Immunotherapy for polyomaviruses

Abstract

To provide polyomavirus epitopes useful for treating cancer or polyomavirus infection.SOLUTION: The present invention provides a peptide comprising a JC virus (JCV) epitope, the epitope being encoded by multiple specific amino acid sequences, the epitope being HLA class II restricted, one or more epitopes including one or more epitopes derived from a non-polyomavirus, and the one or more epitopes derived from a non-polyomavirus including one or more epitopes derived from an adenovirus, an Epstein-Barr virus, or a cytomegalovirus.SELECTED DRAWING: None

Description

[Technical Field]

[0001] Related Applications This application is incorporated by reference in its entirety. The benefit of priority to patent application Ser. No. 62 / 878,105 is claimed. [Background technology]

[0002] Polyomaviruses are ubiquitous viruses that infect a wide range of mammalian species. BK polyomavirus (BKV / human polyomavirus 1), John Cunningham ham) polyomavirus (JCV / human polyomavirus 2), and Merkel cell polyomavirus More than 12 different human polioviruses, including human polyomavirus (MCV / human polyomavirus 5) Identification of several rhesus virus species has been reported.

[0003] Most such polyomaviruses are typically asymptomatic in humans. However, human polyomaviruses associated with the disease often occur in childhood and / or or infect immunocompromised hosts. For example, initial JCV infection occurs via the amygdala or gastrointestinal tract. may occur and remain dormant in the gastrointestinal tract, possibly lymphoid organs, neuronal tissue, and kidneys. The virus remains trapped in the cytoplasm, where it continues to reproduce and shed viral particles. In the setting of immunodeficiency, immunosuppression, or immunodeficiency, both JCV and BKV can reactivate and infect vital organs. may progress to disease.

[0004] Of particular note is the JC virus, which crosses the blood-brain barrier and becomes neurotropic. They are able to penetrate the neurotropic central nervous system (CNS) and act on glial cells (e.g., oligodendrocytes). JCV infection infects cells in the brain (e.g., glial cells and astrocytes) and meningeal cells. in subjects), once reactivated, can lead to white matter demyelination and several pathological syndromes, e.g. For example, JCV granular cell layer neuropathy (JCV GCN), JCV encephalopathy (JCV CPN / JCVE), JCV meningitis (JCV M), and in particular progressive multifocal leukoencephalopathy (PML), a demyelinating disease of the central nervous system with high mortality. PML is associated with PML. It is common in patients with acquired immunodeficiency syndrome (AIDS) and in patients receiving immunosuppressive therapy (e.g., For example, steroids, cytostatics and antiproliferative agents, therapeutic antibodies, calcineurin inhibitors, Patients receiving anti-rejection drugs, such as organ transplants, Hodgkin's lymphoma, multiple sclerosis, psoriasis, It is primarily observed in patients with severe immunodeficiency, such as those with scabies and other autoimmune diseases. Currently, there are no drugs that effectively inhibit or cure viral infections. The goal is to reverse or alleviate the patient's immune deficiency, thereby slowing or halting the progression of the disease. However, such a strategy may require pausing or discontinuing treatment in immunosuppressed patients. This creates the dilemma of requiring a steroid drug and leaving those patients vulnerable to one of two conditions. Therefore, polyomavirus infection and / or polyomavirus-related diseases New therapies are needed to treat and prevent rheumatoid arthritis. Summary of the Invention

[0005] by T lymphocytes (e.g., cytotoxic T lymphocytes (CTLs) and / or helper T lymphocytes) Recognized and associated with polyomavirus infection (e.g., JCV infection), and / or cancer (e.g., polio) and poliovirus-associated cancers, e.g., JCV-associated cancers. a human ovarian tumor virus epitope (e.g., an epitope listed in Tables 1, 2, 3, 4, 5, and / or 6) Compositions and methods relating to the present invention are provided herein. The methods relate to JCV epitopes (e.g., epitopes listed in Tables 1, 2, and 3). In embodiments, the compositions and methods provide for the detection of viral infections within and / or across related viral strains. Hybrid epitopes incorporating sequence variations found in the epitopes (e.g., the epitopes listed in Table 4) Taupe).

[0006] In certain embodiments, one or more epitopes from one or more JCV antigens (e.g., LTA, STA, or or epitopes derived from the VP1 viral antigen, e.g., epitopes listed in Tables 1, 2 and / or 3. epitopes), and / or one or more hybrid epitopes (e.g., epitopes listed in Table 4). Peptides (e.g., isolated and / or recombinant polypeptides) containing the peptides are referred to herein as In some embodiments, the polypeptide comprises multiple such epitopes. In some embodiments, the polypeptide comprises at least two of the plurality of epitopes. In some embodiments, the peptide further comprises an intervening amino acid sequence between , capable of eliciting an immune response upon administration to a mammalian subject, e.g., a human subject.

[0007] In some embodiments, epitopes are selected to provide broad coverage in the human population. In some embodiments, the epitope is selected from HLA-A1, -A2, -A3, -A11, -A23, -A24, -A26, -A29, -A30, -B7, -B8, -B27, -B35, -B38, -B40, -B41, -B44, -B51, -B56, -B57 In some embodiments, the epitope is HLA class I restricted to HLA-B58 or -B58. HLA class II restriction to -DP, -DM, -DOA, -DOB, -DQ, or -DR. In some embodiments, the epitope is HLA class II restricted to HLA-DRB or -DQB. In one embodiment, the peptide comprises an epitope amino acid sequence set forth in SEQ ID NOs: 1-21. In some embodiments, the compositions provided herein are Pharmaceutical compositions comprising the peptides are provided herein.

[0008] In certain embodiments, nucleic acids (e.g., isolated nucleic acids) encoding the peptides disclosed herein are In some embodiments, a gene encoding a nucleic acid comprising such a nucleic acid is provided herein. Present constructs are provided herein. In some embodiments, such expression constructs Provided herein are host cells comprising the vectors provided herein. and expressing the isolated peptide in a host cell comprising the isolated peptide. Methods for producing isolated peptides, including at least partial purification, are described herein. In some embodiments, pharmaceutical compositions comprising the nucleic acids provided herein are Provided herein.

[0009] In certain embodiments, the antibodies described herein presented on HLA (e.g., class I HLA, class II HLA) are T lymphocytes (e.g., isolated T lymphocytes) containing a T cell receptor (TCR) that specifically binds to the epitope described. CD4+ T lymphocytes, CD8+ T lymphocytes) are provided herein. In an embodiment, a method for expanding BK virus-specific T lymphocytes for adoptive immunotherapy is provided. Thus, (i) one or more cells isolated from a subject, comprising T lymphocytes, are provided herein. and (ii) contacting the antigen-presenting cells with BK virus-specific antigen-presenting cells that present the epitope. Culturing one or more cells under conditions such that T lymphocytes proliferate from said one or more cells. In certain embodiments, methods are provided herein that include culturing one or more cells. In some embodiments, the cells are cultured in the presence of IL-2 and / or IL-21. At least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 , 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 ng / ml of IL-2 and / or IL-21 In some embodiments, the cells are cultured at 30, 35, 40, 45, 50, 60, 70, 80, 90, or 100 nM. In some embodiments, the cells are cultured in 10-50, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 15 ... In some embodiments, the cells are cultured with about 40, 25-35, or about 30 ng / ml of IL-2 and / or IL-21. In a specific embodiment, the cells are cultured with 30 ng / ml of IL-2 and / or IL-21. Proliferation in the presence of IL-2 and / or IL-21 is increased compared to proliferation in the absence of IL-2 or IL-21. In the expanded T lymphocyte population, the absolute number of polyomavirus-specific CD4 T cells This results in an increase in the ratio of the absolute number of polyomavirus-specific CD8 T cells.

[0010] In certain embodiments, the peptides, nucleic acids, T cells, or pharmaceutical compositions provided herein In a subject, a polyomavirus infection (e.g., a JCV infection) is detected, comprising administering to the subject a ), and / or to treat or prevent polyomavirus-associated cancers (e.g., JCV-associated cancers). Methods of treating and / or inducing a T lymphocyte immune response are provided herein. In some embodiments, the subject is a mammal, hi some embodiments, the subject is a human. In some embodiments, the subject is immunocompromised.

[0011] In certain embodiments, the T lymphocytes isolated from the subject are treated with the isolated T lymphocytes provided herein. The presence of JCV-specific T lymphocytes was detected by contacting them with the peptides. In some embodiments, a method for detecting JC virus infection in a subject is provided, comprising: The method includes treating a JC virus infection in a subject according to the methods described herein. In some embodiments, the subject is a mammal. In some embodiments, the subject is immunocompromised.

[0012] In certain embodiments, the subject is diagnosed with cancer (e.g., polyomavirus-associated cancer, e.g., J Provided herein are methods for treating CV-related cancers. In some embodiments, the methods The method may include one or more (e.g., at least 1, 2, 3, 4) of the methods listed in Table 1, Table 2, Table 3, and / or Table 4. , 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 Cytotoxicity involving T cell receptors (TCRs) that recognize epitopes (26, 27, 28, 29, 30 or more) In some embodiments, the method further comprises administering to the subject a pharmaceutical composition comprising cytotoxic T cells (CTLs). express human leukocyte antigens (HLA) to which one or more epitopes are restricted. In embodiments, the CTLs are autologous to the subject. In some embodiments, the CTLs are obtained from a CTL library or bank. In some embodiments, the method includes one or more of the compounds listed in Table 1, Table 2, Table 3, and / or Table 4 (e.g., At least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 , 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more) of the epitopes In some embodiments, the method comprises administering to a subject a compound of Table 1, Table 2, Table 3, and / or One or more of the compounds listed in Table 4 (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more) The pharmaceutical composition includes administering epitope-presenting antigen-presenting cells (APCs) to a subject. In one embodiment, the subject has a human leukocyte antigen (HL) having one or more epitopes restricted therein. A).

[0013] In certain embodiments, the method is for treating a polyomavirus infection (e.g., a JCV infection) in a subject. Methods are provided herein. In some embodiments, the subject is immunocompromised. In embodiments, the method comprises using one or more of the compounds listed in Table 1, Table 2, Table 3, and / or Table 4 (e.g., , at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 2 C containing TCRs that recognize epitopes (0, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more) In some embodiments, the subject is administered a pharmaceutical composition comprising the TL. In some embodiments, the CTLs are directed to a subject expressing an HLA that is restricted by one or more epitopes. In some embodiments, the CTLs are not autologous to the subject. In some embodiments, the CTLs are obtained from a CTL library or bank. , one or more (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more epitopes) to a subject. In some embodiments, the method comprises one or more (e.g., 2 or 3) of the compounds listed in Table 1, Table 2, Table 3, and / or Table 4. For example, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more epitopes) In some embodiments, the subject is administered a recombinant antigen-presenting cell (APC). The antibody expresses human leukocyte antigens (HLA) to which one or more epitopes of the antibody are restricted.

[0014] In some embodiments, one or more (e.g., at least one of) those listed in Table 1, Table 2, Table 3, and / or Table 4 are 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 , 23, 24, 25, 26, 27, 28, 29, 30 or more) Provided herein are populations of CTLs comprising:

[0015] In some embodiments, one or more (e.g., at least one of) those listed in Table 1, Table 2, Table 3, and / or Table 4 are 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 A population of APCs presenting epitopes (e.g., 23, 24, 25, 26, 27, 28, 29, 30 or more) is described herein. In some embodiments, the APCs are selected from the group consisting of B cells, antigen-presenting T cells, dendritic cells, and the like. and / or artificial antigen-presenting cells, e.g., aK562 cells. The cells (e.g., aK562 cells) express CD80, CD83, 41BB-L, and / or CD86. In one embodiment, a method for treating cancer (e.g., a cancer-causing agent) in a subject includes administering to the subject an APC described herein. Polyomavirus-associated cancers, e.g., JCV-associated cancers) and / or polyomavirus Methods for treating or preventing a bacterial (eg, JCV) infection are provided herein.

[0016] In some embodiments, one or more (e.g., at least one of) those listed in Table 1, Table 2, Table 3, and / or Table 4 are 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 , 23, 24, 25, 26, 27, 28, 29, 30 or more) of the epitopes described herein. In certain embodiments, one or more of the compounds listed in Table 1, Table 2, Table 3, and / or Table 4 are provided. (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 , 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more epitopes) Nucleic acid molecules (e.g., DNA molecules or RNA molecules) encoding the peptides are provided herein. In some embodiments, the nucleic acid molecule is a vector (e.g., an adenoviral vector). In some embodiments, the polypeptides and / or nucleic acid molecules described herein are Vaccine compositions are provided herein.

[0017] In some embodiments, one or more (e.g., at least one) of the compounds listed in Table 1, Table 2, Table 3, and / or Table 4 may be present. At least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30 or more epitopes) and CTLs. generating and activating polyomavirus-specific CTLs (e.g., JCV-specific CTLs), including contacting the cells with the Methods for inducing activation and / or proliferation of the cells are provided herein. In some embodiments, the CTLs are contacted with APCs in vitro. Presenting T cells, dendritic cells, and / or artificial antigen-presenting cells, such as aK562 cells. In such cases, antigen-presenting cells (e.g., aK562 cells) express CD80, CD83, 41BB-L, and / or CD86. In some embodiments, the CTLs are contacted with APCs in the presence of one or more cytokines. do.

[0018] In some embodiments, one or more of the compounds listed in Table 1, Table 2, Table 3, and / or Table 4 (e.g., At least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 , 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more) of the epitopes; and / or one or more (e.g., at least one, two, three, or four) of the compounds listed in Table 1, Table 2, Table 3, and / or Table 4. , 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 2 4, 25, 26, 27, 28, 29, 30 or more) and a nucleic acid encoding a polypeptide containing the epitope. A method for producing APCs that present the epitopes provided herein, comprising contacting the APCs with the epitopes. In some embodiments, the APC comprises one or more expresses HLA to which the epitope is restricted.

[0019] In some embodiments, one or more epitopes are expressed by two or more polyomaviruses. In some embodiments, the shared epitope comprises at least The region of sequence homology between the two polyomaviruses is also included. In some embodiments, the length of the loop sequence is at least 3, 4, 5, 6, or 7 amino acids. In some embodiments, the two polyomaviruses are BKV and JCV. At least three amino acids are LLL.

[0020] In other aspects, isolating a sample (e.g., a blood or tumor sample) from a subject, as described herein, or encoding an epitope provided in The methods of treatment provided herein, which involve detecting the presence of a nucleic acid (e.g., Identifying subjects suitable for administration of the CTL, APC, or vaccine compositions provided herein Methods are provided herein. In certain embodiments, the subject is a patient receiving a method as described herein. A subject is considered to be a subject of the present invention if he or she expresses an HLA that is restricted by one or more epitopes identified as a genotype. In some embodiments, the present invention provides a method for treating a cancer that is caused by a cancer cell. Subjects identified as suitable for the treatment methods provided in It is treated with [Brief explanation of the drawings]

[0021] [Figure 1] Figure 1 is a graph showing T cell responses to JCV antigens. Briefly, PBMCs from 17 healthy subjects were stimulated with JCV overlapping peptide pools (OPPs), and T cells were expanded for 14 days in the presence of IL-2. On day 14 after stimulation with each peptide pool, cells were assayed for IFN-γ expression using flow cytometry. Compiled data for all 17 donors are presented in graphs showing (A) BKV-specific CD8+ T cell responses and (B) CD4+ T cell responses after stimulation with each BKV OPP. [Figure 2] Figure 2 is a graph showing representative data demonstrating the identification of T cell determinants using a two-dimensional peptide matrix. JCV-specific T cells expanded in vitro using OPP were further characterized by identifying specific T cell determinants. Individual overlapping peptides were used to generate subpools (24 pools; LTA1–LTA24), and T cell responses for each pool were measured by intracellular cytokine staining (ICS) IFN-γ assay, as shown in the bar graph in panel A. Responses using the subpools were overlaid on the two-dimensional matrix, revealing individual peptides common to the pools. The FACs plot in panel B shows the T cell responses for each individual peptide (P29, P30, and P32) when used in the IFN-γ ICS assay, thereby confirming the peptides responsible for eliciting JCV-specific T cell responses. [Figure 3]Figure 3 is a graph showing representative data from HLA class II restriction analysis of epitopes mapped from the JCV-LT antigen. Specifically, the HLA class II restriction of the VDLHAFLSQAVFSNR (LT29), FLSQAVFSNRTVASF (LT30), and TVASFAVYTTKEKAQ (LT32) peptides as HLA DRB1*10:01 is shown. Briefly, a panel of lymphoblastoid cells (LCLs) matched to one monoallele of the donor's HLA type was selected and loaded with each peptide for 1 hour. The loaded LCLs were then used as stimulator cells in an IFN-γ ICS assay. When presented by MHC, the peptides induce IFN-γ responses in JCV-specific T cells. [Figure 4] Figure 4 is a graph showing T cell cross-reactivity between BKV and JCV epitopes. ICS FACS plots show IFN-γ expression in T cells grown with either the BKV epitope (SSGTQQWRGLARYFK) or the JCV epitope (RSGSQQWRGLSRYFK). These primed T cells were stimulated with both BKV and JCV peptides, demonstrating that T cells grown with either of these epitopes recognize both BKV and JCV peptide sequences. [Figure 5] Figure 5 is a graph illustrating JCV-specific T cell proliferation from healthy subjects. The frequency of CD4+ T cells expressing IFN-γ was assessed and the response for each individual subject is shown in the graph. [Figure 6] Figure 6 is a graph showing the polyfunctionality of JCV-specific T cells expanded using pooled peptides. Representative FACs dot plots show the expression of individual effector molecules in CD4+ T cells upon restimulation with JCV peptide pools (a). The polyfunctionality of JCV-specific T cells expressing multiple cytokines is shown in panels (b) and (c). [Figure 7] FIG. 7 is a graph showing the transcription factor and effector profiles of JCV-specific T cells expanded in vitro. DETAILED DESCRIPTION OF THE INVENTION

[0022] general T lymphocytes (e.g., cytotoxic (CD8 + ) T lymphocytes (CTL) and / or helper (CD4 + ) T lymphocytes cytoplasm), and can be associated with polyomavirus infection (e.g., JCV infection) and / or cancer (e.g., and polyomavirus-associated cancers, e.g., JCV-associated cancers). Polyomavirus epitopes (e.g., epitopes listed in Tables 1, 2, 3, and / or 4) that In some embodiments, compositions and methods relating to The compositions and methods provided herein are directed to JCV epitopes (e.g., those listed in Tables 1, 2, and 3). In some embodiments, the compositions and methods relate to BKV and JCV epitopes. These include mutations found within or across epitopes (e.g., epitopes listed in Table 4). It relates to hybrid epitopes.

[0023] definition For convenience, certain terms employed in the specification, examples, and appended claims are referred to herein. collect.

[0024] The articles "a" and "an" are used herein to refer to the grammatical object of the article. is used to refer to one or more than one (i.e., at least one) of. For example, "one An "element" means one element or more than one element.

[0025] As used herein, the term "administer" refers to providing a pharmaceutical agent or composition to a subject. This means administration by a healthcare professional and self-administration, but is not limited to this. Such agents include, for example, the peptides described herein, the antigen-presenting agents provided herein, and the like. The present invention may include the presenting cells and / or CTLs provided herein.

[0026] The term "amino acid" refers to a polymer of naturally occurring amino acids containing both amino and acid functional groups. The term "antibody" is intended to encompass all molecules, natural or synthetic, that can be included in a molecule. The amino acids include natural amino acids, their analogs, derivatives and homologs, and amino acids having variant side chains. Included are amino acid analogs, as well as all stereoisomers of any of the above.

[0027] The terms "bind" or "interact" refer to, for example, electrostatic interactions under physiological conditions. two molecules by interaction, hydrophobic interactions, ionic interactions and / or hydrogen bonding interactions The association may be a stable association between, for example, a TCR and a peptide / HLA. TCRs are T cells that can bind to T cell epitopes when presented on the appropriate HLA. "Recognizes" cellular epitopes.

[0028] The terms "biological sample," "tissue sample," or simply "sample" respectively refer to a biological sample of interest. Refers to a collection of cells obtained from a tissue. The source of the tissue sample can be fresh, frozen, and / or or solid tissue such as from preserved organs, tissue samples, biopsies or aspirates; blood or any Blood components, serum, blood; body fluids, such as cerebrospinal fluid, amniotic fluid, peritoneal or interstitial fluid, urine, saliva, feces It may be stool, tears; or cells from any point in the 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, bones, cartilage, blood and blood vessels. The term "cancer" further encompasses primary and metastatic cancers.

[0030] As used herein, the term "homologous" refers to the difference between two regions of the same sequence strand or between two different sequences. The term "homology" refers to sequence similarity (e.g., nucleic acid or amino acid sequence) between regions of corresponding sequences. , to refer to sequence similarity between two regions of the same sequence strand or between regions of two different sequence strands. For example, amino acid residue positions in both regions are occupied by the same amino acid residue. If the regions are identical at that position, the first region is the If at least one nucleotide residue position is occupied by the same residue, the second region is Homology between two regions is determined by the presence of two identical nucleotides or amino acid residues. The percentages are expressed in terms of the nucleotide or amino acid residue positions of a region. For example, The region having the nucleotide sequence 5'-ATTGCC-3' and the region having the sequence 5'-TATGGC-3' are 50% Preferably, the first region comprises the first portion and the second region comprises the second portion. and whereby at least about 50%, preferably at least about 7%, of each of these portions 5%, at least about 90%, or at least about 95% of the nucleotide residue positions have the same nucleotide More preferably, all nucleotide residues in each of these portions are occupied by The positions are occupied by the same nucleotide residue.

[0031] The term "isolated" refers to a substance that has been removed from its natural state or is otherwise under the control of humans. Isolated material refers to material that has been subjected to a process to produce a product. Isolated material is a material that is free from the components with which it is normally associated in its natural state. substantially or essentially free of, or from, the components with which it is normally associated in its natural state Both can be engineered to be artificial.

[0032] The term "peptide" refers to two amino acids linked together by a peptide bond or a modified peptide bond. As used herein, the terms "peptide," "polypeptide," and "polypeptide" refer to a sequence of one or more amino acids. The terms "protein" and "protein" may be used interchangeably. In certain embodiments, the peptide is a recombinant DNA peptide. DNA or RNA, or DNA or RNA of synthetic origin, or any combination thereof It is produced in a manner that (1) does not associate with peptides normally found in nature, and (2) is not associated with the cells in which it normally resides. (3) isolated free from other proteins from the same cellular source (4) expressed by cells from a different species, or (5) not naturally occurring.

[0033] The term "epitope" refers to a peptide determinant capable of specific binding to an antibody or TCR. An epitope usually refers to a chemically active surface group of a molecule, e.g., an amino acid or A particular epitope is a specific sequence of amino acids to which an antibody can bind. It can be defined by a sequence.

[0034] As used herein, the phrase "pharmaceutically acceptable" means that the Within the limits, without excessive toxicity, irritation, allergic reactions, or other problems or complications suitable for use in contact with human and animal tissues, consistent with a reasonable benefit / risk ratio "Drugs, compounds, materials, compositions, and / or dosage forms" refers to drugs, compounds, materials, compositions, and / or dosage forms that are

[0035] As used herein, the phrase "pharmaceutically acceptable carrier" refers to a carrier that can be administered to a patient in need thereof. Involved in carrying or transporting from one organ or part of a living body to another organ or part of a living body a pharmaceutically acceptable material, composition or vehicle, e.g., a liquid or solid filler, The term "carbohydrate" refers to a material that encapsulates a carrier, diluent, excipient, or solvent. The compound 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: Examples include: (1) sugars, such as lactose, glucose, and sucrose; (2) dextran; starches, e.g., corn starch and potato starch; (3) cellulose and its derivatives; Derivatives of, for example, sodium carboxymethylcellulose, ethylcellulose and acetic acid Cellulose, (4) powdered tragacanth, (5) malt, (6) gelatin, (7) talc, (8) excipients, (9) Oils, e.g., peanut oil, cottonseed oil, saffron, etc. oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, e.g., propyl (11) Polyols, such as glycerin, sorbitol, mannitol, and 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) Ethylene glycol mononitrate (EPO), (20) pH buffer solution, (21) polyester, polycarbonate and / or polypropylene anhydrides, and (22) other non-toxic compatible substances used in pharmaceutical preparations.

[0036] The terms "polynucleotide" and "nucleic acid" are used interchangeably. Any length of ribonucleotides, whether ribonucleotides or their analogs A polynucleotide refers to a polymeric form of nucleotides. A polynucleotide may have any three-dimensional structure. It may perform any function. The following are non-limiting examples of polynucleotides: genes or coding or non-coding regions of gene fragments, loci(s) determined from linkage analysis; Exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA , ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors 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 nucleotides. Modifications to the nucleotide structure, if present, may include nucleotide analogs. The polynucleotide may be administered before or after construction of the construct. All nucleic acid sequences provided herein may be further modified by conjugation. In the string, a U nucleotide is interchangeable with a T nucleotide.

[0037] As used herein, a therapeutic agent that "prevents" a condition is an agent that statistically inhibits or prevents the onset of a disorder or condition. When administered to a statistical sample, the treatment reduce the occurrence of the disorder or condition in the treated sample or in an untreated control sample. delaying the onset of or decreasing the severity of one or more symptoms of a disorder or condition compared to the original It refers to a compound that reduces the severity of symptoms.

[0038] As used herein, "specific binding" refers to the ability of an antibody to bind to a predetermined antigen or This refers to the ability of a peptide to bind to its designated binding partner. Typically, this is an antibody or peptide. Chid is about 10 -7 K below M D with an affinity corresponding to its predetermined antigen or binding partner and nonspecific and irrelevant antigen / binding partners (e.g., BSA, At least 10-fold less, at least 100-fold less, than the affinity for binding to zein or at least 1000 times smaller affinity (K D (such as represented by Binds to antigen / binding partner.

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

[0040] As used herein, the phrases "therapeutically effective amount" and "effective amount" refer to a therapeutically effective amount administered to a subject. In this case, it is possible to induce an appropriate therapeutic response in a subject and to provide a reasonable therapeutic effect applicable to any medical treatment. It refers to the amount of a drug that produces a beneficial result in a subject, given a benefit / risk ratio.

[0041] "Treating" a disease in a subject or "treating" a subject with a disease administering a medicinal agent to a subject to reduce or prevent the worsening of at least one symptom of a disease This refers to administering therapeutic treatment, such as administering a drug.

[0042] The term "vector" refers to a vector by which a nucleic acid can be propagated and / or transferred between organisms, cells, or cellular components. Vectors are plasmids, viruses, and bacteria. phage, provirus, phagemid, transposon, and artificial chromosome. These may or may not be capable of autonomous replication or may be capable of replicating autonomously within a host cell. It may be integrated into the chromosome.

[0043] epitope In certain embodiments, when presented on HLA, they are targeted to immune effector cells (e.g., cytotoxic T cells). Polyomavirus epitopes, e.g., JCV epitopes, recognized by cytotoxic T cells (CTLs) Provided herein are methods and compositions relating to the method. The epitopes described herein are directed to polyomavirus infection (e.g., JCV virus infection) and / or or cancer (e.g., JVC-associated cancers that express the epitopes provided herein). and / or useful in the prevention and / or treatment of polyomavirus infections (e.g., JCV virus). infection) and / or cancer (e.g., polyclonal antibodies expressing the epitopes provided herein). and compositions thereof (e.g., immunizations) useful for the prevention and / or treatment of rhomavirus-associated cancers. In certain embodiments, the present invention is useful for the generation of immune effector cells and / or APCs. In some embodiments, the epitope is a JCV epitope listed in Table 1, Table 2, and / or Table 3. In this form, the epitope is an amino acid sequence derived from both the BKV epitope and the homologous JCV epitope. and / or hybrids containing amino acid variants found in different BKV or JCV strains. Exemplary hybrid epitopes are listed in Table 4. In some embodiments, the compositions and methods described herein may be used to treat additional viruses, such as EBV, CMV, or ADV. In some embodiments, the epitope is HLA class I restricted. In another embodiment, the epitope is an HLA class II-restricted T cell epitope. It's taupe.

[0044] [Table 1]

[0045] [Table 2]

[0046] [Table 3] TIFF2025160241000004.tif142167

[0047] [Table 4] TIFF2025160241000006.tif50169

[0048] In some embodiments, peptides comprising one or more epitopes from Table 1, Table 2, Table 3, and / or Table 4 are provided. In some embodiments, the present invention provides a method for the preparation of a peptide (e.g., a polypeptide) comprising: The peptides disclosed herein may be derived from full-length viral proteins (e.g., full-length BKV and / or JCV proteins). In some embodiments, the peptide is not a full-length viral protein (e.g., In some embodiments, the peptides disclosed herein are The peptides are BKV and JCV epitopes with sequence homology (e.g., those listed in Tables 2, 3, and 4). In some embodiments, the peptides disclosed herein comprise a viral protein. Less than 100, 90, 80, 70, 60, 50, 40, 30, 25, 20, 15, or 10 consecutive amino acids of a protein In some embodiments, the peptides disclosed herein include those listed in Table 1, Table 2, Table 3, and / or The antigen-binding fragments of the present invention comprise two or more epitopes listed in Table 4. For example, in some embodiments, the antigen-binding fragments of the present invention comprise two or more epitopes listed in Table 4. The disclosed peptides may be any of Table 1, Table 2, Table 3 and / or any of Tables 1, 2, 3 and 4 connected by a polypeptide linker. In some embodiments, the antigen-binding fragments provided herein comprise two or more epitopes listed in Table 4. The peptides to be analyzed must be at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 3 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 epitopes (e.g., Table 1, Table 2 , at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 listed in Table 3 and / or Table 4 , 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 peptides) In a preferred embodiment, the peptides disclosed herein are those that bind to the JCV epitopes listed in Table 1. That is, any one of the JCV epitopes set forth in SEQ ID NOs: 1 to 21 or any of them For example, the peptide may be a combination of the amino acid sequences set forth in SEQ ID NOs: 1 to 21. Coded by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 , 16, 17, 18, 19, 20, or all 21 epitopes.

[0049] In certain embodiments, multiple epitopes from BKV or JCV antigens (e.g., large T antigen (LTA)) are used. ), epitopes derived from the small T antigen (STA) or major capsid protein VP1 viral antigen; epitopes listed in Tables 1, 2, 3 or 4), preferably epitopes listed in Table 1 polypeptides (e.g., isolated polypeptides and / or recombinant polypeptides) containing the polypeptides ) is provided herein. More preferably, the polypeptide disclosed herein is Any one of the JCV epitopes set forth in SEQ ID NOs: 1 to 21 or any combination thereof In some such embodiments, the polypeptide comprises at least one of a plurality of epitopes. In some embodiments, the intervening amino acid sequence is The amino acid or amino acid sequence is a proteasome liberation amino acid or amino acid sequence. Non-limiting examples of proteasome-dissociating amino acids or amino acid sequences include AD, K, or R. In some embodiments, the intervening amino acid or amino acid sequence is or comprises TA Typically, the TAP recognition motif has the following formula: (R / N:I / Q:W / Y) n (In the ceremony , n is any integer equal to or greater than 1). Non-limiting examples of TAP recognition motifs include RIW In some embodiments, the epitaxial layers provided herein include RQW, NIW, and NQY. The fragments are identified by a proteasome-dissociating amino acid sequence and, optionally, a TAP recognition motif. In some such embodiments, the nucleotide sequence is linked or associated at the carboxyl terminus of the nucleotide sequence. The polypeptide is encoded by the amino acid sequence set forth in SEQ ID NOs: 1 to 21. Each of the epitopes may comprise or consist essentially of the respective epitopes.

[0050] In some embodiments, the polypeptides provided herein comprise at least one further Viruses such as Epstein-Barr virus (EBV), cytomegalovirus (CMV), and / or adenovirus (ADV). In some embodiments, the peptide comprises epitopes of two or more viruses. In some embodiments, the peptide comprises epitopes from three or more viruses. In some embodiments, the peptide comprises epitopes from four or more viruses. For example, in some embodiments, the peptide comprises an epitope of a JCV virus. , BKV, EBV, CMV, and / or ADV. .

[0051] In some embodiments, polyepitope polypeptides comprising two or more epitopes described herein are used. polypeptides (i.e., amino acids containing multiple T cell epitopes that are not naturally linked) In some embodiments, the T in a polypeptide is The cellular epitopes are connected via an amino acid linker. The T cell epitopes in the peptides are directly linked with no intervening amino acids. Polypeptide, method for producing polyepitope polypeptide, and polyepitope polypeptide - Patents.com Examples of vectors encoding the nucleotide sequences described in Dasari et al., which are incorporated herein by reference in their entirety. ., Molecular Therapy-Methods & Clinical Development(2016) 3, 16058 Cut.

[0052] In certain embodiments, HLA class I and HLA-specific T cells capable of inducing proliferation of peptide-specific T cells are used. and class II-restricted polyomavirus peptide epitopes (e.g., Tables 1, 2, 3, 4, 5, and A pool of immunogenic peptides containing the epitopes listed in (1) and / or (2) above is provided. In embodiments, the pool of immunogenic peptides comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 epitopes (e.g., at least one, two, three, or more of those listed in Table 1, Table 2, Table 3, and / or Table 4) , 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 epitopes) or combinations thereof. In Table 1, the peptide pool contains at least one JCV epitope listed in Table 1, i.e., Any one of the JCV epitopes set forth in SEQ ID NOs: 1 to 21 or any combination thereof For example, the pool of immunogenic peptides may include the amino acid sequences set forth in SEQ ID NOs: 1 to 21. At least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 1 coded by columns It may comprise 5, 16, 17, 18, 19, 20, or all 21 epitopes. Such peptide pools include JCV peptide epitope amino acids set forth in SEQ ID NOS: 1-21. Immunogenic peptides and pools thereof elicit peptide-specific T cells (e.g., For example, peptide-specific cytotoxic T cells and / or CD4 + T cell proliferation do.

[0053] In some embodiments, the compositions and methods provided herein comprise the compositions of Tables 1, 2, and / or 3 For example, in some embodiments, In this case, two or more (e.g., at least 3, 4, 5, 6) of the epitopes listed in Tables 1, 2, and / or 3 are included. , 7, 8, 9 or 10) naturally occurring variants of the polyepitopic polypeptides described herein. Provided.

[0054] In some embodiments, the sequences of the epitopes provided herein are one or more (e.g., one 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) of the amino acids described herein except for conservative sequence modifications. As used herein, the term "conservative sequence modifications" refers to modifications of the TCR and HLA does not significantly affect or inhibit the interaction between peptides containing the amino acid sequences presented above is intended to refer to an amino acid modification that does not alter the amino acid sequence. Such conservative modifications include: Amino acid substitutions, additions (e.g., addition of amino acids to the N- or C-terminus of a peptide) and deletions (e.g., deletion of amino acids from the N-terminus or C-terminus of the peptide). Substitutions are ones in which the 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), amino acids with acidic side chains (e.g., aspartic acid, glutamic acid), non- Amino acids with charged polar side chains (e.g., glycine, asparagine, glutamine, serine) , threonine, tyrosine, cysteine, tryptophan), amino acids with nonpolar side chains ( For example, alanine, valine, leucine, isoleucine, proline, phenylalanine, thionine), amino acids with beta-branched side chains (e.g., threonine, valine, isoleucine, amino acids with aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, etc.) Thus, one or more of the peptides described herein may be used. The above amino acid residues can be substituted with other amino acid residues from the same side chain family. The modified peptides may be used to detect TCR binding (e.g., TCR-binding domains) using methods known in the art. Modifications can be tested for retention of integrity (e.g., antigenicity). Mutagenesis can be achieved by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. It can be introduced into the antibody.

[0055] In some embodiments, the peptides (e.g., polypeptides) described herein are immunogenic. and elicits an immune response upon administration to a subject (e.g., a mammalian subject, e.g., a human subject). In further embodiments, the peptides described herein (e.g., polypeptides) can be used. The immune cells (e.g., immune cells of the subject and / or immune cells from a donor, e.g., the same Endogenous or exogenous processing of peptides by these immune cells, including allogeneic PBMCs An immune response can be elicited after labeling and / or presentation.

[0056] In some embodiments, one or more peptides described herein (e.g., Table 1, Table 2, Table 3 and / or The cells presenting the peptides (peptides containing at least one epitope listed in Table 4) are described herein. In some embodiments, the cell is a mammalian cell. In this state, the cells are antigen-presenting cells (APCs) (e.g., antigen-presenting T cells, dendritic cells, B cells, macrophages, etc.). phage, or artificial antigen-presenting cells, such as aK562 cells). Peptide-presenting cells can be produced by standard techniques known in the art. For example, cells may be pulsed to promote peptide uptake. In some embodiments, the cells transduce a nucleic acid encoding a peptide provided herein. In some embodiments, cells are transfected with a peptide described herein. Provided herein is a method for producing antigen-presenting cells (APCs), comprising pulsing the cells. Illustrative examples of producing antigen-presenting cells can be found in WO2013088114, The entire contents of which are incorporated herein.

[0057] The peptides provided herein can be purified using standard protein purification techniques. It can be isolated from cells or tissue sources by various purification schemes and can be produced by recombinant DNA techniques. They can be produced by ligation and / or chemically synthesized using standard peptide synthesis techniques. The peptides described herein can be used to encode the peptide(s) of the present invention. Produced in a prokaryotic or eukaryotic host cell by expression of a nucleotide sequence encoding the Alternatively, such peptides can be synthesized by chemical methods. Expression of heterologous peptides in recombinant hosts, chemical synthesis of peptides, and in vitro translation Methods of translation are well known in the art and are incorporated herein by reference. Maniatis et al., Molecular Cloning: A Laboratory Manual (1989), 2nd edition, Cold Sprin. g Harbor, NY, Berger and Kimmel, Methods in Enzymology, Volume 152, Guide to Molecule. lar Cloning Techniques (1987), Academic Press, Inc., San Diego, Calif., Merrifie. ld, J. (1969) J. Am. Chem. Soc. 91:501, Chaiken IM (1981) CRC Crit. Rev. Bioc. hem. 11:255, Kaiser et al. (1989) Science 243:187, Merrifield, B. (1986) Science 232: 342, Kent, SBH (1988) Annu. Rev. Biochem. 57:957, Offord, RE (1980) Semi Synthetic Proteins, Wiley Publishing.

[0058] nucleic acid molecule Nucleic acid molecules encoding the epitopes and peptides described herein are provided herein. Nucleic acids may be provided in, for example, whole cells, in a cell lysate, or in a partially purified form. The nucleic acid molecules described herein may be present in purified or substantially pure form. can be isolated using standard molecular biology techniques and the sequence information provided herein. For example, a nucleotide sequence corresponding to one or more of the epitopes listed in Tables 1, 2, 3, or 4. The oligonucleotides can be synthesized by standard synthesis techniques, i.e., automated DNA synthesizers. It can be prepared using

[0059] In some embodiments, vectors (e.g., vectors containing the nucleic acid molecules described herein) are used. A viral vector, such as an adenovirus-based expression vector, is referred to herein as a Viral vectors are provided that contain additional DNA segments that can be ligated into the viral genome. Certain vectors may contain a marker for the host cell into which they are introduced (e.g., bacterial Autonomously replicating vectors (bacterial vectors with a recombinant origin, episomal mammalian vectors) Other vectors (e.g., non-episomal mammalian vectors) can be introduced into a host cell. Upon entry, they are integrated into the host cell genome, allowing them to replicate along with the host genome. Furthermore, certain vectors can direct the expression of genes. These vectors are referred to herein as "recombinant expression vectors" (or simply "expression vectors"). In some embodiments, one or more regulatory sequences (e.g., promoters) are included in the expression vector. In some embodiments, nucleic acids operably linked to a nucleotide sequence of a nucleotide sequence are provided herein. The cells transcribe the nucleic acids provided herein, thereby producing the nucleic acids described herein. The nucleic acid molecule is integrated into the genome of the cell to express the antibody, antigen-binding fragment thereof, or peptide. It may be integrated or it may be extrachromosomal.

[0060] In some embodiments, the nucleic acid vectors or recombinant adenoviruses provided herein The sequence encodes one or more epitopes listed in Tables 1, 2, 3 and / or 4. For example, The nucleic acid vector or recombinant adenovirus may contain more than one epitope from the same table (e.g., Table 1). one or more epitopes from Table 1, one or more epitopes from Table 2, one or more epitopes from Table 3 or one or more epitopes from Table 4). Recombinant adenoviruses can contain one or more epitopes from the same table (e.g., Table 1) and one or more epitopes from a different table (e.g., For example, it may consist of one or more epitopes from Table 2). The nucleic acid vectors or recombinant adenoviruses provided herein are those listed in Tables 1, 2, 3 or 4. In addition to the epitopes listed above, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7 , 6, 5, 4, 3, 2 or 1 amino acid or less.

[0061] In some embodiments, the nucleic acid vector comprises a nucleic acid sequence that has been codon optimized. In such an embodiment, the coding sequence is prepared using a method for assembling the coding sequence. The peptide is constructed by changing the codons in each nucleic acid. Methods for identifying nucleotide sequences that optimize codon usage for construction include at least The method also includes the following steps (a) to (e): and an oligomer encoding a portion of a polypeptide containing a degenerate codon for an amino acid. , together with an oligomer extended to provide a contiguous coding sequence with overlapping sequences. In step (b), oligomers are added to cause assembly of the coding sequence of the peptide. The reassembled peptide is then transferred to an expression system operably linked to a regulatory sequence. In step (c), the expression system is cultured in a suitable host cell. In step (d), the transformed host cell is transfected with The colonies are tested for the level of polypeptide production. Obtaining at least one colony from the expression system that exhibits satisfactory polypeptide production The sequence of the portion of the expression system that encodes the protein is determined. Further codon optimization A description is provided in U.S. Patent Application Publication US2010 / 035768, which is incorporated herein by reference in its entirety. Incorporate into the subsection.

[0062] antigen presenting cells In some embodiments, one or more T cell epitopes provided herein (e.g., Table 1, Table 2) are used. , one or more T cell epitopes listed in Table 3 and / or Table 4) (e.g., on HLA) PC is provided herein. In some embodiments, the HLA is class I HLA. In some embodiments, the HLA is a class II HLA. In some embodiments, the class I HLA is an HLA- HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-g, HLA-K, or HLA-L. In some embodiments, the class II HLA is HLA-DMA, HLA-DOA, HLA-DPA, HLA-DQA, or HLA- In some embodiments, the class II HLA has an alpha chain polypeptide that is HLA-DMB. , HLA-DOB, HLA-DPB, HLA-DQB, or HLA-DRB. In morphology, APC is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 , 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36 37 or 38 T cell epitopes (e.g., at least one of those listed in Table 1, Table 2, Table 3 and / or Table 4). At least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, or 39 T cell epitopes).

[0063] In some embodiments, the APC is a B cell, an antigen-presenting T cell, a dendritic cell, or an artificial antigen-presenting cell. Dendritic cells for use in this process are derived from patient samples. BMCs can be prepared by harvesting them and adhering them to plastic. Generally, the monocyte population remains and all other cells can be washed away. The population is differentiated with IL-4 and GM-CSF to produce monocyte-derived dendritic cells. IL-1β, IL-6, PGE-1, and TNF-α (which upregulate important costimulatory molecules on the surface of dendritic cells) and then contacted with a recombinant adenovirus described herein. do.

[0064] In some embodiments, the APC is an artificial antigen-presenting cell, such as aK562 cell. In some embodiments, the artificial antigen-presenting cells express CD80, CD83, 41BB-L, and / or CD86. Examples of artificial antigen-presenting cells, such as aK562 cells, are described in U.S. Pat. No. 2003 / 0147869, which is incorporated herein by reference.

[0065] In certain embodiments, nucleic acid vectors encoding the T cell epitopes described herein and and / or recombinant adenovirus and / or nucleic acid vectors or compositions described herein. contacting an APC with a polyepitope produced by a recombinant adenovirus, Provided herein are methods for generating APCs that present two or more T cell epitopes described herein. In some embodiments, the APCs are irradiated.

[0066] T cells In certain embodiments, the peptides described herein presented on HLA (e.g., Table 1, Table 2, Table 3 and / or an epitope listed in Table 4) (e.g., αβTCR or γδTCR). T cells and T cell populations (e.g., CD4 T cells and / or CD8 T cells) expressing In some embodiments, the T cells are provided with a T cell antigen as described herein that is presented on class I HLA. In some embodiments, the T cells are CD8 T cells (CTLs) that express a TCR that recognizes the peptide. The cells are CD4 T cells (Human lymphocytes) that recognize the peptides described herein presented on class II HLA. Most preferably, the present disclosure provides a method for detecting, for example, a single immune effector (e.g., a T cell). For example, cells that produce only a single biomarker, e.g., a cytokine or CD107a, also for epitopes (e.g., epitopes listed in Table 1, Table 2, Table 3, and / or Table 4). Polyfunctional T cells, i.e., cells with multiple immune effector functions, provide a more effective immune response. The stimulation and proliferation of T cells capable of inducing polyfunctional, monofunctional, or Furthermore, "exhausted" T cells may be unable to mount an immune response during chronic infection or disease states (e.g., cancer). may dominate and thus adversely affect treatment or protection against virus-related complications. The functional competence and activity of such T cells is determined by the expression of transcription factors such as Tb et and Eomes, and / or cytotoxic effector molecules such as perforin and gran By determining the expression pattern of Zyme B (e.g., expression profile by ICS assay), In some embodiments, T-bet, Eomes, perforin, and The expression of each of the granzymes B is determined for the T cells disclosed herein. Such expression levels may be determined and evaluated as relative measurements, e.g., ratios. In a preferred embodiment, the expression profile of T-bet / Eomes and / or Granzyme B / Perforin is In a preferred embodiment, the T cells disclosed herein (e.g., JCV specific Allergic T cells (i.e., T-bet) express high levels of T-bet and low levels of Eomes (i.e., T-bet hi / Eomes low ) and Similarly, the T cells disclosed herein exhibit high expression of granzyme B and low expression of perforin. phenotype (i.e., granzymes) hi / Perforin low ) may be shown. So, T-bet hi / Eomes low and / or granzymes hi / Perforin low Expression profile Identifying T cells (e.g., JCV-specific T cells) as functionally competent and active Such T cells are selected for use and / or expansion in adoptive T cell immunotherapy. Most preferably, the T cells (e.g., JCV-specific T cells) disclosed herein are , multifunctional (i.e., producing two or more cytokines as described herein), and Tb et hi / Eomes low and / or granzymes hi / Perforin low Expression profiles are shown.

[0067] In some embodiments, T cells (e.g., CTLs) that recognize one or more of the epitopes described herein are used. Provided herein are methods for generating, activating and / or inducing proliferation of IL-1, IL-2, and IL-3. In some embodiments, the sample containing CTLs (i.e., a PBMC sample) is a PBMC sample comprising the CTLs described herein. APCs (e.g., those containing the BKV and / or JCV epitopes described herein on their class I HLA complexes) In some embodiments, the cells are incubated in culture with APCs presenting a peptide containing the antigen. In some embodiments, a sample containing T cells may be incubated with the APCs provided herein more than once. In some embodiments, the T cells are induced in the presence of at least one cytokine. In some embodiments, the cytokines are IL-4, IL-7, IL-8, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, IL-19, IL-20, IL-21, IL-22, IL-23, IL-24, IL-25, IL-26, IL and / or IL-15. An exemplary method for inducing T cell proliferation using APCs is, for example, For example, see U.S. Patent Application Publication No. 2015 / 0017723, which is incorporated herein by reference. be absorbed.

[0068] In some embodiments, one or more T cell epitopes (e.g., those listed in Table 1, Table 2, Table 3, and / or Table 4) are included. A population of CTLs collectively containing T cell receptors that recognize one or more of the T cell epitopes listed In some embodiments, the CTLs are selected from the group consisting of CTLs listed in Table 1, Table 2, Table 3, and / or Table 4. In some embodiments, the population of CTLs recognizes two or more T cell epitopes from JCV, BK T cell epitopes derived from any combination of V, EBV, CMV, ADV and / or other viruses In some embodiments, the population of CTLs collectively comprise T cell receptors that recognize at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 2 3, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37 or 38 T cell epitopes at least 1, 2, 3, 4, 5, 6, or 7 T cell epitopes from Table 1, and and / or at least one, two, three, four, or five of the epitopes listed in Table 1, Table 2, Table 3, and / or Table 4. , 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 , 26, 27, 28, 29 or 30).

[0069] In some aspects, the nucleic acid vectors described herein, peptides generated by the CTLs and / or APCs provided herein (e.g., a composition (e.g., a therapeutic composition) comprising the nucleic acid vector described in In a subject, a polyomavirus infection (e.g., JCV) is diagnosed, comprising administering to the subject a composition comprising: infection) or cancer (e.g., polyomavirus-associated cancer, e.g., JVC-associated cancer) In some embodiments, the CTLs and / or APCs are targeted. are not autologous to the elephant (ie, the CTLs and / or APCs are allogeneic to the subject). In some embodiments, the T cells and / or APCs are autologous to the subject. Alternatively, the T cells and / or APCs may be stored in a cell bank before being administered to a subject.

[0070] Pharmaceutical Composition In some embodiments, the compositions described herein are formulated with a pharmaceutically acceptable carrier. Peptides (e.g., peptides containing epitopes from Table 1), nucleic acids, nucleic acid vectors, recombinant antigens, Compositions containing adenoviruses, antibodies, CTLs, or APCs (e.g., pharmaceutical compositions such as vaccine compositions) and the use of such pharmaceutical compositions to treat cancers (e.g., polyomavirus-associated cancers associated with JCV or polyomavirus infection (e.g., JCV, CMV, EBV, or ADV) In some embodiments, the composition comprises a compound selected from the group consisting of benzodiazepines, ... , including combinations of multiple (e.g., two or more) agents provided herein.

[0071] In some embodiments, the pharmaceutical composition further comprises an adjuvant. When used in combination with other compounds, the term "adjuvant" refers to a compound that affects the immunological or physiological response in a patient or subject. For example, adjuvants are agents that act over time or to target a target of interest such as a tumor. Increases the presence of antigens to the affected area, aids in antigen-presenting cell antigen uptake, and promotes macrophage proliferation. It can activate phages and lymphocytes and support cytokine production. By enhancing the immunological activity of the adjuvant, a smaller dose of the immuno-interactive agent can be used for a particular purpose. This may allow for increased efficacy or safety of the amount of immunointeractive agent. Induced by the use of vasodilators, which prevent T cell depletion and therefore improve the efficacy or safety of certain immune interactive agents. Examples of adjuvants include, but are not limited to, immunomodulatory proteins, adjuvants, and the like. Adjuvant 65, α-GalCer, aluminum phosphate, aluminum hydroxide, calcium phosphate β-glucan peptides, CpG oligodeoxynucleotides, non-CpG oligodeoxynucleotides Reotide, GPI-0100, lipid A and its modified forms (e.g., monophosphorylated lipid A), lipopolysaccharide Lipovant, Montanide, N-acetyl-muramyl-L-alanyl- D-Isoglutamine, Pam3CSK4, Quil A, TLR9 agonist, ODN1a, cationic antibody Bacterial peptides (CAMPs) such as KLK, IC31, and trehalose dimycolate.

[0072] Methods for preparing these formulations or compositions include incorporating an agent described herein into a carrier and, optionally, In general, the formulations comprise the agents described herein in combination with one or more accessory ingredients. The mixture is uniformly and intimately associated with liquid carriers, or finely divided solid carriers, or both, and then optionally If necessary, the product may be shaped by extrusion.

[0073] Pharmaceutical compositions of the present invention suitable for parenteral administration may be prepared by administering one or more pharmaceutically acceptable sterile isotonic solutions. aqueous or non-aqueous solution, dispersion, suspension or emulsion, or aseptically prepared immediately before use As described herein, in combination with sterile powders that can be reconstituted into injectable solutions or sterile injectable dispersions. and also includes sugars, alcohols, antioxidants, buffers, bacteriostats, and formulations. Solutes which render the solution isotonic with the blood of the intended recipient, or suspending or thickening agents may be included. Examples of suitable aqueous and non-aqueous carriers that can be used in the pharmaceutical compositions of the present invention include water, ethanol, alcohols, polyols (glycerol, propylene glycol, polyethylene glycol, etc.) vegetable oils (e.g., olive oil), and injectable organic esters (e.g., oleic acid, ethyl methacrylate, methyl ... Suitable fluidity can be achieved by coating with, for example, lecithin. By using lubricating materials, by maintaining the required particle size in the case of dispersions, and by using surfactants. It can be maintained through use.

[0074] Regardless of the chosen route of administration, the drugs of the present invention can be used in a suitable hydrated form. The agent, and / or pharmaceutical composition of the present invention may be prepared in a pharmaceutically acceptable form by conventional methods known to those skilled in the art. It is formulated into an acceptable dosage form.

[0075] Treatment method JCV sequence and / or protein expression has been observed in several malignancies. and immunodeficiency (e.g., immune deficiency, immune dysfunction, and / or is frequently reported in patients with cancer (e.g., immunosuppressed). , polyomavirus-associated cancers, e.g., JCV-associated cancers) or polyomavirus infections (e.g., Methods for treating and / or preventing a viral infection (e.g., a JCV infection) are provided herein. In some embodiments, the methods include the CTLs, APCs, polypeptides and / or nucleic acid molecules described herein. administering the pharmaceutical composition to the subject.

[0076] In some embodiments, the subject being treated is immunocompromised. For example, in some embodiments, In some embodiments, the subject has a T cell deficiency. In some embodiments, the subject has multiple myeloma. In some embodiments, the subject has HIV, sclerosis, psoriasis, and / or other autoimmune diseases. In some embodiments, the subject is infected with a virus and / or has AIDS. or bone marrow transplant. In some embodiments, the subject is undergoing immunosuppressive therapy, e.g., steroid therapy. loids, cytostatics and antiproliferative agents, therapeutic antibodies, calcineurin inhibitors, anti-rejection drugs, etc. or a combination thereof. In some embodiments, the subject has not received chemotherapy. In some embodiments, the subject has had and / or has received radiation therapy. have and / or are undergoing.

[0077] In a preferred embodiment, the subject is diagnosed with a JCV infection in the central nervous system (e.g., a reactivation of a JCV infection). or newly reactivated virus seeding). In embodiments, JCV infection is associated with destruction of oligodendrocytes and / or white matter demyelination. In certain embodiments, the subject is diagnosed with JCV granular cell layer neuropathy (JCV GCN), JCV encephalopathy (JCV CP), N / JCVE), JCV meningitis (JCVM), and / or progressive multifocal leukoencephalopathy (PML), preferably PML. In some such embodiments, the pathogen (e.g., JCV) is present in the cerebrospinal fluid of the subject. It is detectable in

[0078] In some embodiments, the subject has cancer. The methods described can be used to treat any cancerous or precancerous tumor. In some cases, the cancer may be caused by one or more of the polyomavirus epitopes provided herein (e.g., In some embodiments, the BKV / JCV epitopes are expressed in a specific sequence (e.g., BKV / JCV epitopes listed in Tables 1, 2, 3, and / or 4). In some embodiments, the cancer is a JVC-associated cancer. In some embodiments, the cancer comprises a solid tumor. Typically, the cancer is a gastrointestinal malignancy, such as colon cancer, stomach cancer, gastrointestinal tumors, etc. Preferably, the cancer is a CNS malignancy, such as glioma and all its subtypes (e.g., For example, ependymoma, astrocytoma, brainstem glioma, oligodendroglioma, optic nerve glioma, mixed glioma By way of example and not limitation, these include medulloblastoma, primary neuroectodermal tumor, and neuroblastoma. Cancers that can be treated by the methods and compositions provided herein include, but are not limited to: , bladder, blood, bone, bone marrow, brain, breast, colon, esophagus, gastrointestinal tract, gums, head, kidneys, liver, lungs , including cancer cells derived from the nasopharynx, cervix, ovary, prostate, skin, stomach, testicle, tongue, or uterus In addition, the cancer may be of the following histological types, among others, but not limited to: neoplastic, malignant; Carcinoma; carcinoma, undifferentiated; giant cell carcinoma and spindle cell carcinoma, small cell carcinoma, papillary carcinoma, squamous cell carcinoma, lymphoid carcinoma Skin cancer, basal cell carcinoma, hair matrix carcinoma, transitional cell carcinoma, papillary transitional cell carcinoma, adenocarcinoma, gastrin-producing tumor , Malignant; cholangiocarcinoma, hepatocellular carcinoma, combined hepatocellular carcinoma and cholangiocarcinoma, trabecular adenocarcinoma, adenoid cystic carcinoma, adenomatous Adenocarcinoma in polyps, adenocarcinoma, familial colonic polyposis, solid tumors, carcinoid tumors, malignant Gender; bronchioloalveolar adenocarcinoma, papillary adenocarcinoma, chromophobe carcinoma, acidophil carcinoma, eosinophilic carcinoma gonadal carcinoma (oxyphilic 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, appointment Crine gland carcinoma, sebaceous gland carcinoma, ceruminous gland carcinoma, mucoepidermoid carcinoma, cystadenocarcinoma, papillary cystadenocarcinoma, papillary serous sac Cystadenocarcinoma, Mucinous cystadenocarcinoma, Mucinous adenocarcinoma, Signet ring cell carcinoma, Invasive ductal carcinoma, Medullary carcinoma, Lobular carcinoma, Inflammatory Cancer of the breast, Paget's disease of the breast, acinic cell carcinoma, adenosquamous carcinoma, adenocarcinoma with squamous metaplasia, malignant Thymoma, malignant ovarian stromal tumor, malignant theca cell tumor, malignant granulosa cell tumor, malignant androgen-producing tumor Vivimoma, Sertoli cell tumor, malignant Leydig cell tumor, malignant lipocyte tumor, malignant paraganglioma tumor, malignant extramammary paraganglioma, pheochromocytoma, hemangiosarcoma, malignant melanoma, amelanotic melanoma , superficial spreading melanoma, malignant melanoma in giant pigmented nevus, epithelioid cell melanoma, malignant blue melanoma Nevus, sarcoma, fibrosarcoma, malignant fibrous histiocytoma, myxosarcoma, liposarcoma, leiomyosarcoma, striated muscle Sarcoma, embryonal rhabdomyosarcoma, alveolar rhabdomyosarcoma, stromal sarcoma, malignant mixed tumor, mixed Müllerian tumor Tumor, nephroblastoma, hepatoblastoma, carcinosarcoma, malignant mesenchymoma, malignant Brenner tumor, malignant phyllodes tumor, synovial membrane Sarcoma, malignant mesothelioma, dysgerminoma, embryonal carcinoma, malignant teratoma, malignant ovarian goiter, 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, enamel Meloblastic fibrosarcoma, malignant pinealoma, chordoma, malignant glioma, ependymoma, astrocytoma, protozoan Qualitative astrocytoma, fibrous astrocytoma, astroblastoma, glioblastoma, glioblastoma multiforme, pineal Glioblastoma, oligodendroglioma, primitive neuroectodermal, cerebellar fibroblastoma, somatoblastoma tumor, ganglioneuroblastoma, neuroblastoma, retinoblastoma, olfactory neurogenic tumor, malignant meningioma, neuro Fibrosarcoma, malignant schwannoma, malignant granular cell tumor, malignant lymphoma, Hodgkin's disease, Hodgkin's lymphoma granuloma, small lymphocytic lymphoma, diffuse large cell lymphoma, follicular lymphoma lymphoma, mycosis fungoides, other specified non-Hodgkin's lymphoma, malignant histiocytosis, multiple bone marrow ulcers 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 leukemia.

[0079] In some embodiments, the subject also receives an antiviral drug that inhibits replication of the polyomavirus. For example, in some embodiments, the subject is administered ganciclovir, valganciclovir, or Le, foscarnet, cidofovir, acyclovir, formivirsen, maribavir, BAY 38-4766 or GW275175X will be administered.

[0080] In some embodiments, the subject is also administered an immune checkpoint inhibitor. Checkpoint blockade is produced by cancer cells to prevent or downregulate the immune response. It broadly refers to the inhibition of checkpoints that can Examples of proteins include, but are not limited to, CTLA4, PD-1, PD-L1, PD-L2, and A2AR. , B7-H3, B7-H4, BTLA, KIR, LAG3, TIM-3, or VISTA. Checkpoint inhibitors are antibodies or their antibodies that bind to and inhibit immune checkpoint proteins. Examples of immune checkpoint inhibitors include atezolomide, thiazolinone, and thiazolinone. lizumab, avelumab, camrelizumab, cemiplimab, cetrelimab, durvalumab (MEDI-4736), genolimuzumab, ipilimumab, nivolumab, pembrolizumab, pidiri Izumab, sintilimab, spartalizumab, tislelizumab, toripalimab, AMP-224, A MP-514, AK-104, ASP-8374, AUR-012, BCD-135, BGB-A333, BMS-936559, CBT-502, MCLA- 145, KN-046, MGD-019, MK-4830, MSB-0020718C, RG-7446, SL-279252, STI-A1010, STI- These include, but are not limited to, A1110, TSR-042, XmAb20717, and XmAb23104.

[0081] In some embodiments, the compositions provided herein are directed to treating cancer and / or polyomas. The vaccine is administered prophylactically to prevent a viral infection (e.g., a JCV infection). In some embodiments, the composition may be used prior to or after the detection of cancer cells or polyomavirus infected cells in a subject. can be administered later. Thus, in some such embodiments, The compositions provided herein are directed to immunosuppressive therapy (e.g., steroids, cytostatics, and anti-inflammatory drugs). proliferative agents, therapeutic antibodies, calcineurin inhibitors, anti-rejection drugs, etc., or combinations thereof) In some such embodiments, the composition is administered before or after chemotherapy. Similarly, in some embodiments, the composition is administered before or after radiation therapy. In some embodiments, the peptides, nucleic acids, CTLs and / or antibodies described herein are administered. or after administration of a composition comprising APCs, a proinflammatory response is induced. , proinflammatory cytokines and / or chemokines, such as interferon gamma (IFN-γ ) and / or interleukin 2 (IL-2) production.

[0082] Conjunctive therapy is a treatment in which the therapeutic effect of a first drug administered is delayed until a subsequent treatment is administered. Sequential, simultaneous and separate administration of the active compounds in such a way that they are not completely eliminated when In some embodiments, the second agent is co-formulated with the first agent. or may be formulated into separate pharmaceutical compositions.

[0083] In some aspects, the treatments provided herein (e.g., the medicaments provided herein) and administering a composition to the subject to treat polyomavirus infection, JCV infection, and Provided herein are methods for identifying subjects suitable for the treatment of cancer and / or the management of cancer. In some embodiments, the method comprises collecting a sample (e.g., a blood sample, a tissue sample, a tumor sample, and detecting the presence of an epitope listed in Table 1, 2 or 3 in the sample. In some embodiments, the epitope is detected using an ELISA assay, a Western Blot assay, FACS assay, fluorescence microscopy assay, Edman degradation assay and / or are detected using mass spectrometry assays (e.g., protein sequencing). In such embodiments, for example, the presence of a JCV epitope is determined by the presence of a nucleic acid encoding the JCV epitope. In some embodiments, the nucleic acid encoding the JCV epitope is detected. Acids are detected using nucleic acid probes, nucleic acid amplification assays and / or sequencing assays. Notably, the JC virus genome contains sequences necessary for replication (the origin of viral replication). It contains both the ORI (a specific ORI) and sequences required for transcription (several promoters and cis-regulatory elements). It contains two conserved coding regions separated by a highly variable non-coding control region (NCCR) The highly conserved region containing the ORI contains segments a, b, c, d, e, and f. The JC virus found in the CNS of PML patients often contains rearranged NCCR (e.g., absence of b and d sections and duplication of ace sequence) Differences in the NCCR sequence may contribute to viral fitness in the CNS and thus to the development of PML. Thus, a sample (e.g., a blood sample, a urine sample, a tissue sample, a cerebrospinal fluid sample) is obtained from a subject. , tumor samples) and test for the presence of PML-associated JCV sequence rearrangements (e.g., by nucleic acid amplification, such as nested PCR). Identifying subjects suitable for the treatments provided herein, including detecting Such sequences and detection methods are well known in the art. and is known in, for example, L'Honnner et al., PLoS ONE, 13(6), 2018.

[0084] In some embodiments, the method includes determining the HLA type of the subject. In this embodiment, the subject is a subject in which the subject expresses an HLA bound to an epitope provided herein. Some of the compounds are identified as suitable for treatment by the methods provided herein. In embodiments, the methods provided herein further comprise the therapeutic methods provided herein. treating the identified subject using (e.g., a pharmaceutical composition provided herein) In some embodiments, the subject is administered a therapeutic agent as described herein. a composition comprising the CTLs described in claim 1, wherein the CTLs are HLA-restricted to HLA expressed by the subject; In some embodiments, the antibody comprises a TCR that recognizes an epitope provided herein. The subject is administered an epitope provided herein that is HLA-restricted to an HLA expressed by the subject. In some embodiments, the subject is administered a composition comprising a polypeptide comprising: comprising an epitope provided herein that is HLA-restricted to an HLA expressed by the subject A composition comprising an APC that presents the polypeptide is administered. The epitopes provided herein are HLA-restricted to HLA expressed by the subject. A composition comprising a nucleic acid encoding a polypeptide comprising:

[0085] [Example] [Example 1] CD8 against LTA, VP1 and STA JCV antigens + and CD4 + T cell response PBMCs from 17 healthy volunteers were incubated with JVC overlapping peptide pools (OPPs). These cells were cultured for 14 days in the presence of IL-2. and viral protein 1 (VP1), as well as a peptide matrix for each matrix. The composition of the peptide pool for each was arranged as follows:

[0086] TIFF2025160241000007.tif104168

[0087] TIFF2025160241000008.tif65155

[0088] TIFF2025160241000009.tif53149

[0089] On day 14, these T cell cultures were analyzed for JVC-specific cytokines using an intracellular cytokine (ICS) assay. Notably, in vitro culture of T cells with JVC peptide for 14 days significantly increased the These initial analyses demonstrated that T cell responses were related to LTA, V, and It was clearly shown to be directed towards P1 and STA (see Figure 1).

[0090] [Example 2] JCV epitope HLA restriction To precisely map HLA class I and class II restricted T cell responses, T cell epitopes were identified. For peptide mapping, individual overlapping peptides (15 amino acids) for LTA, STA, and VP1 proteins were analyzed. A two-dimensional peptide matrix was used to identify all the Individual peptides were distributed into small overlapping peptide pools. For example, in the case of the large T antigen, The tricks are arranged so that each peptide in the pool (LTA1–LTA24) appears once on the ordinate. The T cell responses for each pool were analyzed using intracellular cytokine staining (ICS) IF. The data were measured by N-γ assay (see Figure 2A) and displayed on a two-dimensional matrix as follows: Stacked.

[0091] TIFF2025160241000010.tif99159

[0092] Thus, individual peptides common among pools that elicited T cell responses, i.e., row L Peptide 32 (P32) at the intersection of row LTA4 with column LTA16, and at the intersection of row LTA3 with columns LTA23 and LTA24 Peptides P29 and P30 were identified at the nucleus. Fluorescence-activated cell sorting (FACS) was used to identify the individual peptides. We confirm that the peptides P29, P30, and P32 induce JCV-specific T cell responses (see Figure 2B).

[0093] These individual peptides were further evaluated for T cell proliferation and ICS analysis to identify potential JC The V antigen was identified, and the resulting peptides showed high HLA allele coverage for JCV. (See Figure 3 and Table 5.)

[0094] [Table 5]

[0095] [Example 3] JCV-specific T cell expansion and characterization JCV-specific T cells were expanded in vitro after stimulation with pooled JCV epitopes. Specifically, PBMCs from healthy volunteers were stimulated with synthetic JCV peptides (Table 1) for 1 hour, followed by IL-2 (10 ng / ml), IL-7 (10 ng / ml), IL-12 (10 ng / ml) and / or IL-15 (10 ng / ml) were administered. The expanded T cells were cultured for 12–14 days in the presence of a combination of cytokines. , assessed using standard intracellular cytokine assays (Table 6).

[0096] [Table 6]

[0097] [Example 4] T cell cross-reactivity between JCV and BKV epitopes Peptide-specific T cells were stimulated with JCV or BKV epitopes in vitro. and then restimulated with the corresponding homologous peptide epitopes (see Table 2), resulting in the JCV epitopes. Any cross-reactive responses between the IgG and BKV epitopes were observed. PBMCs from subjects were cultured with the synthetic JCV peptide epitope RSGSQQWRGLSRYFK or the synthetic BKV peptide epitope RSGSQQWRGLSRYFK. After initial growth, each sample was incubated with the JCV epitope RSGSQQ. Re-stimulation (recall) was performed with either WRGLSRYFK or the BKV epitope SSGTQQWRGLARYFK (herein (A sample recalled with the same epitope acts as an internal control). Expanded T cells The responsiveness of the homologous ( T cells expanded with either the BKV or JCV peptide sequences were expressed in the presence of either the BKV or JCV homolgous epitope. Recognize.

[0098] [Example 5] Profile of functional and phenotypic characteristics of JCV-specific T cells in healthy individuals and transplant recipients Profiling Recently, T-box transcription factor (T-bet) and Eomesodermin (Eomes) have been shown to mediate CD8 + T cell fate High levels of T-bet have been shown to play an important role in the determination of cytotoxic T cells. Associated with differentiation and upregulation of perforin and granzyme B in antigen-specific cells High levels of Eomes are associated with long-term memory formation. It has been shown that the coordinated expression of these genes is important for infection control. It has also been shown that the loss of either transcription factor results in a failure to suppress infection. Therefore, we aim to clarify the phenotypic characterization of T cells and the understanding of T cell differentiation during both acute and chronic viral infections. It is important to study the expression of these transcription factors, which may help to resolve the JCV-specific The expression patterns of T-bet and Eomes in target T cells are still unknown, and such T cells Analysis of these transcription factors will enable a deeper understanding of JCV-specific T cell differentiation. Detailed studies of the functional characteristics of T cells may also contribute to the development of effective immunity against JCV-associated diseases. This could lead to the development of immunotherapy. An early series of experiments showed that T cells regulate their differentiation. We are investigating the expression of transcription factors T-bet, Eomes, perforin, and granzyme B. , assayed for JCV-specific T cells and CMV-specific T cells using ICS. Initial analysis found moderate to low levels of T bet expression in JCV-specific T cells, whereas CMV-specific We show that high levels of T-bet are found in T cells compared with CMV-specific T cells. In JCV-specific T cells, very low Eomes expression is found. Folin and granzyme B are also found on JCV-specific T cells, which is consistent with CMV-specific T cells. This suggests that JCV-specific T cells are functionally inferior in effector function compared with non-JCV-specific T cells. Therefore, driving the effector function of JCV-specific CTLs is essential for effective adoptive T cell immunity. It will be the focus of research that will contribute to the development of immunotherapy.

[0099] [Example 6] Feasibility of T cell expansion with the proposed peptide pool PBMCs from 15 healthy donors were randomly selected regardless of their HLA type and analyzed as described herein. The peptides disclosed in the document (i.e., peptides containing the amino acid sequences set forth in SEQ ID NOs: 1 to 21) Stimulation with a peptide pool containing IgG1 (IgG1-specific IgG1) resulted in proliferation of JCV-specific T cells. T cells were expanded for 17 days. The 15 donors were then evaluated for JCV responses using an intracellular cytokine staining assay. T cells from 13 of these individuals were resistant to IFN-γ production upon restimulation with a peptide pool. The mice had a JCV-specific T cell response (see Figure 5).

[0100] [Example 7] Functional characterization of JCV-specific T cell products To determine the polyfunctionality of JCV-specific T cells expanded using peptide pools, T Cells were analyzed for expression of IL-2, TNF, IFN-γ, and CD107 by intracellular staining (Figure 6 JCV-specific T cells showed higher expression of TNF along with other cytokines.

[0101] Boolean analysis of the expression patterns of different cytokine combinations revealed JCV-specific We demonstrated that the T cell product was polyfunctional and produced two or more cytokines (Figure 6 To further characterize JCV-specific T cell products, transcription factors (T-bet and Eom) were analyzed. es) and expression of effector molecules (perforin and granzyme B). T-bet hi / Eomes low and granzymes hi / Perforin low profile, which JCV-specific T cells are functionally active and exhibit cytotoxic effects against JCV-infected cells. Such T cells can be expanded in vitro. , can be used to treat JCV-associated diseases (see Figure 7).

Claims

1. A peptide comprising one or more of the epitopes listed in Tables 1-4.

2. Claim 1, wherein the one or more epitopes include a JC virus (JCV) epitope listed in Table 1. The peptide according to claim 1.

3. 1 or 2, wherein the one or more epitopes comprise JCV epitopes set forth in SEQ ID NOs: 1 to 21. is a peptide described in 2.

4. One or more epitopes may be JC virus (JCV) epitopes listed in Table 2 and / or Table 3. The peptide of claim 1, comprising:

5. 10. The method of claim 1, wherein the one or more epitopes comprise a hybrid epitope according to Table 4. peptide.

6. 6. The peptide of claim 1, wherein the peptide comprises multiple epitopes listed in Tables 1 to 4. The peptide described.

7. 7. The method of claim 6, wherein the plurality of epitopes comprises a plurality of JCV epitopes listed in Table 1. peptide.

8. Claim 1, wherein the plurality of epitopes comprises a plurality of JCV epitopes set forth in SEQ ID NOS: 1-21.

7. The peptide according to claim 7.

9. The plurality of epitopes comprises a plurality of JCV epitopes listed in Table 2 and / or Table 3. Item 6. The peptide according to Item 5.

10. Multiple epitopes are included, including the JVC epitopes listed in Table 1 and the epitopes listed in Table 2 and / or Table 3.

7. The peptide of claim 6, comprising a selected JCV epitope.

11. and further comprising an intervening amino acid sequence between at least two of the plurality of epitopes. Item 11. The peptide according to any one of Items 6 to 10.

12. Any of claims 1 to 11, wherein the peptide is capable of inducing an immune response upon administration to a subject. The peptide according to any one of claims 1 to 4.

13. Claims 1-1, wherein the epitopes are selected to provide broad coverage in the human population 3. A peptide according to any one of claims 2.

14. The epitope is HLA class II restricted to HLA-DP, -DM, -DOA, -DOB, -DQ, or -DR.

14. The peptide of claim 13, comprising:

15. 15. The epitope of claim 14, wherein the epitope is HLA class II restricted to HLA-DRB or -DQB. peptides.

16. 16. The method of claim 1, comprising the epitope amino acid sequences set forth in SEQ ID NOs: 1 to 21. The peptide according to any one of claims 1 to 4.

17. 17. The method of claim 1, wherein the antigen-binding fragment essentially consists of the epitope amino acid sequence set forth in SEQ ID NOs: 1 to 21. The peptide according to any one of claims 1 to 4.

18. The peptides according to claims 1 to 21 consist of the epitope amino acid sequences set forth in SEQ ID NOs: 1 to 21.

18. A peptide according to any one of claims 17.

19. The peptide further comprises one or more epitopes derived from Merkel cell virus (MCV). The peptide according to any one of claims 1 to 18.

20. 20. The method of claim 1, further comprising one or more epitopes derived from a non-polyoma virus.

3. The peptide according to claim 1.

21. One or more epitopes from non-polyoma viruses are included in the adenovirus (ADV), Epstein-Barr virus (EPV), and HIV-1. Contains one or more epitopes derived from EBV or cytomegalovirus (CMV). The peptide of claim 20.

22. 22. An isolated nucleic acid encoding the peptide of any one of claims 1 to 21.

23. 23. An expression construct comprising the isolated nucleic acid of claim 22.

24. 24. A host cell comprising the expression construct of claim 23.

25. 25. Expressing the peptide in a host cell according to claim 24, and 2. A method for producing a peptide comprising at least partially purifying the peptide.

26. A pharmaceutical composition comprising the peptide of any one of claims 1 to 21 and a pharmaceutically acceptable carrier. Pharmaceutical composition.

27. 23. A pharmaceutical composition comprising the isolated nucleic acid of claim 22.

28. A vaccine comprising the peptide of any one of claims 1 to 21 and a pharmaceutically acceptable carrier. Cutin composition.

29. 29. The vaccine composition of claim 28, further comprising an adjuvant.

30. A pharmaceutical composition according to claim 26 or 27 or a vaccine composition according to claim 28 or 29. A method for treating or preventing a polyomavirus infection in a subject, comprising administering to the subject a compound ... How to do it.

31. 30. The method of claim 29, wherein the polyomavirus infection is a JC virus (JCV) infection.

32. The subjects are JCV granular cell layer neuropathy (JCV GCN), JCV encephalopathy (JCVE), and JCV meningitis (JCVM).

32. The method of claim 30 or 31, wherein the patient is suffering from progressive multifocal leukoencephalopathy (PML).

33. A pharmaceutical composition according to claim 26 or 27 or a vaccine composition according to claim 28 or 29. and administering to the subject a compound comprising the steps of: How to prevent it.

34. 34. The method of claim 33, wherein the polyomavirus-associated cancer is a JCV-associated cancer.

35. Polyomavirus-associated cancers include gastrointestinal malignancies, e.g., colon cancer, stomach cancer, and / or or a gastrointestinal tumor.

36. Polyomavirus-associated cancers include central nervous system (CNS) malignancies, such as gliomas and medulloblastomas.

35. The method of claim 33 or 34, wherein the tumor is a primary neuroectodermal tumor, a primary neuroectodermal tumor and / or a neuroblastoma.

37. A pharmaceutical composition according to claim 26 or 27 or a vaccine composition according to claim 28 or 29. A method of inducing a T cell immune response in a subject, comprising administering to the subject an

38. HLA class I and / or class II restriction can induce peptide-specific T cell proliferation The epitope amino acid sequences of SEQ ID NOs: 1 to 21 are included in the JCV peptide epitopes. A pool of immunogenic peptides comprising at least one or a combination thereof.

39. At least one of the JCV peptide epitope amino acid sequences listed in Table 1 or a combination thereof 39. The pool of immunogenic peptides of claim 38, further comprising a combination of:

40. A vaccine comprising each of the JCV peptide epitope amino acid sequences set forth in SEQ ID NOs: 1 to 21.

40. A pool of immunogenic peptides according to claim 38 or 39.

41. The epitope is HLA class II restricted to HLA-DP, -DM, -DOA, -DOB, -DQ, or -DR.

41. A pool of immunogenic peptides according to any one of claims 38 to 40, comprising:

42. 42. The method of claim 41, wherein the epitope is HLA class II restricted to HLA-DRB or -DQB. A pool of immunogenic peptides.

43. The epitopes are DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*10:01, and DRB1*1 1:01, DRB1*13:01, DRB1*14:04, DRB1*15:01, DRB1*16:01, DQB1*02:02 or DQB1*05:03 Any one of claims 38 to 42 is bound by any one of the HLA specificities selected from A pool of immunogenic peptides according to any one of claims 1 to 4.

44. Claims 38-43, wherein the peptide-specific T cells exhibit a polyfunctional immune effector profile. A pool of immunogenic peptides according to any one of claims 1 to 4.

45. Immunogenic peptides can induce the proliferation of peptide-specific cytotoxic T lymphocytes (CTLs). A pool of immunogenic peptides according to any one of claims 38 to 44.

46. Peptide-specific cytotoxic T cells (CTLs) display a polyfunctional immune effector profile 46. ​​The pool of immunogenic peptides according to claim 45.

47. 1. A method of expanding JC virus-specific T cells for adoptive immunotherapy, comprising: (i) treating one or more cells isolated from a subject with a peptide according to any one of claims 1 to 21; or contacting with a pool of immunogenic peptides according to any one of claims 38 to 46; and (ii) growing JC virus-specific T cells from said one or more cells under conditions such that JC virus-specific T cells proliferate from said one or more cells; Culturing the above cells A method comprising:

48. The peptide or pool of immunogenic peptides is a JCV peptide epitope set forth in SEQ ID NOs: 1-21.

48. The method of claim 47, consisting essentially of each of the top amino acid sequences.

49. The one or more cells isolated from the subject may include peripheral blood mononuclear cells (PBMCs) from a healthy donor.

47. The method of claim 46.

50. 47. The method of claim 47, wherein the one or more cells isolated from the subject comprise PBMCs from an immunocompromised donor. is the method described in 46.

51. 51. The method of claim 50, wherein the donor is undergoing immunosuppressive therapy.

52. 52. The method of claim 50 or 51, wherein the donor is an organ transplant recipient. 。

53. 53. The method according to any one of claims 50 to 52, wherein the donor is a donor undergoing antiviral therapy. The method described.

54. Claim 47. The JC virus-specific T cells exhibit a polyfunctional immune effector profile.

54. A method according to any one of claims 1 to 53.

55. The method further comprises administering JC virus-specific T cells to a subject suffering from a JCV infection.

55. The method of any one of claims 47 to 54.

56. Administering the JC virus-specific T cells according to any one of claims 47 to 54 to a subject. A method of treating or preventing a JCV infection in a subject, comprising:

57. A CTL prepared by the method of any one of claims 47 to 54.

58. A method for treating or preventing JCV infection in a subject, comprising administering to the subject the CTL of claim 57. How to prevent it.

59. Exposure to an immunogenic peptide or a pool of immunogenic peptides induces JCV peptide-specific T cells.

59. The method of claim 58, wherein the method induces stimulation and proliferation of

60. 59. The method of claim 58, wherein the CTLs administered to the subject are autologous.

61. 59. The method of claim 58, wherein the CTLs administered to the subject are not autologous.

62. 62. The method of any one of claims 56 to 61, wherein the infection is a recurrent JCV infection.

63. 63. The method of any one of claims 56 to 62, wherein the JCV infection is drug resistant.

64. 64. The method of any one of claims 56 to 63, wherein the subject is an organ transplant recipient.

65. The subjects are JCV granular cell layer neuropathy (JCV GCN), JCV encephalopathy (JCVE), and JCV meningitis (JCVM). and / or progressive multifocal leukoencephalopathy (PML). How to post.

66. Targeting the expanded JC virus-specific T lymphocytes according to any one of claims 45 to 54 - A method for treating or preventing polyomavirus-associated cancer in a subject, comprising administering 。

67. 67. The method of claim 66, wherein the polyomavirus-associated cancer is a JCV-associated cancer.

68. A method of contacting T lymphocytes isolated from a subject with a peptide according to any one of claims 1 to 21. detecting the presence of JCV-specific T lymphocytes in a subject by administering a How to detect a virus infection.

69. The method further comprises detecting JCV-specific DNA in a sample of cerebrospinal fluid isolated from the subject. The method of claim 68.

70. JCV-specific DNA is characterized by the absence of sequences b and d in the non-coding control region (NCCR) and the overlap of sequence ace.

70. The method of claim 69, comprising:

71. Any one of the epitope amino acid sequences set forth in SEQ ID NOs: 1 to 21 or a combination thereof and administering to the subject an adoptive immunotherapy composition comprising JC virus-specific T cells that target the JC virus. The method of any one of claims 68 to 70, further comprising:

72. 72. The method of any one of claims 30 to 37 or 47 to 71, wherein the subject is a mammal.

73. 73. The method of claim 72, wherein the subject is a human.

74. 74. The method of claim 72 or 73, wherein the subject is immunocompromised.

75. Cytotoxicity involving a T cell receptor (TCR) that recognizes one or more epitopes listed in Tables 1-4 and administering to the subject a pharmaceutical composition comprising cytotoxic T cells (CTLs). is a way to prevent it.

76. Claim 7, wherein the one or more epitopes include a JC virus (JCV) epitope listed in Table 1.

5. The method described in 5.

77. One or more epitopes include JC virus (JCV) epitopes set forth in SEQ ID NOs: 1-21. The method of claim 75.

78. One or more epitopes may be JC virus (JCV) epitopes listed in Table 2 and / or Table 3.

77. The method of claim 75 or 76, comprising:

79. Claims 76 to 78, wherein the one or more epitopes include a hybrid epitope as set forth in Table 4.

78. The method of any one of claims 78 to 78.

80. 80. The method of any one of claims 76 to 79, wherein the cancer is a polyomavirus-associated cancer. 。

81. 81. The method of claim 80, wherein the polyomavirus is JC virus (JCV).

82. Polyomavirus-associated cancers include gastrointestinal malignancies, e.g., colon cancer, stomach cancer, and / or or a gastrointestinal tumor.

83. Polyomavirus-associated cancers include central nervous system (CNS) malignancies, such as gliomas and medulloblastomas.

82. The method of claim 80 or 81, wherein the tumor is a primary neuroectodermal tumor, a primary neuroectodermal tumor and / or a neuroblastoma.

84. Cytotoxicity involving a T cell receptor (TCR) that recognizes one or more epitopes listed in Tables 1-4 and administering to the subject a pharmaceutical composition comprising cytotoxic T cells (CTLs). A method for treating or preventing viral infections.

85. Claim 8, wherein the one or more epitopes comprise a JC virus (JCV) epitope listed in Table 1.

4. The method described in 4.

86. One or more epitopes include JC virus (JCV) epitopes set forth in SEQ ID NOs: 1-21. The method of claim 85.

87. One or more epitopes may be JC virus (JCV) epitopes listed in Table 2 and / or Table 3.

87. The method of any one of claims 84 to 86, comprising:

88. Claims 84 to 88, wherein the one or more epitopes include a hybrid epitope as set forth in Table 4.

87. A method according to any one of claims 87 to 87.

89. 89. The method of claim 84, wherein the polyomavirus is JC virus (JCV). method.

90. Any one of claims 75 to 89, wherein at least one of the TCRs recognizes a VP1 epitope from JCV. The method described in paragraph .

91. Any one of claims 75 to 90, wherein at least one of the TCRs recognizes an LTA epitope from JCV. The method described in paragraph .

92. Any one of claims 75 to 91, wherein at least one of the TCRs recognizes a STA epitope from JCV. The method described in paragraph .

93. CTLs collect TCRs that recognize at least two of the epitopes set forth in SEQ ID NOs: 1 to 21.

93. The method of any one of claims 75 to 92, comprising

94. CTLs are collected from TCRs that recognize at least five of the epitopes set forth in SEQ ID NOs: 1 to 21.

94. The method of claim 93, wherein the method comprises:

95. CTLs containing TCRs that recognize at least 10 of the epitopes set forth in SEQ ID NOs: 1 to 21.

95. The method of claim 94, collectively comprising:

96. The CTLs collectively comprise TCRs that recognize each of the epitopes set forth in SEQ ID NOS: 1-21.

96. The method of claim 95.

97. Claim 75: The TCR collectively recognizes epitopes from at least two different viruses.

96. The method of any one of claims 1 to 96.

98. Claim 97, wherein the TCR collectively recognizes epitopes from at least three different viruses. The method described below.

99. Claim 98, wherein the TCR collectively recognizes epitopes from at least four different viruses. The method described below.

100. Claim 99: The TCR collectively recognizes epitopes from at least five different viruses. The method described below.

101. Claim 75: The TCRs collectively recognize one or more epitopes from non-polyoma viruses.

101. The method of any one of claims 1 to 100.

102. One or more epitopes from non-polyoma viruses are included in the adenovirus (ADV), Epstein-Barr virus (EPV), and HIV-1. Contains one or more epitopes derived from EBV or cytomegalovirus (CMV). The method of claim 101.

103. the subject expresses a human leukocyte antigen (HLA) to which the one or more epitopes are restricted; 103. The method of any one of claims 75 to 102.

104. The method of any one of claims 75 to 103, wherein the CTLs are autologous to the subject.

105. The method of any one of claims 75 to 103, wherein the CTLs are not autologous to the subject.

106. The method of claim 105, wherein the CTL is obtained from a CTL library or bank.

107. 107. The method of any one of claims 75 to 106, wherein the subject is immunocompromised.

108. 108. The method of claim 75, wherein the CTLs exhibit a polyfunctional immune effector profile. The method described.

109. One or more polyomavirus peptides containing any one of the epitopes listed in Tables 1-4. Polyomavirus-specific immunoglobulins (CTLs) are produced by contacting CTLs with antigen-presenting cells (APCs) that present the CTLs with CTLs. A method for inducing proliferation of allergic cytotoxic T cells (CTL).

110. Claim 109: One or more peptides comprise a JC virus (JCV) epitope listed in Table 1. The method described below.

111. One or more peptides are selected from any one of SEQ ID NOs: 1 to 21.

111. The method of claim 110, comprising a pitope.

112. One or more peptides contain a JC virus (JCV) epitope listed in Table 2 and / or Table 3. The method of any one of claims 109 to 111.

113. Claims 109-1, wherein one or more peptides comprise a hybrid epitope as set forth in Table 4.

13. The method of any one of claims 12.

114. The method of any one of claims 109 to 113, wherein the CTLs are contacted with APCs in vitro.

115. The one or more peptides comprise one or more epitopes derived from a non-polyoma virus.

115. The method according to any one of paragraphs 109 to 114.

116. One or more peptides derived from non-polyoma viruses are used to express the peptides of adenovirus (ADV), Epstein-Barr virus (EBV), and HIV-1. Contains one or more epitopes derived from Epstein-Barr virus (EBV) or cytomegalovirus (CMV) 116. The method of claim 115.

117. Any of claims 109-116, wherein the CTL is contacted with the APC in the presence of one or more cytokines.

10. The method according to claim 1.

118. The method of any one of claims 109 to 117, wherein the APC comprises a B cell.

119. 119. The method of any one of claims 109 to 118, wherein the APC comprises an antigen-presenting T cell.

120. 120. The method of any one of claims 109 to 119, wherein the APC comprises a dendritic cell.

121. The method of any one of claims 109 to 120, wherein the APCs comprise aK562 cells.

122. 122. The method of claim 109, wherein the CTLs are derived from a sample of peripheral blood mononuclear cells (PBMCs). method.

123. Polyomavirus-specific cytotoxic T cells are stored in a CTL library or bank. The method of any one of claims 109 to 122.

124. Polyomavirus-specific cytotoxic T cells exhibit a multifunctional immune effector profile The method according to any one of claims 109 to 123, wherein

125. administering to a subject a vaccine composition comprising one or more epitopes listed in Tables 1-4 10. A method for treating or preventing cancer in a subject, comprising:

126. Claim 1, wherein the one or more epitopes include a JC virus (JVC) epitope listed in Table 1.

25. The method described in

127. One or more epitopes include JC virus (JVC) epitopes set forth in SEQ ID NOs: 1-21. The method of claim 126.

128. One or more epitopes may be JC virus (JCV) epitopes listed in Table 2 and / or Table 3.

128. The method of any one of claims 125 or 127, comprising:

129. Claim 125: One or more epitopes include a hybrid epitope set forth in Table 4 19. The method of any one of claims 1 to 128.

130. The method according to any one of claims 125 to 129, wherein the cancer is a polyomavirus-associated cancer. Law.

131. Polyomavirus-associated cancers include gastrointestinal malignancies, e.g., colon cancer, stomach cancer, and / or or a gastrointestinal tumor.

132. Polyomavirus-associated cancers include central nervous system (CNS) malignancies, such as gliomas and medulloblastomas.

131. The method of claim 130, wherein the tumor is a primary neuroectodermal tumor, a primary neuroectodermal tumor and / or a neuroblastoma.

133. 133. The method of any one of claims 130 to 132, wherein the polyomavirus is JC virus (JCV). How to do it.

134. administering to a subject a vaccine composition comprising one or more epitopes listed in Tables 1-4 10. A method of treating or preventing polyomavirus infection in a subject, comprising:

135. Claim 1, wherein the one or more epitopes include a JC virus (JCV) epitope listed in Table 1.

34. The method according to claim 34.

136. One or more epitopes include JC virus (JCV) epitopes set forth in SEQ ID NOs: 1-21. The method of claim 135.

137. One or more epitopes may be JC virus (JCV) epitopes listed in Table 2 and / or Table 3.

137. The method of any one of claims 134 to 136, comprising:

138. Claim 134, wherein the one or more epitopes comprise a hybrid epitope set forth in Table 4 138. The method of any one of claims 1 to 137.

139. 139. The method of any one of claims 134 to 138, wherein the polyomavirus is JC virus (JCV). How to do it.

140. the vaccine composition further comprises one or more epitopes from a non-polyoma virus; 140. The method of any one of claims 125 to 139.

141. One or more epitopes from non-polyoma viruses are included in the adenovirus (ADV), Epstein-Barr virus (EPV), and HIV-1. Contains one or more epitopes derived from EBV or cytomegalovirus (CMV). The method of claim 140.

142. The one or more epitopes are selected from at least two of the epitopes set forth in SEQ ID NOs: 1 to 21.

142. The method of any one of claims 125 to 141, comprising:

143. One or more epitopes are selected from at least five of the epitopes set forth in SEQ ID NOs: 1-21.

143. The method of claim 142, comprising:

144. One or more epitopes are selected from at least 10 of the epitopes set forth in SEQ ID NOs: 1-21.

144. The method of claim 143, comprising:

145. The one or more epitopes are selected from at least each of the epitopes set forth in SEQ ID NOs: 1-21.

145. The method of claim 144, comprising:

146. the subject expresses a human leukocyte antigen (HLA) to which the one or more epitopes are restricted; 146. The method of any one of claims 125 to 145.

147. 147. The vaccine composition of any one of claims 125 to 146, wherein the vaccine composition further comprises an adjuvant. method.

148. Any one of claims 125-147, wherein the subject is immunodeficient, immunologically impaired, or immunocompromised. The method described in paragraph .

149. The method of any one of claims 75 to 148, wherein the subject is a human.

150. 48. The method of claim 47, wherein the cells are cultured in the presence of IL-2.

151. 151. The method of claim 150, wherein IL-2 is present at a concentration of about 120 IU / ml.

152. The method of any one of claims 109 to 123, further comprising culturing the CTL in the presence of IL-2. How to post.

153. 153. The method of claim 152, wherein IL-2 is present at a concentration of about 120 IU / ml.

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