Novel peptides and combination of peptides for use in immunotherapy against hepatocellular carcinoma (hcc) and other cancers

Abstract

The present invention relates to peptides, proteins, nucleic acids and cells for use in immunotherapeutic methods. In particular, the present invention relates to the immunotherapy of cancer. The present invention furthermore relates to tumor-associated T-cell peptide epitopes, alone or in combination with other tumor-associated peptides that can for example serve as active pharmaceutical ingredients of vaccine compositions that stimulate anti-tumor immune responses, or to stimulate T cells ex vivo and transfer into patients. Peptides bound to molecules of the major histocompatibility complex (MHC), or peptides as such, can also be targets of antibodies, soluble T-cell receptors, and other binding molecules. In particular, the present invention relates to several novel peptide sequences and their variants derived from HLA class I and class II molecules of human tumor cells that can be used in vaccine compositions for eliciting anti-tumor immune responses or as targets for the development of pharmaceutically/immunologically active compounds and cells.

1 . A product comprising a peptide comprising an amino acid sequence of SEQ ID 303, and/or a variant sequence thereof which is at least 88% homologous to SEQ ID No. 303, and wherein said variant binds to MHC and/or induces T cells cross-reacting with said variant peptide; wherein the product is in the form of a pharmaceutical acceptable salt of said peptide or variant, wherein said peptide or variant is not a full-length polypeptide and further wherein said peptide or variant is optionally modified and/or includes non-peptide bonds. 
     
     
         2 . The product according to  claim 1 , wherein said peptide has the ability to bind to a molecule of the human major histocompatibility complex (MHC) class-I or -II, and wherein said peptide, when bound to MHC, is capable of being recognized by CD4 and/or CD8 T cells. 
     
     
         3 . The product according to  claim 1 , wherein the amino acid sequence thereof comprises a continuous stretch of amino acids according SEQ ID No. 303. 
     
     
         4 . The product according to  claim 1 , wherein said peptide or variant has an overall length of from 8 to 100, optionally from 8 to 30, and optionally from 8 to 16 amino acids, and optionally wherein the peptide consists or consists essentially of an amino acid sequence according to SEQ ID 303. 
     
     
         5 . The product according to any of  claim 1 , wherein said peptide is modified and/or includes non-peptide bonds. 
     
     
         6 . The product according to  claim 1 , wherein said peptide is part of a fusion protein, optionally comprising N-terminal amino acids of the HLA-DR antigen-associated invariant chain (Ii). 
     
     
         7 . A nucleic acid, encoding a peptide or variant of the product according to  claim 1 , optionally linked to a heterologous promoter sequence. 
     
     
         8 . An expression vector capable of expressing the nucleic acid according to  claim 7 . 
     
     
         9 . The product according to  claim 1 , capable of being used in medicine. 
     
     
         10 . A host cell comprising the product according to  claim 1 , wherein said host cell optionally is an antigen presenting cell optionally comprising a dendritic cell. 
     
     
         11 . A method for producing the peptide or variant of the product according to  claim 1 , the method comprising culturing a host cell that presents the peptide or variant thereof, and isolating the peptide or variant from the host cell or a culture medium. 
     
     
         12 . An in vitro method for producing activated T lymphocytes, the method comprising contacting in vitro one or more T cells with antigen loaded human class I or II MHC molecules expressed on the surface of a suitable antigen-presenting cell or an artificial construct mimicking an antigen-presenting cell for a period of time sufficient to activate said T cells in an antigen specific manner, wherein said antigen is a peptide or variant of the product according to  claim 1 . 
     
     
         13 . An activated T cell, produced by the method according to  claim 12 , that selectively recognizes a cell which presents a polypeptide comprising an amino acid sequence that is at least 88% homologous to SEQ ID No. 303. 
     
     
         14 . A method for killing target cells in a patient which target cells present a polypeptide comprising an amino acid sequence sequence that is at least 88% homologous to SEQ ID No. 303, the method comprising administering to the patient an effective number of activated T cells as defined in  claim 13 . 
     
     
         15 . An antibody, soluble or membrane-bound, that specifically recognizes the peptide or variant of the product according to  claim 1 , optionally the peptide or variant is bound to an MHC molecule and optionally the antibody carries a further effector function optionally comprising an immune stimulating domain or toxin. 
     
     
         16 . A product according to  claim 1  capable of being used for treatment of cancer and/or in the manufacture of a medicament against cancer. 
     
     
         17 . The product according to  claim 16 , wherein said cancer is selected from the group of HCC, brain cancer, kidney cancer, pancreatic cancer, colon or rectal cancer or leukemia and other tumors that show an overexpression of optionally APOB, FASN, COPA, optionally GLUL, GPAM, PLIN2, SLC16A1, SLC9A3R1, PCBD1, SEC16A, AKR1C4, ABCB11, HAL, CYP2E1, C4A, C4B, ALDH1L1, CRP, ACSL4, EEF2, HLTF, FBXO22, GALK1, TMCO1, TMEM33, ZNF318, IP09, AMACR, C1QTNF3, CYP4F8, CYP4F3, CYP4F11, CYP4F12, CYP4F2, MOCOS, A1CF, COL18A1, HPR, LBP, C19orf80, CFHR5, ITIH4, TMEM110, LARP4, LMF2, SLC10A5, SLC16A11, and optionally ANKFY1, C12orf44, C16orf58, CPSF1, DCAF8, PEX19, DDX11, DDX12P, DECR2, NME4, DENND5B, DYM, EDC4, ERI3, FAM20A, FNDC3A, GPR107, GYG2, HEATR2, IFT81, KCTD3, SHKBP1, KIAA1324L, KLHL24, MARCH6, MBTPS2, MIR1279, CPSF6, NOC4L, NXF1, PANK2, PCNXL3, PIPSL, PSMD4, PSMD14, SLC35B1, TCP11L2, THNSL2, THOC2, TOMM5, TRAPPC6B, TRIM54, TRIM55, TRIM63, UGGT2, URB1, VPS54, WIZ, ZNF45, RFTN2, SCFD1, SERINC5, CCT7P2, CMAS, ANKS1A, C17orf70, CCT7, CDK5RAP2, CLPTM1, and another protein from which a peptide SEQ ID No. 303 is derived from. 
     
     
         18 . A kit comprising:
 (a) a container comprising a pharmaceutical composition containing the product according to  claim 1  in solution or in lyophilized form;   (b) optionally, a second container containing a diluent or reconstituting solution for the lyophilized formulation;   (c) optionally, at least one more peptide selected from the group consisting of SEQ ID No. 1 to SEQ ID No. 346, and   (d) optionally, instructions for (i) use of the solution or (ii) reconstitution and/or use of the lyophilized formulation.   
     
     
         19 . The kit according to  claim 18 , further comprising one or more of (iii) a buffer, (iv) a diluent, (v) a filter, (vi) a needle, or (v) a syringe. 
     
     
         20 . The kit according to  claim 18 , wherein said product consists essentially of SEQ ID No. 303. 
     
     
         21 . A method for producing a personalized anti-cancer vaccine for a compound-based and/or cellular therapy for an individual patient using a product of  claim 1 , said method comprising:
 a) identifying tumor-associated peptides (TUMAPs) presented by a tumor sample from the individual patient;   b) comparing the peptides as identified in a) with a warehouse of peptides that have been prescreened for immunogenicity and/or over-presentation in tumors as compared to normal tissues   c) selecting at least one peptide from the warehouse that matches a tumor-associated peptide identified in the patient; and   d) manufacturing the personalized vaccine or compound-based or cellular therapy product based on step c).   
     
     
         22 . A T-cell receptor, soluble or membrane-bound, that is reactive with an HLA ligand, wherein said ligand has at least 75% identity to an amino acid sequence selected from the group consisting of SEQ ID No. 303. 
     
     
         23 . The T-cell receptor according to  claim 22 , wherein said amino acid sequence is at least 88% identical to SEQ ID No. 303. 
     
     
         24 . The T-cell receptor according to  claim 22 , wherein said amino acid sequence consists of SEQ ID No. 303. 
     
     
         25 . The T-cell receptor according to  claim 22 , wherein said T-cell receptor is provided as a soluble molecule and optionally carries a further effector function optionally comprising an immune stimulating domain or toxin. 
     
     
         26 . A nucleic acid, encoding for a TCR according to  claim 22 , optionally linked to a heterologous promoter sequence. 
     
     
         27 . An expression vector capable of expressing the nucleic acid according to  claim 26 . 
     
     
         28 . A host cell comprising the nucleic acid according to  claim 26 , wherein said host cell optionally is a T cell or NK cell. 
     
     
         29 . A method for producing the T cell receptor according to  claim 22 , said method comprising culturing a host cell, and isolating said T cell receptor from said host cell and/or a culture medium. 
     
     
         30 . A pharmaceutical composition comprising at least one active ingredient selected from the group consisting of
 a) a peptide selected from the group consisting of SEQ ID No. 303;   b) a T-cell receptor reactive with a peptide and/or the peptide-MHC complex according to a);   c) a fusion protein comprising a peptide according to a), and the N-terminal amino acids 1 to 80 of the HLA-DR antigen-associated invariant chain (Ii);   d) a nucleic acid encoding for any of a) to c) or an expression vector comprising said nucleic acid,   e) a host cell comprising the expression vector of d,   f) an activated T-lymphocyte, obtained by a method comprising contacting in vitro T cells with a peptide according to a) expressed on the surface of a suitable antigen-presenting cell for a period of time sufficient to activate said T cell in an antigen specific manner, as well as a method to transfer these activated T cells into the autologous or other patients;   g) an antibody, or soluble T-cell receptor, reactive to a peptide and/or the peptide—MHC complex according to a) and/or a cell presenting a peptide according to a), and potentially modified by fusion with for example immune-activating domains or toxins,   h) an aptamer recognizing a peptide of SEQ ID No. 303 and/or a complex of a peptide of SEQ ID No. 303 with a MHC molecule,   i) a conjugated or labelled peptide or scaffold according to any of a) to h) and a pharmaceutically acceptable carrier, and optionally, pharmaceutically acceptable excipients and/or stabilizers.   
     
     
         31 . An aptamer that specifically recognizes the product according to  claim 1 , optionally the peptide or variant or said product thereof is bound to an MHC molecule.