiosarcoma, malignant hemangioendothelioma, Kaposi's sarcoma, malignant hemangiopericytoma, lymphangiosarcoma, osteosarcoma, parosteal osteosarcoma, chondrosarcoma, malignant chondroblastoma, mesenchymal chondrosarcoma, giant cell tumor of bone, Ewing's sarcoma, malignant odontogenic tumor, ameloblastic odontosarcoma , malignant ameloblastoma, ameloblastic fibrosarcoma, malignant pinealoma, chordoma, malignant glioma, ependymoma, astrocytoma, protoplasmic astrocytoma, fibrous astrocytoma, astroblastoma, glioblastoma, oligodendroglioma, oligodendroglioma, primitive neuroectodermal, cerebellar sarcoma, ganglioneuroblastoma, neuroblastoma, retinoblastoma, olfactory neurogenic tumor, malignant meningioma, neurofibrosarcoma, malignant neurilemmoma, malignant granular cell tumor, malignant lymphoma, Hodgkin's disease, Hodgkin's lymphoma, lateral granuloma, Small lymphocytic lymphoma, diffuse large cell lymphoma, follicular lymphoma, mycosis fungoides, other specified non-Hodgkin's lymphoma, malignant histiocytosis, multiple myeloma, mast cell sarcoma, immunoproliferative small intestinal disease, leukemia, lymphocytic leukemia, plasma cell leukemia, erythroleukemia, lymphosarcoma cell leukemia, myeloid leukemia, basophilic leukemia, eosinophilic leukemia, monocytic leukemia, mast cell leukemia, megakaryoblastic leukemia, myeloid sarcoma, and hairy cell leukemia.

[0085] In some embodiments, the subject is also administered an anti-cancer compound. Examples of anti-cancer compounds include, but are not limited to, alemtuzumab (Campath®), alitretinoin (Panretin®), anastrozole (Arimidex®), bevacizumab (Avastin®), bexarotene (Targretin®), bortezomib (Velcade®), bosutinib (Bosulif®), and rivaroxaban (Renfee®). Registered Trademark)], brentuximab vedotin [Adcetris®], cabozantinib [Cometriq™], carfilzomib [Kyprolis™], cetuximab [Erbitux®], crizotinib [Xalkori®], dasatinib [Sprycel®], denileukin diftitox [Ontak®], erlotinib hydrochloride [Tarcine®] (Tarceva®), everolimus (Afinitor®), exemestane (Aromasin®), fulvestrant (Faslodex®), gefitinib (Iressa®), ibritumomab tiuxetan (Zevalin®), imatinib mesylate (Gleevec®), ipilimumab (Yervoy™), Rapamycin (Rafenib®), rituximab ... Tinib ditosylate [Tykerb®], letrozole [Femara®], nilotinib [Tasigna®], ofatumumab [Arzerra®], panitumumab [Vectibix®], pazopanib hydrochloride [Votrient®], pertuzumab [Perjeta™], pralatrexate [Folotyn®],Regorafenib (Stivarga®), rituximab (Rituxan®), romidepsin (Istodax®), sorafenib tosylate (Nexavar®), sunitinib malate (Sutent®), tamoxifen, temsirolimus (Torisel®), toremifene (Fareston®), tositumomab, and 131I - Tositumomab (Bexxar®), trastuzumab (Herceptin®), tretinoin (Vesanoid®), vandetanib (Caprelsa®), vemurafenib (Zelboraf®), vorinostat (Zolinza®), and ziv-aflibercept (Zaltrap®).

[0086] In some embodiments, the subject is also administered a chemotherapeutic agent. Examples of chemotherapeutic agents include, but are not limited to, alkylating agents such as thiotepa and cyclophosphamide; alkylsulfonates such as busulfan, improsulfan, and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethyleneimines and methylamelamines such as altretamine, triethylenemelamine, triethylenephosphoramide, triethylenethiophosphaoramide, and trimethylolmelamine. ylolomelamine, etc.; acetogenins (especially bullatacin and bullatacinone); camptothecin (including the synthetic analog topotecan); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin, and bizelesin synthetic analogs); cryptophycins (especially cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin ) (including synthetic analogs, KW-2189 and CB1-TM1); eleutherobin; pancratistatin; sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, chlorophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard, and the like;nitrosureas, such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimustine; antibiotics, such as enediyne antibiotics (e.g., calicheamicin, especially calicheamicin γ1I and calicheamicin ω1I; dynemicin, including dynemicin A); bisphosphonates such as clodronate; esperamicin;and neocarzinostatin chromophores and related chromoprotein enediynes. Antibiotic chromophores, aclacinomycins, actinomycin, authrarnycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detoxin, thiazolinone ... Detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin, and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; antimetabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogs such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine, etc.;Pyrimidine analogues, such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine, etc.; androgens, such as calusterone, dromostanolone propionate, epithiostanol, mepitiostane, testolactone, etc.; antiadrenal agents, such as aminoglutethimide, mitotane, trilostane, etc.; folic acid replenishers, such as frolinic acid, etc.; Aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elfomithine; elliptinium acetate acetate); epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids, such as maytansine and ansamitocin; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; podophyllinic acid; 2-ethylhydrazide; procarbazine; PSK polysaccharide complex; razoxane; rhizoxin; sizofuran; spirogermanium; tenuazonic acid acid; triaziquone; 2,2',2''-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A, and anguidine); urethane; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside ("Ara-C"); cyclophosphamide; thiotepa; taxoids, such as paclitaxel and docetaxel; chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine;methotrexate; platinum coordination complexes such as cisplatin, oxaliplatin, and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine; vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (e.g., CPT-11); topoisomerase inhibitor RFS 2000; difluoromethylornithine (DMFO); retinoids such as retinoic acid; capecitabine; and pharmaceutically acceptable salts, acids, or derivatives of the foregoing.

[0087] In some embodiments, the subject is also administered an immunotherapy agent. Immunotherapy refers to treatments that utilize a subject's immune system to treat cancer, such as the use of cancer vaccines, cytokines, cancer-specific antibodies, T-cell therapy, and dendritic cell therapy.

[0088] In some embodiments, the subject is also administered an immunomodulatory protein. Examples of immunomodulatory proteins include, but are not limited to, B lymphocyte chemoattractant ("BLC"), CC motif chemokine 11 ("eotaxin-1"), eosinophil chemoattractant protein 2 ("eotaxin-2"), granulocyte colony-stimulating factor ("G-CSF"), granulocyte-macrophage colony-stimulating factor ("GM-CSF"), 1-309, intercellular adhesion molecule 1 ("ICAM-1"), interferon gamma ("IFN-γ"), interleukin-1 alpha ("IL-1α"), interleukin-1 beta ("IL-1β"), interleukin-1 receptor antagonist ("IL-1"). ra"), interleukin-2 ("IL-2"), interleukin-4 ("IL-4"), interleukin-5 ("IL-5"), interleukin-6 ("IL-6"), interleukin-6 soluble receptor ("IL-6 sR"), interleukin-7 ("IL-7"), interleukin-8 ("IL-8"), interleukin-10 ("IL-10"), interleukin-11 ("IL-11"), interleukin-12 subunit beta ("IL-12 p40" or "IL-12 p40"), p70"), interleukin-13 ("IL-13"), interleukin-15 ("IL-15"), interleukin-16 ("IL-16"), interleukin-17 ("IL-17"), chemokine (CC motif) ligand 2 ("MCP-1"), macrophage colony-stimulating factor ("M-CSF"), gamma interferon-inducible monokine ("MIG"), chemokine (CC motif) ligand 2 ("MIP-1 alpha"), chemokine (CC motif) ligand 4 ("MIP-1 beta"), macrophage inflammatory protein-1-delta ("MIP-1 delta"), platelet-derived growth factor subunit B ("PDGF-BB"), chemokine (CC motif) ligand 5, Regulated on Activation, Normal T cell Expressed and SecretedSecreted) ("RANTES"), TIMP metallopeptidase inhibitor 1 ("TIMP-1"), TIMP metallopeptidase inhibitor 2 ("TIMP-2"), tumor necrosis factor lymphotoxin-alpha ("TNFα"), tumor necrosis factor lymphotoxin-beta ("TNFβ"), soluble TNF receptor type 1 ("sTNFRI"), sTNFRIIAR, brain-derived neurotrophic factor ("BDNF"), basic fibroblast growth factor ("bFGF"), bone morphogenetic protein 4 ("BMP-4"), bone morphogenetic protein 5 ("BMP-5"), bone morphogenetic protein 7 ("BMP-7"), nerve growth factor ("b-NGF"), epidermal growth factor ("EGF"), epidermal growth factor receptor ("EGFR"), endocrine-derived vascular endothelial growth factor ("EGF"). -VEGF"), fibroblast growth factor 4 ("FGF-4"), keratinocyte growth factor ("FGF-7"), growth differentiation factor 15 ("GDF-15"), glial cell line-derived neurotrophic factor ("GDNF"), growth hormone, heparin-binding EGF-like growth factor ("HB-EGF"), hepatocyte growth factor ("HGF"), insulin-like growth factor binding protein 1 ("IGFBP-1"), insulin-like growth factor binding protein 2 ("IGFBP-2"), insulin-like growth factor binding protein 3 ("IGFBP-3"), insulin-like growth factor binding protein 4 ("IGFBP-4"), insulin-like growth factor binding protein 6 ("IGFBP-6"), insulin-like growth factor 1 ("IGF-1"), insulin, macrophage colony-stimulating factor ("M-CSF"). R"), nerve growth factor receptor ("NGF R"), neurotrophin-3 ("NT-3"), neurotrophin-4 ("NT-4"), osteoprotegerin ("osteoprotegerin"), platelet-derived growth factor receptor ("PDGF-AA"), phosphatidylinositol-glycan biosynthesis factor ("PIGF"), Skp, Cullin, F-box-containing complex ("SCF"), stem cell factor receptor ("SCFTransforming growth factor alpha ("TGFα"), transforming growth factor beta-1 ("TGFβ1"), transforming growth factor beta-3 ("TGFβ3"), vascular endothelial growth factor ("VEGF"), vascular endothelial growth factor receptor 2 ("VEGFR2"), vascular endothelial growth factor receptor 3 ("VEGFR3"), VEGF-D 6Ckine, tyrosine protein kinase receptor UFO ("Axl"), betacellulin ("BTC"), mucosal-associated epithelial chemokine ("CCL28"), chemokine (C-C motif) ligand 27 ("CTACK"), chemokine (C-X-C motif) ligand 16 ("CXCL16"), C-X-C motif chemokine 5 ("ENA-78"), chemokine (C-C motif) ligand 26 ("eotaxin-3"), granulocyte chemoattractant protein 2 ("GCP-2"), GRO, chemokine (C-C motif) ligand 14 ("HCC-l"), chemokine (C-C motif) ligand 16 ("HCC-4"), interleukin-9 ("IL-9"), interleukin-17 F ("IL-17F"), interleukin-18 binding protein ("IL-18 BPa"); Interleukin-28 A ("IL-28A"), interleukin-29 ("IL-29"), interleukin-31 ("IL-31"), C-X-C motif chemokine 10 ("IP-10"), chemokine receptor CXCR3 ("I-TAC"), leukemia inhibitory factor ("LIF"), Light, chemokine (C motif) ligand ("lymphotactin"), monocyte chemotactic protein 2 ("MCP-2"), monocyte chemotactic protein 3 ("MCP-3"), monocyte chemotactic protein 4 ("MCP-4"), macrophage-derived chemokine ("MDC"), macrophage migration inhibitory factor ("MIF"), chemokine (C-C motif) ligand 20 ("MIP-3α"), CC motif chemokine 19 ("MIP-3β"), chemokine (CC motif) ligand 23 ("MPIF-1"), macrophage-stimulating protein alpha chain ("MSPalpha"), nucleosome assembly protein 1-like 4 ("NAP-2"), secreted phosphoprotein 1 ("osteopontin"), lung and activation-regulating cytokine ("PARC"), platelet factor 4 ("PF4"), stromal cell-derived factor-1 alpha ("SDF-1α"), chemokine (CC motif) ligand 17 ("TARC"), thymus-expressed chemokine ("TECK"), thymic stromal lymphopoietin ("TSLP"), 4-IBB"), CD166 antigen ("ALCAM"), cluster of differentiation 80 ("B7-1"), tumor necrosis factor receptor superfamily member 17 ("BCMA"), cluster of differentiation 14 ("CD14"), cluster of differentiation 30 ("CD30"), cluster of differentiation 40 ("CD40 ligand"), carcinoembryonic antigen-related cell adhesion molecule 1 ("biliary glycoprotein") ("CEACAM-1"), death receptor 6 ("DR6"), deoxythymidine kinase ("Dtk") "), type 1 membrane glycoprotein ("endoglin"), receptor tyrosine protein kinase erbB-3 ("ErbB3"), endothelial leukocyte adhesion molecule 1 ("E-selectin"), apoptosis antigen 1 ("Fas"), Fms-like tyrosine kinase 3 ("Flt-3L"), tumor necrosis factor receptor superfamily member 1 ("GITR"), tumor necrosis factor receptor superfamily member 14 ("HVEM"), intercellular adhesion molecule 3 ("ICAM-3"), IL-1 R4, IL-1 RI, IL-10R beta, IL-17R, IL-2R gamma, IL-21R, lysosomal membrane protein 2 ("LIMPII"), neutrophil gelatinase-associated lipocalin ("lipocalin-2"), CD62L ("L-selectin"), lymphatic endothelial cell ("LYVE-1"), MHC class I polypeptide-related sequence A ("MICA"), MHC class I polypeptide-related sequence B ("MICB"), NRGl-beta1, platelet-derived growth factor receptor beta ("PDGF R beta"), platelet endothelial cell adhesion molecule ("PECAM-1"), RAGE, hepatitis A virus intercellular receptor 1 ("TIM-1"), tumor necrosis factor receptor superfamily member IOC ("TRAIL-1"), and R3), trapin protein transglutaminase binding domain ("trapin-2"), urokinase receptor ("uPAR"), vascular cell adhesion protein 1 ("VCAM-1"), XEDAR, activin A, Agouti-related protein ("AgRP"), ribonuclease 5 ("angiogenin"), angiopoietin 1, angiostatin, cathepsin S, CD40, Cryptic family protein IB ("Cripto-1"), DAN, Dickkopf-related protein 1 ("DKK-1"), E-cadherin, epithelial cell adhesion molecule ("EpCAM"), Fas ligand (FasL or CD95L), Fcg RIIB / C, FoUistatin, galectin-7, intercellular adhesion molecule 2 ("ICAM-2"), IL-13 Rl, IL-13R2, IL-17B, IL-2Ra, IL-2Rb, IL-23, LAP, neural cell adhesion molecule ("NrCAM"), plasminogen activator inhibitor-1 ("PAI-1"), platelet-derived growth factor receptor ("PDGF-AB"), resistin, stromal cell-derived factor 1 ("SDF-1β"), sgpl30, secreted frizzled-related protein 2 ("ShhN"), sialic acid-binding immunoglobulin-type lectin ("Siglec-5"), ST2, transforming growth factor beta 2 ("TGFβ2"), Tie-2, thrombopoietin ("TPO"), tumor necrosis factor receptor superfamily member 10D ("TRAIL-1"), and IL-13R2.R4"), Triggering Receptor Expressed on Myeloid Cells 1 ("TREM-1"), Vascular Endothelial Growth Factor C ("VEGF-C"), VEGFRl, Adiponectin, Adipsin ("AND"), Alpha Fetoprotein ("AFP"), Angiopoietin-Like 4 ("ANGPTL4"), Beta-2-Microglobulin ("B2M"), Basal Cell Adhesion Molecule ("BCAM"), Carbohydrate Antigen 1 25 ("CA125"), cancer antigen 15-3 ("CA15-3"), carcinoembryonic antigen ("CEA"), cAMP receptor protein ("CRP"), human epidermal growth factor receptor 2 ("ErbB2"), follistatin, follicle-stimulating hormone ("FSH"), chemokine (CXC motif) ligand 1 ("GRO alpha"), human chorionic gonadotropin ("βHCG"), insulin-like growth factor 1 receptor ("IGF-1 sR"), IL-1 sRII, IL-3, IL-18 Rb, IL-21, leptin, matrix metalloproteinase-1 ("MMP-1"), matrix metalloproteinase-2 ("MMP-2"), matrix metalloproteinase-3 ("MMP-3"), matrix metalloproteinase-8 ("MMP-8"), matrix metalloproteinase-9 ("MMP-9"), matrix metalloproteinase-10 ("MMP-10"), matrix metalloproteinase-13 ("MMP-13"), neural cell adhesion molecule ("NCAM-1"), entactin ("nidogen-1"), neuron-specific enolase ("NSE"), oncostatin M ("OSM"), procalcitonin, prolactin, prostate-specific antigen ("PSA"), sialic acid-binding Ig-like lectin 9 ("Siglec-9"), ADAM 17 endopeptidase ("TACE"), thyroglobulin, inhibitor of metalloproteinase 4 ("TIMP-4"), TSH2B4, a disintegrin and metalloproteinase domain-containing protein 9 ("ADAM-9"), angiopoietin 2, tumor necrosis factor ligand superfamily member 13 / acidic leucine-rich nuclear phosphoprotein 32 family member B ("APRIL"), bone morphogenetic protein 2 ("BM"), and thyroglobulin. P-2"), bone morphogenetic protein 9 ("BMP-9"), complement component 5a ("C5a"), cathepsin L, CD200, CD97, chemerin, tumor necrosis factor receptor superfamily member 6B ("DcR3"), fatty acid binding protein 2 ("FABP2"), fibroblast activation protein, alpha ("FAP"), fibroblast growth factor 19 ("FGF-19"), galectin-3, hepatocyte growth factor receptor ("HGF R"), IFN-alpha / beta R2, insulin-like growth factor 2 ("IGF-2"), insulin-like growth factor 2 receptor ("IGF-2")R”), interleukin-1 receptor 6 (“IL-1R6”), interleukin-24 (“IL-24”), interleukin-33 (“IL-33”), kallikrein 14, asparagine endopeptidase (“legumain”), oxidized low-density lipoprotein receptor 1 (“LOX-1”), mannose-binding lectin (“MBL”), neprilysin (“NEP”), Notch homolog 1, translocation-associated (Drosophila) ( "Notch-1"), nephroblastoma overexpression ("NOV"), osteoactivin, programmed cell death protein 1 ("PD-1"), N-acetylmuramoyl-L-alanine amidase ("PGRP-5"), serpin A4, secreted frizzled-related protein 3 ("sFRP-3"), thrombomodulin, Toll-like receptor 2 ("TLR2"), tumor necrosis factor receptor superfamily member 10A ("TRAIL"), and ATP. R1), transferrin ("TRF"), WIF-1ACE-2, albumin, AMICA, angiopoietin 4, B-cell activating factor ("BAFF"), carbohydrate antigen 19-9 ("CA19-9"), CD163, clusterin, CRT AM, chemokine (C-X-C motif) ligand 14 ("CXCL14"), cystatin C, decorin ("DCN"), Dickkopf-related protein 3 ("Dkk-3"), delta-like protein 1 ("DLL1"), fetuin A, heparin-binding growth factor 1 ("aFGF"), folate receptor alpha ("FOLR1"), Furin, GPCR-associated sorting protein 1 ("GASP-1"), GPCR-associated sorting protein 2 ("GASP-2"), granulocyte colony-stimulating factor receptor ("GCSF"). R"), serine protease hepsin ("HAI-2"), interleukin-17B receptor ("IL-17B R"), interleukin-27 ("IL-27"), lymphocyte activation gene 3 ("LAG-3"), apolipoprotein AV ("LDLR"), pepsinogen I, retinol binding protein 4 ("RBP4"), SOST, heparan sulfate proteoglycan ("syndecan-1"), tumor necrosis factor receptor superfamily member 13B ("TACI"), tissue factor pathway inhibitor ("TFPI"), TSP-1, tumor necrosis factor receptor superfamily, member 10b ("TRAIL R2"), TRANCE, troponin I, urokinase plasminogen activator ("uPA"), cadherin 5, type 2 or VE-cadherin (vascular endothelial), also known as CD144 ("VE-cadherin"), WNT1-inducible signaling pathway protein 1 ("WISP-1"), and receptor activator of nuclear factor-κB ("RANK").

[0089] In some embodiments, the subject is also administered an immune checkpoint inhibitor. Immune checkpoint inhibition broadly refers to inhibiting checkpoints that cancer cells can produce to prevent or downregulate an immune response. Examples of immune checkpoint proteins include, but are not limited to, CTLA-4, PD-1, PD-L1, PD-L2, A2AR, B7-H3, B7-H4, BTLA, KIR, LAG3, TIM-3, or VISTA. The immune checkpoint inhibitor may be an antibody or antigen-binding fragment thereof that binds to and inhibits an immune checkpoint protein. Examples of immune checkpoint inhibitors include, but are not limited to, nivolumab, pembrolizumab, pidilizumab, AMP-224, AMP-514, STI-A1110, TSR-042, RG-7446, BMS-936559, MEDI-4736, MSB-0020718C, AUR-012, and STI-A1010.

[0090] In some embodiments, the compositions provided herein (e.g., vaccine compositions provided herein) are administered prophylactically to prevent cancer, precancerous lesions, and / or HPV infection. In some embodiments, the vaccine is administered to inhibit tumor cell growth. The vaccine can be administered before or after detection of cancer cells, precancerous lesions, or HPV-infected cells in a patient. Inhibition of tumor cell growth is understood to refer to preventing, stopping, slowing the growth of tumor cells, or killing tumor cells. In some embodiments, a proinflammatory response is induced after administration of a vaccine comprising a peptide, nucleic acid, antibody, or APC described herein. The proinflammatory immune response includes the production of proinflammatory cytokines and / or chemokines, such as interferon gamma (IFN-γ) and / or interleukin 2 (IL-2). Proinflammatory cytokines and chemokines are well known in the art.

[0091] Conjunctive therapy includes sequential, simultaneous and separate, and / or co-administration of active compounds in such a way that the therapeutic effect of the first agent administered is not completely eliminated when the subsequent treatment is administered. In some embodiments, the second agent may be co-formulated with the first agent or may be formulated in a separate pharmaceutical composition.

[0092] Actual dosage levels of the active ingredients in the pharmaceutical compositions provided herein may be varied to achieve an amount, composition, and mode of administration of the active ingredients that is effective to achieve the desired therapeutic response for a particular patient without being toxic to the patient.

[0093] The selected dosage level will depend upon a variety of factors, such as the activity of the particular agent used, the route of administration, the time of administration, the rate of excretion or metabolism of the particular compound used, the duration of treatment, other drugs, compounds and / or materials used in combination with the particular compound used, the age, sex, weight, condition, general health and previous medical history of the patient being treated, and similar factors well known in the medical arts.

[0094] In some aspects, provided herein are methods for identifying a subject suitable for a treatment provided herein (a method for treating HPV infection, cancer, and / or precancerous lesions in a subject, comprising administering to the subject a pharmaceutical composition provided herein). In some embodiments, the method comprises isolating a sample (e.g., a blood sample, a tissue sample, a tumor sample) from the subject and detecting the presence of an HPV epitope listed in Table 1 in the sample. In some embodiments, the epitope is detected using an ELISA assay, a Western blot assay, a FACS assay, a fluorescence microscopy assay, an Edman degradation assay, and / or a mass spectrometry assay (e.g., protein sequencing). In some embodiments, the presence of an HPV epitope is detected by detecting a nucleic acid encoding the HPV epitope. In some embodiments, the nucleic acid encoding the HPV epitope is detected using a nucleic acid probe, a nucleic acid amplification assay, and / or a sequencing assay.

[0095] Examples of nucleic acid amplification assays that can be used in the methods provided herein include, but are not limited to, polymerase chain reaction (PCR), LATE-PCR, ligase chain reaction (LCR), strand displacement amplification (SDA), transcription-mediated amplification (TMA), self-sustained sequence replication (3SR), Qβ replicase-based amplification, nucleic acid sequence-based amplification (NASBA), repair chain reaction (RCR), boomerang DNA amplification (BDA), and / or rolling circle amplification (RCA).

[0096] In some embodiments, the products of the amplification reaction are detected as an indication of the presence and / or identity of bacteria in a sample. In some embodiments, the amplification products are detected after the amplification reaction is completed (i.e., endpoint detection). Examples of endpoint detection methods include gel electrophoresis-based methods, probe binding-based methods (e.g., molecular beacons, HPA probes, light-on / light-off probes), and double-stranded DNA-binding fluorescent dye-based methods (e.g., ethidium bromide, SYBR-Green). In some embodiments, the amplification products are detected as they are produced during the amplification reaction (i.e., real-time detection). Examples of real-time detection methods include probe binding-based methods (e.g., molecular beacons, TaqMan probes, Scorpion probes, light-on / light-off probes), and double-stranded DNA-binding fluorescent dye-based methods (e.g., ethidium bromide, SYBR-Green). In some embodiments, the products of the amplification reaction are detected and / or identified by sequencing (e.g., through the use of a sequencing assay described herein).

[0097] In some embodiments, detecting the nucleic acid sequence comprises contacting the nucleic acid sequence with a nucleic acid probe that specifically hybridizes to the nucleic acid sequence. In some embodiments, the probe is detectably labeled. In some embodiments, the probe is labeled (directly or indirectly) with a fluorescent moiety. Examples of fluorescent moieties useful in the methods provided herein include, but are not limited to, allophycocyanin, fluorescein, phycoerythrin, peridinin-chlorophyll protein conjugate, Alexa Fluor 350, Alexa Fluor 405, Alexa Fluor 430, Alexa Fluor 488, Alexa Fluor 514, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 555, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 633, Alexa Fluor 635, Alexa Fluor 647, Alexa Fluor 660, Alexa Fluor 680, Alexa Fluor 700, Alexa Fluor 750, Alexa Fluor 790, GFP, RFP, YFP, EGFP, mPlum, mCherry, mOrange, mKO, EYFP, mCitrine, Venus, YPet, Emerald, Cerulean, and CyPet. In some embodiments, the probe is a molecular beacon probe, a molecular torch probe, a TaqMan probe, an SDA probe, a Scorpion probe, an HPA probe, or a light-on / light-off probe.

[0098] In some embodiments, nucleic acid sequences are detected by sequencing (e.g., whole genome sequencing, transcriptome sequencing, and / or targeted gene sequencing). Examples of sequencing methods that can be used in the methods provided herein include, but are not limited to, chain termination sequencing, massively parallel signature sequencing, ion semiconductor sequencing, polony sequencing, Illumina sequencing, sequencing by ligation, sequencing by synthesis, pyrosequencing, single molecule real-time sequencing, SOLiD sequencing, DNA nanoball sequencing, heliscope single molecule sequencing, single molecule real-time sequencing, 454 sequencing, nanopore sequencing, tunneling current DNA sequencing, or sequencing by hybridization.

[0099] In some embodiments, the methods provided herein further include treating the identified subject using the therapeutic methods provided herein (e.g., by administering to the subject a pharmaceutical composition provided herein). [Example]

[0100] [Example 1] Characterization of HPV-specific T cell responses to facilitate the development of immunotherapeutic strategies for HPV A total of 50 volunteers will be recruited into the study, including patients who have not yet received treatment, are currently undergoing treatment, or have completed definitive radiation therapy with or without systemic treatment for HPV-related oropharyngeal cancer. In addition to the patient cohort, up to 21 healthy donors will be recruited into the study. An initial blood sample of up to 70 mL will be collected from each participant, with approximately 20 mL collected into EDTA tubes for HLA typing and approximately 50 mL collected for immunological assays. Three additional blood samples (50 mL each) will be collected from participants to follow up on HPV immunity (particularly in patients diagnosed with HPV-positive cancer). If participants require surgery after the consent period, fresh cancerous or precancerous specimens will be collected at the time of surgery. If sufficient tissue is available after specimen removal for standard pathological analysis, the samples will be examined for histopathology and immunological testing.

[0101] HPV-specific T cell phenotype and function are assessed ex vivo or after short-term in vitro culture. Tests include, but are not limited to, cell surface staining, peptide-MHC multimer analysis, ELISPOT, and intracellular cytokine staining assays. Gene expression and epigenetic analysis are performed to assess the molecular regulation of effector function and phenotype in the patient's virus-specific T cells compared to healthy donors, or virus-specific T cells compared to non-virus-specific T cells.

[0102] Total DNA will be extracted from participants' cells or plasma, and quantitative real-time PCR will then be used to assess the HPV DNA load in these samples. Where possible, cells from HPV-associated lesions will also be used to assess immune responses and antigen expression in tissues, as well as the expression of specific proteins and receptors that may regulate the immune response.

[0103] [Example 2] CD8 against HPV16 and HPV18 antigens + and CD4 + T cell response Virus-specific T cells derived from PBMCs collected from HNC (head and neck cancer) were expanded in vitro. Briefly, PBMC samples were incubated with either HPV16 or HPV18 HPV antigen pepmix peptide pools as described in Figures 1 and 2, respectively, and these cells were cultured for 14 days in the presence of IL-2.

[0104] On day 14, these T cell cultures were assessed for HPV antigen specificity using an ICS (intracellular cytokine staining) assay. A cutoff value for positivity was obtained down to 1% and identified IFN-γ. + CD8 + and IFN-γ + CD4 + As can be seen in Figure 1, for all HPV16 antigens except E4, the dominant CD8 + response (i.e., IFN-γ + ) was observed. + In our population, we observed dominant responses to all HPV antigens except E4 and E5, whereas Figure 2 illustrates the low level of HPV18 antigen-specific T cell responses observed in HNC patients.

[0105] [Example 3] HPV T cell epitope mapping Peripheral blood mononuclear cells (PBMCs) from HNC patients were isolated and stimulated with either HPV16 or HPV18 HPV antigen pepmix peptide pools in separate cultures as described above and prepared for intracellular cytokine staining (ICS) assays (unstimulated controls were run in parallel). T cell responses to the pepmix peptide pools were analyzed to identify individual peptides. These individual peptides were further evaluated for T cell proliferation, and potential epitopes were identified by ICS analysis. After identifying 15-mer peptides, further minimization of the epitope sequence was performed to identify optimal T cell epitope sequences. The 15-mer peptide sequences were trimmed from both the N- and C-termini to a minimum peptide length of 9–14 amino acids. After identifying the minimal peptide sequence, further confirmation was performed using a limited-dose titration ICS assay. After mapping the minimal epitope sequence, the HLA restriction of the epitope was identified by stimulating T cells using peptide-loaded HLA-matched and mismatched PHA blasts (PHAs). The complete process of epitope mapping is shown in the flow chart provided in FIG.

[0106] Representative data showing that HPV-specific T cells from HNC patients recognized HPV16-E6 and HPV18-E6 antigens can be found in Figures 1 and 2, respectively. To map T cell epitopes, further analysis was performed using subpools of E6 peptides. For example, with regard to HPV18-E6 peptides, pools E6-2, E6-3, and E6-9 were shown to be stimulatory by intracellular cytokine analysis. When analyzed on the HPV peptide matrix layout, a common peptide sequence between the responsive pools was identified (see Figure 4). The fine-mapping process revealed that TVLELTEVFEFA was associated with the HPV18-E6 CD4. + This was identified as a T cell epitope (see Figure 5). Similarly, CD4 epitope fine mapping of the HPV16-E6 pool identified KQRFHNIRGRWTGRC (see Figure 6). A list of HPV epitopes mapped by this method in this study is listed in Table 1.

[0107] [Example 4] HPV CD8 and CD4 polyepitope sequences A series of HPV polyepitope peptides were designed. + T cell epitopes were selected (see Table 1) to generate the HPV CD8 polyepitope (see Figure 7A, individual epitopes are indicated by alternating bold and underlined italic letters). + T cell epitopes were selected from Table 1 to generate the HPV CD4 polyepitope. + The polyepitope contains an ER (endoplasmic reticulum) signal sequence at the amino terminus and a lysosomal signal sequence at the carboxy terminus (see Figure 7B). + and CD4 + In this case, the polyepitope sequence was separated by an internal ribosome entry site (IRES; derived from encephalomyocarditis virus) (see Figures 7C and 7D). + , CD8 + The DNA sequence encoding the CD8IRESCD4 polyepitope was obtained from Atum Bio in the pJ201 cloning vector. The nucleotide sequence is 5'Nhe1 and 3'Kpn1 (CD4 + and CD8 + The polyepitope nucleotide sequences were released from the cloning vector by digestion with 5'NheI and 3'NotI (for the CD8IRESCD4 polyepitope) and 5'NheI and 3'NotI (for the CD8IRESCD4 polyepitope). These polyepitope nucleotide sequences were cloned into the pShuttle2 vector to generate mammalian expression cassettes. The recombinant pShuttle2 vector was digested with I-CeuI and PI-SceI restriction enzymes to generate the HPV CD4 + , CD8 + The mammalian expression cassette encoding the HPV CD8IRESCD4 polyepitope was released and then ligated into the Ad5F35 vector digested with I-CeuI and PI-SceI restriction enzymes (see Figure 8). + , CD8 +All recombinant adenovirus vectors expressing the CD8IRESCD4 or CD8IRESCD4 polyepitope were confirmed by PCR. The vectors were then linearized with PacI restriction enzyme to expose the inverted terminal repeats and packaged with Ad5F35 DNA. To generate recombinant adenovirus, HEK293 cells were transfected with the linear DNA, and the primary recombinant virus stock was harvested on day 6 by lysing the HEK293 cells with a freeze-thaw cycle. To obtain high-titer recombinant adenovirus, HEK293 cells were repeatedly infected with the primary recombinant virus stock. HPV CD4 + , CD8 + The presence of the CD8IRESCD4 polyepitope nucleotide sequence in the encapsidated adenovirus genome was assessed by PCR (see Figure 9).

[0108] [Example 5] Evaluation of immunogenicity of recombinant AdHPVCD8 To investigate the immunogenicity of AdHPVCD8poly, cells were pulsed with AdHPVCD8poly recombinant virus for 1 hour. Cells were then washed and incubated overnight, and activation of a panel of HPV-specific T cells was assessed by measuring intracellular expression of IFN-γ. Representative data shown in Figure 10 demonstrate that the HPV16-E2 HLA A02:01-restricted epitope derived from HPV16-E2 and E6 antigens, and the HLA A01:01-restricted epitope derived from HPV16-E2 antigen, are more efficiently processed and activate HPV-specific CD8 T cells. + HPV-specific CD8 + The frequency of was similar to that in JuSt fibroblasts pulsed with HPV pepmix.

[0109] [Example 6] HPV-specific CD8 from HPV HNC patients using recombinant AdHPVCD8 + T cell proliferation To further evaluate the immunogenicity of AdHPVCD8 poly, PBMCs from HPV HNC patients were stimulated with the virus in the presence of IL-2 for 14 days. + T cell proliferation was assessed by measuring IFN-γ secretion. Representative data shown in Figure 11 demonstrate that HPV AdCD8 polyclonal antibody increased HPV-specific CD8 T cell proliferation in the majority of patients. + It shows that T cell proliferation was induced and proliferation was observed against multiple antigens (E2, E4, E5, E6, and E7) from two different HPV strains (HPV16 and HPV18).

[0110] [Example 7] Assessment of immunogenicity of AdHPVCD4 poly To investigate the immunogenicity of HPV AdCD4 poly, PBMCs from one of the HPV HNC patients were stimulated with AdHPVCD4 poly and then cultured for 14 days in the presence of IL-2. The data shown in Figure 12 show the HPV-specific CD4 T cell proliferation after stimulation of PBMCs with HPV AdCD4 poly compared to stimulation of PBMCs with HPV pepmix and T cell proliferation against multiple HPV16 E2, E6, and E7 antigens. + It shows stable proliferation of T cells. Interestingly, CD8 + Longer CD4 T cell epitopes + Possibly incorporating T cell epitopes, HPV AdCD4 polyclonal antibodies stimulated HPV-specific CD8 T cells against HPV16 E6 and E7 antigens. + simultaneously stimulates the proliferation of T cells and these CD8 + The frequency of T cells was dramatically higher than in PBMC stimulated with HPV pepmix (Figure 12).

[0111] [Example 8] Evaluation of immunogenicity of AdCD8IRESCD4 recombinant viruses To evaluate the immunogenicity of HPV AdCD8IRESCD4 poly, PBMCs from six different HPV HNC patients were stimulated with virus in the presence of IL-2 for 14 days. Another set of PBMCs from the same patients was stimulated with AdHPVCD4 poly and AdHPVCD8 poly to elicit HPV-specific CD4 + and CD8 + The ability of AdCD8IRESCD4 poly to expand HPV-specific CD4 + and CD8 + T cell proliferation was determined by measuring IFN-γ secretion. Representative data shown in Figures 13A and B demonstrate that AdCD8IRESCD4 poly(A) inhibited the proliferation of HPV-specific CD4 T cells against HPV16 E1, E6, and E7 from two donors. + The data shown in Figures 13C and 13D show that AdCD8IRESCD4 poly also induced T cell proliferation, and the frequency of expanded T cells did not show a clear pattern compared to PBMCs expanded with HPV AdCD4 poly and HPV AdCD8 poly. In addition, the data shown in Figures 13C and 13D show that AdCD8IRESCD4 poly also induced HPV-specific CD8 T cells from multiple donors against HPV16 E5, E6, and E7 antigens. + demonstrated that HPV-specific CD4 T cell proliferation was induced by HPV HNC patients. + and CD8 + 1 shows the ability of HPV AdCD8IRESCD4poly as a single recombinant virus to expand T cells.

[0112] Incorporation by Reference All publications, patents, patent applications, and sequence accession numbers mentioned herein are hereby incorporated by reference in their entirety as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. In the case of conflict, the present application will control, including any definitions herein.

[0113] equivalent Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein which equivalents are intended to be encompassed by the following claims.

[0114] <110> THE COUNCIL OF THE QUEENSLAND INSTITUTE OF MEDICAL RESEARCH <120> HPV IMMUNOTHERAPY <130> PA25-239 <150> US 62 / 621,279 <151> 2018-01-24 <160> 63 <170> PatentIn version 3.5 <210> 1 <211> 10 <212> PRT <213> Human papillomavirus <400> 1 Leu Gln Asp Val Ser Leu Glu Val Tyr Leu 1 5 10 <210> 2 <211> 11 <212> PRT <213> Human papillomavirus <400> 2 Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe 1 5 10 <210> 3 <211> 9 <212> PRT <213> Human papillomavirus <400> 3 Ser Pro Ala Thr Ala Phe Thr Val Tyr 1 5 <210> 4 <211> 9 <212> PRT <213> Human papillomavirus <400> 4 Ser Ala Phe Arg Cys Phe Ile Val Tyr 1 5 <210> 5 <211> 9 <212> PRT <213> Human papillomavirus <400> 5 Phe Glu Leu Ser Gln Met Val Gln Trp 1 5 <210> 6 <211> 10 <212> PRT <213> Human papillomavirus <400> 6 Thr Leu Leu Gln Gln Tyr Cys Leu Tyr Leu 1 5 10 <210> 7 <211> 9 <212> PRT <213> Human papillomavirus <400> 7 Ser Glu Ile Ala Tyr Lys Tyr Ala Gln 1 5 <210> 8 <211> 9 <212> PRT <213> Human papillomavirus <400> 8 Arg Pro Phe Lys Ser Asn Lys Ser Thr 1 5 <210> 9 <211> 11 <212> PRT <213> Human papillomavirus <400> 9 Thr Leu Gln Asp Val Ser Leu Glu Val Tyr Leu 1 5 10 <210> 10 <211> 11 <212> PRT <213> Human papillomavirus <400> 10 Val Trp Glu Val His Ala Gly Gly Gln Val Ile 1 5 10 <210> 11 <211> 9 <212> PRT <213> Human papillomavirus <400> 11 Trp Pro Thr Thr Pro Pro Arg Pro Ile 1 5 <210> 12 <211> 9 <212> PRT <213> Human papillomavirus <400> 12 Asn Leu Asp Thr Ala Ser Thr Thr Leu 1 5 <210> 13 <211> 9 <212> PRT <213> Human papillomavirus <400> 13 His Asp Ile Ile Leu Glu Cys Val Tyr 1 5 <210> 14 <211> 9 <212> PRT <213> Human papillomavirus <400> 14 Lys Leu Pro Gln Leu Cys Thr Glu Leu 1 5 <210> 15 <211> 10 <212> PRT <213> Human papillomavirus <400> 15 Thr Ile His Asp Ile Ile Leu Glu Cys Val 1 5 10 <210> 16 <211> 9 <212> PRT <213> Human papillomavirus <400> 16 Phe Arg Asp Leu Cys Ile Val Tyr Arg 1 5 <210> 17 <211> 9 <212> PRT <213> Human papillomavirus <400> 17 Ala Phe Arg Asp Leu Cys Ile Val Tyr 1 5 <210> 18 <211> 10 <212> PRT <213> Human papillomavirus <400> 18 Ile Arg Cys Ile Asn Cys Gln Lys Pro Leu 1 5 10 <210> 19 <211> 10 <212> PRT <213> Human papillomavirus <400> 19 Gly Arg Trp Thr Gly Arg Cys Met Ser Cys 1 5 10 <210> 20 <211> 12 <212> PRT <213> Human papillomavirus <400> 20 Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe Ala 1 5 10 <210> 21 <211> 11 <212> PRT <213> Human papillomavirus <400> 21 Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe 1 5 10 <210> 22 <211> 9 <212> PRT <213> Human papillomavirus <400> 22 Leu Leu Met Gly Thr Leu Gly Ile Val 1 5 <210> 23 <211> 10 <212> PRT <213> Human papillomavirus <400> 23 Asp Arg Ala His Tyr Asn Ile Val Thr Phe 1 5 10 <210> 24 <211> 11 <212> PRT <213> Human papillomavirus <400> 24 Leu Glu Asp Leu Leu Met Gly Thr Leu Gly Ile 1 5 10 <210> 25 <211> 15 <212> PRT <213> Human papillomavirus <400> 25 Trp Lys Ser Phe Phe Ser Arg Thr Trp Ser Arg Leu Ser Leu His 1 5 10 15 <210> 26 <211> 15 <212> PRT <213> Human papillomavirus <400> 26 His Ile Asp Tyr Trp Lys His Met Arg Leu Glu Cys Ala Leu Tyr 1 5 10 15 <210> 27 <211> 15 <212> PRT <213> Human papillomavirus <400> 27 Ser Val Asp Ser Ala Pro Ile Leu Thr Ala Phe Asn Ser Ser His 1 5 10 15 <210> 28 <211> 23 <212> PRT <213> Human papillomavirus <400> 28 Val Tyr Asp Tyr Ala Phe Arg Asp Leu Cys Ile Val Tyr Arg Asp Gly 1 5 10 15 Asn Pro Tyr Ala Val Cys Asp 20 <210> 29 <211> 19 <212> PRT <213> Human papillomavirus <400> 29 Arg Cys Ile Asn Cys Gln Lys Pro Leu Cys Pro Glu Glu Lys Gln Arg 1 5 10 15 His Leu Asp <210> 30 <211> 27 <212> PRT <213> Human papillomavirus <400> 30 Glu Lys Gln Arg His Leu Asp Lys Lys Gln Arg Phe His Asn Ile Arg 1 5 10 15 Gly Arg Trp Thr Gly Arg Cys Met Ser Cys Cys 20 25 <210> 31 <211> 19 <212> PRT <213> Human papillomavirus <400> 31 Thr Pro Thr Leu His Glu Tyr Met Leu Asp Leu Gln Pro Glu Thr Thr 1 5 10 15 Asp Leu Tyr <210> 32 <211> 15 <212> PRT <213> Human papillomavirus <400> 32 Tyr Glu Gln Leu Asn Asp Ser Ser Glu Glu Glu Asp Glu Ile Asp 1 5 10 15 <210> 33 <211> 19 <212> PRT <213> Human papillomavirus <400> 33 Val Gln Ser Thr His Val Asp Ile Arg Thr Leu Glu Asp Leu Leu Met 1 5 10 15 Gly Thr Leu <210> 34 <211> 164 <212> PRT <213> Artificial Sequence <220> <223> Description of Artificial Sequence: Synthetic polypeptide <400> 34 Met Phe Glu Leu Ser Gln Met Val Gln Trp Thr Leu Leu Gln Gln Tyr 1 5 10 15 Cys Leu Tyr Leu Ser Glu Ile Ala Tyr Lys Tyr Ala Gln Arg Pro Phe 20 25 30 Lys Ser Asn Lys Ser Thr Thr Leu Gln Asp Val Ser Leu Glu Val Tyr 35 40 45 Leu Val Trp Glu Val His Ala Gly Gly Gln Val Ile Trp Pro Thr Thr 50 55 60 Pro Pro Arg Pro Ile Asn Leu Asp Thr Ala Ser Thr Thr Leu Ser Ala 65 70 75 80 Phe Arg Cys Phe Ile Val Tyr Ser Pro Ala Thr Ala Phe Thr Val Tyr 85 90 95 His Asp Ile Ile Leu Glu Cys Val Tyr Lys Leu Pro Gln Leu Cys Thr 100 105 110 Glu Leu Phe Arg Asp Leu Cys Ile Val Tyr Arg Ile Arg Cys Ile Asn 115 120 125 Cys Gln Lys Pro Leu Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe 130 135 140 Ala Leu Leu Met Gly Thr Leu Gly Ile Val Asp Arg Ala His Tyr Asn 145 150 155 160 Ile Val Thr Phe <210> 35 <211> 510 <212> DNA <213> Artificial Sequence <220> <223> Description of Artificial Sequence: Synthetic polynucleotide <400> 35 gctagcatgt tcgagctgtc gcaaatggtg cagtggaccc tgctgcaaca gtactgcctg 60 tacttgtccg agatcgctta caaatacgcc cagcggccct ttaagagcaa caagtcaacc 120 accctgcaag acgtcagcct cgaagtgtac ctcgtgtggg aagtccacgc gggtggacag 180 gtcatctggc ccacaactcc tccgaggcca atcaatctgg atacggcgtc cactaccctc 240 tccgccttcc ggtgcttcat cgtgtactcc cctgccactg ccttcaccgt gtatcacgac 300 attattctgg aatgcgtgta caagctcccg cagctttgta ccgagctgtt ccgcgatctg 360 tgcatcgtgt accgcattcg gtgcatcaac tgtcagaagc cgctgactgt gctggagctg 420 accgaagtgt ttgagttcgc cctgttgatg ggcacccttg ggattgtgga cagagcacat 480 tacaacatcg tcaccttctg ataaggtacc 510 <210> 36 <211> 220 <212> PRT <213> Artificial Sequence <220> <223> Description of Artificial Sequence: Synthetic polypeptide <400> 36 Met Arg Tyr Met Ile Leu Gly Leu Leu Ala Leu Ala Ala Val Cys Ser 1 5 10 15 Ala Trp Lys Ser Phe Phe Ser Arg Thr Trp Ser Arg Leu Ser Leu His 20 25 30 His Ile Asp Tyr Trp Lys His Met Arg Leu Glu Cys Ala Leu Tyr Ser 35 40 45 Val Asp Ser Ala Pro Ile Leu Thr Ala Phe Asn Ser Ser His Val Tyr 50 55 60 Asp Tyr Ala Phe Arg Asp Leu Cys Ile Val Tyr Arg Asp Gly Asn Pro 65 70 75 80 Tyr Ala Val Cys Asp Arg Cys Ile Asn Cys Gln Lys Pro Leu Cys Pro 85 90 95 Glu Glu Lys Gln Arg His Leu Asp Glu Lys Gln Arg His Leu Asp Lys 100 105 110 Lys Gln Arg Phe His Asn Ile Arg Gly Arg Trp Thr Gly Arg Cys Met 115 120 125 Ser Cys Cys Thr Pro Thr Leu His Glu Tyr Met Leu Asp Leu Gln Pro 130 135 140 Glu Thr Thr Asp Leu Tyr Tyr Glu Gln Leu Asn Asp Ser Ser Glu Glu 145 150 155 160 Glu Asp Glu Ile Asp Val Gln Ser Thr His Val Asp Ile Arg Thr Leu 165 170 175 Glu Asp Leu Leu Met Gly Thr Leu Thr Leu Ile Pro Ile Ala Val Gly 180 185 190 Gly Ala Leu Ala Gly Leu Val Leu Ile Val Leu Ile Ala Tyr Leu Val 195 200 205 Gly Arg Lys Arg Ser His Ala Gly Tyr Gln Thr Ile 210 215 220 <210> 37 <211> 678 <212> DNA <213> Artificial Sequence <220> <223> Description of Artificial Sequence: Synthetic polynucleotide <400> 37 gctagcatgc gctacatgat tctggggctc cttgcactcg cggccgtgtg ctcagcctgg 60 aagtcctttt tctcccggac ttggtcgaga ctgtcactcc atcatatcga ctactggaag 120 cacatgcgcc tggaatgcgc cctgtactcg gtggattccg ccccgatcct gaccgctttc 180 aactcctccc acgtctatga ctacgccttc cgggacctct gtattgtcta ccgggatggg 240 aacccgtacg ccgtgtgtga ccggtgcatc aattgccaga agccactctg ccctgaggaa 300 aagcagaggc atctggacga gaagcaacgc catttggata agaaacagcg gttccacaac 360 atcagaggtc gctggactgg ccggtgcatg tcctgctgca cccccaccct gcacgagtac 420 atgctggatc tgcagcccga gactaccgac ctgtactacg aacagcttaa cgacagctcc 480 gaggaagagg acgaaatcga cgtgcaaagc acccacgtgg acatcaggac cctggaagat 540 ctcctgatgg gcaccctgac gttgatccct attgctgtcg gtggagcact tgccggcctg 600 gtgctgatcg tgctgatcgc ctatctcgtg ggacgcaaga gaagccacgc gggataccag 660 actatttgat aaggtacc 678 <210> 38 <211> 383 <212> PRT <213> Artificial Sequence <220> <223> Description of Artificial Sequence: Synthetic polypeptide <220> <221> NON_CONS <222> (164)..(165) <223> These positions are non-consecutive and are separated by an IRES sequence <400> 38 Met Phe Glu Leu Ser Gln Met Val Gln Trp Thr Leu Leu Gln Gln Tyr 1 5 10 15 Cys Leu Tyr Leu Ser Glu Ile Ala Tyr Lys Tyr Ala Gln Arg Pro Phe 20 25 30 Lys Ser Asn Lys Ser Thr Thr Leu Gln Asp Val Ser Leu Glu Val Tyr 35 40 45 Leu Val Trp Glu Val His Ala Gly Gly Gln Val Ile Trp Pro Thr Thr 50 55 60 Pro Pro Arg Pro Ile Asn Leu Asp Thr Ala Ser Thr Thr Leu Ser Ala 65 70 75 80 Phe Arg Cys Phe Ile Val Tyr Ser Pro Ala Thr Ala Phe Thr Val Tyr 85 90 95 His Asp Ile Ile Leu Glu Cys Val Tyr Lys Leu Pro Gln Leu Cys Thr 100 105 110 Glu Leu Phe Arg Asp Leu Cys Ile Val Tyr Arg Ile Arg Cys Ile Asn 115 120 125 Cys Gln Lys Pro Leu Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe 130 135 140 Ala Leu Leu Met Gly Thr Leu Gly Ile Val Asp Arg Ala His Tyr Asn 145 150 155 160 Ile Val Thr Phe Met Arg Tyr Met Ile Leu Gly Leu Leu Ala Leu Ala 165 170 175 Ala Val Cys Ser Ala Trp Lys Ser Phe Phe Ser Arg Thr Trp Ser Arg 180 185 190 Leu Ser Leu His His Ile Asp Tyr Trp Lys His Met Arg Leu Glu Cys 195 200 205 Ala Leu Tyr Ser Val Asp Ser Ala Pro Ile Leu Thr Ala Phe Asn Ser 210 215 220 Ser His Tyr Asp Tyr Ala Phe Arg Asp Leu Cys Ile Val Tyr Arg Asp 225 230 235 240 Gly Asn Pro Tyr Ala Val Cys Asp Arg Cys Ile Asn Cys Gln Lys Pro 245 250 255 Leu Cys Pro Glu Glu Lys Gln Arg His Leu Asp Glu Lys Gln Arg His 260 265 270 Leu Asp Lys Lys Gln Arg Phe His Asn Ile Arg Gly Arg Trp Thr Gly 275 280 285 Arg Cys Met Ser Cys Cys Thr Pro Thr Leu His Glu Tyr Met Leu Asp 290 295 300 Leu Gln Pro Glu Thr Thr Asp Leu Tyr Tyr Glu Gln Leu Asn Asp Ser 305 310 315 320 Ser Glu Glu Glu Asp Glu Ile Asp Val Gln Ser Thr His Val Asp Ile 325 330 335 Arg Thr Leu Glu Asp Leu Leu Met Gly Thr Leu Thr Leu Ile Pro Ile 340 345 350 Ala Val Gly Gly Ala Leu Ala Gly Leu Val Leu Ile Val Leu Ile Ala 355 360 365 Tyr Leu Val Gly Arg Lys Arg Ser His Ala Gly Tyr Gln Thr Ile 370 375 380 <210> 39 <211> 570 <212> DNA <213> Viral encephalomyocarditis <400> 39 cccctaacg ttactggccg aagccgcttg gaataaggcc ggtgtgcgtt tgtctatatg 60 ttattttcca ccatattgcc gtcttttggc aatgtgaggg cccggaaacc tggccctgtc 120 ttcttgacga gcattcctag gggtctttcc cctctcgcca aaggaatgca aggtctgttg 180 aatgcgtga aggaagcagt tcctctggaa gcttcttgaa gacaaacaac gtctgtagcg 240 accctttgca ggcagcggaa ccccccacct ggcgacaggt gcctctgcgg ccaaaagcca 300 cgtgtataag atacacctgc aaaggcggca caaccccagt gccacgttgt gagttggata 360 gttgtggaaa gagtcaaatg gctctcctca agcgtattca acaaggggct gaaggatgcc 420 cagaaggtac cccattgtat gggatctgat ctggggcctc ggtacacatg ctttacatgt 480 gtttagtcga ggttaaaaaa cgtctaggcc ccccgaacca cggggacgtg gttttccttt 540 gaaaaacacg atgataatat ggccacaacc 570 <210> 40 <211> 1757 <212> DNA <213> Artificial Sequence <220> <223> Description of Artificial Sequence: Synthetic polynucleotide <400> 40 atgttcgagc tgtcgcaaat ggtgcagtgg accctgctgc aacagtactg cctgtacttg 60 tccgagatcg cttacaaata cgcccagcgg ccctttaaga gcaacaagtc aaccaccctg 120 caagacgtca gcctcgaagt gtacctcgtg tgggaagtcc acgcgggtgg acaggtcatc 180 tggcccacaa ctcctccgag gccaatcaat ctggatacgg cgtccactac cctctccgcc 240 ttccggtgct tcatcgtgta ctcccctgcc actgccttca ccgtgtatca cgacattatt 300 ctggaatgcg tgtacaagct cccgcagctt tgtaccgagc tgttccgcga tctgtgcatc 360 gtgtaccgca ttcggtgcat caactgtcag aagccgctga ctgtgctgga gctgaccgaa 420 gtgtttgagt tcgccctgtt gatgggcacc cttgggattg tggacagagc acattacaac 480 atcgtcacct tctgataata aggtctctaa aattccgccc cccccctaac gttactggcc 540 gaagccgctt ggaataaggc cggtgtgcgt ttgtctatat gttattttcc accatattgc 600 cgtcttttgg caatgtgagg gcccggaaac ctggccctgt cttcttgacg agcattccta 660 ggggtctttc ccctctcgcc aaaggaatgc aaggtctgtt gaatgtcgtg aaaggaagcag 720 ttcctctgga agcttcttga cgtctgtagc gaccctttgc accccccacc tggcgacagg tgcctctgcg gccaaaagcc acgtgtata gatacacctg 840 caaaggcggc acaaccccag tgccacgttg tgagttggat agttgtgga aggtcaaat ggctctcctc aagcgtattc aacaaggggc tgaaggatgc ccagaaggta ccccattgta 960 tgggatctga tctggggcct cggtacacat gctttacatg tgtttagtcg aggttaaaaa acgtctaggc cccccgaacc acggggacgt ggttttcctt tgaaaaacac gatgataata tggccacaac catgcgctac atgattctgg ggctccttgc actcgcggcc gtgtgctcag cctggaagtc ctttttctcc cggacttggt cgagactgtc actccatcat atcgactact ggagcacat gcgcctgga tgcgccctgt actcggtgga ttccgccccg atcctgaccg 1320. ctttcaactc ctcccacgtc tatgactacg ccttccgggga cctctgtatt gtctaccggg <h2 style=";text-align:left;direction:ltr">atgggaaccc gtacgccgtg tgtgaccggt gcatcaattg ccagaagcca ctctgccctg 1380<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> aggaaaagca gaggcatctg gacgagaagc aacgccattt ggataagaaa cagcggttcc 1440<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> acaacatcag aggtcgctgg actggccggt gcatgtcctg ctgcacccc accctgcacg 1500<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> agtacatgct ggatctgcag cccgagacta ccgacctgta ctacgaacag cttaacgaca 1560<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> gctccgagga agaggacgaa atcgacgtgc aaagcaccca cgtggacatc aggaccctgg 1620<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> aagatctcct gatggggcacc ctgacgttga tccctattgc tgtcggtgga gcacttgccg 1680<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> gcctggtgct gatcgtgctg atcgcctatc tcgtggggacg caagagaagc cacgcgggat 1740<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> 1757<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <210> 41<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <211> 15<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <212> PRT<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <213> Human papillomavirus<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <400> 41<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> Lys Gln Arg Phe His Asn Ile Arg Gly Arg Trp Thr Gly Arg Cys<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> 1 5 10 15<h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <h2 style=";text-align:left;direction:ltr"> <210> 42 <211> 19 <212> PRT <213> Human papillomavirus <400> 42 Val Tyr Cys Lys Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe Ala 1 5 10 15 Phe Lys Asp <210> 43 <211> 18 <212> PRT <213> Human papillomavirus <400> 43 Val Tyr Cys Lys Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe Ala 1 5 10 15 Phe Lys <210> 44 <211> 17 <212> PRT <213> Human papillomavirus <400> 44 Val Tyr Cys Lys Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe Ala 1 5 10 15 Phe <210> 45 <211> 16 <212> PRT <213> Human papillomavirus <400> 45 Val Tyr Cys Lys Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe Ala 1 5 10 15 <210> 46 <211> 15 <212> PRT <213> Human papillomavirus <400> 46 Val Tyr Cys Lys Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe 1 5 10 15 <210> 47 <211> 14 <212> PRT <213> Human papillomavirus <400> 47 Val Tyr Cys Lys Thr Val Leu Glu Leu Thr Glu Val Phe Glu 1 5 10 <210> 48 <211> 13 <212> PRT <213> Human papillomavirus <400> 48 Val Tyr Cys Lys Thr Val Leu Glu Leu Thr Glu Val Phe 1 5 10 <210> 49 <211> 12 <212> PRT <213> Human papillomavirus <400> 49 Val Tyr Cys Lys Thr Val Leu Glu Leu Thr Glu Val 1 5 10 <210> 50 <211> 11 <212> PRT <213> Human papillomavirus <400> 50 Val Tyr Cys Lys Thr Val Leu Glu Leu Thr Glu 1 5 10 <210> 51 <211> 10 <212> PRT <213> Human papillomavirus <400> 51 Val Tyr Cys Lys Thr Val Leu Glu Leu Thr 1 5 10 <210> 52 <211> 9 <212> PRT <213> Human papillomavirus <400> 52 Val Tyr Cys Lys Thr Val Leu Glu Leu 1 5 <210> 53 <211> 18 <212> PRT <213> Human papillomavirus <400> 53 Tyr Cys Lys Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe Ala Phe 1 5 10 15 Lys Asp <210> 54 <211> 17 <212> PRT <213> Human papillomavirus <400> 54 Cys Lys Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe Ala Phe Lys 1 5 10 15 Asp <210> 55 <211> 16 <212> PRT <213> Human papillomavirus <400> 55 Lys Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe Ala Phe Lys Asp 1 5 10 15 <210> 56 <211> 15 <212> PRT <213> Human papillomavirus <400> 56 Thr Val Leu Glu Leu Thr Glu Val Phe Glu Phe Ala Phe Lys Asp 1 5 10 15 <210> 57 <211> 14 <212> PRT <213> Human papillomavirus <400> 57 Val Leu Glu Leu Thr Glu Val Phe Glu Phe Ala Phe Lys Asp 1 5 10 <210> 58 <211> 13 <212> PRT <213> Human papillomavirus <400> 58 Leu Glu Leu Thr Glu Val Phe Glu Phe Ala Phe Lys Asp 1 5 10 <210> 59 <211> 12 <212> PRT <213> Human papillomavirus <400> 59 Glu Leu Thr Glu Val Phe Glu Phe Ala Phe Lys Asp 1 5 10 <210> 60 <211> 11 <212> PRT <213> Human papillomavirus <400> 60 Leu Thr Glu Val Phe Glu Phe Ala Phe Lys Asp 1 5 10 <210> 61 <211> 10 <212> PRT <213> Human papillomavirus <400> 61 Thr Glu Val Phe Glu Phe Ala Phe Lys Asp 1 5 10 <210> 62 <211> 9 <212> PRT <213> Human papillomavirus <400> 62 Glu Val Phe Glu Phe Ala Phe Lys Asp 1 5 <210> 63 <211> 525 <212> DNA <213> Artificial Sequence <220> <223> Description of Artificial Sequence: Synthetic polynucleotide <400> 63 gctagcatgt tcgagctgtc gcaaatggtg cagtggaccc tgctgcaaca gtactgcctg 60 tacttgtccg agatcgctta caaatacgcc cagcggccct ttaagagcaa caagtcaacc 120 accctgcaag acgtcagcct cgaagtgtac ctcgtgtggg aagtccacgc gggtggacag 180 gtcatctggc ccacaactcc tccgaggcca atcaatctgg atacggcgtc cactaccctc 240 tccgccttcc ggtgcttcat cgtgtactcc cctgccactg ccttcaccgt gtatcacgac 300 attattctgg aatgcgtgta caagctcccg cagctttgta ccgagctgtt ccgcgatctg 360 tgcatcgtgt accgcattcg gtgcatcaac tgtcagaagc cgctgactgt gctggagctg 420 accgaagtgt ttgagttcgc cctgttgatg ggcacccttg ggattgtgga cagagcacat 480 tacaacatcg tcaccttctg ataataaggt ctctaaaatt ccgcc 525

Claims

1. An isolated peptide consisting of a cytotoxic T cell epitope having an amino acid sequence selected from the cytotoxic T cell epitope amino acid sequences set forth in SEQ ID NOs: 1 to 24.

2. An isolated polyepitope peptide comprising multiple T cell epitope amino acid sequences selected from the T cell epitope amino acid sequences listed in Table 1.

3. 3. The isolated polyepitope peptide of claim 2, comprising an amino acid sequence set forth in any one of SEQ ID NOs: 34, 36, and 38.

4. An isolated nucleic acid comprising a nucleotide sequence encoding a peptide consisting of a cytotoxic T cell epitope having an amino acid sequence selected from SEQ ID NOs: 1-24.

5. The nucleic acid of claim 4, which is an expression vector.

6. The nucleic acid of claim 5, wherein the expression vector is a viral vector.

7. The nucleic acid of claim 6, wherein the viral vector is an adenovirus-based expression vector.

8. A vaccine composition comprising a peptide according to any one of claims 1 to 3 or a nucleic acid according to any one of claims 4 to 7.

9. 9. The vaccine composition of claim 8, comprising a peptide and an adjuvant.

10. An isolated polypeptide comprising a plurality of isolated HPV CTL epitopes having an amino acid sequence selected from the HPV CTL amino acid sequences set forth in SEQ ID NOs: 1-24.

11. 10. The isolated polypeptide of claim 9, comprising the amino acid sequence set forth in any one of SEQ ID NOs: 34 and 38.

12. A method for preparing a composition for use in inducing CTLs in a subject, the method comprising mixing at least one peptide consisting essentially of an amino acid sequence set forth in Table 1 with a pharmaceutically acceptable carrier, diluent or excipient.

13. A method of treating cancer in a subject, comprising administering to the subject a pharmaceutical composition comprising cytotoxic T cells (CTLs) comprising a T cell receptor (TCR) that specifically binds to one or more HPV epitope peptides bound to an HLA class I or HLA class II molecule comprising one or more epitope peptides listed in Table 1 presented on class I MHC.

14. A method of treating a precancerous condition in a subject, comprising administering to the subject a pharmaceutical composition comprising cytotoxic T cells (CTLs) comprising a T cell receptor (TCR) that specifically binds to one or more HPV epitope peptides bound to an HLA class I or HLA class II molecule that comprises one or more epitope peptides listed in Table 1 presented on class I MHC.

15. A method for treating a human papillomavirus (HPV) infection in a subject, comprising administering to the subject a pharmaceutical composition comprising cytotoxic T cells (CTLs) comprising a T cell receptor (TCR) that specifically binds to one or more HPV epitope peptides bound to an HLA class I or HLA class II molecule comprising one or more epitope peptides listed in Table 1 presented on class I MHC.

16. 16. The method of any one of claims 13 to 15, wherein the CTLs are autologous to the subject.

17. The method of any one of claims 13 to 15, wherein the CTLs are not autologous to the subject.

18. The method of claim 17, wherein the CTL is obtained from a library or bank of CTLs.

19. A method for inducing proliferation of HPV-specific cytotoxic T cells (CTLs), comprising incubating a sample containing CTLs with antigen-presenting cells (APCs) that present one or more HPV peptides comprising one or more epitopes listed in Table 1, thereby inducing proliferation of peptide-specific CTLs in the sample.

20. 20. The method of claim 19, wherein the sample further comprises one or more cytokines.

21. The method of claim 19 or 20, wherein the APC is a B cell.

22. The method of claim 19 or 20, wherein the APC is an antigen-presenting T cell.

23. The method of claim 19 or 20, wherein the APC is a dendritic cell.

24. The method of claim 20 or 21, wherein the APC is an aK562 cell.

25. 24. The method of any one of claims 19 to 23, wherein the sample comprises peripheral blood mononuclear cells (PBMCs).

26. 26. The method of any one of claims 19 to 25, wherein the HPV peptide is 20 amino acids or less in length.

27. 27. The method of claim 26, wherein the HPV peptide is 15 amino acids or less in length.

28. 27. The method of claim 26, wherein the HPV peptide is 10 amino acids or less in length.

29. 26. The method of any one of claims 19 to 25, wherein the HPV peptide is an HPV16-E1 antigen.

30. 30. The method of claim 29, wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 5-8 and 20.

31. 26. The method of any one of claims 19 to 25, wherein the HPV peptide is an HPV16-E2 antigen.

32. 32. The method of claim 31 , wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 1, 9, 10, 26, and 27.

33. 26. The method of any one of claims 19 to 25, wherein the HPV peptide is HPV16-E4 antigen.

34. 34. The method of claim 33, wherein the HPV peptide comprises the sequence WPTTPPRPI (SEQ ID NO: 11).

35. 26. The method of any one of claims 19 to 25, wherein the HPV peptide is HPV18-E6 antigen.

36. 36. The method of claim 35, wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 2, 20 and 21.

37. 26. The method of any one of claims 19 to 25, wherein the HPV peptide is HPV18-E5 antigen.

38. 38. The method of claim 37, wherein the HPV peptide comprises the sequence SPATAFTVY (SEQ ID NO: 3).

39. 26. The method of any one of claims 19 to 25, wherein the HPV peptide is an HPV16-E5 antigen.

40. 40. The method of claim 39, wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 4 and 12.

41. 26. The method of any one of claims 19 to 25, wherein the HPV peptide is HPV16-E6 antigen.

42. 42. The method of claim 41, wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 13-19, and 28-30.

43. 26. The method of any one of claims 19 to 25, wherein the HPV peptide is an HPV16-E7 antigen.

44. 44. The method of claim 43, wherein the HPV peptide comprises a sequence set forth in any one of SEQ ID NOs: 22, 23, and 24.

45. A peptide comprising an amino acid sequence listed in Table 1, wherein the peptide does not contain more than 30 consecutive amino acids of an HPV protein.

46. 46. ​​The peptide of claim 45, wherein the amino acid sequence listed in Table 1 is LQDVSLEVYL, TVLELTEVFEF, SPATAFTVY, or SAFRCFIVY.

47. 47. The peptide of claim 45 or 46, comprising two or more sequences listed in Table 1.

48. 48. A vaccine composition comprising a peptide according to any one of claims 45 to 47.

49. 49. The vaccine composition of claim 48, further comprising an adjuvant.

50. 50. A method of treating and / or preventing cancer in a subject, comprising administering to the subject one or more vaccine compositions of claim 48 or 49.

51. 50. A method of treating and / or preventing a precancerous condition in a subject comprising administering to the subject one or more vaccine compositions of claim 48 or 49.

52. 50. A method of treating and / or preventing HPV infection in a subject comprising administering to the subject one or more vaccine compositions of claim 48 or 49.

53. 48. A method of treating and / or preventing cancer in a subject, comprising administering to the subject one or more peptides according to any one of claims 45 to 47.

54. 48. A method of treating and / or preventing a precancerous condition in a subject, comprising administering to the subject one or more peptides according to any one of claims 45 to 47.

55. 48. A method of treating and / or preventing HPV infection in a subject, comprising administering to the subject one or more peptides according to any one of claims 45 to 47.

56. 48. An antigen-presenting cell (APC) comprising a peptide according to any one of claims 45 to 47, presented on class I MHC.

57. 57. The APC of claim 56, which is an antigen-presenting T cell.

58. 57. The APC of claim 56, which is a dendritic cell.

59. The APC of claim 56, which is a B cell.

60. The APC of claim 56, which is an artificial APC.

61. The APC of claim 56, wherein the artificial APC is an aK562 cell.

62. 48. A method for generating antigen-presenting cells (APCs) that present one or more HPV peptides, comprising incubating antigen-presenting cells with one or more peptides described in any one of claims 45 to 47, or one or more nucleic acids encoding one or more peptides described in any one of claims 45 to 47.

63. The method of claim 62, wherein the APC is an antigen-presenting T cell.

64. The method of claim 62, wherein the APC is a dendritic cell.

65. The method of claim 62, wherein the APC is a B cell.

66. The method of claim 62, wherein the APC is an artificial APC.

67. 63. The method of claim 62, wherein the artificial APC is aK562 cell.

68. 62. A method for treating or preventing cancer in a subject, the method comprising administering to the subject an APC described in any one of claims 56 to 61.

69. The method of claim 68, wherein the APCs are autologous to the subject.

70. The method of claim 68, wherein the APCs are not autologous to the subject.

71. 62. A method for treating or preventing a precancerous condition in a subject, the method comprising administering to the subject an APC of any one of claims 56 to 61.

72. The method of claim 71, wherein the APCs are autologous to the subject.

73. The method of claim 71, wherein the APCs are not autologous to the subject.

74. 62. A method of treating or preventing HPV infection in a subject, comprising administering to the subject the APC of any one of claims 56 to 61.

75. The method of claim 74, wherein the APCs are autologous to the subject.

76. The method of claim 74, wherein the APCs are not autologous to the subject.

77. 48. A nucleic acid encoding a peptide according to any one of claims 45 to 47.

78. 78. The nucleic acid of claim 77, which is an expression vector.

79. 79. The nucleic acid of claim 78, wherein the expression vector is a viral vector.

80. 80. The nucleic acid of claim 79, wherein the viral vector is an adenovirus-based expression vector.

81. 81. A vaccine composition comprising the nucleic acid of any one of claims 77 to 80.

82. 82. A method of treating and / or preventing cancer in a subject, comprising administering to the subject the vaccine composition of claim 81.

83. 82. A method of treating and / or preventing a precancerous condition in a subject, comprising administering to the subject the vaccine composition of claim 81.

84. 82. A method of treating or preventing HPV infection in a subject comprising administering to the subject the vaccine composition of claim 81.

85. An antibody or antigen-binding fragment thereof that binds to an HPV epitope listed in Table 1.

86. full-length immunoglobulin molecules, scFv, Fab fragments, Fab' fragment, F(ab')2, Fv, camel antibodies, Disulfide-linked Fv, Designed Ankyrin Repeat Protein (DARPin) 86. The antibody or antigen-binding fragment thereof of claim 85,

87. 87. A method of treating cancer in a subject, comprising administering to the subject the antibody or antigen-binding fragment thereof of claim 85 or 86.

88. 87. A method of treating a precancerous condition in a subject, comprising administering to the subject the antibody or antigen-binding fragment thereof of claim 85 or 86.

89. 87. A method of treating an HPV infection in a subject comprising administering to the subject the antibody or antigen-binding fragment thereof of claim 85 or 86.

90. A T cell expressing a T cell receptor (TCR) that binds to one or more peptides containing one or more epitopes listed in Table 1 presented on the major histocompatibility complex (MHC).

91. 91. The T cell of claim 90, which is a cytotoxic T cell (CTL).

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