Novel peptides and combination of peptides for use in immunotherapy against lung cancer, including nsclc, sclc and other cancers

Abstract

To provide peptides, proteins, nucleic acids and cells for use in immunotherapeutic methods.SOLUTION: 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, which can serve, for example, as active pharmaceutical ingredients of vaccine compositions that stimulate anti-tumor immune responses, or stimulate T cells ex vivo and transfer into patients. Peptides bound to molecules of the major histocompatibility complex (MHC), or peptides as such, may also be targets of antibodies, soluble T-cell receptors, and other binding molecules.SELECTED DRAWING: None

Description

[Technical field]

[0001] The present invention relates to peptides, proteins, nucleic acids and cells used in immunotherapy.In particular, the present invention relates to the immunotherapy of cancer.The present invention further relates to tumor-associated T-cell peptide epitopes, alone or in combination with other tumor-associated peptides, which can act as active pharmaceutical ingredients of vaccine compositions, for example, to stimulate anti-tumor immune responses or to stimulate T cells ex vivo and transfer to patients.Peptides bound to molecules of major histocompatibility complex (MHC), or peptides themselves, can also be targets of antibodies, soluble T-cell receptors and other binding molecules.

[0002] The present invention relates to several novel peptide sequences and their variants derived from HLA class I molecules of human tumor cells, which can be used in vaccine compositions to elicit anti-tumor immune responses or as targets for the development of pharmacological / immunologically active compounds and cells. [Background technology]

[0003] Lung cancer is the leading cause of cancer-related deaths in both men and women. Globally, lung cancer is the most common cancer in terms of both incidence and mortality. In 2012, there were over 1.8 million new cases (13% of total cancer incidence) and 1.6 million deaths due to lung cancer (20% of total cancer mortality). Lung cancer is the leading cause of cancer death in men in 87 countries and in women in 26 countries. More than one-third of newly diagnosed cases occurred in China. The highest rates are in North America, Europe, and East Asia (World Cancer Report, 2014).

[0004] Since 1987, more women have died each year from lung cancer than from breast cancer. Mortality rates have continued to decline significantly in men, by about 1.9% per year from 1991 to 2003. Lung cancer mortality rates in women are approaching a plateau after decades of continuous increases. These trends in lung cancer mortality reflect the decline in smoking rates over the past 30 years.

[0005] According to the National Cancer Institute (NCI), an estimated 230,000 new cases of lung cancer and 160,000 deaths due to lung cancer are predicted in the United States in 2013.

[0006] Historically, small cell lung cancer (SCLC) has been distinct from non-small cell lung cancer (NSCLC), including adenocarcinoma, squamous cell carcinoma, and large cell carcinoma histologies. However, over the past decade, the distinction between adenocarcinoma and squamous cell carcinoma has increasingly been recognized due to significant differences in genetics and response to specific therapies. Thus, lung cancers are increasingly classified according to molecular subtypes, based on specific genetic alterations that drive and maintain lung tumorigenesis (Travis et al., 2013).

[0007] Prognosis is generally poor. 10-15% of all lung cancer patients survive 5 years after diagnosis. Poor survival in lung cancer patients is due, at least in part, to the 80% of patients being diagnosed with metastatic disease and the majority of patients with distant metastases (SEER STAT facts, 2014). At presentation, 30-40% of NSCLC cases are stage IV and 60% of SCLC are stage IV.

[0008] The 1-year relative survival rate for lung cancer has increased slightly from 35% in 1975-1979 to 44% in 2010, mainly due to improvements in surgical techniques and combination therapies. However, the 5-year survival rate for all stages combined is only 17%. In cases detected when the disease is still localized, the survival rate is 54%; however, only 16% of lung cancers are diagnosed at this early stage (SEER STAT facts, 2014).

[0009] Treatment options are determined by the cancer type (small cell or non-small cell) and stage, and include surgery, radiation therapy, chemotherapy, and targeted biological therapies such as bevacizumab (AVASTIN®) and erlotinib (TARCEVA®). For localized cancer, surgery is usually the treatment of choice. Recent studies suggest that survival in early-stage non-small cell lung cancer is improved by chemotherapy following surgery. Because the disease is usually widespread by the time of detection, radiation therapy and chemotherapy are frequently used, sometimes in combination with surgery. Chemotherapy alone or in combination with radiation is the usual treatment of choice for small cell lung cancer; with this regimen, the majority of patients experience remission, which in some surgical cases lasts for a long time (S3-Leitlinie Lungenkarzinom, 2011).

[0010] Advanced lung cancer is resistant to traditional chemotherapy. However, recent advances have led to exciting developments in histology- and genetics-dependent therapies. The level of scrutiny is exemplified by an adjuvant chemotherapy trial designed to discriminate not only between mutations between codons 12 and 13 of KRAS, but also between different amino acid substitutions determined by specific mutations in codon 12 (Shepherd et al., 2013).

[0011] Different immunotherapeutic approaches have been tested or are still under investigation to expand treatment options for NSCLC. Vaccination with L-BLP25 or MAGEA3 failed to demonstrate a vaccine-mediated survival benefit in NSCLC patients, whereas an allogeneic cell line-derived vaccine showed promising clinical trial results. Furthermore, further vaccination trials targeting epidermal growth factor receptors, gangliosides, and several other antigens are currently underway. An alternative strategy to boost antitumor T cell responses in patients consists of blocking inhibitory T cell receptors or their ligands with specific antibodies. The therapeutic potential of some of these antibodies, including ipilimumab, nivolumab, pembrolizumab, MPDL3280A, and MEDI-4736 in NSCLC, is currently being evaluated in clinical trials (Reinmuth et al., 2015). Summary of the Invention [Problem to be solved by the invention]

[0012] Considering the severe side effects and costs associated with cancer treatment, there is a need to identify factors that can be used in the treatment of cancer in general, and lung cancer in particular (including NSCLC and SCLC). There is also a need to identify factors that represent biomarkers for cancer in general, and lung cancer in particular (including NSCLC and SCLC), that can lead to better diagnosis of cancer, assessment of prognosis, and prediction of treatment success. [Means for solving the problem]

[0013] Cancer immunotherapy represents an option to specifically target cancer cells while minimizing side effects. Cancer immunotherapy exploits the presence of tumor-associated antigens.

[0014] The current classification of tumor-associated antigens (TAA) comprises the following main groups: a) Cancer-Testis Antigens: The first identified TAAs that can be recognized by T cells belong to this class and were originally called cancer-testis (CT) antigens because their members are expressed in histologically distinct human tumors and are present in normal tissues only in spermatocytes / spermatogonia of the testis and occasionally in the placenta. Since cells of the testis do not express class I and II HLA molecules, these antigens cannot be recognized by T cells of normal tissues and are therefore considered immunologically tumor-specific. Well-known examples of CT antigens are the MAGE family members and NY-ESO-1. b) Differentiation antigens: These TAAs are shared between tumors and the normal tissues from which they arise. Most of the known differentiation antigens are found in melanomas and normal melanocytes. Many of these melanocyte-related proteins are involved in melanin biosynthesis and therefore are not tumor-specific, but are nevertheless widely exploited for cancer immunotherapy. Examples include, but are not limited to, tyrosinase and Melan-A / MART-1 for melanoma, or PSA for prostate cancer. c) Overexpressed TAAs: Genes encoding ubiquitously expressed TAAs have been detected in histologically distinct types of tumors and generally at lower expression levels in many normal tissues. While many of the epitopes processed and potentially presented by normal tissues may be below the threshold level for T cell recognition, their overexpression in tumor cells may initiate anti-cancer responses by breaking previously established immune tolerance. Prominent examples of this class of TAAs are Her-2 / neu, survivin, telomerase, or WT1. d) Tumor-specific antigens: These unique TAAs arise from mutations in normal genes (β-catenin, CDK4, etc.). Some of these molecular changes are associated with neoplastic transformation and / or progression. Tumor-specific antigens can usually induce a strong immune response without the risk of an autoimmune reaction against normal tissues. On the other hand, these TAAs are most often associated only with the very tumor on which they were identified and are usually not shared between many individual tumors. In proteins with tumor-specific (associated) isoforms, tumor specificity (or association) of peptides may also arise if the peptide is derived from a tumor (associated) exon. e) TAAs resulting from aberrant post-translational modifications: Such TAAs may arise from proteins that are neither specific nor overexpressed in tumors, but nevertheless become tumor-associated by post-translational processes that are primarily active in tumors. Examples of this class arise from altered glycosylation patterns that result in novel epitopes in tumors, such as MUC1, or from protein splicing events during degradation that may or may not be tumor specific. f) Oncoviral proteins: These TAAs are viral proteins that may play an important role in the carcinogenic process and, being foreign (non-human), they can induce T cell responses. An example of such a protein is the human papillomavirus type 16 proteins E6 and E7, which are expressed in cervical cancer.

[0015] T cell-based immunotherapy targets tumor-associated or tumor-specific protein-derived peptide epitopes presented by molecules of the major histocompatibility complex (MHC). The antigens, i.e., their epitopes, recognized by tumor-specific T lymphocytes can be molecules derived from all protein classes, such as enzymes, receptors, transcription factors, etc., that are expressed in the respective tumor cells and are usually upregulated compared to non-modified cells of the same origin.

[0016] There are two classes of MHC molecules: MHC class I and MHC class II. MHC class I molecules are composed of α heavy chains and β2 microglobulin, while MHC class II molecules are composed of α and β chains. Their three-dimensional structure provides a binding groove that is used for non-covalent interactions with peptides.

[0017] MHC class I molecules are found on most nucleated cells. They present peptides that are mainly derived from endogenous proteins, defective ribosomal products (DRIPs), and proteolytic cleavage of larger peptides. However, peptides derived from endosomal compartments or exogenous sources are also frequently found on MHC class I molecules. This non-classical mode of class I presentation is referred to in the literature as cross-presentation (Brossart and Bevan, 1997; Rock et al., 1990). MHC class II molecules are found mostly on professional antigen-presenting cells (APCs) and mainly present peptides of exogenous or transmembrane proteins that are taken up by the APCs, for example during endocytosis, and subsequently processed. Complexes of peptides and MHC class I are recognized by CD8-positive T cells bearing the appropriate T cell receptor (TCR), while complexes of peptides and MHC class II molecules are recognized by CD4-positive helper T cells bearing the appropriate TCR. As a result, it is well known that TCR, peptide, and MHC are present in a 1:1:1 stoichiometric amount.

[0018] CD4+ helper T cells play a key role in inducing and maintaining effective responses by CD8+ cytotoxic T cells. Identification of CD4+ T cell epitopes derived from tumor-associated antigens (TAA) is crucial for the development of drugs that trigger antitumor immune responses (Gnjatic et al., 2003). At the tumor site, T helper cells maintain a cytokine environment that favors cytotoxic T cells (CT) (Mortara et al., 2006) and attract effector cells, such as CTLs, natural killer (NK) cells, macrophages, and granulocytes (Hwang et al., 2007).

[0019] In the absence of inflammation, expression of MHC class II molecules is primarily restricted to cells of the immune system, particularly professional antigen-presenting cells (APCs), such as monocytes, monocyte-derived cells, macrophages, dendritic cells, etc. In cancer patients, tumor cells have been found to express MHC class II molecules (Dengjel et al., 2006).

[0020] Extended (longer) peptides of the invention can act as MHC class II active epitopes.

[0021] T helper cells activated by MHC class II epitopes play an important role in orchestrating the effector functions of CTLs in antitumor immunity. T helper cell epitopes that initiate TH1-type T helper cell responses support the effector functions of CD8-positive killer T cells, including cytotoxicity directed against tumor cells that present tumor-associated peptide / MHC complexes on their cell surface. Thus, tumor-associated T helper cell peptide epitopes, alone or in combination with other tumor-associated peptides, can serve as active pharmaceutical ingredients of vaccine compositions that stimulate antitumor immune responses.

[0022] In mammalian models, such as mice, it has been shown that CD4 T cells are sufficient to inhibit tumor development through the inhibition of angiogenesis by secreting interferon-γ (IFNγ), even in the absence of CD8 T lymphocytes (Beatty and Paterson, 2001; Mumberg et al., 1999). There is evidence that CD4 T cells are direct antitumor effectors (Braumuller et al., 2013; Tran et al., 2014).

[0023] Since constitutive expression of HLA class II molecules is usually restricted to immune cells, it was not previously thought that it might be possible to isolate class II peptides directly from primary tumors, but Dengjel et al. succeeded in identifying several MHC class II epitopes directly from tumors (WO 2007 / 028574; EP 1760088 B1).

[0024] Because both types of CD8- and CD4-dependent responses jointly and synergistically contribute to antitumor effects, the identification and characterization of tumor-associated antigens recognized by either CD8+ T cells (ligand: MHC class I molecule + peptide epitope) or CD4-positive T helper cells (ligand: MHC class II molecule + peptide epitope) is important for the development of tumor vaccines.

[0025] For an MHC class I peptide to initiate (elicit) a cellular immune response, it must also bind to an MHC molecule. This process depends on the allele of the MHC molecule and on the specific polymorphism of the peptide's amino acid sequence. MHC class I binding peptides are usually 8-12 amino acid residues long and usually contain two conserved residues ("anchors") in their sequence that interact with the corresponding binding groove of the MHC molecule. Thus, each MHC allele has a "binding motif" that determines which peptides can specifically bind to the binding groove.

[0026] In an MHC class I-dependent immune response, not only can peptides bind to specific MHC class I molecules expressed by tumor cells, but they must also be subsequently recognized by T cells bearing specific T cell receptors (TCRs).

[0027] In order for a protein to be recognized by T lymphocytes as a tumor-specific or tumor-associated antigen and to be utilized in therapy, certain prerequisites must be met. The antigen should be expressed mainly by tumor cells and not expressed or expressed in relatively low amounts by healthy tissues. In a preferred embodiment, the peptide should be over-presented by tumor cells compared to healthy tissues. It is further desirable that the respective antigen is not only present in certain tumors, but also present in high concentrations (i.e., copy number per cell of the respective peptide). Tumor-specific and tumor-associated antigens are often derived from proteins that are directly involved in the transformation of normal cells into tumor cells, for example due to their function in cell cycle regulation or apoptosis suppression. Furthermore, downstream targets of the proteins directly responsible for transformation may be upregulated and thus indirectly tumor-associated. Such indirect tumor-associated antigens may also be targets for vaccination approaches (Singh-Jasuja et al., 2004). To ensure that such peptides ("immunogenic peptides") are derived from tumor-associated antigens and result in an in vitro or in vivo T cell response, it is essential that an epitope is present within the amino acid sequence of the antigen.

[0028] Essentially, any peptide capable of binding to an MHC molecule may serve as a T cell epitope. A prerequisite for the induction of an in vitro or in vivo T cell response is the presence of T cells bearing the corresponding TCR and the absence of immune tolerance to this particular epitope.

[0029] Therefore, TAAs are the starting point for the development of T cell-based therapeutics, including but not limited to tumor vaccines. Methods for identifying and characterizing TAAs are usually based on the use of T cells that can be isolated from patients or healthy individuals, or they are based on the generation of differential transcriptional profiles or peptide expression patterns between tumor and normal tissues. However, the identification of genes that are overexpressed in tumor tissues or human tumor cell lines, or selectively expressed in such tissues or cell lines, does not provide accurate information regarding the use of antigens transcribed from these genes in immunotherapy. This is because only individual subpopulations of epitopes of these antigens are suitable for such applications, because T cells with corresponding TCR must exist, and immune tolerance to this particular epitope must be absent or minimal. Therefore, in a highly preferred embodiment of the present invention, it is important to select only peptides that are over- or selectively presented for which there are functional and / or proliferative T cells. Such functional T cells are defined as T cells that are capable of clonally expanding upon stimulation with a specific antigen and capable of carrying out effector functions ("effector T cells").

[0030] When targeting peptide-MHC with a specific TCR (e.g., a soluble TCR) and an antibody or other binding molecule (scaffold) according to the invention, the immunogenicity of the underlying peptide is secondary. In these cases, presentation is the determining factor. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0031] In a first aspect of the invention, the present invention relates to a peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:489, or a variant thereof that is at least 77%, preferably at least 88% homologous (preferably at least 77% or at least 88% identical) to SEQ ID NO:1 to SEQ ID NO:489, wherein said variant binds to MHC and / or induces cross-reactivity of T cells with said peptide or a pharma- ceutically acceptable salt thereof, and wherein said peptide is not the underlying full-length polypeptide.

[0032] The present invention further relates to a peptide of the present invention comprising a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:489, or a variant thereof that is at least 77% and preferably at least 88% homologous (preferably at least 77% or at least 88% identical) to SEQ ID NO:1 to SEQ ID NO:489, wherein said peptide or variant thereof has an overall length of 8 to 100, preferably 8 to 30, most preferably 8 to 14 amino acids.

[0033] The following table shows the peptides according to the invention, their respective SEQ ID NOs, and the predicted origin (basic) genes of those peptides. In Table 1, peptides with SEQ ID NOs: 1 to 83 are identified as HLA-A * 24 and the peptides having SEQ ID NO: 84 to SEQ ID NO: 133 bind to HLA-A * The peptides having SEQ ID NO: 134 to SEQ ID NO: 201 bind to HLA-A * The peptides having SEQ ID NOs: 202 to 219 bind to HLA-A * The peptides having SEQ ID NO:220 to SEQ ID NO:295 bind to HLA-B * The peptides having SEQ ID NOs: 296 to 318 bind to HLA-B * The peptides having SEQ ID NOs: 319 to 374 bind to HLA-B *44. The peptides in Table 2 have been previously disclosed in a large list as a result of high-throughput screening with a high error rate or calculated using an algorithm, but have never been associated with cancer before. In Table 2, peptides with SEQ ID NO: 375 to SEQ ID NO: 387 bind to HLA-A * 24 and the peptides having SEQ ID NOs: 388 to 393 bind to HLA-A * The peptides having SEQ ID NOs: 394 to 452 bind to HLA-A * The peptides having SEQ ID NOs: 453 to 458 bind to HLA-A * The peptides having SEQ ID NOs: 459 to 475 bind to HLA-B * The peptides having SEQ ID NOs: 476 to 489 bind to HLA-B * The peptides in Table 3 are additional peptides that may be useful in combination with other peptides of the invention. In Table 3, peptides having SEQ ID NO: 490 to SEQ ID NO: 508 bind to HLA-A 44. * 24 and peptides having SEQ ID NOs: 509 to 528 bind to HLA-A * The peptides having SEQ ID NOs: 529 to 530 bind to HLA-B * The peptide having SEQ ID NO: 531, which binds to HLA-B * Combines with 44.

[0034] Table 1: Peptides according to the invention [Table 1-1] [Table 1-2] [Table 1-3] [Table 1-4] [Table 1-5] [Table 1-6] [Table 1-7] [Table 1-8] [Table 1-9]

[0035] Table 2: Additional peptides according to the invention with no previously known cancer association [Table 2-1] [Table 2-2] [Table 2-3]

[0036] Table 3: Peptides according to the invention useful, for example, in personalized cancer therapy [Table 3-1] [Table 3-2]

[0037] The present invention further relates generally to peptides according to the invention for use in the treatment of proliferative diseases such as, for example, acute myeloid leukemia, breast cancer, bile duct cancer, brain cancer, chronic lymphocytic leukemia, colorectal cancer, esophageal cancer, gallbladder cancer, gastric cancer, squamous cell carcinoma of the head and neck, hepatocellular carcinoma, melanoma, non-Hodgkin's lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, renal cell carcinoma, urinary bladder cancer, uterine cancer, etc.

[0038] Particularly preferred are peptides according to the invention, alone or in combination, selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 489. More preferred are peptides, alone or in combination, selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 374 (see Table 1), and their use in the immunotherapy of lung cancer (including NSCLC and SCLC), acute myeloid leukemia, breast cancer, cholangiocarcinoma, brain cancer, chronic lymphocytic leukemia, colorectal cancer, esophageal cancer, gallbladder cancer, gastric cancer, squamous cell carcinoma of the head and neck, hepatocellular carcinoma, melanoma, non-Hodgkin's lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, renal cell carcinoma, urinary bladder cancer, uterine cancer, and preferably lung cancer (including NSCLC and SCLC).

[0039] Therefore, another aspect of the present invention relates to the use of a peptide according to the invention for the combined treatment of a proliferative disease, preferably selected from the group of lung cancer (including NSCLC and SCLC), acute myeloid leukemia, breast cancer, cholangiocarcinoma, brain cancer, chronic lymphocytic leukemia, colorectal cancer, esophageal cancer, gallbladder cancer, gastric cancer, squamous cell carcinoma of the head and neck, hepatocellular carcinoma, melanoma, non-Hodgkin's lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, renal cell carcinoma, urinary bladder cancer, uterine cancer.

[0040] The present invention further relates to peptides according to the invention which have the ability to bind to molecules of the human major histocompatibility complex (MHC) class I or, in extended forms such as length variants, have the ability to bind to MHC class II.

[0041] The present invention further relates to a peptide according to the invention, said peptide consisting or consisting essentially of the amino acid sequence set forth in SEQ ID NO: 1 to SEQ ID NO: 489 (respectively).

[0042] The present invention further relates to a peptide according to the invention, said peptide being modified and / or comprising a non-peptide bond.

[0043] The present invention further relates to a peptide according to the invention, said peptide being part of a fusion protein, in particular fused to the N-terminal amino acid of the HLA-DR antigen-associated invariant chain (Ii) or fused to (or in the sequence of) an antibody, e.g. an antibody specific for dendritic cells.

[0044] The present invention further relates to a nucleic acid encoding a peptide according to the invention.The present invention further relates to a nucleic acid according to the invention which is DNA, cDNA, PNA, RNA or a combination thereof.

[0045] The present invention further relates to an expression vector capable of expressing and / or which expresses a nucleic acid according to the invention.

[0046] The present invention further relates to a peptide according to the invention, a nucleic acid according to the invention or an expression vector according to the invention for use in the treatment of diseases and in medicine, in particular in the treatment of cancer.

[0047] The present invention further relates to antibodies specific for the peptides according to the invention or for complexes of said peptides according to the invention with MHC, and to methods for their production.

[0048] The invention further relates to T cell receptors (TCRs), in particular soluble TCRs (sTCRs) and cloned TCRs incorporated into autologous or allogeneic T cells; methods for producing these; and methods for producing NK cells or other cells bearing or cross-reacting with said TCRs.

[0049] Antibodies and TCRs are further embodiments of immunotherapeutic applications of the peptides according to the invention.

[0050] The present invention further relates to a host cell comprising a nucleic acid or an expression vector according to the invention as described above.The present invention further relates to a host cell according to the invention which is an antigen-presenting cell, preferably a dendritic cell.

[0051] The present invention further relates to a method for producing a peptide according to the invention, comprising the steps of culturing a host cell according to the invention and isolating the peptide from said host cell or its culture medium.

[0052] The present invention further relates to a method according to the invention, in which a sufficient amount of antigen is contacted with an antigen-presenting cell, thereby loading the antigen onto class I or II MHC molecules expressed on the surface of a suitable antigen-presenting cell or artificial antigen-presenting cell.

[0053] The present invention further relates to a method according to the present invention, wherein the antigen-presenting cell comprises an expression vector capable of expressing or expressing said peptide containing SEQ ID NO:1 to SEQ ID NO:489, preferably containing SEQ ID NO:1 to SEQ ID NO:374 or a mutant amino acid sequence.

[0054] The present invention further relates to activated T cells produced by the method according to the invention, said T cells selectively recognizing cells expressing a polypeptide comprising an amino acid sequence according to the invention.

[0055] The present invention further relates to a method of killing target cells in a patient which aberrantly express a polypeptide comprising any amino acid sequence according to the present invention, comprising the step of administering to the patient an effective number of T cells produced according to the present invention.

[0056] The present invention further relates to the use of any of the described peptides, a nucleic acid according to the invention, an expression vector according to the invention, a cell according to the invention, an activated T lymphocyte, a T cell receptor or antibody or other peptide and / or peptide MHC binding molecule according to the invention as a medicament or in the manufacture of a medicament, preferably said medicament being effective against cancer.

[0057] Preferably, the agent is a cell therapy, a vaccine or a protein based on a soluble TCR or an antibody.

[0058] The present invention further relates to a use according to the present invention, wherein said cancer cells are lung cancer (including NSCLC and SCLC), acute myeloid leukemia, breast cancer, cholangiocarcinoma, brain cancer, chronic lymphocytic leukemia, colorectal cancer, esophageal cancer, gallbladder cancer, gastric cancer, squamous cell carcinoma of the head and neck, hepatocellular carcinoma, melanoma, non-Hodgkin's lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, renal cell carcinoma, urinary bladder cancer, uterine cancer, and preferably lung cancer (including NSCLC and SCLC) cells.

[0059] The present invention further relates to a peptide-based biomarker according to the present invention, referred to herein as "target", which can be used in the diagnosis of cancer, preferably lung cancer (including NSCLC and SCLC). The marker can be the over-presentation of the peptide itself, or the over-expression of the corresponding gene. The marker can also be used to predict the probability of success of a treatment, preferably an immunotherapy, most preferably an immunotherapy that targets the same target identified by the biomarker. For example, an antibody or soluble TCR can be used to stain tumor sections to detect the presence of the peptide of interest complexed with MHC.

[0060] Optionally, the antibody possesses additional effector functions, such as an immunostimulatory domain or a toxin.

[0061] The present invention also relates to the use of these novel targets in the context of cancer therapy.

[0062] Stimulation of an immune response depends on the presence of antigens that are recognized as foreign by the host immune system. The discovery of the existence of tumor-associated antigens has raised the possibility of harnessing the host's immune system to intervene in tumor growth. Various mechanisms that harness both the humoral and cellular arms of the immune system are currently being explored for cancer immunotherapy.

[0063] Specific elements of the cellular immune response can specifically recognize and destroy tumor cells. Isolation of T cells from tumor-infiltrating cell populations or from peripheral blood suggests that such cells play a key role in the innate immune defense against cancer. CD8+ T cells that recognize class I molecules of major histocompatibility complex (MHC)-bearing peptides, usually of 8-10 amino acid residues, derived from proteins or defective ribosomal products (DRIPS) located in the cytosol, play a key role in this response. MHC molecules in humans are also called human leukocyte antigens (HLA).

[0064] As used herein, all terms are defined as set forth below unless otherwise stated.

[0065] The term "T cell response" refers to the specific proliferation and activation of effector functions induced by peptides in vitro or in vivo. For MHC class I-restricted cytotoxic T cells, the effector functions may be lysis of peptide-pulsed, peptide precursor-pulsed, or naturally peptide-presenting target cells; secretion of cytokines, preferably interferon-γ, TNF-α, or IL-2, induced by the peptide; secretion of effector molecules, preferably granzymes or perforins, induced by the peptide; or degranulation.

[0066] The term "peptide" is used herein to designate a series of amino acid residues that are typically linked together by peptide bonds between the alpha amino and carbonyl groups of adjacent amino acids. Peptides are preferably 9 amino acids in length, but can be as short as 8 amino acids in length, 10, 11, or 12 or more, and in the case of MHC class II peptides (extended variants of the peptides of the invention), they can be 13, 14, 15, 16, 17, 18, 19, or 20 or more amino acids in length.

[0067] Furthermore, the term "peptide" is intended to include salts of a series of amino acid residues that are typically linked together by peptide bonds between the α-amino and carbonyl groups of adjacent amino acids. Preferably, the salts are pharma- ceutically acceptable salts of peptides, such as, for example, chloride salts or acetate salts (trifluoroacetates). It should be noted that peptides are not salts in vivo, so that salts of peptides according to the present invention have substantially different in vivo states than peptides.

[0068] The term "peptide" is also intended to include "oligopeptide." The term "oligopeptide" is used herein to designate a series of amino acid residues that are typically linked together by peptide bonds between the alpha amino and carbonyl groups of adjacent amino acids. The length of the oligopeptide is not critical to the invention, provided the correct epitope or epitopes are retained therein. Oligopeptides are typically less than about 30 amino acid residues in length and more than about 15 amino acids in length.

[0069] The term "polypeptide" refers to a series of amino acid residues that are typically linked together by peptide bonds between the alpha amino and carbonyl groups of adjacent amino acids. The length of the polypeptide is not critical to the present invention, provided that the correct epitope is retained. In contrast to the term peptide or oligopeptide, the term polypeptide is intended to refer to a molecule that contains more than about 30 amino acid residues.

[0070] A peptide, oligopeptide, protein or polynucleotide encoding such a molecule is "immunogenic" if it is capable of inducing an immune response (and therefore is an "immunogen" in the present invention). In the present invention, immunogenicity is more specifically defined as the ability to induce a T cell response. Thus, an "immunogen" is a molecule capable of inducing an immune response, and in the present invention, a molecule capable of inducing a T cell response. In another embodiment, the immunogen can be a peptide, a peptide-MHC complex, an oligopeptide, and / or a protein used to generate specific antibodies or TCRs against it.

[0071] A class IT cell "epitope" requires a short peptide bound to a class I MHC receptor to form a ternary complex (MHC class I α chain, β-2-microglobulin, and peptide) that can be recognized by a T cell bearing a compatible T cell receptor that binds to the MHC / peptide complex with appropriate affinity. Peptides bound to MHC class I molecules are typically 8-14 amino acids in length, most typically 9 amino acids in length.

[0072] In humans, there are three distinct genetic loci that code for MHC class I molecules (human MHC molecules also called human leukocyte antigens (HLA)): HLA-A, HLA-B, and HLA-C. * 01. HLA-A * 02, and HLA-B * 07 are examples of different MHC class I alleles that can be expressed from these loci.

[0073] Table 4: HLA-A * 02. HLA-A * 01. HLA-A * 03. HLA-A * 24. HLA-B * 07. HLA-B * 08, and HLA-B * The frequency of occurrence of 44 serotypes F. The haplotype frequency Gf was obtained from a study using HLA typing data from a registry of over 6.5 million volunteer donors in the United States (Gragert et al., 2013). Haplotype frequency is the frequency of different alleles on an individual chromosome. Due to the diploid set of chromosomes in mammalian cells, the frequency of genotype occurrence of this allele is higher and can be calculated using the Hardy-Weinberg principle (F = 1 - (1-Gf)2). [Table 4]

[0074] The peptides of the invention, when included in the vaccines of the invention described herein, preferably * 02, A * 01, A * 03, A * 24, B * 07, B * 08 or B * 44. The vaccine may also comprise a pan-binding MHC class II peptide. Thus, the vaccine of the present invention can be used to * 02-, A * 01-, A * 03-, A * 24-, B * 07-, B * 08- or B * Due to the pan-binding properties of these peptides, there is no need to select for MHC class II allotypes, while the cancer of patients who are 44-positive can be treated.

[0075] A of the present invention * 02 If the peptide is, for example, A * When combined with a peptide that binds to another allele, such as HLA-A 24, a higher percentage of any patient population may be treated compared to addressing any one of the MHC class I alleles alone. In the majority of populations, less than 50% of patients could be addressed by any one of the alleles alone, while HLA-A 25 and HLA-A 26 may be combined with a peptide that binds to another allele, such as HLA-A 27 and HLA-A 28. * 24 and HLA-A * A vaccine comprising the 02 epitope may treat at least 60% of patients in any reasonable population. Specifically, at least one of these alleles is positive in the following percentages of patients in various geographic regions: United States 61%, Western Europe 62%, China 75%, South Korea 77%, Japan 86% (calculated from www.allelefrequencies.net).

[0076] Table 5: HLA allele coverage in European Caucasian populations (from (Gragert et al., 2013) calculated). [Table 5]

[0077] In a preferred embodiment, the term "nucleotide sequence" refers to a heteropolymer of deoxyribonucleotides.

[0078] Nucleotide sequences encoding particular peptides, oligopeptides, or polypeptides may be of natural origin or they may be synthetically constructed. Generally, DNA fragments encoding the peptides, polypeptides, and proteins of the invention are constructed from cDNA fragments and short oligonucleotide linkers, or from a series of oligonucleotides to provide synthetic genes that can be expressed in recombinant transcription units comprising regulatory elements derived from microbial or viral operons.

[0079] As used herein, the term "nucleotide sequence encoding a peptide" refers to a nucleotide sequence that encodes a peptide that includes artificial start and stop codons that are compatible with the biological system in which the sequence is expressed, for example, by a dendritic cell or another cell line useful for producing a TCR.

[0080] As used herein, reference to a nucleic acid sequence includes both single-stranded and double-stranded nucleic acids. Thus, for example, a specific sequence refers to the single-stranded DNA of such sequence, the double strand of such sequence and its complement (double-stranded DNA), and the complement of such sequence, unless the context clearly indicates otherwise.

[0081] The term "coding region" refers to that portion of a gene that naturally or normally encodes an expression product of the gene in its natural genomic environment, i.e., the region that encodes the gene's natural expression product in vivo.

[0082] The coding region may be derived from a non-mutated ("normal"), mutated or altered gene, or may even be derived from a DNA sequence or gene that is entirely synthesized in the laboratory using methods well known to those skilled in the art of DNA synthesis.

[0083] The term "expression product" refers to a polypeptide or protein that is the natural translation product of a gene and of any nucleic acid sequence that, due to the degeneracy of the genetic code, codes for an equivalent and therefore codes for the same amino acid.

[0084] The term "fragment", when referring to a coding sequence, means a portion of DNA comprising less than the complete coding region, whose expression product retains essentially the same biological function or activity as the expression product of the complete coding region.

[0085] The term "DNA segment" refers to a polymer of DNA, either in the form of a separate fragment or as a component of a larger DNA construct, that is derived from DNA that has been isolated at least once, in a substantially pure form, i.e., free from contaminating endogenous material, in an amount or concentration that allows the segment and its constituent nucleotide sequences to be identified, manipulated, and recovered, for example, by standard biochemical methods using a cloning vector. Such segments are provided in the form of an open reading frame that is uninterrupted by internal non-translated sequences or introns that are typically present in eukaryotic genes. Non-translated DNA sequences may be present downstream of the open reading frame, where they do not interfere with the manipulation or expression of the coding region.

[0086] The term "primer" means a short nucleic acid sequence that can pair with a single strand of DNA and provide a free 3'-OH end at which DNA polymerase initiates deoxyribonucleotide chain synthesis.

[0087] The term "promoter" refers to a region of DNA involved in binding RNA polymerase to initiate transcription.

[0088] The term "isolated" means that the material is removed from its original environment (e.g., the natural environment if it is of natural origin). For example, a naturally occurring polynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleotide or polypeptide separated from some or all of the coexisting materials in the natural system is isolated. Such a polynucleotide may be part of a vector and / or such a polynucleotide or polypeptide may be part of a composition, but is still isolated in the sense that such a vector or composition is not part of its natural environment.

[0089] The polynucleotides and recombinant or immunogenic polypeptides disclosed by the present invention may be in "purified" form. The term "purified" does not necessarily mean completely pure; rather, it is intended to be a relative definition and may include highly purified preparations, or only partially purified preparations, as these terms are understood by those skilled in the art. For example, individual clones isolated from a cDNA library have been conventionally purified to electrophoretic homogeneity. Purification of the starting material or natural material to at least one order of magnitude, preferably two or three orders of magnitude, more preferably four or five orders of magnitude, is expressly contemplated. Furthermore, the claimed polypeptides are expressly encompassed, preferably having a purity of 99.999%, or at least 99.99% or 99.9% by weight; more desirably 99% or greater.

[0090] The nucleic acid and polypeptide expression products disclosed by the present invention, as well as expression vectors containing such nucleic acids and / or such polypeptides, may be in "enriched form". As used herein, the term "enriched" refers to a concentration of a substance that is (for example) at least about 2, 5, 10, 100, or 1000 times its natural concentration, advantageously 0.01% by weight, preferably at least about 0.1% by weight. Enriched preparations of about 0.5%, 1%, 5%, 10%, and 20% by weight are also contemplated. The sequences, constructs, vectors, clones, and other substances that make up the present invention may advantageously be in enriched or isolated form. The term "active fragment" refers to a peptide, polypeptide, or fragment of a nucleic acid sequence that generates an immune response (i.e., has immunogenicity) when administered, usually alone or optionally with a suitable adjuvant or in a vector, to an animal, such as a mammal, including, for example, a rabbit or mouse, and also to a human, such immune response taking the form of stimulating a T-cell response in a recipient animal, such as a human. Alternatively, the "active fragments" may also be used to induce T cell responses in vitro.

[0091] As used herein, when used in the context of a polypeptide, the terms "portion," "segment," and "fragment" refer to a sequence of consecutive residues, such as amino acid residues, which form a subset of a larger sequence. For example, if a polypeptide is treated with any of the common endopeptidases, such as trypsin or chymotrypsin, the oligopeptides resulting from such treatment will represent a portion, segment, or fragment of the starting polypeptide. When used in reference to a polynucleotide, these terms refer to the products resulting from the treatment of said polynucleotide with any of the endonucleases.

[0092] According to the present invention, when referring to a sequence, the term "percentage of identity" or "percent identical" means that the sequence is compared to the claimed or described sequence ("reference sequence") after alignment of the sequence to be compared ("comparison sequence") with the described or claimed sequence. The percentage of identity is then determined according to the following formula: Percent identity=100[1-(C / R)] where C is the number of differences between the reference sequence and the compared sequence over the alignment length between the reference sequence and the compared sequence, (i) each base or amino acid in the reference sequence that does not have a corresponding aligned base or amino acid in the comparison sequence; and (ii) each gap in the reference sequence, and (iii) each aligned base or amino acid in the reference sequence that differs from an aligned base or amino acid in the comparison sequence constitutes a difference; (iiii) the alignment must start at position 1 of the matching sequence; R is the number of bases or amino acids in the reference sequence over the length of the alignment with the comparison sequence, and any gaps that occur in the reference sequence are also counted as bases or amino acids.

[0093] If there is an alignment between a comparison sequence and a reference sequence for which the identity percentage is calculated as above that is about or exceeds a particular minimum identity percentage, then the comparison sequence has a particular minimum identity percentage with the reference sequence, even if there is an alignment therein whose identity percentage calculated as above is less than the particular identity percentage.

[0094] Thus, as mentioned above, the present invention provides a peptide comprising a sequence selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 489, or a variant thereof that is 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 489, or a variant thereof that cross-reacts T cells with said peptide. The peptide of the present invention has the ability to bind human major histocompatibility complex (MHC) class I molecules or extended versions of said peptides to class II.

[0095] In the present invention, the term "homologous" refers to the degree of identity between two amino acid sequences, i.e., peptide or polypeptide sequences (see percentage identity above). Said "homology" is determined by comparing two sequences aligned under optimal conditions across the sequences being compared. Such sequence homology can be calculated, for example, by creating an alignment using the ClustalW algorithm. Publicly available sequence analysis software, more specifically Vector NTI, GENETYX or other tools, are provided by public databases.

[0096] One skilled in the art would be able to assess whether T cells induced by a particular peptide variant are capable of cross-reacting with the peptide itself (Appay et al., 2006; Colombetti et al., 2006; Fong et al., 2001; Zaremba et al., 1997).

[0097] By "mutant" of a given amino acid sequence, we mean that, for example, the side chains of one or two of the amino acid residues are altered (e.g., by replacing them with the side chains of another naturally occurring amino acid residue, or with other side chains), such that the peptide is still able to bind to an HLA molecule substantially similarly to a peptide consisting of the given amino acid sequence consisting of SEQ ID NO:1 to SEQ ID NO:489. * It may be modified to at least maintain, if not improve, its ability to interact with and bind to the binding groove of an appropriate MHC molecule, such as -02 or -DR, and thus it at least maintains, if not improves, its ability to bind to the TCR of an activated T cell.

[0098] These T cells can subsequently cross-react with and kill cells expressing a polypeptide containing the native amino acid sequence of the cognate peptide as defined in the embodiments of the present invention. As can be deduced from the academic literature and databases (Rammensee et al., 1999; Godkin et al., 1997), certain positions of HLA-binding peptides are typically anchor residues, forming a core sequence that fits the binding motif of the HLA receptor defined by the polar, electrophysical, hydrophobic, and spatial properties of the polypeptide chain that constitute the binding groove. Thus, one skilled in the art could modify the amino acid sequences set forth in SEQ ID NO: 1 to SEQ ID NO: 489 by retaining the known anchor residues and determine whether such variants maintain the ability to bind to MHC class I or II molecules. The variants of the present invention maintain the ability to bind to the TCR of activated T cells, which can subsequently cross-react with and kill cells expressing a polypeptide containing the native amino acid sequence of the cognate peptide as defined in the embodiments of the present invention.

[0099] The original (unmodified) peptides disclosed herein may be modified by substitution of one or more residues at different, possibly selective, sites in the peptide chain, unless otherwise specified. Preferably, these substitutions are located at the ends of the amino acid chain. Such substitutions may be of a conservative nature, e.g., an amino acid is replaced by an amino acid of similar structure and characteristics, such as a hydrophobic amino acid being replaced by another hydrophobic amino acid. Even more conservative substitutions are the replacement of amino acids of the same or similar size and chemical properties, such as the replacement of leucine by isoleucine. In studies of sequence diversity of naturally occurring homologous protein families, certain amino acid substitutions are often tolerated better than others, and these often show a correlation with the similarity of size, charge, polarity, and hydrophobicity between the original amino acid and its replacement, which is the basis for the definition of "conservative substitution".

[0100] Conservative substitutions are defined herein as exchanges within one of the following five groups: Group 1 - small aliphatic, non-polar or slightly polar residues (Ala, Ser, Thr, Pro, Gly); Group 2 - polar negatively charged residues and their amides (Asp, Asn, Glu, Gln); Group 3 - polar positively charged residues (His, Arg, Lys); Group 4 - large aliphatic non-polar residues (Met, Leu, Ile, Val, Cys); and Group 5 - large aromatic residues (Phe, Tyr, Trp).

[0101] A less conservative substitution might involve the substitution of another amino acid with similar characteristics but somewhat different in size, such as the substitution of an isoleucine residue for an alanine. A highly non-conservative substitution might involve the substitution of a polar amino acid with an acidic amino acid, or even a basic amino acid. However, even such "radical" substitutions cannot be dismissed as potentially ineffective, since chemical effects are not completely predictable, and free radical substitutions can lead to fortuitous effects not predictable from simple chemical principles.

[0102] Of course, such substitutions may involve structures other than the usual L-amino acids. Thus, D-amino acids may be substituted for L-amino acids normally found in the antigenic peptides of the invention and still be encompassed by the disclosure herein. Furthermore, non-standard amino acids (i.e., other than the common naturally occurring proteogenic amino acids) may also be used for substitution purposes to produce immunogens and immunogenic polypeptides according to the invention.

[0103] When substitutions at two or more positions are found to result in a peptide with substantially equal or greater antigenic activity as defined below, combinations of these substitutions are tested to determine whether the combination of substitutions results in an additive or synergistic effect on the antigenicity of the peptide. At a maximum, no more than four positions in a peptide are substituted simultaneously.

[0104] Peptides consisting essentially of amino acid sequences as shown herein may have one or two non-anchor amino acids (see below for anchor motifs) exchanged without substantially altering or adversely affecting their ability to bind to human major histocompatibility complex (MHC) class I or II molecules, as compared to the unmodified peptide. In another embodiment, in peptides consisting essentially of amino acid sequences as shown herein, one or two amino acids may be exchanged with their conservative exchange partners (see below), as compared to the unmodified peptide, without substantially altering or adversely affecting their ability to bind to human major histocompatibility complex (MHC) class I or II molecules.

[0105] Amino acid residues that do not substantially contribute to the interaction with the T cell receptor may be modified by substitution with other amino acids whose incorporation does not substantially affect T cell reactivity or preclude binding to the relevant MHC. Thus, except for the provisos given, a peptide of the invention may be any peptide (we include in that term an oligopeptide or polypeptide) comprising an amino acid sequence as given or a portion or variant thereof.

[0106] Table 6: Variants and motifs of peptides set forth in SEQ ID NOs: 4, 13, 90, 93, 138, 171, 202, 204, 224, 294, 306, 316, 322, and 327 [Table 6-1] [Table 6-2] [Table 6-3] [Table 6-4]

[0107] Longer (extended) peptides may also be suitable. MHC class I epitopes are usually 8-11 amino acids long, but can be generated by peptide processing from longer peptides or proteins that contain the actual epitope. The residues flanking the actual epitope are preferably those that do not substantially affect the proteolytic cleavage required to expose the actual epitope during processing.

[0108] The peptides of the invention may be extended by up to 4 amino acids, i.e. 1, 2, 3 or 4 amino acids may be added to either end in any combination between 4:0 and 0:4. Extension combinations according to the invention are given in Table 7.

[0109] Table 7: Combinations of extensions of peptides of the invention [Table 7]

[0110] The amino acids for extension / lengthening can be the peptides of the original protein sequence or any other amino acids. Extensions can be used to increase the stability or solubility of the peptides.

[0111] Thus, epitopes of the present invention may be identical to naturally occurring tumor-associated or tumor-specific epitopes, or may include epitopes that differ from the reference peptide by no more than four residues, so long as they have substantially the same antigenic activity.

[0112] In alternative embodiments, the peptide is extended on one or both sides by more than four amino acids, preferably up to a total length of 30 amino acids. This may result in an MHC class II binding peptide. Binding to MHC class II may be tested by methods known in the art.

[0113] Thus, the present invention provides peptides and variants of MHC class I epitopes, where the peptides or variants have an overall length of 8-100, 9-100, 10-100, 11-100, 12-100, preferably 8-30, and 9-30, 10-30, 11-30, 12-30, most preferably 8-14, 9-14, 10-14, 11-14, 12-14. The present invention further provides peptides and variants of MHC class I epitopes, where the peptides or variants have an overall length of 8, 9, 10, 11, 12, 13 or 14 amino acids, where in case of extended class II binding peptides the length can also be 15, 16, 17, 18, 19, 20, 21 or 22 amino acids.

[0114] Of course, the peptides or variants according to the invention have the ability to bind to molecules of the human major histocompatibility complex (MHC) class I or II. The binding of the peptides or variants to the MHC complexes may be tested by methods known in the art.

[0115] Preferably, when T cells specific for a peptide according to the invention are tested with a substituted peptide, the peptide concentration at which the substituted peptide achieves half-maximal increase in lysis over background is about 1 mM or less, preferably about 1 μM or less, more preferably about 1 nM or less, even more preferably about 100 pM or less, and most preferably about 10 pM or less. It is also preferred that the substituted peptide is recognized by T cells from more than one individual, at least two, and more preferably three individuals.

[0116] In a particularly preferred embodiment of the invention, the peptide consists or consists essentially of the amino acid sequence set forth in SEQ ID NO:1 to SEQ ID NO:489.

[0117] "Consisting essentially of" is intended to mean that the peptide according to the invention contains, in addition to a sequence as set forth in any of SEQ ID NO: 1 to SEQ ID NO: 489 or a variant thereof, an additional N- and / or C-terminally located sequence of amino acids which do not necessarily constitute part of the peptide that functions as an epitope for an MHC molecule epitope.

[0118] Nevertheless, these sequences may be important to provide efficient transfer of the peptide according to the invention into cells. In one embodiment of the invention, the peptide is part of a fusion protein comprising the 80 N-terminal amino acids of the HLA-DR antigen-associated invariant chain (p33, hereafter "Ii"), e.g. from NCBI, GenBank accession number X00497. In other fusions, the peptide of the invention may be fused to an antibody as described herein, or a functional part thereof, in particular to an antibody sequence, so as to be specifically targeted by said antibody, or may be fused to or in an antibody specific for dendritic cells, e.g. as described herein.

[0119] Furthermore, the peptides or variants may be further modified to improve stability and / or binding to MHC molecules in order to elicit a stronger immune response. Such methods of optimizing peptide sequences are well known in the art and include, for example, the introduction of reverse peptide bonds or non-peptide bonds.

[0120] In reverse peptide bonds, amino acid residues are not linked by peptide (-CO-NH-) bonds, but peptide bonds are reversed. Such retro-inverso peptidomimetics may be produced using methods known in the art, such as those described in Meziere et al (1997) (Meziere et al., 1997), which is incorporated herein by reference. This approach involves creating pseudopeptides that contain changes that involve the main chain, not the direction of the side chain. Meziere et al. (Meziere et al., 1997) show that these pseudopeptides are useful for MHC binding and T helper cell response. Retro-inverse peptides that contain NH-CO bonds instead of CO-NH peptide bonds are much more resistant to proteolysis.

[0121] Non-peptide bonds are, for example, -CH2-NH, -CH2S-, -CH2CH2-, -CH=CH-, -COCH2-, -CH(OH)CH2-, and -CH2SO-. U.S. Pat. No. 4,897,445 provides a method for the solid phase synthesis of non-peptide bonds (-CH2-NH) in polypeptide chains, involving polypeptides synthesized by standard procedures and non-peptide bonds synthesized by reacting amino acids with amino aldehydes in the presence of NaCNBH3.

[0122] Peptides comprising the above sequences may be synthesized with additional chemical groups present at their amino and / or carboxy termini to improve the stability, bioavailability, and / or affinity of the peptides. For example, hydrophobic groups such as carbobenzoxyl, dansyl, or t-butyloxycarbonyl groups may be added to the amino termini of the peptides. Similarly, an acetyl group or a 9-fluorenylmethoxycarbonyl group may be placed at the amino termini of the peptides. Additionally, hydrophobic groups, t-butyloxycarbonyl, or amide groups may be added to the carboxy termini of the peptides.

[0123] Furthermore, the peptides of the present invention may be synthesized to modify their configuration. For example, the D-isomer of one or more amino acid residues of the peptide may be used instead of the usual L-isomer. Still further, at least one of the amino acid residues of the peptide of the present invention may be substituted with one of the well-known non-naturally occurring amino acid residues. Modifications such as these may help to increase the stability, bioavailability and / or binding activity of the peptide of the present invention.

[0124] Similarly, the peptides or variants of the invention may be chemically modified by reacting specific amino acids either before or after peptide synthesis. Examples of such modifications are well known in the art and are summarized, for example, in R. Lundblad, Chemical Reagents for Protein Modification, 3rd ed. CRC Press, 2004 (Lundblad, 2004), which is incorporated herein by reference. Chemical modifications of amino acids include, but are not limited to, acylation, amidination, pyridoxylation of lysine, reductive alkylation, trinitrobenzylation of amino groups with 2,4,6-trinitrobenzenesulfonic acid (TNBS), amide and sulfhydryl modification of carboxyl groups by performic acid oxidation of cysteine ​​to cysteic acid, mercury derivative formation, mixed disulfide formation with other thiol compounds, reaction with maleimide, carboxymethylation with iodoacetic acid or iodoacetamide, and carbamoylation with cyanate at alkaline pH. In this regard, those skilled in the art are referred to Chapter 15 of Current Protocols In Protein Science, Eds. Coligan et al. (John Wiley and Sons NY 1995-2000) (Coligan et al., 1995) for more detailed procedures regarding the chemical modification of proteins.

[0125] Briefly, for example, the modification of arginyl residues in proteins is often based on the reaction of vicinal dicarbonyl compounds such as phenylglyoxal, 2,3-butanedione, and 1,2-cyclohexanedione to form adducts. Another example is the reaction of arginine residues with methylglyoxal. Cysteines can be modified without the concomitant modification of other nucleophilic sites such as lysines and histidines. As a result, a large number of reagents are available for cysteine ​​modification. Websites of companies such as Sigma-Aldrich (http: / / www.sigma-aldrich.com) provide information on specific reagents.

[0126] Selective reduction of disulfide bonds in proteins is also common. Disulfide bonds can be formed and oxidized during heat treatment of biopharmaceuticals. Specific glutamic acid residues may be modified using Woodward's reagent K. Intramolecular crosslinks can be formed between lysine and glutamic acid residues using N-(3-(dimethylamino)propyl)-N'-ethylcarbodiimide. For example, diethylpyrocarbonate is a reagent for histidyl residue modification in proteins. Histidine can also be modified using 4-hydroxy-2-nonenal. Reactants of lysine residues and other α-amino groups are useful, for example, in binding peptides to surfaces or protein / peptide crosslinking. Lysine is the site of attachment of poly(ethylene) glycol and is the primary modification site for glycosylation of proteins. Methionine residues in proteins can be modified, for example, by iodoacetamide, bromoethylamine, and chloramine T.

[0127] Tyrosyl residues can be modified using tetranitromethane and N-acetylimidazole. Cross-linking through the formation of dityrosine can be achieved with hydrogen peroxide / copper ion.

[0128] Recent studies on the modification of tryptophan have used N-bromosuccinimide, 2-hydroxy-5-nitrobenzyl bromide or 3-bromo-3-methyl-2-(2-nitrophenylmercapto)-3H-indole (BPNS-skatole).

[0129] Successful modification of therapeutic proteins and peptides with PEG is often associated with increased circulatory half-life, while cross-linking of proteins with glutaraldehyde, polyethylene glycol diacrylate, and formaldehyde is used for hydrogel preparation. Chemical modification of allergens for immunotherapy is often achieved by carbamylation with potassium cyanate.

[0130] Peptides or peptide variants which are modified or contain non-peptide bonds are preferred embodiments of the present invention.

[0131] Another embodiment of the present invention relates to a non-naturally occurring peptide, the peptide consisting of or consisting essentially of the amino acid sequence set forth in SEQ ID NO:1 to SEQ ID NO:489, synthetically produced (e.g., synthesized) as a pharma- ceutically acceptable salt. Methods for synthetically producing peptides are well known in the art. Since peptides produced in vivo are not salts, the salts of the peptides according to the present invention are substantially different from the in vivo state of the peptide. The non-naturally occurring salt form of the peptide mediates the solubility of the peptide, especially in the context of pharmaceutical compositions comprising the peptide, such as the peptide vaccines disclosed herein. Sufficient, at least substantial, solubility of the peptide is necessary to efficiently provide the peptide to the subject being treated. Preferably, the salt is a pharma- ceutically acceptable salt of the peptide. These salts according to the present invention include PO4 as the anion. 3- , SO4 2- , CH3COO - , Cl - , Br - , NO3 - , ClO4 - , I - , SCN - , and NH4 as the cation + , Rb + , K + , Na + , Cs + , Li + , Zn 2+ , Mg 2+ , Ca 2+ , Mn 2+ , Cu 2+ and Ba 2+In particular, the salts include alkali and alkaline earth salts such as the Hofmeister series salts comprising (NH4)3PO4, (NH4)2HPO4, (NH4)H2PO4, (NH4)2SO4, NH4CH3COO, NH4Cl, NH4Br, NH4NO3, NH4CIO4, NH4I, NH4SCN, Rb3PO4, Rb2HPO4, RbH2PO4, Rb2SO4, Rb4CH3COO, Rb4Cl, Rb4Br, Rb4NO3, Rb4CIO4, Rb4I, Rb4SCN, K3PO4, K2HPO4, KH2PO4, K2SO4, KCH3COO, KCl, KBr, KNO3, KClO4, KI, KSCN, Na3PO4, Na2HPO4, NaH2PO4, Na2SO4, NaCH3COO, NaCl, NaB r, NaNO3, NaCIO4, NaI, NaSCN, ZnCI2Cs3PO4, Cs2HPO4, CsH2PO4, Cs2SO4, CsCH3COO, CsCl, CsBr, CsNO3, CsCIO4, CsI , CsSCN, Li3PO4, Li2HPO4, LiH2PO4, Li2SO4, LiCH3COO, LiCl, LiBr, LiNO3, LiClO4, LiI, LiSCN, Cu2SO4, Mg3(PO4) 2, Mg2HPO4, Mg(H2PO4)2, Mg2SO4, Mg(CH3COO)2, MgCl2, MgBr2, Mg(NO3)2, Mg(ClO4)2, MgI2, Mg(SCN)2, MnCl2, Ca3( PO4), Ca2HPO4, Ca(H2PO4)2, CaSO4, Ca(CH3COO)2, CaCl2, CaBr2, Ca(NO3)2, Ca(ClO4)2, CaI2, Ca(SCN)2, Ba3(PO4)2, Ba2HPO4, Ba(H2PO4)2, BaSO4, Ba(CH3COO)2, BaCl2, BaBr2, Ba(NO3)2, Ba(ClO4)2, BaI2, and Ba(SCN)2. Particularly preferred are NH acetates, such as, for example, chlorides or acetates (trifluoroacetates), MgCl2, KH2PO4, Na2SO4, KCl, NaCl, and CaCl2.

[0132] In general, peptides and variants (at least those containing peptide bonds between amino acid residues) may be synthesized by the Fmoc-polyamide mode of solid-phase peptide synthesis as disclosed by Lukas et al. (Lukas et al., 1981) and the references cited therein. Temporary N-amino group protection is provided by the 9-fluorenylmethyloxycarbonyl (Fmoc) group. Repetitive cleavage of this highly base-labile protecting group is carried out using 20% ​​piperidine in N,N-dimethylformamide. Side chain functional groups may be protected as their butyl ethers (for serine, threonine, and tyrosine), butyl esters (for glutamic acid and aspartic acid), butyloxycarbonyl derivatives (for lysine and histidine), trityl derivatives (for cysteine), and 4-methoxy-2,3,6-trimethylbenzenesulfonyl derivatives (for arginine). When glutamine or asparagine is the C-terminal residue, a 4,4'-dimethoxybenzhydryl group is utilized to protect the side chain amide functionality. The solid support is based on a polydimethyl-acrylamide polymer, composed of three monomers: dimethylacrylamide (backbone monomer), bisacryloylethylenediamine (crosslinker), and acryloylsarcosine methyl ester (functionalizer). The peptide-to-resin cleavable linker used is an acid-labile 4-hydroxymethyl-phenoxyacetic acid derivative. All amino acid derivatives are added as their preformed symmetrical anhydride derivatives, except for asparagine and glutamine, which are added using a reverse N,N-dicyclohexyl-carbodiimide / 1-hydroxybenzotriazole-mediated conjugation procedure. All conjugation and deprotection reactions are monitored using ninhydrin, trinitrobenzenesulfonic acid or isatin test procedures. Upon completion of synthesis, the peptide is cleaved from the resin support and the side chain protecting groups are simultaneously removed by treatment with 95% trifluoroacetic acid containing a 50% scavenger mixture. Commonly used scavengers include ethanedithiol, phenol, anisole, and water, with the exact choice depending on the constituent amino acids of the peptide being synthesized.A combination of solid-phase and solution-phase methods for the synthesis of peptides is also possible (see, for example, (Bruckdorfer et al., 2004) and references cited therein).

[0133] Trifluoroacetic acid is removed by evaporation in vacuo, followed by trituration with diethyl ether to give the crude peptide. Any scavengers present are removed by a simple extraction procedure which, on lyophilization of the aqueous phase, gives the scavenger-free crude peptide. Reagents for peptide synthesis are commonly available, for example from Calbiochem-Novabiochem (Nottingham, UK).

[0134] Purification may be achieved by any one or combination of techniques such as recrystallization, size exclusion chromatography, ion exchange chromatography, hydrophobic interaction chromatography, and (usually) reverse-phase high performance liquid chromatography using, for example, an acetonitrile / water gradient separation.

[0135] Analysis of peptides may be carried out using thin layer chromatography, electrophoresis, in particular capillary electrophoresis, solid phase extraction (CSPE), reversed-phase high performance liquid chromatography, amino acid analysis after acid hydrolysis, by fast atom bombardment (FAB) mass spectrometry, as well as by MALDI and ESI-Q-TOF mass spectrometry.

[0136] To select over-represented peptides, a presentation profile is calculated, which shows the median sample presentation as well as the replicate variation. The profile juxtaposes the samples of the tumor entity of interest to the baseline of normal samples. Then, by calculating the p-value of the linear mixed-effects model (Pinheiro et al., 2015) and correcting for multiple testing by false discovery rate (Benjamini and Hochberg, 1995), each of these profiles can be combined into an over-representation score (see Example 1, Figure 1).

[0137] For identification and relative quantification of HLA ligands by mass spectrometry, HLA molecules from shock-frozen samples were purified and HLA-associated peptides were isolated. The isolated peptides were separated and sequenced by online nanoelectrospray ionization (nanoESI) liquid chromatography mass spectrometry (LC-MS) experiments. The resulting peptide sequences were confirmed by comparison of the fragmentation patterns of native tumor-associated peptides (TUMAPs) recorded from lung cancer (including NSCLC and SCLC) samples (N=201 samples) with those of corresponding synthetic standard peptides of identical sequences. Since the peptides were directly identified as ligands of HLA molecules in primary tumors, these results provide direct evidence of native processing and presentation of the identified peptides on primary cancer tissues obtained from 201 lung cancer (including NSCLC and SCLC) patients.

[0138] The discovery pipeline XPRESIDENT® v2.1 (see, e.g., U.S. Patent No. 2013-0096016, the entire contents of which are incorporated herein by reference) enables the identification and selection of plausible over-presented peptide vaccine candidates based on direct relative quantification of HLA-restricted peptide levels on cancer tissues compared to several different non-cancerous tissues and organs. This was achieved by development of label-free differential quantification combining algorithms for sequence identification, spectral clustering, ion counting, retention time alignment, charge state deconvolution, and normalization using acquired LC-MS data processed with a proprietary data analysis pipeline.

[0139] Presentation levels were established, including error estimates for each peptide and sample. Peptides that are exclusively presented on tumor tissues and peptides that are over-presented in tumors compared to non-cancerous tissues and organs were identified.

[0140] HLA-peptide complexes from lung cancer (including NSCLC and SCLC) tissue samples were purified to isolate HLA-associated peptides and analyzed by LC-MS (see Example 1). All TUMAPs included in this application were identified on lung cancer (including NSCLC and SCLC) samples by this approach and their presentation on lung cancer (including NSCLC and SCLC) was confirmed.

[0141] TUMAPs identified on multiple lung cancers (including NSCLC and SCLC) and normal tissues were quantified using ion counts of label-free LC-MS data. The method assumes that the LC-MS signal area of ​​a peptide correlates with its abundance in the sample. All quantitative signals of a peptide in different LC-MS experiments were normalized based on central tendency, averaged per sample, and merged into a bar graph called the presentation profile. The presentation profile integrates different analytical methods such as protein database searching, spectral clustering, charge state deconvolution, and retention time alignment and normalization.

[0142] In addition to over-representation of peptides, mRNA expression of underlying genes was examined. mRNA data was obtained through RNASeq analysis of normal and cancer tissues (see Example 2, Figure 2). An additional source of normal tissue data was a publicly available database of RNA expression data derived from approximately 3000 normal tissue samples (Lonsdale, 2013). Peptides derived from proteins whose mRNAs are highly expressed in cancer tissues but very low or absent in vital normal tissues are preferably included in the present invention.

[0143] The present invention provides peptides useful for treating cancer / tumor, preferably lung cancer (including NSCLC and SCLC), which overly or exclusively present the peptides of the present invention.These peptides have been shown by mass spectrometry to be naturally presented by HLA molecules on primary human lung cancer (including NSCLC and SCLC) samples.

[0144] Many of the original genes / proteins (also referred to as "full-length proteins" or "basal proteins") from which the peptides are derived have been shown to be highly overexpressed in cancer compared to normal tissues, demonstrating the high tumor relevance of the original genes, where "normal tissue" in the context of the present invention shall mean either healthy lung cells or other normal tissue cells (see Example 2). Furthermore, the peptides themselves are strongly over-represented on tumor tissues, but not on normal tissues, where "tumor tissue" in the context of the present invention shall mean samples derived from patients suffering from lung cancer (including NSCLC and SCLC) (see Example 1).

[0145] HLA-bound peptides can be recognized by the immune system, particularly T lymphocytes, which can destroy cells that present the recognized HLA / peptide complex, such as lung cancer (including NSCLC and SCLC) cells that present the derived peptide.

[0146] The peptides of the invention have been shown to be capable of stimulating T cell responses and / or being over-presented, and therefore can be used according to the invention for the manufacture of antibodies and / or TCRs, such as soluble TCRs (see examples 3, 4). Furthermore, the peptides, when complexed with the respective MHC, can also be used for the manufacture of antibodies and / or TCRs, in particular TCRs, according to the invention. The respective methods are well known to those skilled in the art and can also be found in the respective references (see also below). The peptides of the invention are therefore useful for generating an immune response in a patient, by which tumor cells can be destroyed. The immune response in a patient can be induced by administering the described peptides, or suitable precursors (e.g. extended peptides, proteins, or nucleic acids encoding these peptides), directly to the patient, ideally in combination with agents that enhance immunogenicity (i.e. adjuvants). Since the target peptides of the invention are not presented in comparable copy numbers on normal tissues, the immune response resulting from such therapeutic vaccination can be expected to be highly specific against tumor cells, preventing the risk of unwanted autoimmune reactions against normal cells of the patient.

[0147] The present specification further relates to a T cell receptor (TCR) comprising an alpha chain and a beta chain ("alpha / beta TCR"). Also provided are peptides according to the invention which, when presented by an MHC molecule, are capable of binding to a TCR and an antibody.

[0148] The present specification also relates to fragments of the TCRs according to the invention, which are capable of binding to peptide antigens according to the invention when presented by HLA molecules. This term particularly relates to soluble TCR fragments, e.g. TCRs lacking the transmembrane portion and / or the constant region, single chain TCRs and fusions thereof, e.g. Igs.

[0149] The present specification also relates to nucleic acids, vectors, and host cells for expressing the TCRs and peptides of the present specification; and methods of using the same.

[0150] The term "T cell receptor" (abbreviated as TCR) refers to a heterodimeric molecule comprising an alpha polypeptide chain (alpha chain) and a beta polypeptide chain (beta chain), which heterodimeric receptor can bind to peptide antigens presented by HLA molecules. The term also includes the so-called gamma / delta TCRs.

[0151] In one embodiment, an embodiment provides a method of producing a TCR as described herein, the method comprising culturing a host cell capable of expressing the TCR under conditions suitable to promote expression of the TCR.

[0152] Another embodiment relates to a method described herein in which a sufficient amount of antigen is contacted with an antigen-presenting cell to load the antigen onto class I or II MHC molecules expressed on the surface of a suitable antigen-presenting cell or artificial antigen-presenting cell, or the antigen / class I or II MHC complex monomers are tetramerized to load the antigen onto class I or II MHC tetramers.

[0153] The α and β chains of α / β TCRs, and the γ and δ chains of γ / δ TCRs, are generally considered to have two "domains" each: a variable and a constant domain. The variable domain consists of a variable region (V) linked to a joining region (J). The variable domain may also include a leader region (L). The β and δ chains may also include a diversity region (D). The α and β constant domains may also include a C-terminal transmembrane (TM) domain that anchors the α and β chains to the cell membrane.

[0154] With respect to gamma / delta TCRs, the term "TCR gamma variable domain" as used herein refers to the junction of the TCR gamma V (TRGV) region without the leader region (L) and the TCR gamma J (TRGJ) region, and the term TCR gamma constant domain refers to the extracellular TRGC region or to a C-terminal truncated TRGC sequence. Similarly, the term "TCR delta variable domain" refers to the junction of the TCR delta V (TRDV) region without the leader region (L) and the TCR delta D / J (TRDD / TRDJ) region, and the term "TCR delta constant domain" refers to the extracellular TRDC region or to a C-terminal truncated TRDC sequence.

[0155] The TCRs herein preferably bind to peptide-HLA molecule complexes with a binding affinity (KD) of about 100 μM or less, about 50 μM or less, about 25 μM or less, or about 10 μM or less. More preferred are high affinity TCRs having a binding affinity of about 1 μM or less, about 100 nM or less, about 50 nM or less, or about 25 nM or less. Non-limiting examples of preferred binding affinity ranges for the TCRs of the present invention include about 1 nM to about 10 nM; about 10 nM to about 20 nM; about 20 nM to about 30 nM; about 30 nM to about 40 nM; about 40 nM to about 50 nM; about 50 nM to about 60 nM; about 60 nM to about 70 nM; about 70 nM to about 80 nM; about 80 nM to about 90 nM; and about 90 nM to about 100 nM.

[0156] As used herein, in the context of TCRs herein, "specific binding" and grammatical variants thereof are used to mean a TCR that has a binding affinity (KD) of 100 μM or less for a peptide-HLA molecule complex.

[0157] The α / β heterodimeric TCRs herein may have a disulfide bond introduced between their constant domains. Preferred TCRs of this type include those having a TRAC constant domain sequence and a TRBC1 or TRBC2 constant domain sequence, with the proviso that Thr48 of TRAC and Ser57 of TRBC1 or TRBC2 are replaced by cysteine ​​residues which form a disulfide bond between the TRAC constant domain sequence and the TRBC1 or TRBC2 constant domain sequence of the TCR.

[0158] In the presence or absence of the above-described introduced interchain bond, the α / β heterodimeric TCR of the present specification may have a TRAC constant domain sequence and a TRBC1 or TRBC2 constant domain sequence, and the TRAC constant domain sequence of the TCR and the TRBC1 or TRBC2 constant domain sequence may be linked by a native disulfide bond between Cys4 of exon 2 of TRAC and Cys2 of exon 2 of TRBC1 or TRBC2.

[0159] The TCRs herein may comprise a detectable label selected from the group consisting of a radionuclide, a fluorophore, and biotin. The TCRs herein may be conjugated to a therapeutically active agent, such as a radionuclide, a chemotherapeutic agent, or a toxin.

[0160] In one embodiment, the TCRs herein having at least one mutation in the alpha chain and / or having at least one mutation in the beta chain have modified glycosylation compared to the non-mutated TCR.

[0161] In one embodiment, a TCR comprising at least one mutation in the TCR alpha and / or beta chain has at least twice the binding affinity and / or binding half-life to a peptide-HLA molecule complex as a TCR comprising a non-mutated TCR alpha and / or beta chain. The affinity enhancement of tumor-specific TCRs and their utilization depend on the existence of a window of optimal TCR affinity. The existence of such a window is based on the observation that TCRs specific for HLA-A2-restricted pathogens generally have about 10-fold lower KD values ​​compared to TCRs specific for HLA-A2-restricted tumor-associated self-antigens. Although the KD values ​​may be in a slightly different range for TCRs specific for pathogens restricted by other alleles compared to tumor-associated self-antigens, there is no general difference between different alleles in terms of their potential to generate TCRs. It is now known that tumor antigens have the potential to be immunogenic, but because tumors arise from an individual's own cells, only mutant proteins or proteins with altered translational processing are considered foreign by the immune system. Upregulated or overexpressed antigens (so-called self-antigens) do not necessarily induce a functional immune response against tumors; T cells expressing highly reactive TCRs against these antigens are negatively selected in the thymus by a process known as central immune tolerance, i.e., only T cells with low affinity TCRs against self-antigens remain. Thus, the affinity of the TCR or variants herein for peptides can be increased by methods well known in the art.

[0162] The present specification further relates to a method for identifying and isolating TCRs according to the present specification, comprising the steps of incubating PBMCs from healthy donors negative for this allele with HLA / peptide monomers, incubating the PBMCs with tetrameric phycoerythrin (PE), and isolating high avidity T cells by fluorescence-activated cell sorting (FACS) Calibur analysis.

[0163] The present specification further relates to a method for identifying and isolating TCRs according to the present specification, comprising the steps of obtaining a transgenic mouse carrying a fully human TCR αβ gene locus (1.1 and 0.7 Mb) whose T cells express a diverse human TCR repertoire that complements the mouse TCR deficiency, immunizing the mouse with peptide, culturing PBMC obtained from the transgenic mouse with tetrameric phycoerythrin (PE), and isolating high avidity T cells by fluorescence-activated cell sorting (FACS) Calibur analysis.

[0164] In one embodiment, to obtain T cells expressing the TCR of the present invention, the nucleic acid encoding the TCR-α and / or TCR-β chain of the present invention is cloned into an expression vector such as a gamma retrovirus or lentivirus. The recombinant virus is produced and then tested for function, such as antigen specificity and functional binding activity. An aliquot of the final product is then used to transduce a target T cell population (generally purified from the patient's PBMC) and expanded before infusion into the patient.

[0165] In another embodiment, to obtain T cells expressing the TCRs herein, TCR RNA is synthesized by techniques known in the art, such as, for example, in vitro transcription. The in vitro synthesized TCR RNA is then introduced by electroporation into primary CD8+ T cells obtained from healthy donors to re-express the tumor-specific TCR-α and / or TCR-β chains.

[0166] To increase expression, the nucleic acids encoding the TCRs herein may be operably linked to strong promoters such as retroviral long terminal repeat (LTR), cytomegalovirus (CMV), murine stem cell virus (MSCV) U3, phosphoglycerate kinase (PGK), β-actin, ubiquitin, and simian virus 40 (SV40) / CD43 composite promoter, elongation factor (EF)-1a, and spleen focus forming virus (SFFV) promoter. In a preferred embodiment, the promoter is heterologous to the nucleic acid to be expressed.

[0167] In addition to a strong promoter, the TCR expression cassettes herein may contain additional elements that can enhance transgene expression, including the central polypurine tract (cPPT), which facilitates nuclear translocation of the lentiviral construct (Follenzi et al., 2000), and the woodchuck hepatitis virus post-transcriptional regulator (wPRE), which increases RNA stability and therefore enhances levels of transgene expression (Zufferey et al., 1999).

[0168] The α and β chains of the TCR of the present invention may be encoded by nucleic acids on separate vectors or may be encoded by polynucleotides on the same vector.

[0169] Achieving high levels of TCR surface expression requires high levels of transcription of both the TCR-α and TCR-β chains of the introduced TCR. To do this, the TCR-α and TCR-β chains herein may be cloned into a bicistronic construct in a single vector, which has been shown to overcome this obstacle. The use of a viral internal ribosome entry site between the TCR-α and TCR-β chains results in coordinated expression of both chains, since the TCR-α and TCR-β chains are generated from a single transcript that is split into two proteins during translation to ensure the generation of equimolar TCR-α and TCR-β chains (Schmitt et al., 2009).

[0170] The nucleic acids encoding the TCRs herein may be codon-optimized to increase expression from host cells. Redundancy in the genetic code allows some amino acids to be coded for by more than one codon, but certain codons are less "optimal" than others due to the relative availability of compatible tRNAs as well as other factors (Gustafsson et al., 2004). Modifying the TCR-α and TCR-β gene sequences so that each amino acid is coded for by the optimal codon for mammalian gene expression, as well as removing mRNA instability motifs or potential splice sites, has been shown to significantly enhance TCR-α and TCR-β gene expression (Scholten et al., 2006).

[0171] Furthermore, mispairing between the introduced and endogenous TCR chains can lead to the acquisition of specificity that poses significant autoimmune risks. For example, the formation of mixed TCR dimers may reduce the number of CD3 molecules available to form properly paired TCR complexes, thus significantly reducing the functional avidity of cells expressing the introduced TCR (Kuball et al., 2007).

[0172] To reduce mispairing, the C-terminal regions of the introduced TCR chains herein may be modified to increase interchain affinity while decreasing the ability of the introduced chains to pair with endogenous TCRs. These strategies include replacing the C-terminal regions of human TCR-α and TCR-β with their murine counterparts (murinized C-terminal regions); creating a second interchain disulfide bond in the C-terminal regions by introducing a second cysteine ​​residue in both the TCR-α and TCR-β chains of the introduced TCR (cysteine ​​modification); exchanging interacting residues in the C-terminal regions of the TCR-α and TCR-β chains ("knobs-in-holes"); and fusing the variable regions of the TCR-α and TCR-β chains directly to CD3ζ (CD3ζ fusion) (Schmitt et al., 2009).

[0173] In one embodiment, the host cell is genetically engineered to express the TCR of the present disclosure. In a preferred embodiment, the host cell is a human T cell or T cell precursor. In some embodiments, the T cell or T cell precursor is obtained from a cancer patient. In other embodiments, the T cell or T cell precursor is obtained from a healthy donor. The host cell herein can be allogeneic or autologous with respect to the patient being treated. In one embodiment, the host is a gamma / delta T cell transformed to express an alpha / beta TCR.

[0174] A "pharmaceutical composition" is a composition suitable for administration to humans in a medical context. Preferably, the pharmaceutical composition is sterile and manufactured in accordance with GMP guidelines.

[0175] The pharmaceutical composition comprises the peptide either in free form or in the form of a pharmaceutically acceptable salt (see also above).In one embodiment, the peptide described herein is in the form of a pharmaceutically acceptable salt.In another embodiment, the peptide in the form of a pharmaceutical salt is in crystalline form.

[0176] In one aspect, pharma- ceutically acceptable salts as described herein refer to salts that have a toxicity profile within an acceptable range for pharmaceutical use.

[0177] As used herein, "pharmaceutical acceptable salts" refers to derivatives of the disclosed peptides, where the peptides are modified by producing acid or base salts of the drug. For example, acid salts are prepared from the free base (where the neutral form of the drug typically has a neutral -NH2 group) by reaction with a suitable acid. Suitable acids for preparing acid salts include both organic acids, such as, for example, acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, malic acid, malonic acid, succinic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and inorganic acids, such as, for example, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like. Conversely, preparations of base salts of acid moieties that may be present on the peptides are prepared using pharmaceutical acceptable bases, such as sodium hydroxide, potassium hydroxide, ammonium hydroxide, calcium hydroxide, trimethylamine, and the like.

[0178] In one aspect, pharmaceutically acceptable salts may enhance the solubility and / or stability of the peptides described herein.In another aspect, the pharmaceutical salts described herein may be prepared by conventional means from the corresponding carrier peptides or complexes, for example, by reacting a suitable acid or base with the peptides or complexes as described herein.In another aspect, the pharmaceutically acceptable salts are in crystalline or semi-crystalline form. In yet another embodiment, pharma- ceutically acceptable salts include those described, for example, in Handbook of Pharmaceutical Salts: Properties, Selection, and Use By P.H. Stahl and C.G. Wermuth (Wiley-VCH 2002); and L.D. Bighley, S.M. Berge, D.C. Monkhouse, in "Encyclopedia of Pharmaceutical Technology". Eds. J. Swarbrick and J.C. Boylan, Vol. 13, Marcel Dekker, Inc., New York, Basel, Hong Kong 1995, pp. 453-499, each of which is incorporated herein by reference in its entirety.

[0179] In a particularly preferred embodiment, the pharmaceutical composition comprises the peptide as a salt of acetic acid (acetate), trifluoroacetic acid or hydrochloric acid (chloride).

[0180] Preferably, the medicament of the present invention is an immunotherapy such as a vaccine. It may be administered id, im, sc, ip, and iv directly to the patient, to the affected organ, or systemically, or applied ex vivo to cells derived from the patient or human cell lines, which are subsequently administered to the patient, or used ex vivo to select a subpopulation of immune cells derived from the patient, which are then readministered to the patient. When the nucleic acid is administered ex vivo to cells, it may be useful to transfect the cells to co-express an immune stimulating cytokine, such as interleukin 2. The peptide may be substantially pure, or combined with an immune stimulating adjuvant (see below), or used in combination with an immunostimulating cytokine, or administered by a suitable delivery system, such as, for example, liposomes. The peptide may also be conjugated to a suitable carrier, such as keyhole limpet hemocyanin (KLH) or mannan (see WO 95 / 18145 and (Longenecker et al., 1993)). The peptide may also be labeled, may be a fusion protein, or may be a hybrid molecule. The peptides whose sequences are described in the present invention are predicted to stimulate CD4 or CD8 T cells. However, the stimulation of CD8 T cells is more efficient in the presence of the help provided by CD4 T helper cells. Thus, for MHC class I epitopes that stimulate CD8 T cells, the fusion partner or section of the hybrid molecule appropriately provides an epitope that stimulates CD4 positive T cells. CD4 and CD8 stimulating epitopes are well known in the art and include those identified in the present invention.

[0181] In one embodiment, the vaccine comprises at least one peptide having an amino acid sequence as set forth in SEQ ID NO: 1 to SEQ ID NO: 489 and at least one additional peptide, preferably 2 to 50, more preferably 2 to 25, even more preferably 2 to 20, most preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 or 18 peptides. The peptides may be derived from one or more specific TAAs and may bind to MHC class I molecules.

[0182] A further aspect of the invention provides nucleic acids (e.g. polynucleotides) encoding the peptides or peptide variants of the invention. The polynucleotide may be, for example, either single-stranded and / or double-stranded DNA, cDNA, PNA, RNA or a combination thereof, or may be a native or stabilized form of polynucleotide, such as a polynucleotide with a phosphorothioate backbone, which may or may not contain introns, so long as it encodes the peptide. Of course, only peptides containing natural amino acid residues linked by naturally occurring peptide bonds may be encoded by the polynucleotide. A still further aspect of the invention provides an expression vector capable of expressing the polypeptide according to the invention.

[0183] A variety of methods have been developed to link polynucleotides, particularly DNA, to vectors, for example, via complementary cohesive ends. For example, a complementary homopolymer sequence can be added to the DNA segment to be inserted into the vector DNA. The vector and DNA segment are then linked by hydrogen bonding between the complementary homopolymer tails to form a recombinant DNA molecule.

[0184] Synthetic linkers containing one or more restriction sites provide an alternative method of joining DNA segments to vectors. Synthetic linkers containing a variety of restriction endonuclease sites are commercially available from several sources, including International Biotechnologies Inc., New Haven, Connecticut, USA.

[0185] A desirable method for modifying the DNA encoding the polypeptide of the present invention is to use the polymerase chain reaction as disclosed in Saiki RK, et al. (Saiki et al., 1988). This method may be used to introduce the DNA into a suitable vector, for example, by engineering suitable restriction sites, or it may be used to modify the DNA in other useful ways known in the art. If a viral vector is used, a poxvirus or adenovirus vector is preferred.

[0186] The DNA (or RNA in the case of retroviral vectors) may then be expressed in a suitable host to produce a polypeptide comprising the peptide or variant of the invention. Thus, according to known techniques, appropriately modified in view of the teachings contained herein, the DNA encoding the peptide or variant of the invention may be used to construct an expression vector, which is then used to transform a suitable host cell for the expression and production of the polypeptide of the invention. Such techniques include, for example, those disclosed in U.S. Pat. Nos. 4,440,859, 4,530,901, 4,582,800, 4,677,063, 4,678,751, 4,704,362, 4,710,463, 4,757,006, 4,766,075, and 4,810,648.

[0187] The DNA (or in the case of retroviral vectors, RNA) encoding the polypeptide constituting the compound of the invention may be joined to a wide variety of other DNA sequences for introduction into an appropriate host. The companion DNA will depend on the nature of the host, the manner of the introduction of the DNA into the host, and whether episomal maintenance or integration is desired.

[0188] Generally, DNA is inserted into an expression vector such as a plasmid in the proper direction and correct reading frame for expression. If necessary, DNA may be linked to the appropriate transcriptional and translational regulatory control nucleotide sequences recognized by the desired host, such controls are generally available in the expression vector. The vector is then introduced into the host through standard techniques. Generally, not all hosts are transformed by the vector. Therefore, it becomes necessary to select transformed host cells. One selection technique involves incorporating into an expression vector a DNA sequence with any necessary control elements that encodes a selectable trait in transformed cells, such as antibiotic resistance.

[0189] Alternatively, the gene for such selectable trait can be on another vector, which is used to cotransform the desired host cell.

[0190] Host cells transformed with the recombinant DNA of the present invention can then be cultured under appropriate conditions known to those of skill in the art for a sufficient period of time to allow for expression of the polypeptide, which can then be recovered, given the teachings disclosed herein.

[0191] Numerous expression systems are known, including bacteria (e.g., E. coli and Bacillus subtilis), yeast (e.g., Saccharomyces cerevisiae), filamentous fungi (e.g., Aspergillus), plant cells, animal cells, and insect cells. Preferably, the expression system may be mammalian cells, such as CHO cells, available from the ATCC Cell Biology Collection.

[0192] A typical mammalian cell vector plasmid for constitutive expression comprises a CMV or SV40 promoter with an appropriate polyA tail and a resistance marker such as neomycin. One example is pSVL available from Pharmacia, Piscataway, NJ, USA. An example of an inducible mammalian expression vector, pMSG, is also available from Pharmacia. Useful yeast plasmid vectors are pRS403-406 and pRS413-416, typically available from Stratagene Cloning Systems, La Jolla, Calif., 92037. Plasmids pRS403, pRS404, pRS405, and pRS406 are Yeast Integrating Plasmids (YIps) and incorporate the yeast selectable markers HIS3, TRP1, LEU2, and URA3. Plasmid pRS413-416 is a Yeast Centromeric Plasmid (Ycps). CMV promoter-based vectors (e.g., from Sigma-Aldrich) provide transient or stable expression, cytoplasmic expression or secretion, and N- or C-terminal tagging with various combinations of FRAG, 3xFLAG, c-myc, or MAT. These fusion proteins allow recombinant proteins to be detected, purified, and analyzed. Dual-label fusions offer versatility in detection.

[0193] The strong human cytomegalovirus (CMV) promoter regulatory region increases constitutive protein expression levels as high as 1 mg / L in COS cells. In less potent cell lines, protein levels are typically around 0.1 mg / L. The presence of the SV40 origin of replication results in high levels of DNA replication in SV40 replication-permissive COS cells. CMV vectors may contain, for example, the pMB1 (a derivative of pBR322) origin of replication in bacterial cells, the b-lactamase gene for ampicillin resistance selection in bacteria, hGH polyA, and the f1 origin. Vectors containing a preprotrypsin leader (PPT) sequence may direct FRAG fusion protein secretion into the culture medium for purification using anti-FRAG antibodies, resins, and plates. Other vectors and expression systems for use with a variety of host cells are well known in the art.

[0194] In another embodiment, two or more peptides or peptide variants of the invention are encoded and thus expressed sequentially (similar to a "beads and beads" construct), whereby the peptides or peptide variants may be linked or fused together by a stretch of linker amino acids, such as LLLLLL, or may be linked without any additional peptide between them. These constructs may also be used for cancer therapy and may induce immune responses involving both MHC I and MHC II.

[0195] The present invention also relates to host cells transformed with the polynucleotide vector constructs of the present invention. Host cells can be either prokaryotic or eukaryotic. Bacterial cells may be preferred prokaryotic host cells in some circumstances, typically E. coli strains such as E. coli DH5 available from Bethesda Research Laboratories Inc., Bethesda, MD, USA, and RR1 (ATCC No. 31343) available from the American Type Culture Collection (ATCC), Rockville, MD, USA. Preferred eukaryotic host cells include yeast, insect, and vertebrate cells such as mammalian cells, preferably those derived from mouse, rat, monkey, or human fibroblast and colon cell lines. Yeast host cells include YPH499, YPH500, and YPH501, which are generally available from Stratagene Cloning Systems, La Jolla, CA 92037. Preferred mammalian host cells include Chinese hamster ovary (CHO) cells available from ATCC as CCL61, NIH Swiss mouse embryo cells NIH / 3T3 available from ATCC as CRL1658, monkey kidney derived COS-1 cells available from ATCC as CRL1650, and human fetal kidney cells 293 cells. Preferred insect cells are Sf9 cells which can be transfected with baculovirus expression vectors. Reviews on the selection of suitable host cells for expression can be found, for example, in the textbook "Methods in Molecular Biology Recombinant Gene Expression, Reviews and Protocols," Part One, Second Edition, ISBN 978-1-58829-262-9 by Paulina Balbas and Argelia Lorence, and other references known to those skilled in the art.

[0196] Transformation of suitable cell hosts with the DNA constructs of the present invention is accomplished by well-known methods that typically depend on the type of vector used. For transformation of prokaryotic host cells, see, for example, Cohen et al. (Cohen et al., 1972) and (Green and Sambrook, 2012). Transformation of yeast cells is described in Sherman et al. (Sherman et al., 1986). The method of Beggs (Beggs, 1978) is also useful. For vertebrate cells, reagents useful for transfecting such cells, such as, for example, calcium phosphate and DEAE-dextran or liposome formulations, are available from Life Technologies Inc., Gaithersburg, Maryland, 20877. Electroporation is also useful for transforming and / or transfecting cells and is well known in the art for transforming yeast cells, bacterial cells, insect cells, and vertebrate cells.

[0197] Successfully transformed cells, i.e., cells containing the DNA construct of the present invention, can be identified by well-known techniques such as PCR. Alternatively, antibodies can be used to detect the presence of protein in the supernatant.

[0198] It will be appreciated that certain host cells of the invention, such as, for example, bacteria, yeast, and insect cells, are useful in preparing the peptides of the invention. However, other host cells may be useful in certain therapeutic methods. For example, antigen-presenting cells, such as dendritic cells, may be usefully used to express the peptides of the invention so that they may be loaded into the appropriate MHC molecules. Thus, the invention provides a host cell comprising a nucleic acid or expression vector according to the invention.

[0199] In a preferred embodiment, the host cell is an antigen-presenting cell, particularly a dendritic cell or an antigen-presenting cell.The APC loaded with recombinant fusion protein containing prostatic acid phosphatase (PAP) was approved by the US Food and Drug Administration (FDA) on April 20, 2010 to treat asymptomatic or minimally symptomatic metastatic HRPC (Sipuleucel-T) (Rini et al., 2006; Small et al., 2006).

[0200] A further aspect of the invention provides a method for producing a peptide or a variant thereof comprising the steps of culturing a host cell and isolating the peptide from the host cell or its culture medium.

[0201] In another embodiment, the peptide, nucleic acid or expression vector of the present invention is used in medicine. For example, the peptide or its variants may be formulated for intravenous (iv), subcutaneous (sc), intradermal (id), intraperitoneal (ip) or intramuscular (im) injection. Preferred methods of peptide injection include sc, id, ip, im, and iv. Preferred methods of DNA injection include id, im, sc, ip, and iv. For example, a dose of 50 μg to 1.5 mg, preferably 125 μg to 500 μg of peptide or DNA may be administered, depending on the respective peptide or DNA. This range of doses has been used successfully in previous clinical trials (Walter et al., 2012).

[0202] The polynucleotides used for active vaccination may be substantially pure or may be contained in a suitable vector or delivery system. The nucleic acid may be DNA, cDNA, PNA, RNA or a combination thereof. Methods for designing and introducing such nucleic acids are well known in the art. A review is provided, for example, by Teufel et al. (Teufel et al., 2005). Polynucleotide vaccines are easy to prepare, but the mechanism of action of these vectors in inducing immune responses is not fully understood. Suitable vectors and delivery systems include viral DNA and / or RNA, such as adenovirus, vaccinia virus, retrovirus, herpes virus, adeno-associated virus or hybrid-based systems containing components of two or more viruses. Non-viral delivery systems include cationic lipids and cationic polymers and are well known in the DNA delivery art. Physical delivery, such as via a "gene gun", may also be used. The peptide or peptides encoded by the nucleic acid may be a fusion protein with an epitope that stimulates T cells of the respective inverse CDR, for example as described above.

[0203] The medicament of the present invention may also include one or more adjuvants. Adjuvants are substances that non-specifically promote or enhance immune responses (e.g., immune responses to antigens mediated by CD8 positive T cells and helper T (TH) cells) and are therefore considered useful in the medicament of the present invention. Suitable adjuvants include 1018 ISS, aluminum salts, AMPLIVAX®, AS15, BCG, CP-870,893, CpG7909, CyaA, dSLIM, flagellin or flagellin-derived TLR5 ligand, FLT3 ligand, GM-CSF, IC30, IC31, imiquimod (ALDARA®), resiquimod, ImuFact IMP321, interleukins such as IL-2, L-13 and IL-21, interferon-α or -β or their PEGylated derivatives, IS patch, ISS, ISCOMATRIX, ISCOM, JuvImmune®, LipoVac, MALP2, MF59, monophosphoryl lipid A, Montanide IMS1312, Montanide ISA206, Montanide ISA50V, Montanide ISA-51, water in oil and and oil-in-water emulsions, OK-432, OM-174, OM-197-MP-EC, ONTAK, OspA, PepTel® vector system, poly(lactide-co-glycolide) [PLG]-based and dextran microparticles, talactoferrin SRL172, virosomes and other virus-like particles, YF-17D, VEGF trap, R848, β-glucan, Pam3Cys, Aquila's QS21 stimulon derived from saponin, mycobacterial extracts and synthetic bacterial cell wall mimics, and other proprietary adjuvants such as Ribi's Detox or Quil or Superfos. Adjuvants such as Freund's or GM-CSF are preferred. Several immunological adjuvants (e.g. MF59) specific for dendritic cells and their preparations have been previously described (Allison and Krummel, 1995). Cytokines may also be used.Several cytokines have been directly implicated in influencing the migration of dendritic cells to lymphoid tissues (e.g., TNF-), accelerating the maturation of dendritic cells into efficient antigen-presenting cells for T lymphocytes (e.g., GM-CSF, IL-1, and IL-4) (U.S. Pat. No. 5,849,589, the entire contents of which are specifically incorporated by reference herein), and acting as immune enhancers (e.g., IL-12, IL-15, IL-23, IL-7, IFN-α, IFN-β) (Gabrilovich et al., 1996).

[0204] CpG immunostimulatory oligonucleotides have also been reported to enhance adjuvant effects in a vaccine environment. Without being bound by theory, CpG oligonucleotides act by activating the innate (non-adaptive) immune system through Toll-like receptors (TLRs), primarily TLR9. CpG-induced TLR9 activation enhances antigen-specific humoral and cellular responses to a wide variety of antigens, including peptide or protein antigens, live or killed viruses, dendritic cell vaccines, autologous cell vaccines, and polysaccharide conjugates in both prophylactic and therapeutic vaccines. More importantly, it enhances dendritic cell maturation and differentiation, leading to enhanced activation of TH1 cells and potent cytotoxic T lymphocyte (CTL) generation, even in the absence of CD4 T cell help. The TH1 bias induced by TLR9 stimulation is maintained even in the presence of vaccine adjuvants such as alum or incomplete Freund's adjuvant (IFA), which normally promote a TH2 bias. CpG oligonucleotides, when formulated or co-administered with other adjuvants, or in formulations such as microparticles, nanoparticles, lipid emulsions or similar formulations, still show higher adjuvant activity, which is especially necessary to induce strong responses when the antigen is relatively weak. They also accelerate immune responses, and in some experiments allow for almost two orders of magnitude reduction in antigen dose with antibody response equivalent to the total vaccine dose without CpG (Krieg, 2006). US Patent No. 6,406,705 B1 describes the combination of CpG oligonucleotides, non-nucleic acid adjuvants, and antigens to induce antigen-specific immune responses. The CpG TLR9 antagonist is dSLIM (double stem loop immunomodulator) from Mologen (Berlin, Germany), which is a preferred component of the pharmaceutical composition of the present invention. Other TLR binding molecules, such as RNA-binding TLR7, TLR8 and / or TLR9, may also be used.

[0205] Other examples of useful adjuvants include chemically modified CpG (e.g., CpR, Idera); dsRNA analogs such as poly(I:C) and their derivatives (e.g., AmpliGen®, Hiltonol®, poly(ICLC), poly(IC-R), poly(I:C12U), non-CpG bacterial DNA or RNA; and cyclophosphamide, sunitinib, bevacizumab®, Celebrex, NCX-4016, sildenafil, tadalafil, vardenafil, sorafenib, temozolomide, temsirolimus, XL-999, CP-547632, pazopanib, VEGF Immunoactive small molecules and antibodies, such as Trap, ZD2171, AZD2171, anti-CTLA4; other antibodies targeting key structures of the immune system (e.g., anti-CD40, anti-TGFβ, anti-TNFα receptor); SC58175, which may act therapeutically and / or as adjuvants. The amounts and concentrations of adjuvants and additives useful in the context of the present invention can be readily determined by one of skill in the art without undue experimentation.

[0206] Preferred adjuvants are anti-CD40, imiquimod, resiquimod, GM-CSF, cyclophosphamide, sunitinib, bevacizumab, interferon alpha, CpG oligonucleotides and derivatives, poly(I:C) and derivatives, RNA, sildenafil, and PLG or virosome microparticle formulations.

[0207] In a preferred embodiment of the pharmaceutical composition according to the invention, the adjuvant is selected from the group consisting of colony stimulating factors such as granulocyte-macrophage colony stimulating factor (GM-CSF, sargramostim), cyclophosphamide, imiquimod, resiquimod, and interferon alpha.

[0208] In a preferred embodiment of the pharmaceutical composition according to the invention, the adjuvant is selected from the group consisting of colony stimulating factors such as granulocyte macrophage colony stimulating factor (GM-CSF, sargramostim), cyclophosphamide, imiquimod, and resiquimod. In a preferred embodiment of the pharmaceutical composition according to the invention, the adjuvant is cyclophosphamide, imiquimod or resiquimod. Even more preferred adjuvants are Montanide IMS 1312, Montanide ISA 20, Montanide ISA 50V, Montanide ISA-51, poly-ICLC (Hiltonol®), and anti-CD40mAB or combinations thereof.

[0209] The composition is used for parenteral administration, such as subcutaneous, intradermal, intramuscular, or oral administration. For this purpose, the peptide and optionally other molecules are dissolved or suspended in a pharma- ceutically acceptable, preferably aqueous, carrier. The composition may further contain excipients, such as buffers, binding agents, blasting agents, diluents, flavors, lubricants, etc. The peptide may also be administered together with immune stimulants, such as cytokines. A detailed list of excipients that may be used in such compositions may be taken, for example, from A. Kibbe, Handbook of Pharmaceutical Excipients (Kibbe, 2000). The composition may be used for the prevention, prophylaxis and / or treatment of adenomatous or cancerous diseases. Exemplary formulations are, for example, in EP 2112253.

[0210] In one embodiment, the peptide or another molecule described herein may be combined with an aqueous carrier.In one embodiment, the aqueous carrier is selected from ion exchangers; alumina; aluminum stearate; magnesium stearate; lecithin; serum proteins such as human serum albumin; buffer substances such as phosphates, glycine, sorbic acid, and potassium sorbate; partial glyceride mixtures of saturated vegetable fatty acids; salts or electrolytes such as protamine sulfate, disodium hydrogen phosphate, dicalcium phosphate, potassium hydrogen phosphate, sodium chloride, and zinc salts; colloidal silica; magnesium trisilicate; polyvinylpyrrolidone; polyvinylpyrrolidone-vinyl acetate; cellulose-based substances (e.g., microcrystalline cellulose, hydroxypropyl methylcellulose, hydroxypropyl methylcellulose acetate succinate, hydroxypropyl methylcellulose phthalate); starch; lactose monohydrate; mannitol; trehalose sodium lauryl sulfate; and croscarmellose sodium; polyethylene glycol; sodium carboxymethylcellulose; polyacrylates; polymethacrylates, waxes; polyethylene-polyoxypropylene block polymers; polyethylene glycol; and wool fat.

[0211] In one embodiment, the aqueous carrier contains multiple components, such as water, combined with non-aqueous carrier components, such as those described herein. In another embodiment, the aqueous carrier, when combined with the peptides or other molecules described herein, can provide improved properties, such as, for example, improved solubility, efficacy, and / or improved immunotherapy. The composition may further contain excipients, such as buffers, binders, blasting agents, diluents, flavors, lubricants, and the like. "Pharmaceutically acceptable diluents" include, for example, physiologically compatible solvents, bulking agents, stabilizers, dispersion media, coatings, antibacterial and antifungal agents, isotonicity agents, and absorption delaying agents. Examples of pharmaceutically acceptable diluents include one or more of saline, phosphate buffered saline, dextrose, glycerol, ethanol, and the like, and combinations thereof. In many cases, it is preferable to include one or more isotonicity agents in the composition, such as, for example, sugars, such as trehalose and sucrose, polyalcohols, such as mannitol and sorbitol, or sodium chloride. Pharmaceutically acceptable substances such as wetting agents or minor amounts of wetting or emulsifying agents, preservatives or auxiliary substances such as buffers are also within the scope of the present invention. Additionally, the compositions may contain excipients such as buffers, binding agents, blasting agents, diluents, flavoring agents, and lubricants.

[0212] It is important to understand that the immune response induced by the vaccine according to the invention attacks cancers at different cell division stages and different developmental stages. Moreover, different cancer-associated signaling pathways are attacked. This is an advantage over vaccines that may only address one or a few targets, leading to easy adaptation of the tumor to the attack (tumor escape). Moreover, not all individual tumors express the same pattern of antigens. Thus, the combination of several tumor-associated peptides ensures that each and every tumor has at least some of the targets. The composition is designed with the expectation that each tumor expresses some of the antigens, covering several independent pathways necessary for tumor growth and maintenance. Thus, the vaccine can be easily used "off the shelf" for a larger patient population. This means that the pre-selection of patients to be treated with the vaccine can be limited to HLA typing and does not require any additional biomarker assessment of antigen expression, but still ensures that several targets are simultaneously attacked by the induced immune response, which is important for efficacy (Banchereau et al., 2001; Walter et al., 2012).

[0213] As used herein, the term "scaffold" refers to a molecule that specifically binds to a (e.g., antigenic) determinant. In one embodiment, the scaffold can also direct the entity to which it is attached (e.g., a (second) antigen-binding moiety) to a type target site, such as, for example, a specific tumor cell or tumor stroma bearing an antigenic determinant (e.g., a peptide-MHC complex as described herein). In another embodiment, the scaffold can activate signaling through its target antigen, such as, for example, a T cell receptor complex antigen. Scaffolds include, but are not limited to, antibodies and fragments thereof, antibody antigen-binding domains comprising an antibody heavy chain variable region and an antibody light chain variable region, binding proteins comprising at least one ankyrin repeat motif and a single domain antigen-binding (SDAB) molecule, aptamers, (soluble) TCRs, and (modified) cells such as allogeneic or autologous T cells. To assess whether a molecule is a scaffold that binds to a target, a binding assay can be performed.

[0214] "Specific" binding means that the scaffold binds to the peptide-MHC-complex of interest better than other natural peptide-MHC-complexes, so that the scaffold equipped with an active molecule capable of killing cells bearing a specific target cannot kill other cells that do not have the specific target but present other peptide-MHC complexes. If the peptide of the cross-reactive peptide-MHC is not naturally occurring, i.e., does not originate from the human HLA peptidome, binding to other peptide-MHC complexes is irrelevant. Tests to evaluate target cell killing are well known in the art. They should be performed using target cells (primary cells or cell lines) with unmodified peptide-MHC presentation, or cells loaded with peptide to reach naturally occurring peptide-MHC levels.

[0215] Each scaffold may comprise a label, which provides that the binding scaffold may be detected by determining the presence or absence of the signal provided by the label. For example, the scaffold may be labeled with a fluorescent dye or any other applicable cell marker molecule. Such marker molecules are well known in the art. For example, the fluorescent label provided by a fluorescent dye may provide visualization of the bound aptamer by fluorescence or laser scanning microscopy or flow cytometry.

[0216] Each scaffold can be conjugated to a second active molecule, such as, for example, IL-21, anti-CD3, and anti-CD28.

[0217] For further information regarding polypeptide scaffolds, see, e.g., the Background section of WO 2014 / 071978 A1 and the references cited therein.

[0218] The present invention further relates to aptamers.Aptamers (see, for example, WO 2014 / 191359 and the references cited therein) are short single-stranded nucleic acid molecules that can fold into a predetermined three-dimensional structure and recognize specific target structures.They have appeared to be a suitable alternative for developing targeted therapy.Aptamers have been shown to selectively bind to a variety of complex targets with high affinity and specificity.

[0219] Aptamers that recognize molecules located on the cell surface have been identified within the past decade, providing a means to develop diagnostic and therapeutic approaches. Aptamers have been shown to be nearly free of toxicity and immunogenicity, making them promising candidates for biomedical applications. Indeed, aptamers, such as the prostate-specific membrane antigen-recognizing aptamer, have been successfully used for targeted therapy and have been shown to function in xenograft in vivo models. Furthermore, aptamers that recognize specific tumor cell lines have been identified.

[0220] DNA aptamers can be selected to exhibit broad-spectrum recognition properties against various cancer cells, especially those derived from solid tumors, while not recognizing non-tumorigenic and primary healthy cells. If an identified aptamer not only recognizes a specific tumor subtype, but rather interacts with a range of tumors, this makes the aptamer applicable as a so-called broad-spectrum diagnostic and therapeutic agent.

[0221] Furthermore, investigation of the cell binding behavior by flow cytometry showed that the aptamer displayed very good apparent affinity in the nanomolar range.

[0222] Aptamers are useful for diagnostic and therapeutic purposes. Furthermore, it has been shown that some aptamers are taken up by tumor cells and thus can function as molecular vehicles for targeted delivery of anticancer drugs, such as siRNA, into tumor cells.

[0223] Aptamers can be selected using cell SELEX (enriched evolution by in vitro sequencing) technology against complex targets such as cells and tissues, and against peptide complexes comprising, and preferably consisting of, any of the sequences set forth in SEQ ID NO:1 to SEQ ID NO:489 according to the present invention and an MHC molecule.

[0224] Using the peptides of the present invention, specific antibodies against MHC / peptide complexes can be produced and developed. These can be used for therapeutics to target toxins or radioactive materials to diseased tissues. Another use of these antibodies can be to target radionuclides to diseased tissues for imaging purposes such as PET. This use can help detect small metastases or determine the size and precise location of diseased tissues.

[0225] It is therefore a further aspect of the present invention to provide a method for producing a recombinant antibody that specifically binds to human major histocompatibility complex (MHC) class I or II molecule complexed with an HLA-restricted antigen (preferably a peptide according to the present invention), comprising the steps of: immunizing a genetically engineered non-human mammal comprising cells expressing said human major histocompatibility complex (MHC) class I or II with a soluble form of an MHC class I or II molecule complexed with said HLA-restricted antigen; isolating mRNA molecules from antibody-producing cells of said non-human mammal; creating a phage display library displaying protein molecules encoded by said mRNA molecules; and isolating at least one phage from said phage display library, wherein at least one phage displays said antibody that specifically binds to said human major histocompatibility complex (MHC) class I or II complexed with said HLA-restricted antigen (preferably a peptide according to the present invention).

[0226] It is therefore a further aspect of the invention to provide an antibody that specifically binds to human major histocompatibility complex (MHC) class I or II complexed with an HLA-restricted antigen, wherein the antibody is preferably a polyclonal, monoclonal, bispecific and / or chimeric antibody.

[0227] Respective methods for producing such antibodies and single-chain class I major histocompatibility complexes, as well as other tools for producing these antibodies, are disclosed in WO 03 / 068201, WO 2004 / 084798, WO 01 / 72768, WO 03 / 070752, and in the literature (Cohen et al., 2003a; Cohen et al., 2003b; Denkberg et al., 2003), the contents of which are all expressly incorporated by reference in their entirety for the purposes of the present invention.

[0228] Preferably, the antibody binds to the complex with a binding affinity of less than 20 nanomolar, preferably less than 10 nanomolar, which is also considered "specific" in the context of the present invention.

[0229] The present invention relates to a peptide comprising a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:489, or a variant thereof that is at least 88% homologous (preferably identical) to SEQ ID NO:1 to SEQ ID NO:489, or a variant thereof that cross-reacts with T cells with said peptide, wherein said peptide is not the underlying full-length polypeptide.

[0230] The present invention further relates to a peptide comprising a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:489, or a variant thereof that is at least 88% homologous (preferably identical) to SEQ ID NO:1 to SEQ ID NO:489, said peptide or variant having an overall length of 8 to 100, preferably 8 to 30, most preferably 8 to 14 amino acids.

[0231] The present invention further relates to a peptide according to the invention having the ability to bind to a molecule of the human major histocompatibility complex (MHC) class I or II.

[0232] The present invention further relates to a peptide according to the invention, wherein the peptide consists of or consists essentially of the amino acid sequence set forth in SEQ ID NO:1 to SEQ ID NO:489.

[0233] The present invention further relates to a peptide according to the invention, wherein the peptide is (chemically) modified and / or comprises non-peptide bonds.

[0234] The present invention further relates to a peptide according to the invention, which is part of a fusion protein, in particular comprising the N-terminal amino acids of the HLA-DR antigen-associated invariant chain (Ii), or which is fused to (or into) an antibody, e.g. a dendritic cell-specific antibody.

[0235] The present invention further relates to a nucleic acid encoding a peptide according to the invention, with the proviso that the peptide is not the complete (full-length) human protein.

[0236] The present invention further relates to a nucleic acid according to the invention which is DNA, cDNA, PNA, RNA or a combination thereof.

[0237] The present invention further relates to an expression vector capable of expressing a nucleic acid according to the invention.

[0238] The present invention further relates to a peptide according to the invention, a nucleic acid according to the invention or an expression vector according to the invention for use in medicine, in particular in the treatment of lung cancer (including NSCLC and SCLC).

[0239] The present invention further relates to a host cell comprising a nucleic acid according to the invention or an expression vector according to the invention.

[0240] The present invention further relates to a host cell according to the invention which is an antigen-presenting cell, preferably a dendritic cell.

[0241] The present invention further relates to a method for producing a peptide according to the invention, comprising the steps of culturing a host cell according to the invention and isolating the peptide from said host cell or its culture medium.

[0242] The invention further relates to a method according to the invention, wherein a sufficient amount of antigen is contacted with an antigen-presenting cell, thereby loading the antigen onto class I or II MHC molecules expressed on the surface of a suitable antigen-presenting cell.

[0243] The present invention further relates to a method according to the present invention, wherein the antigen-presenting cell comprises an expression vector capable of expressing the peptide containing SEQ ID NO: 1 to SEQ ID NO: 489 or the heterologous amino acid sequence.

[0244] The present invention further relates to activated T cells produced by the method according to the invention, said T cells selectively recognizing cells which aberrantly express a polypeptide comprising an amino acid sequence according to the invention.

[0245] The present invention further relates to a method of killing target cells in a patient which aberrantly express a polypeptide comprising any amino acid sequence according to the present invention, comprising the step of administering to the patient an effective number of T cells according to the present invention.

[0246] The present invention further relates to the use of any of the described peptides, the nucleic acid according to the invention, the expression vector according to the invention, the cell according to the invention or the activated cytotoxic T lymphocytes according to the invention as a medicament or in the manufacture of a medicament. The present invention further relates to the use according to the invention, wherein the medicament is effective against cancer.

[0247] The present invention further relates to a use according to the present invention, wherein the medicament is a vaccine.The present invention further relates to a use according to the present invention, wherein the medicament is effective against cancer.

[0248] The invention further relates to the use according to the invention, wherein said cancer cells are lung cancer (including NSCLC and SCLC) cells or other solid or hematological tumor cells such as acute myeloid leukemia, breast cancer, cholangiocarcinoma, brain cancer, chronic lymphocytic leukemia, colorectal cancer, esophageal cancer, gallbladder cancer, gastric cancer, squamous cell carcinoma of the head and neck, hepatocellular carcinoma, melanoma, non-Hodgkin's lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, renal cell carcinoma, urinary bladder cancer, uterine cancer.

[0249] The present invention further relates to specific peptide-based labeled proteins and biomarkers according to the present invention, referred to herein as "targets", which can be used in the diagnosis and / or prognosis of lung cancer (including NSCLC and SCLC). The present invention also relates to the use of these novel targets for cancer therapy.

[0250] The term "antibody" or "antibodies" is used broadly herein and includes both polyclonal and monoclonal antibodies. In addition to intact or "intact" immunoglobulin molecules, the term "antibody" also includes fragments (e.g., CDR, Fv, Fab, and Fc fragments) or polymers of these immunoglobulin molecules and humanized versions of immunoglobulin molecules, so long as they exhibit any of the desired properties according to the invention (e.g., specific binding of a lung cancer (including NSCLC and SCLC) marker (poly)peptide, delivery of a toxin to lung cancer (including NSCLC and SCLC) cells expressing an increased level of a cancer marker gene, and / or inhibiting the activity of a lung cancer (including NSCLC and SCLC) marker polypeptide).

[0251] Whenever possible, the antibody of the present invention may be purchased from a commercial source. The antibody of the present invention may also be produced using well-known methods. Those skilled in the art will understand that either full-length lung cancer (including NSCLC and SCLC) marker polypeptide or its fragment may be used to generate the antibody of the present invention. The polypeptide used to produce the antibody of the present invention may be partially or completely purified from natural sources, or may be produced using recombinant DNA technology.

[0252] For example, cDNA encoding a peptide according to the present invention, such as the peptides set forth in SEQ ID NO:1 to SEQ ID NO:489 polypeptides, or variants or fragments thereof, can be expressed in prokaryotic cells (e.g., bacteria) or eukaryotic cells (e.g., yeast, insect, or mammalian cells), and the recombinant protein can then be purified and used to generate monoclonal or polyclonal antibody preparations that specifically bind to lung cancer (including NSCLC and SCLC) cancer marker polypeptides, which are used to generate antibodies according to the present invention.

[0253] Those skilled in the art will appreciate that the generation of two or more distinct sets of monoclonal or polyclonal antibodies maximizes the chances of obtaining antibodies with the required specificity and affinity for their intended use (e.g., ELISA, immunohistochemistry, in vivo imaging, immunotoxin therapy). Depending on the purpose for which the antibody is to be used, the antibodies are tested for the desired activity by known methods (e.g., ELISA, immunohistochemistry, immunotherapy, etc.; see, for further guidance on antibody production and testing, for example, Greenfield, 2014 (Greenfield, 2014)). For example, antibodies may be tested in ELISA assays, or Western blots, immunohistochemical staining of formalin-fixed cancer or frozen tissue sections. After their initial in vitro characterization, antibodies intended for therapeutic or in vivo diagnostic use are tested by known clinical testing methods.

[0254] The term "monoclonal antibody", as used herein, refers to an antibody obtained from a substantially homogeneous antibody population; i.e., the individual antibodies constituting the population are identical except for possible naturally occurring mutations that may be present in minor amounts. As used herein, "monoclonal antibody" specifically includes "chimeric" antibodies in which a portion of the heavy and / or light chain is identical or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain is identical or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired antagonistic activity (U.S. Pat. No. 4,816,567, the entire contents of which are incorporated herein by reference).

[0255] Monoclonal antibodies of the invention may be prepared using the hybridoma method, in which a mouse or other suitable host animal is typically immunized with an immunizing agent to give rise to lymphocytes that produce, or are capable of producing, antibodies that specifically bind to the immunizing agent. Alternatively, lymphocytes may be immunized in vitro.

[0256] The monoclonal antibodies may also be produced by recombinant DNA methods, such as those described in U.S. Patent No. 4,816,567. DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes capable of binding specifically to genes encoding the heavy and light chains of murine antibodies).

[0257] In vitro methods are also suitable for preparing monovalent antibodies. Digestion of antibodies to generate antibody fragments, particularly Fab fragments, can be accomplished using conventional techniques known in the art. For example, digestion can be performed using papain. Examples of papain digestion are described in WO 94 / 29348 and U.S. Pat. No. 4,342,566. Papain digestion of antibodies typically produces two identical antigen-binding fragments, called Fab fragments, each of which has a single antigen-binding site, and a remaining Fc fragment. Pepsin treatment results in F(ab')2 fragments and pFc' fragments.

[0258] Antibody fragments may also contain insertions, deletions, substitutions, or other selected modifications of specific regions or specific amino acid residues, whether attached to other sequences or not, provided that the activity of the fragment is not significantly altered or impaired compared to the unmodified antibody or antibody fragment. These modifications may provide some additional properties, such as removing / adding amino acids capable of disulfide bonding, increasing its biological lifespan, altering its secretion properties, etc. In any case, the antibody fragment must have bioactive properties, such as binding activity, binding modulation in the binding region, etc. Functional or active regions of the antibody may be identified by mutagenesis of specific regions of the protein, followed by expression and testing of the expressed polypeptide. Such methods are readily apparent to a skilled practitioner in the art and may include site-directed mutagenesis of the nucleic acid encoding the antibody fragment.

[0259] The antibodies of the invention may further comprise humanized or human antibodies. Humanized forms, such as non-human (e.g. murine) antibodies, are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab' or other antigen-binding subsequences of antibodies) that contain minimal sequence derived from non-human immunoglobulin. Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementarity determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity, and capacity. In some cases, Fv framework (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences. Generally, a humanized antibody will comprise substantially all of at least one, and typically two, variable regions, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are of human immunoglobulin consensus sequences. Optimally, the humanized antibody will also comprise at least a portion of an immunoglobulin constant region (Fc), typically a human immunoglobulin constant region.

[0260] Methods for humanizing non-human antibodies are well known in the art. Usually, a humanized antibody has one or more amino acid residues introduced from a non-human source. These non-human amino acid residues are often referred to as "import" residues, which are typically obtained from an "import" variable domain. Humanization can essentially be performed by replacing rodent CDR(s) or CDR(s) sequences with corresponding human antibody sequences. Such "humanized" antibodies are thus chimeric antibodies (U.S. Pat. No. 4,816,567) in which substantially less than a complete human variable domain has been replaced by the corresponding sequence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues have been replaced by residues from analogous sites in rodent antibodies.

[0261] Upon immunization, transgenic animals (e.g. mice) can be used that can produce a full repertoire of human antibodies in the absence of endogenous immunoglobulin production. For example, it has been described that homozygous deletion of antibody heavy chain joining region genes in chimeric and germline mutant mice results in complete inhibition of endogenous antibody production. Transfer of human germline immunoglobulin gene arrays in such germline mutant mice results in the production of human antibodies upon antigen challenge. Human antibodies can also be generated in phage display libraries.

[0262] The antibody of the present invention is preferably administered to a subject in a pharma- ceutically acceptable carrier. Typically, an appropriate amount of a pharmacologically acceptable salt is used in the formulation to make the formulation isotonic. Examples of pharmacologically acceptable carriers include physiological saline, Ringer's solution, and dextrose solution. The pH of the solution is preferably about 5 to about 8, more preferably about 7 to about 7.5. Further carriers include sustained release formulations of semipermeable matrices of solid hydrophobic polymers containing the antibody, the matrices being in the form of shaped articles, such as films, liposomes, or microparticles. It will be apparent to one skilled in the art that certain carriers may be more preferable depending, for example, on the route of administration and the concentration of the antibody to be administered.

[0263] The antibody may be administered to a subject, patient, or cell by injection (e.g., intravenous, intraperitoneal, subcutaneous, intramuscular) or other methods such as infusion that ensure delivery to the bloodstream in its effective form. The antibody may also be administered by intratumoral or peritumoral routes to exert local as well as systemic therapeutic effects. Local or intravenous injection is preferred.

[0264] Effective dosages and schedules for administering the antibody may be empirically determined, and making such determinations is within the skill of the art. Those skilled in the art will appreciate that the antibody dose to be administered will vary depending, for example, on the subject receiving the antibody, the route of administration, the particular antibody type used, and other agents administered. A typical daily dose of an antibody used alone may range from about 1 (μg / kg up to 100 mg / kg body weight or more per day, depending on the factors mentioned above. Following antibody administration, preferably for treating lung cancer (including NSCLC and SCLC), the efficacy of the therapeutic antibody may be assessed in a variety of ways well known to the skilled practitioner. For example, standard tumor imaging techniques may be used to monitor the size, number, and / or distribution of cancer in the treated subject. A therapeutically administered antibody that halts tumor growth, causes tumor shrinkage, and / or prevents the development of new tumors compared to the disease course that would occur in the absence of antibody administration is an effective antibody for cancer treatment.

[0265] It is also a further aspect of the present invention to provide a method for producing soluble T cell receptors (sTCRs) that recognize specific peptide-MHC complexes. Such soluble T cell receptors can be generated from specific T cell clones, and their affinity can be increased by targeted mutagenesis of complementarity determining regions. For the purpose of selecting T cell receptors, phage display can be used (US 2010 / 0113300, (Liddy et al., 2012)). For the purpose of stabilizing T cell receptors in phage display and in pharmaceutical applications, the α and β chains can be linked, for example, by non-natural disulfide bonds, other covalent bonds (single-chain T cell receptors), or dimerization domains (Boulter et al., 2003; Card et al., 2004; Willcox et al., 1999). T cell receptor can be linked to toxins, drugs, cytokines (see, for example, US 2013 / 0115191), and effector cell recruiting domains such as anti-CD3 domains, etc., to exert specific functions on target cells. It can also be expressed in T cells used for adoptive transfer. Further information can be found in WO 2004 / 033685 A1 and WO 2004 / 074322 A1. sTCR combinations are described in WO 2012 / 056407 A1. Further manufacturing methods are disclosed in WO 2013 / 057586 A1.

[0266] Additionally, the peptides and / or TCRs or antibodies or other binding molecules of the present invention may be used to confirm a pathologist's cancer diagnosis based on a biopsy sample.

[0267] The antibody or TCR may also be used for in vivo diagnostic assay.Usually, the antibody is labeled with radioactive nucleotide (such as 111In, 99Tc, 14C, 131I, 3H, 32P or 35S) using immunoscintigraphy so that tumors can be localized.In one embodiment, the antibody or its fragment binds to the extracellular domain of two or more targets of proteins selected from the group consisting of the above-mentioned proteins, and has an affinity (Kd) of less than 1x10 μM.

[0268] Diagnostic antibodies may be labeled with probes suitable for detection by various imaging methods. Probe detection methods include, but are not limited to, fluorescence, optical, confocal and electron microscopy; magnetic resonance imaging and spectroscopy; fluoroscopy, computed tomography and positron emission tomography. Suitable probes include, but are not limited to, fluorescein, rhodamine, eosin and other fluorophores, radioisotopes, gold, gadolinium and other lanthanides, paramagnetic iron, fluorine-18 and other positron-emitting radionuclides. Furthermore, the probes may be bifunctional or multifunctional and may be detectable by more than one of the listed methods. These antibodies may be directly or indirectly labeled with said probes. Particularly well-recognized attachment of probes to antibodies includes covalent binding of probes, incorporation of probes into antibodies, and covalent binding of chelating compounds for probe binding. For immunohistochemistry, diseased tissue samples may be fresh or frozen, or may be paraffin-embedded and fixed with a preservative such as formalin. Fixed or embedded sections containing the sample are contacted with labeled primary and secondary antibodies, and the antibodies are used to detect in situ protein expression.

[0269] Another aspect of the invention includes an in vitro method of producing activated T cells, the method comprising contacting ex vivo T cells with antigen-loaded human MHC molecules expressed on the surface of suitable antigen-presenting cells for a time sufficient to activate the T cells in an antigen-specific manner, the antigen being a peptide according to the invention. Preferably, a sufficient amount of antigen is used in conjunction with the antigen-presenting cells.

[0270] Preferably, the mammalian cell has no or reduced levels or function of the TAP peptide transporter. Suitable cells lacking the TAP peptide transporter include T2, RMA-S, and Drosophila cells. TAP is a transporter involved in antigen processing.

[0271] The human peptide loading depletion cell line T2 is available from the American Type Culture Collection, 12301 Parklawn Drive, Rockville, Maryland 20852, USA, under catalog number CRL1992; the Drosophila cell line Schneider strain 2 is available from the ATCC under catalog number CRL19863; the mouse RMA-S cell line is described in Ljunggren et al. (Ljunggren and Karre, 1985).

[0272] Preferably, before transfer, the host cells do not substantially express MHC class I molecules. It is also preferred that the stimulator cells express molecules important for providing costimulatory signals for T cells, such as any of B7.1, B7.2, ICAM-1, and LFA3. Numerous nucleic acid sequences of MHC class I molecules and costimulatory molecules are publicly available from the GenBank and EMBL databases.

[0273] When an MHC class I epitope is used as the antigen, the T cell is a CD8 positive T cell.

[0274] When antigen-presenting cells are transfected to express such epitopes, preferably the cells comprise an expression vector capable of expressing a peptide containing SEQ ID NO:1 to SEQ ID NO:489, or a variant amino acid sequence thereof.

[0275] Several other methods may be used to generate T cells ex vivo. For example, autologous tumor-infiltrating lymphocytes may be used to generate CTLs. Plebanski et al. (Plebanski et al., 1995) utilized autologous peripheral blood lymphocytes (PLBs) in the preparation of T cells. In addition, autologous T cells can be generated by pulsing dendritic cells with peptides or polypeptides or infecting them with recombinant viruses. B cells may also be used in the production of autologous T cells. In addition, macrophages pulsed with peptides or polypeptides or infected with recombinant viruses may be used in the preparation of autologous CTLs. S. Walter et al. (Walter et al., 2003) described the ex vivo priming of T cells using artificial antigen-presenting cells (aAPCs), which is also a suitable method for producing T cells against selected peptides. In the present invention, aAPCs are generated by conjugating preformed MHC:peptide complexes to surface polystyrene particles (microbeads) by biotin:streptavidin biochemistry. This system allows precise regulation of MHC density on aAPCs, which allows selectively eliciting high or low avidity antigen-specific T cell responses from blood samples with high efficiency. Besides MHC:peptide complexes, aAPCs should carry other proteins with costimulatory activity, such as anti-CD28 antibodies, conjugated to their surface. Furthermore, such aAPC-based systems often require the addition of appropriate soluble factors, such as cytokines like interleukin-12.

[0276] In preparing T cells, allogeneic cells may also be used, and methods are detailed in WO 97 / 26328, which is incorporated herein by reference. For example, in addition to Drosophila cells and T2 cells, other cells may be used to present antigens, such as CHO cells, baculovirus-infected insect cells, bacteria, yeast, and vaccinia-infected target cells. In addition, plant viruses may be used (see, for example, Porta et al., who describe the development of cowpea mosaic virus as a high-yield system for exogenous peptide presentation (Porta et al., 1994)).

[0277] Activated T cells directed against the peptides of the invention are useful in therapy. Thus, a further aspect of the invention provides activated T cells obtainable by the methods of the invention described above.

[0278] The activated T cells produced by the above method selectively recognize cells that abnormally express a polypeptide comprising an amino acid sequence of any of SEQ ID NOs:1 to 489.

[0279] Preferably, the T cells recognize cells by interaction with (e.g. binding to) HLA / peptide complexes through their TCR. The T cells are useful in a method of killing target cells in a patient whose target cells aberrantly express a polypeptide comprising an amino acid sequence of the invention, to which the patient is administered an effective number of activated T cells. The T cells administered to the patient may be derived from the patient and activated as described above (i.e., they are autologous T cells). Alternatively, the T cells are derived from another individual, not the patient. Of course, it is preferred if the individual is a healthy individual. By "healthy individual", we mean that the individual is generally in good health, preferably has a competent immune system, and more preferably is not suffering from any disease that can be easily tested for and detected.

[0280] In vivo, target cells for CD8 positive T cells according to the present invention may be tumor cells (which sometimes express MHC class II) and / or stromal cells surrounding the tumor (tumor cells) (which sometimes also express MHC class II; (Dengjel et al., 2006)).

[0281] The T cells of the present invention may be used as an active ingredient of a therapeutic composition.Thus, the present invention also provides a method of killing target cells in a patient, the target cells of which abnormally express a polypeptide comprising an amino acid sequence of the present invention, the method comprising administering to the patient an effective number of T cells as defined above.

[0282] By "aberrantly expressed" we also mean that the polypeptide is overexpressed, or that the gene is silent in the tissue from which the tumor originates, but is expressed in the tumor, compared to the expression level in normal tissue. By "overexpressed" we mean that the polypeptide is present at a level of at least 1.2 times the level present in normal tissue; preferably at least 2 times, more preferably at least 4 or 6 times the level present in normal tissue.

[0283] T cells may be obtained by methods known in the art, such as those described above.

[0284] Protocols for this so-called adoptive transfer of T cells are well known in the art and are reviewed in Gattioni et al. and Morgan et al. (Gattinoni et al., 2006; Morgan et al., 2006).

[0285] Another aspect of the invention involves the use of peptides that complex with MHC to generate T cell receptors whose nucleic acids are cloned and introduced into host cells, preferably T cells. This engineered T cell can then be transferred into a patient for cancer treatment.

[0286] Any of the molecules of the present invention, i.e. peptides, nucleic acids, antibodies, expression vectors, cells, activated T cells, T cell receptors or nucleic acids encoding same, are useful for treating disorders characterized by cells that escape immune responses. Thus, any of the molecules of the present invention may be used as a medicament or in the manufacture of a medicament. The molecules may be used alone or in combination with other molecules of the present invention or known molecules.

[0287] The present invention relates to (a) a container containing the above-mentioned pharmaceutical composition in solution or in lyophilized form; (b) optionally, a second container containing a diluent or reconstitution solution for the lyophilized formulation; and (c) optionally, (i) using a solution, or (ii) reconstituting a lyophilized formulation and / or or instructions for use The present invention is further directed to a kit comprising:

[0288] The kit may further comprise one or more of: (iii) a buffer, (iv) a diluent, (v) a filter, (vi) a needle, or (v) a syringe. The container is preferably a bottle, a vial, a syringe, or a test tube; it may be a multi-use container. The pharmaceutical composition is preferably lyophilized.

[0289] The kit of the present invention preferably comprises the lyophilized formulation of the present invention in a suitable container and instructions for its reconstitution and / or use. Suitable containers include, for example, bottles, vials (e.g., dual-chamber vials), syringes (such as dual-chamber syringes), and test tubes. The containers may be formed from a variety of materials, such as glass or plastic. Preferably, the kit and / or container includes instructions on or associated with the container, which indicate reconstitution and / or use directions. For example, the label may indicate that the lyophilized formulation is reconstituted to a peptide concentration as described above. The label may further indicate that the formulation is useful or intended for subcutaneous administration.

[0290] The container housing the formulation may be a multi-use vial, which allows for repeated administration (e.g., 2-6 administrations) of the reconstituted formulation. The kit may further comprise a second container comprising a suitable diluent (e.g., sodium bicarbonate solution).

[0291] Upon mixing of the diluent and the lyophilized formulation, the final peptide concentration in the reconstituted formulation is preferably at least 0.15 mg / mL / peptide (=75 μg), and preferably no more than 3 mg / mL / peptide (=1500 μg). The kit may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions.

[0292] The kits of the invention may have a single container containing a pharmaceutical composition formulation according to the invention, with or without added other components (e.g., other compounds or pharmaceutical compositions of these other compounds), or may have separate containers for each component.

[0293] Preferably, the kit of the invention comprises a formulation of the invention packaged for use in conjunction with the co-administration of a second compound (such as an adjuvant (e.g., GM-CSF), a chemotherapeutic agent, a natural product, a hormone or antagonist, an anti-angiogenic agent or inhibitor, an apoptosis inducer or chelator, or a pharmaceutical composition thereof). The components of the kit may be premixed or each component may be in a separate, distinct container prior to administration to a patient. The components of the kit may be provided in one or more liquid solutions, preferably aqueous solutions, more preferably sterile aqueous solutions. The components of the kit may also be provided as solids, which may be converted to liquids by the addition of a suitable solvent, preferably provided in another, distinct container.

[0294] The container of the therapeutic kit may be a vial, test tube, flask, bottle, syringe, or any other means of containing a solid or liquid. Usually, when there are two or more components, the kit contains a second vial or another container to allow separate dosing. The kit may also contain another container for pharma-ceutically acceptable liquid. Preferably, the therapeutic kit contains a device (e.g., one or more needles, syringes, eyedroppers, pipettes, etc.) to allow administration of the agent of the present invention that is a component of the kit.

[0295] The formulation is suitable for administration of the peptide by any acceptable means, such as oral (enteral), nasal, ocular, subcutaneous, intradermal, intramuscular, intravenous or transdermal. Preferably, administration is sc, and most preferably id, optionally by infusion pump.

[0296] Since the peptides of the invention were isolated from lung cancers (including NSCLC and SCLC), the agents of the invention are preferably used to treat lung cancers (including NSCLC and SCLC).

[0297] The present invention further relates to a method for producing a personalized medicine for an individual patient, comprising the step of producing a pharmaceutical composition comprising at least one peptide selected from the reservoir of pre-screened TUMAPs, wherein at least one peptide used in the pharmaceutical composition is selected for suitability in the individual patient.In one embodiment, the pharmaceutical composition is a vaccine.The method can also be adapted to produce T cell clones for downstream applications such as TCR isolation, or soluble antibodies, and other therapeutic options.

[0298] "Personalized medicine" shall mean a therapy that is specifically tailored for an individual patient, including proactive personalized cancer vaccines and adoptive cellular therapies using autologous patient tissue, used exclusively for the treatment of such individual patient.

[0299] As used herein, the term "reservoir" refers to a group or set of peptides that have been pre-screened for immunogenicity and / or over-presentation in a particular tumor type. The term "reservoir" is not intended to imply that the particular peptides included in the vaccine are pre-manufactured and stored in a physical facility, although this possibility is contemplated. It is expressly contemplated that peptides may be produced de novo for each individualized vaccine produced, or may be pre-manufactured and stored. The reservoir (e.g., in the form of a database) is composed of tumor-associated peptides that are highly overexpressed in tumor tissues of lung cancer (including NSCLC and SCLC) patients with diverse HLA-A, HLA-B, and HLA-C alleles. It may contain MHC class I and MHC class II peptides or extended MHC class I peptides. In addition to tumor-associated peptides taken from several lung cancer (including NSCLC and SCLC) tissues, the reservoir may also contain peptides that are highly overexpressed in tumor tissues of lung cancer (including NSCLC and SCLC) patients with HLA-A, HLA-B, and HLA-C alleles. * 02. HLA-A * 01. HLA-A * 03. HLA-A * 24. HLA-B * 07. HLA-B *08, and HLA-B * 44 marker peptides. These peptides allow quantitative comparison of the magnitude of T cell immunity induced by TUMAP, and therefore important conclusions can be drawn about the vaccine's ability to induce antitumor responses. Secondly, they serve as important positive control peptides derived from "non-self" antigens in cases where no vaccine-induced T cell response against TUMAPs derived from "self" antigens is observed in patients. Thirdly, it may allow conclusions to be drawn about the immunocompetence status of patients.

[0300] TUMAPs for the reservoir are identified using an integrated functional genomics approach that combines gene expression analysis, mass spectrometry, and T cell immunology (XPresident®). The approach ensures that only TUMAPs that are truly present on a high percentage of tumors, but not or only minimally expressed on normal tissues, are selected for further analysis. For initial peptide selection, lung cancer (including NSCLC and SCLC) samples from patients and blood from healthy donors were analyzed in a stepwise approach: 1. HLA ligands from malignant agents were identified by mass spectrometry 2. Genome-wide messenger ribonucleic acid (mRNA) expression analysis was used to identify gene overexpression in malignant tissues (including lung cancer (NSCLC and SCLC)) compared with a range of normal organs and tissues. 3. The identified HLA ligands were compared with gene expression data. Preferably, peptides that are over- or selectively presented on tumor tissues, encoded by selectively expressed or over-expressed genes as detected in step 2, were considered as suitable TUMAP candidates for multi-peptide vaccines. 4. A literature search was conducted to identify additional evidence supporting the validity of the identified peptides as TUMAPs. 5. The association of overexpression at the mRNA level was confirmed by re-detection of selected TUMAPs from step 3 on tumor tissues and their absence (or rare) detection in healthy tissues. 6. To assess whether the selected peptides are capable of inducing T cell responses in vivo, in vitro immunogenicity assays were performed using human T cells from healthy donors and lung cancer (including NSCLC and SCLC) patients.

[0301] In one embodiment, peptides are pre-screened for immunogenicity before being included in the reservoir. As a non-limiting example, the immunogenicity of peptides included in the reservoir is determined by a method comprising ex vivo T cell priming through repeated stimulation of CD8+ T cells from healthy donors with artificial antigen-presenting cells loaded with peptide / MHC complexes and anti-CD28 antibodies.

[0302] This method is favorable for rare cancers and for patients with rare expression profiles. In contrast to a multiple peptide mixture with a fixed composition, the currently developed reservoir allows a significantly higher matching of the vaccine with the actual expression of the antigen in the tumor. In a multi-target approach, several "off-the-shelf" peptides are selected for each patient, either single or in combination. In theory, an approach based on the selection of, for example, 5 different antigenic peptides from a library of 50 antigenic peptides would result in approximately 17 million possible drug product (DP) compositions.

[0303] In one aspect, peptides are selected for inclusion in the vaccine based on their suitability for an individual patient based on the methods according to the invention as described herein or as follows.

[0304] HLA phenotype, transcriptomic and peptidomic data are collected from patient tumor material and blood samples to identify the most relevant peptides for each patient, containing the "reservoir" and patient-specific (i.e. mutated) TUMAPs. Peptides are selected that are selectively or overexpressed in the patient's tumor and, if possible, show strong in vitro immunogenicity when tested with the patient's individual PBMCs.

[0305] Preferably, the peptides to be included in the vaccine are identified by a method comprising the steps of: (a) identifying tumor associated peptides (TUMAPs) presented by tumor samples from individual patients; (b) comparing the peptides identified in (a) with the peptide repository (database) described above; and (c) selecting at least one peptide from the repository (database) that is related to the tumor associated peptides identified in the patient. For example, the TUMAPs presented by tumor samples are identified by the steps of: (a1) comparing expression data from the tumor sample with expression data from a normal tissue sample corresponding to the tissue type of the tumor sample to identify proteins that are overexpressed or aberrantly expressed in the tumor sample; and (a2) correlating the expression data with sequences of MHC ligands that bind to MHC class I and / or class II molecules in the tumor sample to identify MHC ligands derived from proteins that are overexpressed or aberrantly expressed by the tumor. Preferably, the sequences of the MHC ligands are identified by eluting bound peptides from MHC molecules isolated from the tumor sample and sequencing the eluted ligands. Preferably, the tumor sample and normal tissue are obtained from the same patient.

[0306] In addition to or as an alternative to using a reservoir (database) model to select peptides, TUMAPs may be identified de novo in patients and then included in vaccines. As an example, candidate TUMAPs may be identified in patients by: (a1) comparing expression data from tumor samples with expression data from normal tissue samples corresponding to the tissue type of the tumor sample to identify proteins that are overexpressed or aberrantly expressed in the tumor sample; and (a2) correlating the expression data with sequences of MHC ligands that bind to MHC class I and / or class II molecules in the tumor sample to identify MHC ligands derived from proteins that are overexpressed or aberrantly expressed by the tumor. As another example, proteins containing mutations unique to tumor samples may be identified by comparing with normal counterpart tissues from individual patients, and TUMAPs that specifically target the mutations may be identified. For example, the genome of the tumor and the genome of the corresponding normal tissue may be sequenced by whole genome sequencing. To discover nonsynonymous mutations in the protein coding regions of genes, genomic DNA and RNA are extracted from tumor tissues, and normal non-mutated genomic germline DNA is extracted from peripheral blood mononuclear cells (PBMCs). The applied NGS approach is limited to resequencing of protein coding regions (exome resequencing). For this purpose, exonic DNA from human samples is captured using target enrichment kits provided by the supplier, followed by sequencing, for example by HiSeq2000 (Illumina). In addition, tumor mRNA is sequenced for direct quantification of gene expression and for validity assessment that mutated genes are expressed in the patient's tumor. The resulting millions of sequence reads are processed through software algorithms. The output list contains mutations and gene expression. Tumor-specific somatic mutations are determined and prioritized by comparison with PBMC-derived germline diversity. The newly identified peptides can then be tested for immunogenicity as described above for the reservoir, and candidate TUMAPs that retain the appropriate immunogenicity are selected for inclusion in the vaccine.

[0307] In one exemplary embodiment, peptides to be included in the vaccine are identified by: (a) identifying tumor-associated peptides (TUMAPs) presented by tumor samples from individual patients by the methods described above; (b) comparing the peptides identified in a) with a reservoir of peptides preselected for immunogenicity and over-presentation in tumors compared to corresponding normal tissues; (c) selecting at least one peptide from the reservoir that is related to the tumor-associated peptides identified in the patient; and (d) optionally selecting at least one newly identified peptide in (a) and confirming its immunogenicity.

[0308] In one exemplary embodiment, peptides to be included in the vaccine are identified by: (a) identifying tumor-associated peptides (TUMAPs) presented by tumor samples from individual patients; and (b) selecting at least one newly identified peptide in (a) and confirming its immunogenicity.

[0309] Once peptides for a personalized peptide-based vaccine are selected, the vaccine is manufactured, preferably as a liquid formulation consisting of individual peptides dissolved in 20-40% DMSO, such as about 33% DMSO, preferably about 30-35% DMSO.

[0310] Each peptide included in the product is dissolved in DMSO. The concentration of the single peptide solution must be selected according to the number of peptides included in the product. The single peptide DMSO solutions are mixed in equal amounts to obtain a solution containing all peptides included in the product at a concentration of approximately 2.5 mg / ml per peptide. The mixed solution is then diluted 1:3 with water for injection to obtain a concentration of 0.826 mg / ml per peptide in 33% DMSO. The diluted solution is filtered through a 0.22 μm sterile filter. The final bulk solution is obtained.

[0311] The final bulk solution is filled into vials and stored at -20°C until use. Each vial contains 700 μL of solution containing 0.578 mg of each peptide. Of this, 500 μL (approximately 400 μg per peptide) is applied for intradermal injection.

[0312] In addition to being useful for treating cancer, the peptides of the present invention are also useful as diagnostic agents. Because the peptides were produced from lung cancer (including NSCLC and SCLC) cells, and because these peptides were determined to be absent or present at lower levels in normal tissues, these peptides can be used to diagnose the presence of cancer.

[0313] The presence of the claimed peptides on tissue biopsies in blood samples can assist pathologists in cancer diagnosis. Detection of a particular peptide by means of antibodies, mass spectrometry or other methods known in the art can tell a pathologist that a tissue sample is malignant, or inflammatory, or generally diseased, or can be used as a biomarker for lung cancer (including NSCLC and SCLC). The presence of peptide groups can allow classification or subclassification of diseased tissue.

[0314] The detection of peptides on diseased tissue samples allows the evaluation of the benefits of treatments involving the immune system, especially when T lymphocytes are known or predicted to be involved in the mechanism of action. Loss of MHC expression is a well-described mechanism by which infected malignant cells escape immune surveillance. The presence of peptides therefore indicates that this mechanism is not exploited by the analyzed cells.

[0315] The peptides of the present invention may be used to analyze lymphocyte responses to these peptides, such as T cell or antibody responses to peptides or peptides complexed with MHC molecules. These lymphocyte responses may be used as prognostic markers to determine further treatment steps. These responses may also be used as surrogate response markers in immunotherapy approaches that aim to induce lymphocyte responses by different means, such as vaccination with proteins, nucleic acids, autologous materials, or adoptive transfer of lymphocytes. In the setting of gene therapy, lymphocyte responses to peptides may be taken into account in the evaluation of side effects. Monitoring lymphocyte responses may also be a useful tool for follow-up examinations of transplantation therapy, such as for example detection of graft-versus-host disease and host-versus-graft disease.

[0316] The present invention will now be described in the following examples which depict preferred embodiments thereof and with reference to the accompanying drawings, in which: For purposes of the present invention, all references cited herein are incorporated by reference in their entirety. [Brief description of the drawings]

[0317] Figures 1A to 1N show the over-representation of various peptides in different cancer tissues (black dots). Top: Median MS signal intensity from technical replicates plotted as points for single positive normal (grey dots) and tumor samples (black dots) on which the peptide was detected. Tumor and normal samples are grouped by organ of origin, and box plots represent the median, 25th and 75th percentiles (boxes), and minimum and maximum (whiskers) of normalized signal intensity across multiple samples. Normal organs are ordered by risk category. (Blood cells, blood vessels, brain, liver, lungs: high risk, grey dots; genitals, breast, prostate: low risk, grey dots; all other organs: medium risk, grey dots). Bottom: Relative peptide detection frequency in each organ is shown as a bar graph. Numbers below the panels indicate the number of samples in which the peptide was detected out of the total number of samples analyzed for each organ. If a peptide was detected on a sample but could not be quantified for technical reasons, the sample is included in this detection frequency display but no dot is shown at the top of the figure. [Figure 1A] Figure 1 shows over-representation of various peptides on HLA-A*24 cancer tissues compared to a panel of HLA-A*24 normal samples (N=19 normal samples, N=94 tumor samples). Tissues (from left to right): Normal samples: blood vessels; brain; heart; liver; lung; kidney; pituitary. Tumor samples: GBM: glioblastoma; GC: gastric cancer; HCC: hepatocellular carcinoma; NSCLC adenocarcinoma (non-small cell lung cancer adenocarcinoma); NSCLC other (non-small cell lung cancer); NSCLC squamous (non-small cell lung cancer squamous cell); SCLC: small cell lung cancer. Figure 1A) Gene symbol: URB1, peptide: LYQEILAQL (SEQ ID NO: 62), Figure 1B) Gene symbol: CKAP5, peptide: VYPASKMFPFI (SEQ ID NO: 65). [Figure 1B] Same as above [Figure 1C]Over-representation of various peptides on HLA-A*02 cancer tissues compared to a panel of HLA-A*02 normal samples (N=469 normal samples, N=528 tumor samples). Tissues (from left to right): Normal samples: Blood cells; bloodvess (blood vessels); brain; heart; liver; lung; adipose (adipose tissue); adren.gl. (adrenal gland); bile duct; bladder; BM (bone marrow); esoph (esophagus); eye; gallb (gallbladder); head and neck; kidney; arge_int (large intestine); LN (lymph node); nerve; pancreas; parathyr (parathyroid); perit (peritoneum); pituit (pituitary gland); pleura; skel.mus (skeletal muscle); skin; small_int (small intestine); spleen; stomach; thyroid; trachea; ureter; breast; ovary; placenta; prostate; testis; thymus; uterus. Tumor samples: AML: acute myeloid leukemia; BRCA: breast cancer; CCC: cholangiocarcinoma; CLL: chronic lymphocytic leukemia; CRC: colorectal cancer; GBC: gallbladder cancer; GBM: glioblastoma; GC: gastric cancer; GEJC: gastric cardia-esophageal cancer; HCC: hepatocellular carcinoma; HNSCC: head and neck cancer; MEL: melanoma; NHL: non-Hodgkin's lymphoma; NSCLC adenocarcinoma (non-small cell lung cancer adenocarcinoma); NSCLC other (non-small cell lung cancer); NSCLC squamous (non-small cell lung cancer squamous cell); OC: ovarian cancer; OSCAR: esophageal cancer; PACA: pancreatic cancer; PRCA: prostate cancer; RCC: renal cell carcinoma; SCLC: small cell lung cancer; UBC: bladder cancer; UEC: uterine and endometrial cancer. Figure 1C) Gene symbol: BMS1, peptide: VLYDKDAVYV (SEQ ID NO: 129), Figure 1D) Gene symbol: GORASP2, peptide: NLWGGQGLLGV (SEQ ID NO: 130). [Figure 1D] Same as above [Figure 1E]Figure 1 shows over-representation of various peptides on HLA-A*01 cancer tissues compared to a panel of HLA-A*01 normal samples (N=13 normal samples, N=40 tumor samples). Tissues (from left to right): Normal samples: Blood cells; Brain; Heart; Liver; Lung. Tumor samples: GBM: Glioblastoma; HCC: Hepatocellular carcinoma; NSCLC Adenocarcinoma (non-small cell lung cancer adenocarcinoma); NSCLC Other (non-small cell lung cancer); NSCLC Squamous (non-small cell lung cancer squamous cell); SCLC: Small cell lung cancer. Figure 1E) Gene symbol: ZNF439, peptide: LLDISQKNLY (SEQ ID NO: 154), Figure 1F) Gene symbol: MMP12, peptide: SADDIRGIQSLY (SEQ ID NO: 174). [Figure 1F] Same as above [Figure 1G] Figure 1 shows over-representation of various peptides on HLA-A*03 cancer tissues compared to a panel of HLA-A*03 normal samples (N=12 normal samples, N=28 tumor samples). Tissues (from left to right): Normal samples: blood cells; bloodvess (blood vessels); brain; heart; liver; lung. Tumor samples: GBM: glioblastoma; GC: gastric cancer; NHL: non-Hodgkin's lymphoma; NSCLC adenocarcinoma (non-small cell lung cancer adenocarcinoma); NSCLC other (non-small cell lung cancer); NSCLC squamous (non-small cell lung cancer squamous cell); SCLC: small cell lung cancer. Figure 1G) Gene symbol: KRT81, KRT121P, KRT83, KRT85, KRT86, peptide: KLAELEGALQK (SEQ ID NO: 202), Figure 1H) Gene symbol: NDC80, peptide: SINKPTSER (SEQ ID NO: 457). [Figure 1H] Same as above [Figure 1I]Figure 1 shows over-representation of various peptides on HLA-B*07 cancer tissues compared to a panel of HLA-B*07 normal samples (N=13 normal samples, N=36 tumor samples). Tissues (from left to right): Normal samples: blood cells; bloodvess (blood vessels); brain; heart; liver; lung. Tumor samples: GBM: glioblastoma; NSCLC adenocarcinoma (non-small cell lung cancer adenocarcinoma); NSCLC other (non-small cell lung cancer); NSCLC squamous (non-small cell lung cancer squamous cell); OC: ovarian cancer; SCLC: small cell lung cancer. Figure 1I) Gene symbol: CTHRC1, peptide: SPQRLRGLL (SEQ ID NO: 291), Figure 1J) Gene symbol: MANEA, peptide: RPHKPGLYL (SEQ ID NO: 475). [Figure 1J] Same as above [Figure 1K] Figure 1 shows over-representation of various peptides on HLA-B*08 cancer tissues compared to a panel of HLA-B*08 normal samples (N=1 normal sample, N=22 tumor samples). Tissues (from left to right): Normal samples: Lung. Tumor samples: GBM: glioblastoma; NSCLC adenocarcinoma (non-small cell lung cancer adenocarcinoma); NSCLC other (non-small cell lung cancer); NSCLC squamous (non-small cell lung cancer squamous cell); SCLC: small cell lung cancer. Figure 1K) Gene symbol: VPS13B, peptide: DIYQRALNL (SEQ ID NO: 315), Figure 1L) Gene symbol: ARID4A, peptide: LVKVKVLL (SEQ ID NO: 317). [Figure 1L] Same as above [Figure 1M] Figure 1 shows over-representation of various peptides on HLA-B*44 cancer tissues compared to a panel of HLA-B*44 normal samples (N=15 normal samples, N=25 tumor samples). Tissues (from left to right): Normal samples:; Brain; Heart; Liver; Lung. Tumor samples: GBM: glioblastoma; NSCLC adenocarcinoma (non-small cell lung cancer adenocarcinoma); NSCLC other (non-small cell lung cancer); NSCLC squamous (non-small cell lung cancer squamous cell); SCLC: small cell lung cancer. Figure 1M) Gene symbol: NUP155, peptide: SEKGVIQVY (SEQ ID NO: 362), Figure 1N) Gene symbol: CLSPN, peptide: SEIGKAVGF (SEQ ID NO: 489). [Figure 1N] Same as above [Figure 2A]Figure 1 shows an exemplary exon expression profile of the origin gene of the present invention that is overexpressed in different cancer samples. Tumor (black dots) and normal (gray dots) samples are grouped by organ of origin, and the box plots represent the median, 25th and 75th percentiles (boxes), and the minimum and maximum (whiskers) RPKM values. Normal organs are ordered by risk category. FPKM = fragments per kilobase per million mapped reads. Normal Sample: Blood cells; bloodvess: Blood vessels; brain; heart; liver; lung; adipose: Adipose tissue; adren.gl.: Adrenal gland; bile duct; bladder; BM: Bone marrow; cartilage; esoph: Esophagus; eye; gallb: Gallbladder; head and neck; kidney; large_int: Large intestine; LN: Lymph node; nerve; pancreas; parathyr: Parathyroid gland; pituit: Pleura; skel.mus: Skeletal muscle; skin; small_int: Small intestine; Spleen; Stomach; Thyroid; Trachea; Bladder; Breast; Ovary; Placenta; Prostate; Testis; Thymus; Uterus. Tumor samples: AML: acute myeloid leukemia; BRCA: breast cancer; CCC: cholangiocarcinoma; CLL: chronic lymphocytic leukemia; CRC: colorectal cancer; GBC: gallbladder cancer; GBM: glioblastoma; GC: gastric cancer; HCC: hepatocellular carcinoma; HNSCC: head and neck cancer; MEL: melanoma; NHL: non-Hodgkin's lymphoma; NSCLC adenocarcinoma: non-small cell lung cancer adenocarcinoma; NSCLC other: non-small cell lung cancer; NSCLC squamous: non-small cell lung cancer squamous cell; OC: ovarian cancer; OSCAR: esophageal cancer; PACA: pancreatic cancer; PRCA: prostate cancer; RCC: renal cell carcinoma; SCLC: small cell lung cancer; UBC: bladder cancer; UEC: uterine and endometrial cancer.FIG. 2A) Gene symbol: ADAMTS12, peptide: QYDPTPLTW (SEQ ID NO: 1); FIG. 2B) Gene symbol: MMP12, peptide: VWSNVTPLKF (SEQ ID NO: 2); FIG. 2C) Gene symbol: MMP12, peptide: YVDINTFRL (SEQ ID NO: 84); FIG. 2D) Gene symbol: KIF26B, peptide: TLYPYQISQL (SEQ ID NO: 87); FIG. 2E) Gene symbol: CT83, peptide: NTDNNLAVY (SEQ ID NO: 164); FIG. 2F) Gene symbol: LAMA1, peptide: VSDSECLSRY (SEQ ID NO: 189); FIG. 2G) Gene symbol: KIF26B, peptide: KVKDTPGLGK (SEQ ID NO: 203); FIG. 2H) Gene symbol: SP6, peptide: SLDGAARPK (SEQ ID NO: 205), Figure 2I) Gene symbol: PRAME, peptide: SPSVSQLSVL (SEQ ID NO: 220), Figure 2J) Gene symbol: MMP1, peptide: NPFYPEVEL (SEQ ID NO: 222), Figure 2K) Gene symbol: NLRP2, peptide: FNKRKPLSL (SEQ ID NO: 298), Figure 2L) Gene symbol: KIF26B, peptide: VASPKHCVL (SEQ ID NO: 300), Figure 2M) Gene symbol: MAGEA3, MAGEA6, peptide: MEVDPIGHVYIF (SEQ ID NO: 320), Figure 2N) Gene symbol: MMP12, peptide: QEMQHFLGL (SEQ ID NO: 326). [Figure 2B] Same as above [Figure 2C] Same as above [Figure 2D] Same as above [Figure 2E] Same as above [Figure 2F] Same as above [Figure 2G] Same as above [Figure 2H] Same as above [Figure 2I] Same as above [Figure 2J] Same as above [Figure 2K] Same as above [Figure 2L] Same as above [Figure 2M] Same as above [Figure 2N] Same as above [Diagram 3]Figure 1 shows exemplary results of peptide-specific in vitro CD8+ T cell responses of healthy HLA-A*02+ donors. CD8+ T cells were primed using anti-CD28 mAb and artificial APCs coated with HLA-A*02 complexed with SEQ ID NO:520 peptide (KIQEMQHFL, SEQ ID NO:520) (A, left panel). After three cycles of stimulation, detection of peptide-reactive cells was performed by 2D multimer staining with A*02 / SEQ ID NO:520 (A). The right panel (B) shows control staining of cells stimulated with an irrelevant A*02 / peptide complex. Viable singlet cells were gated on CD8+ lymphocytes. Boolean gates helped to eliminate false positive events detected by multimers specific for different peptides. The frequency of specific multimer+ cells among CD8+ lymphocytes is shown. [Figure 4] Exemplary results of peptide-specific in vitro CD8+ T cell responses of healthy HLA-A*24+ donors are shown. CD8+ T cells were primed using anti-CD28 mAb and artificial APCs coated with HLA-A*24 complexed with SEQ ID NO:504 peptide (A, left panel). After three stimulation cycles, detection of peptide-reactive cells was performed by 2D multimer staining with A*24 / SEQ ID NO:504 (VYEKNGYIYF, SEQ ID NO:504) (A). The right panel (B) shows control staining of cells stimulated with an irrelevant A*24 / peptide complex. Viable singlet cells were gated on CD8+ lymphocytes. Boolean gates helped to eliminate false positive events detected by multimers specific for different peptides. The frequency of specific multimer+ cells among CD8+ lymphocytes is shown. [Diagram 5]Figure 1 shows exemplary results of peptide-specific in vitro CD8+ T cell responses of healthy HLA-A*01+ donors. CD8+ T cells were primed using anti-CD28 mAb and artificial APCs coated with HLA-A*01 complexed with SEQ ID NO: 153 peptide (KLDRSVFTAY, SEQ ID NO: 153) (A, left panel) and SEQ ID NO: 173 peptide (RTEFNLNQY, SEQ ID NO: 173) (B, left panel), respectively. After three cycles of stimulation, detection of peptide-reactive cells was performed by 2D multimer staining with A*01 / SEQ ID NO: 153 (A) or A*01 / SEQ ID NO: 173. The right panel (A and B) shows the control staining of cells stimulated with irrelevant A*01 / peptide complex. Viable single cells were gated for CD8+ lymphocytes. Boolean gates helped to exclude false positive events detected by multimers specific for different peptides. The frequency of specific multimer+ cells among CD8+ lymphocytes is shown. [Figure 6] Figure 1 shows exemplary results of peptide-specific in vitro CD8+ T cell responses of healthy HLA-A*02+ donors. CD8+ T cells were primed using anti-CD28 mAb and artificial APCs coated with HLA-A*02 complexed with SEQ ID NO:89 peptide (ILSTTMVTV, SEQ ID NO:89) (A, left panel) and SEQ ID NO:88 peptide (VQMVITEAQKV, SEQ ID NO:88) (B, left panel), respectively. After three cycles of stimulation, detection of peptide-reactive cells was performed by 2D multimer staining with A*02 / SEQ ID NO:89 (A) or A*02 / SEQ ID NO:88 (B). The right panels (A and B) show control staining of cells stimulated with irrelevant A*02 / peptide complex. Viable single cells were gated for CD8+ lymphocytes. Boolean gates helped to exclude false positive events detected by multimers specific for different peptides. The frequency of specific multimer+ cells among CD8+ lymphocytes is shown. [Figure 7]Figure 1 shows exemplary results of peptide-specific in vitro CD8+ T cell responses of healthy HLA-A*03+ donors. CD8+ T cells were primed using anti-CD28 mAb and artificial APCs coated with HLA-A*03 complexed with SEQ ID NO:208 peptide (GLASRILDAK, SEQ ID NO:208) (A, left panel) and SEQ ID NO:210 peptide (ATSGVPVYK, SEQ ID NO:210) (B, left panel), respectively. After three cycles of stimulation, detection of peptide-reactive cells was performed by 2D multimer staining with A*03 / SEQ ID NO:208 (A) or A*03 / SEQ ID NO:210 (B). The right panels (A and B) show control staining of cells stimulated with irrelevant A*03 / peptide complex. Viable single cells were gated for CD8+ lymphocytes. Boolean gates helped to exclude false positive events detected by multimers specific for different peptides. The frequency of specific multimer+ cells among CD8+ lymphocytes is shown. [Figure 8] Figure 1 shows exemplary results of peptide-specific in vitro CD8+ T cell responses of healthy HLA-A*24+ donors. CD8+ T cells were primed using anti-CD28 mAb and artificial APCs coated with HLA-A*24 complexed with SEQ ID NO:15 peptide (KYALLLQDL, SEQ ID NO:15) (A, left panel) and SEQ ID NO:11 peptide (YYSKSVGFMQW, SEQ ID NO:11) (B, left panel), respectively. After three cycles of stimulation, detection of peptide-reactive cells was performed by 2D multimer staining with A*24 / SEQ ID NO:15 (A) or A*24 / SEQ ID NO:11 (B). The right panels (A and B) show control staining of cells stimulated with irrelevant A*24 / peptide complex. Viable single cells were gated for CD8+ lymphocytes. Boolean gates helped to exclude false positive events detected by multimers specific for different peptides. The frequency of specific multimer+ cells among CD8+ lymphocytes is shown. [Figure 9]Exemplary results of peptide-specific in vitro CD8+ T cell responses of healthy HLA-B*07+ donors are shown. CD8+ T cells were primed using anti-CD28 mAb and artificial APCs coated with HLA-B*07 complexed with SEQ ID NO:225 peptide (LPFDGPGGIL, SEQ ID NO:225) (A, left panel) and SEQ ID NO:248 peptide (IPNWARQDL, SEQ ID NO:248) (B, left panel), respectively. After three cycles of stimulation, detection of peptide-reactive cells was performed by 2D multimer staining with B*07 / SEQ ID NO:225 (A) or B*07 / SEQ ID NO:248 (B). The right panels (A and B) show control staining of cells stimulated with irrelevant B*07 / peptide complex. Viable single cells were gated for CD8+ lymphocytes. Boolean gates helped to exclude false positive events detected by multimers specific for different peptides. The frequency of specific multimer+ cells among CD8+ lymphocytes is shown. [Figure 10] Figure 1 shows exemplary results of peptide-specific in vitro CD8+ T cell responses of healthy HLA-B*08+ donors. CD8+ T cells were primed using anti-CD28 mAb and artificial APCs coated with HLA-B*08 complexed with SEQ ID NO:299 peptide (MAQFKEISL, SEQ ID NO:299) (A, left panel) and SEQ ID NO:297 peptide (RAQLKLVAL, SEQ ID NO:297) (B, left panel), respectively. After three cycles of stimulation, detection of peptide-reactive cells was performed by 2D multimer staining with B*08 / SEQ ID NO:299 (A) or B*08 / SEQ ID NO:297 (B). The right panels (A and B) show control staining of cells stimulated with irrelevant B*08 / peptide complex. Viable single cells were gated for CD8+ lymphocytes. Boolean gates helped to exclude false positive events detected by multimers specific for different peptides. The frequency of specific multimer+ cells among CD8+ lymphocytes is shown. [Figure 11]Illustrates exemplary results of peptide-specific in vitro CD8+ T cell responses of healthy HLA-B*44+ donors. CD8+ T cells were primed using anti-CD28 mAb and artificial APCs coated with HLA-B*44, complexed with SEQ ID NO:325 peptide (QEQDVDLVQKY, SEQ ID NO:325) (A, left panel) and SEQ ID NO:331 peptide (EDAQGHIW, SEQ ID NO:331) (B, left panel), respectively. After three cycles of stimulation, detection of peptide-reactive cells was performed by 2D multimer staining with B*44 / SEQ ID NO:325 (A) or B*44 / SEQ ID NO:331 (B), and single cells were gated for CD8+ lymphocytes. The right panels (A and B) show control staining of cells stimulated with an irrelevant B*44 / peptide complex. Viable single cells were gated for CD8+ lymphocytes. Boolean gating helped to eliminate false positive events detected by multimers specific for different peptides. The frequency of specific multimer+ cells among CD8+ lymphocytes is shown. EXAMPLES

[0318] Example 1 Identification and quantification of cell surface-displayed tumor-associated peptides Tissue samples Patient tumor tissues were obtained from Asterand (Detroit, MI, USA and Royston, Hertfordshire, UK); Bio-Options Inc. (Brea, CA, USA); Geneticist Inc. (Glendale, CA, USA); University Hospital Heidelberg (Heidelberg, Germany); ProteoGenex Inc. (Culver City, CA, USA); Tissue Solutions Ltd (Glasgow, UK); and University Hospital Munich (Munich, Germany). Normal tissues were obtained from Asterand (Detroit, MI, USA and Royston, Hertfordshire, UK); Bio-Options Inc. (Blair, CA, USA); BioServe (Beltsville, MD, USA); Capital BioScience Inc. (Rockville, MD, USA); Centre for Clinical Transfusion Medicine Tuebingen (Tübingen, Germany); Geneticist Inc. (Glendale, CA, USA); Kyoto Prefectural University of Medicine (KPUM) (Kyoto, Japan); Osaka City University (OCU) (Osaka, Japan); ProteoGenex Inc. (Culver City, CA, USA); Tissue Solutions Ltd (Glasgow, UK); University Hospital Geneva (Geneva, Switzerland); University Hospital Heidelberg (Heidelberg, Germany); University Hospital Tubingen (Tübingen, Germany); and University Hospital Munich (Munich, Germany). All patients gave informed consent before surgery or autopsy. Tissues were shock frozen immediately after resection and stored below −70°C until isolation of TUMAPs.

[0319] Isolation of HLA peptides from tissue samples HLA peptide pooling from shock-frozen tissue samples was performed using HLA-A peptide pooling according to a slightly modified protocol (Falk et al., 1991; Seeger et al., 1999).* The 02-specific antibody BB7.2, the HLA-A, -B, -C specific antibody W6 / 32, the HLA-DR specific antibody L243 and the HLA DP specific antibody B7 / 21 were obtained from solid tissues by immunoprecipitation using CNBr-activated Sepharose, acid treatment and ultrafiltration.

[0320] mass spectrometry The resulting HLA peptide pool was separated according to their hydrophobicity by reversed-phase chromatography (nanoAcquity UPL C system, Waters) and the eluted peptides were analyzed in an LTQ-velos and fusion hybrid mass spectrometer (ThermoElectron) equipped with an ESI source. The peptide pool was directly inserted onto an analytical fused silica microcapillary column (75 μm i.d. × 250 mm) packed with 1.7 μm C18 reversed-phase material (Waters) applying a flow rate of 400 nL per minute. Peptides were subsequently separated using a two-step 180 min binary gradient from 10% to 33% B at a flow rate of 300 nL per minute. The gradient consisted of solvent A (0.1% formic acid in water) and solvent B (0.1% formic acid in acetonitrile). Gold-coated glass capillaries (PicoTip, New Objective) were used for introduction into the nanoESI source. The LTQ-Orbitrap mass spectrometer was operated in data-dependent mode using the TOP5 strategy. Briefly, a scan cycle was started with a full scan at high mass accuracy in the Orbitrap (R = 30000), followed by an MS / MS scan of the five most abundant precursor ions, also in the Orbitrap (R = 7500), while previously selected ions were dynamically excluded. Tandem mass spectra were interpreted with a fixed false discovery rate (q ≤ 0.05) and additional manual controls, or by SEQUEST. In cases where the identified peptide sequence was uncertain, it was further validated by comparison of the generated native peptide fragmentation pattern with that of a synthetic sequence-identical reference peptide.

[0321] Label-free relative LC-MS quantification was performed by ion counting, i.e., by extraction and analysis of LC-MS features (Mueller et al., 2007). This method assumes that the LC-MS signal area of ​​a peptide correlates with its abundance in the sample. The extracted features were further processed by charge state deconvolution and retention time alignment (Mueller et al., 2008; Sturm et al., 2008). Finally, all LC-MS features were cross-referenced with the sequence identification results to combine quantitative data of the different samples and tissue-to-peptide presentation profiles. The quantitative data were normalized in a two-stage method according to central tendency that took into account technical and biological intra-replicate variability. In this way, each identified peptide can be associated with quantitative data, allowing relative quantification between samples and tissues. Furthermore, all quantitative data obtained for peptide candidates were manually inspected to ensure data consistency and to check the accuracy of the automated analysis. Presentation profiles were calculated for each peptide, showing the average sample presentation as well as the replicate variability. The profiles juxtapose the cancer samples to a baseline of normal tissue samples. Exemplary presentation profiles of over- or exclusively-presented peptides on tumors are shown in FIG.

[0322] Table 8B shows the presentation of various cancer entities for selected peptides and therefore indicates the specific relevance of the mentioned peptides with respect to the diagnosis and / or treatment of the indicated cancers (e.g., peptide SEQ ID NO:3 for hepatocellular carcinoma, peptide SEQ ID NO:11 for melanoma, ovarian cancer, and uterine cancer).

[0323] Table 8: Summary of the presentation of selected tumor-associated peptides of the invention across entities AML = acute myeloid leukemia, BRCA = breast cancer, CCC = cholangiocarcinoma, GBM = brain cancer, CLL = chronic lymphocytic leukemia, CRC= colorectal carcinoma, OSCAR = esophageal cancer, GBC = gallbladder adenocarcinoma, GC = gastric cancer, HNSCC = head and neck squamous cell carcinoma, HCC = hepatocellular carcinoma, MEL = melanoma, NHL= non-Hodgkin lymphoma, OC = ovarian cancer, PACA = pancreatic cancer, PRCA = prostate cancer and benign prostatic hyperplasia, RCC = renal cell carcinoma, UBC = urinary bladder cancer, UEC= uterine cancer. [Table 8-1] [Table 8-2] [Table 8-3] [Table 8-4] [Table 8-5] [Table 8-6] [Table 8-7] [Table 8-8] [Table 8-9]

[0324] Example 2 Expression profiling of genes encoding the peptides of the present invention Over- or specific presentation of peptides on tumor cells compared to normal cells is sufficient for their usefulness in immunotherapy, and some peptides are tumor-specific, even though their origin proteins are also present in normal tissues. Nevertheless, mRNA expression profiling can increase the level of safety in the selection of peptide targets for immunotherapy. In particular, for therapeutic options with high safety risks, such as affinity-matured TCR, the ideal target peptide would be derived from a protein that is unique to tumors and not found on normal tissues.

[0325] RNA origin and preparation Surgically removed tissue specimens were provided as described above after informed consent was obtained from each patient (see Example 1). Tumor tissue specimens were snap frozen immediately after surgery and then homogenized with a mortar and pestle under liquid nitrogen. Total RNA was prepared from these samples using TRI Reagent (Ambion, Darmstadt, Germany), followed by purification with RNeasy (QIAGEN, Hilden, Germany); both methods were performed according to the manufacturer's protocols.

[0326] Total RNA from healthy human tissues for RNASeq experiments was obtained from Asterand (Detroit, MI, USA and Royston, Hertfordshire, UK); Bio-Options Inc. (Brea, CA, USA); BioCat GmbH (Heidelberg, Germany); BioServe (Beltsville, MD, USA); Capital BioScience Inc. (Rockville, MD, USA); Geneticist Inc. (Glendale, CA, USA); Heidelberg University Hospital (Thoraxklinik, Heidelberg, Germany); Istituto Nazionale Tumori "Pascale" (Naples, Italy); and ProteoGenex Inc. (Culver City, CA, USA).

[0327] Total RNA from tumor tissues for RNASeq experiments was obtained from Asterand (Detroit, MI, USA and Royston, Hertfordshire, UK); Geneticist Inc. (Glendale, CA, USA); ProteoGenex Inc. (Culver City, CA, USA); Tissue Solutions Ltd (Glasgow, UK); University Hospital Bonn (Bonn, Germany); and University Hospital Tübingen (Tübingen, Germany).

[0328] The quality and quantity of all RNA samples were assessed on an Agilent 2100 Bioanalyzer (Agilent) using the RNA 6000 Pico LabChip kit (Agilent, Waldbronn, Germany).

[0329] RNAseq experiments Gene expression analysis of tumor and normal tissue RNA samples was performed by next-generation sequencing (RNAseq) by CeGaT (Tübingen, Germany). Briefly, the Illumina HiSeq v4 reagent kit, including RNA fragmentation, cDNA conversion, and addition of sequencing adapters, is used to generate sequencing libraries according to the vendor's protocol (Illumina Inc., San Diego, CA, USA). Libraries derived from multiple samples are mixed equimolarly and sequenced on an Illumina HiSeq 2500 sequencing instrument according to the manufacturer's instructions, generating 50 bp single-end reads. Processed reads are mapped to the human genome (GRCh38) using STAR software. Expression data are provided at the transcript level as RPKM (Reads Per Kilobase per Million mapped reads, generated by the software Cufflinks) and at the exon level (total reads, generated by the software Bedtools) based on annotations in the ensembl sequence database (Ensembl77). Exon reads are normalized for exon length and alignment size to obtain RPKM values.

[0330] Representative expression profiles of source genes of the invention that are highly overexpressed or exclusively expressed in lung cancers (including NSCLC and SCLC) are shown in Figure 2. Expression scores of additional exemplary genes are shown in Table 9.

[0331] Table 9: Expression scores. The table lists peptides from genes that are very highly overexpressed (+++) in lung cancer tissues (NSCLC adenocarcinoma = non-small cell lung cancer adenocarcinoma; NSCLC squamous cell = non-small cell lung cancer squamous cell; NSCLC other = non-small cell lung cancer, other subtypes; SCLC = small cell lung cancer) compared to a panel of normal tissues; highly overexpressed (++) in tumors compared to a panel of normal tissues; or overexpressed (+) in tumors compared to a panel of normal tissues. Baseline scores were calculated from measurements in relevant normal tissues: adipose tissue, adrenal gland, bile duct, blood cells, blood vessels, bone marrow, brain, cartilage, esophagus, eye, gallbladder, heart, head and neck, kidney, large intestine, liver, lung, lymph node, nerve, parathyroid, pancreas, pituitary, pleura, skeletal muscle, skin, small intestine, spleen, stomach, thyroid, trachea, bladder, ureter. When expression data of several samples of the same tissue type were available, the arithmetic mean of all individual samples was used for calculations. [Table 9-1] [Table 9-2] [Table 9-3] [Table 9-4] [Table 9-5] [Table 9-6] [Table 9-7] [Table 9-8] [Table 9-9]

[0332] Example 3 In vitro immunogenicity of MHC class I-presented peptides To obtain information on the immunogenicity of the TUMAPs of the invention, the inventors carried out studies using an in vitro T cell priming assay based on repeated stimulation of CD8+ T cells with artificial antigen presenting cells (aAPCs) loaded with peptide / MHC complexes and anti-CD28 antibodies. * 02:01, HLA-A * 24:02, HLA-A * 01:01, HLA-A * 03:01, HLA-B * 07:02, HLA-B * 08:01, and HLA-B * The immunogenicity of 44:02-restricted TUMAPs could be demonstrated, demonstrating that these peptides are T cell epitopes against which CD8+ precursor T cells are present in humans (Tables 10a and 10b).

[0333] Ex vivo priming of CD8+ T cells To perform ex vivo stimulation with artificial antigen-presenting cells loaded with peptide-MHC complexes (pMHC) and anti-CD28 antibodies, we first isolated fresh HLA-A antigen-presenting cells through positive selection with CD8 microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) from healthy donors obtained after informed consent from the University clinics in Mannheim, Germany. * 02. HLA-A * 24. HLA-A * 01. HLA-A * 03. HLA-B * 07. HLA-B * 08 or HLA-B * CD8+ T cells were isolated from 44 leukapheresis products.

[0334] PBMCs and isolated CD8+ lymphocytes or PBMCs were incubated in T cell medium (TCM) consisting of RPMI-Glutamax (Invitrogen, Karlsruhe, Germany) supplemented with 10% heat-inactivated human AB serum (PAN-Biotech, Aidenbach, Germany), 100 U / ml penicillin / 100 μg / ml streptomycin (Cambrex, Cologne, Germany), 1 mM sodium pyruvate (CC Pro, Oberdurra, Germany), 20 μg / ml gentamicin (Cambrex) until use. 2.5 ng / ml IL-7 (PromoCell, Heidelberg, Germany) and 10 U / ml IL-2 (Novartis Pharma, Nuremberg, Germany) were also added to the TCM at this stage.

[0335] Generation of pMHC / anti-CD28 coated beads, T cell stimulation, and readout were performed in a highly defined in vitro system using four different pMHC molecules per stimulation condition and eight different pMHC molecules per readout condition.

[0336] Purified costimulatory mouse IgG2a anti-human CD28 Ab9.3 (Jung et al., 1987) was chemically biotinylated using sulfo-N-hydroxysuccinimide biotin as recommended by the manufacturer (Perbio, Bonn, Germany). The beads used were 5.6 μm diameter streptavidin-coated polystyrene particles (Bangs Laboratories, IL, USA).

[0337] The pMHC used for positive and negative control stimulation were, respectively, A * 02:01 / MLA-001 (peptide ELAGIGILTV (SEQ ID NO: 532) derived from modified Melan-A / MART-1) and A * 02:01 / DDX5-001 (YLLPAIVHI derived from DDX5, SEQ ID NO:533).

[0338] 800,000 beads / 200 μl were coated in a 96-well plate in the presence of 4×12.5 ng of different biotin pMHC, washed, and subsequently added 600 ng of biotin anti-CD28 in a volume of 200 μl. 1×10 6 2 × 10 CD8+ T cells 5 Stimulation was initiated in 96-well plates by co-incubation with 10 ... Multimer analysis evaluation was performed using FlowJo software (Tree Star, Oregon, USA). Ex vivo priming of specific multimer+ CD8+ lymphocytes was detected by comparison with negative control stimulation. Immunogenicity of a given antigen was detected if at least one evaluable ex vivo stimulation well of one healthy donor was found to contain specific CD8+ T cell lines after ex vivo stimulation (i.e., this well contained at least 1% specific multimer+ in CD8+ T cells, and the percentage of specific multimer+ cells was at least 10 times the median of negative control stimulation).

[0339] In vitro immunogenicity of lung cancer (including NSCLC and SCLC) peptides For the HLA class I peptides tested, in vitro immunogenicity could be demonstrated by generation of peptide-specific T cell lines. Exemplary flow cytometry results after TUMAP-specific multimer staining for 16 peptides of the invention, along with the corresponding negative controls, are shown in Figures 3-11. Results for 152 peptides from the invention are summarized in Tables 10a and 10b.

[0340] Table 10a: In vitro immunogenicity of HLA class I peptides of the invention Exemplary results of in vitro immunogenicity experiments of the peptides of the invention carried out by the Applicant: <20% = +; 20%- 49% = ++; 50% - 69% = +++; >= 70% = ++++ [Table 10a]

[0341] Table 10b: In vitro immunogenicity of HLA class I peptides of the invention Exemplary results of in vitro immunogenicity experiments of the peptides of the invention carried out by the Applicant: <20% = +; 20%- 49% = ++; 50% - 69% = +++; >= 70% = ++++ [Table 10b-1] [Table 10b-2] [Table 10b-3] [Table 10b-4]

[0342] Example 4 Peptide synthesis All peptides were synthesized using standard, well-established solid-phase peptide synthesis using the Fmoc strategy. Identity and purity of individual peptides were determined by mass spectrometry and analytical RP-HPLC. Peptides were obtained as white to off-white lyophilizates (trifluoroacetate salts) with purity >50%. All TUMAPs are preferably administered as trifluoroacetate or acetate salts, although other salt forms are also possible.

[0343] Example 5 MHC binding assay Candidate peptides for T cell-based therapy according to the present invention were further tested for their MHC binding capacity (affinity). Individual peptide-MHC complexes were generated by UV-ligand exchange, and the UV-sensitive peptides were cleaved upon UV irradiation and exchanged with the peptide of interest to be analyzed. Only peptide candidates that can effectively bind and stabilize peptide-receptive MHC molecules prevent the dissociation of the MHC complex. To determine the yield of the exchange reaction, an ELISA based on the detection of the light chain (β2m) of the stabilized MHC complex was performed. The assay was performed as generally described in Rodenko et al. (Rodenko et al., 2006).

[0344] 96-well MAXISorp plates (NUNC) were coated with 2ug / ml streptavidin in PBS overnight at room temperature, washed 4 times, and blocked in 2% BSA containing blocking buffer for 1 hour at 37°C. Refolded HLA-A *02:01 / MLA-001 monomer served as a standard covering the range of 15-500ng / ml. Peptide-MHC monomers for UV exchange reactions were diluted 100-fold in block buffer. Samples were incubated for 1 hour at 37°C, washed 4 times, incubated with 2ug / ml HRP-conjugated anti-β2m for 1 hour at 37°C, washed again, and detected with TMB solution stopped with NH2SO4. Absorbance was measured at 450nm. For the generation and manufacture of antibodies or their fragments, and / or T-cell receptors or their fragments, candidate peptides that show high exchange yields (preferably higher than 50%, most preferably higher than 75%) are generally preferred, as they show sufficient binding activity to MHC molecules and prevent dissociation of the MHC complex.

[0345] Table 11: MHC Class I Binding Score HLA-A * Binding of HLA class I restricted peptides to 01 varied with peptide exchange yield: >10% = +; >20% = ++; >50 = +++; > 75% = ++++ [Table 11-1] [Table 11-2] [Table 11-3] [Table 11-4]

[0346] Table 12: MHC Class I Binding Score HLA-A * Binding of HLA class I restricted peptides to 02 varied with peptide exchange yield: >10% = +; >20% = ++; >50 = +++; > 75% = ++++ [Table 12-1] [Table 12-2]

[0347] Table 13: MHC Class I Binding Score HLA-A * Binding of HLA class I restricted peptides to 03 varied with peptide exchange yield: >10% = +; >20% = ++; >50 = +++; > 75% = ++++ [Table 13]

[0348] Table 14: MHC Class I Binding Score HLA-A * Binding of HLA class I restricted peptides to 24 varied with peptide exchange yield: >10% = +; >20% = ++; >50 = +++; >75% = ++++ [Table 14-1] [Table 14-2] [Table 14-3]

[0349] Table 15: MHC Class I Binding Score HLA-B * Binding of HLA class I restricted peptides to 07 varied with peptide exchange yield: >10% = +; >20% = ++; >50 = +++; > 75% = ++++ [Table 15-1] [Table 15-2] [Table 15-3]

[0350] Table 16: MHC Class I Binding Score HLA-B * Binding of HLA class I restricted peptides to 08 varied with peptide exchange yield: >10% = +; >20% = ++; >50 = +++; > 75% = ++++ [Table 16]

[0351] Table 17: MHC Class I Binding Score HLA-B * Binding of HLA class I restricted peptides to 44 varied with peptide exchange yield: >10% = +; >20% = ++; >50 = +++; >75% = ++++ [Table 17-1] [Table 17-2] [Table 17-3]

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Claims

1. A peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:489, and variants thereof that are at least 88% homologous to SEQ ID NO:1 to SEQ ID NO:489, and pharma- ceutically acceptable salts thereof; wherein said variants bind to major histocompatibility complex (MHC) molecules and / or cause T cells to cross-react with said variant peptide; and wherein said peptide is not a full-length polypeptide.

2. 2. The peptide of claim 1, which has the ability to bind to an MHC class I or II molecule and, upon binding to said MHC, becomes capable of being recognized by CD4 and / or CD8 T cells.

3. 3. The peptide or variant thereof according to claim 1 or 2, the amino acid sequence of which comprises a stretch of amino acids according to any one of SEQ ID NOs: 1 to 489.

4. 4. The peptide or variant thereof according to any one of claims 1 to 3, wherein the peptide or variant thereof has an overall length of 8 to 100, preferably 8 to 30, more preferably 8 to 16 amino acids, and most preferably the peptide consists or essentially consists of an amino acid sequence as set forth in any of SEQ ID NO: 1 to SEQ ID NO:

489.

5. A peptide or variant thereof according to any one of claims 1 to 4, wherein the peptide is modified and / or comprises a non-peptide bond.

6. The peptide or variant thereof according to any one of claims 1 to 5, wherein said peptide is part of a fusion protein comprising in particular the N-terminal amino acids of the HLA-DR antigen-associated invariant chain (Ii).

7. An antibody, preferably a monoclonal antibody or a fragment thereof, in particular a soluble or membrane-bound antibody, which specifically recognizes a peptide or a variant thereof according to any one of claims 1 to 5, preferably a peptide or a variant thereof according to any one of claims 1 to 5, when bound to an MHC molecule.

8. A T cell receptor, preferably soluble or membrane bound, or a fragment thereof, which, when bound to an MHC molecule, reacts with an HLA ligand which is a peptide or a variant thereof according to any one of claims 1 to 5, preferably a peptide or a variant thereof according to any one of claims 1 to 5.

9. 9. The T cell receptor of claim 8, wherein the ligand amino acid sequence is at least 88% identical to any one of SEQ ID NOs: 1 to 489, or the ligand amino acid sequence consists of any one of SEQ ID NOs: 1 to 489.

10. 10. The T cell receptor of claim 8 or 9, wherein the T cell receptor is provided as a soluble molecule, optionally carrying additional effector functions such as an immunostimulatory domain or a toxin.

11. An aptamer which specifically recognizes a peptide according to any one of claims 1 to 5 or a variant thereof, preferably a peptide according to any one of claims 1 to 5 or a variant thereof bound to an MHC molecule.

12. A nucleic acid encoding a peptide or variant thereof according to any one of claims 1 to 5, an antibody or fragment thereof according to claim 7, a T cell receptor or fragment thereof according to claim 8 or 9, optionally linked to a heterologous promoter sequence or an expression vector expressing said nucleic acid.

13. A recombinant host cell comprising a peptide according to any one of claims 1 to 6, an antibody or fragment thereof according to claim 7, a T cell receptor or fragment thereof according to claim 8 or 9, or a nucleic acid or expression vector according to claim 12, preferably selected from an antigen presenting cell such as a dendritic cell, a T cell or a NK cell.

14. 10. An in vitro method of producing activated T lymphocytes comprising ex vivo contacting T cells with antigen-loaded human class I or II MHC molecules expressed on the surface of a suitable antigen-presenting cell or on the surface of an artificial construct that mimics an antigen-presenting cell for a time sufficient to activate said T cells in an antigen-specific manner, wherein said antigen is a peptide according to any one of claims 1 to 4.

15. 15. An activated T lymphocyte produced by the method of claim 14, which selectively recognizes a cell presenting a polypeptide comprising the amino acid sequence of any one of claims 1 to 4.

16. A pharmaceutical composition comprising at least one active ingredient selected from the group consisting of a peptide according to any one of claims 1 to 6, an antibody or fragment thereof according to claim 7, a T cell receptor or fragment thereof according to claim 8 or 9, an aptamer according to claim 11, a nucleic acid or expression vector according to claim 12, a host cell according to claim 13, or an activated T lymphocyte according to claim 15, or a conjugated or labelled active ingredient, together with a pharma- ceutically acceptable carrier, and, optionally, pharma-ceutically acceptable excipients and / or stabilizers.

17. A method for producing a peptide or variant thereof according to any one of claims 1 to 6, an antibody or fragment thereof according to claim 7, or a T cell receptor or fragment thereof according to claim 8 or 9, comprising the steps of culturing a host cell according to claim 13, and isolating the peptide or variant thereof, antibody or fragment thereof, or T cell receptor or fragment thereof from the host cell and / or a culture medium thereof.

18. A peptide according to any one of claims 1 to 6, an antibody or fragment thereof according to claim 7, a T cell receptor or fragment thereof according to claim 8 or 9, an aptamer according to claim 11, a nucleic acid or expression vector according to claim 12, a host cell according to claim 13, or an activated T lymphocyte according to claim 15 for use in medicine.

19. A method of killing target cells in a patient, the target cells presenting a polypeptide comprising an amino acid sequence according to any one of claims 1 to 4, comprising the step of administering to the patient an effective number of activated T cells as defined in claim 15.

20. A peptide according to any one of claims 1 to 6, an antibody or fragment thereof according to claim 7, a T cell receptor or fragment thereof according to claim 8 or 9, an aptamer according to claim 11, a nucleic acid or expression vector according to claim 12, a host cell according to claim 13, or an activated T lymphocyte according to claim 15 for use in the diagnosis and / or treatment of cancer or for use in the manufacture of a medicament against cancer.

21. 21. The use according to claim 20, wherein said cancer is selected from the group of lung cancer (including NSCLC and SCLC), acute myeloid leukemia, breast cancer, cholangiocarcinoma, brain cancer, chronic lymphocytic leukemia, colorectal cancer, esophageal cancer, gallbladder cancer, gastric cancer, squamous cell carcinoma of the head and neck, hepatocellular carcinoma, melanoma, non-Hodgkin's lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, renal cell carcinoma, urinary bladder cancer, uterine cancer and other tumors that show overexpression of the proteins from which peptides SEQ ID NO:1 to SEQ ID NO:489 are derived.

22. (a) a container comprising a pharmaceutical composition comprising the peptide or variant according to any one of claims 1 to 6, the antibody or fragment thereof according to claim 7, the T cell receptor or fragment thereof according to claim 8 or 9, the aptamer according to claim 11, the nucleic acid or expression vector according to claim 12, the host cell according to claim 13, or the activated T lymphocyte according to claim 15, in solution or in lyophilized form; (b) optionally, a second container containing a diluent or reconstitution 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:531, and (d) optionally, (i) using a solution; or (ii) freezing A kit comprising instructions for reconstitution and / or use of the dry formulation.

23. 23. The kit of claim 22, further comprising one or more of: (iii) a buffer; (iv) a diluent; (v) a filter; (vi) a needle; or (v) a syringe.

24. a) identifying tumor associated peptides (TUMAPs) presented by tumor samples from said individual patients; b) comparing said peptides identified in a) to a pool of peptides prescreened for immunogenicity and / or over-presentation in tumors compared to normal tissues; c) selecting at least one peptide from said reservoir that matches a TUMAP identified in said patient; d) creating and / or formulating a personalized vaccine or a compound-based or cell therapy based on step c); 23. A method for producing a personalized anti-cancer vaccine for compound-based and / or cell therapy for an individual patient, comprising:

25. The TUMAP is a1) comparing expression data from the tumor sample with expression data from a normal tissue sample corresponding to the tissue type of the tumor sample to identify proteins that are overexpressed or aberrantly expressed in the tumor sample; a2) correlating the expression data with sequences of MHC ligands bound to MHC class I / or class II molecules in the tumor sample to identify MHC ligands derived from proteins that are overexpressed or aberrantly expressed by the tumor.

26. 26. The method of claim 24 or 25, wherein the sequence of the MHC ligand is identified by eluting bound peptides from the MHC molecules isolated from the tumor sample and sequencing the eluted ligands.

27. The method according to any one of claims 24 to 26, wherein the normal tissue corresponding to the tissue type of the tumor sample is obtained from the same patient.

28. The peptide contained in the reservoir is aa. performing genome-wide messenger ribonucleic acid (mRNA) expression analysis by highly parallel methods such as microarray or sequencing-based expression profiling, comprising identifying genes that are overexpressed in malignant tissues compared to normal tissues or tissue groups; ab. selecting peptides encoded by the selectively expressed or overexpressed genes detected in step aa; ac. determining the induction of an in vivo T cell response by the selected peptides, comprising an in vitro immunogenicity assay using human T cells from healthy donors or the patient; or b. Identifying HLA ligands from the tumor sample using mass spectrometry; bb. performing genome-wide messenger ribonucleic acid (mRNA) expression analysis by highly parallel methods such as microarray or sequencing-based expression profiling, comprising identifying genes that are overexpressed in malignant tissue compared to normal tissue or tissue groups; bc. comparing the identified HLA ligands to the gene expression data; bd. selecting peptides encoded by the selectively expressed or overexpressed genes detected in step bc; be. Redetecting the TUMAPs selected from step bd on tumor tissue, whereby the absence or rare detection on healthy tissue supports the association of overexpression at the mRNA level; bf. Determining the induction of an in vivo T cell response by the selected peptides, comprising an in vitro immunogenicity assay using human T cells from healthy donors or the patient. The method according to any one of claims 24 to 27, wherein the marker is identified based on

29. The method of any one of claims 24 to 28, wherein the immunogenicity of the peptides contained in the reservoir is determined by a method comprising in vitro immunogenicity assays, patient immune monitoring for individual HLA binding, MHC multimer staining, ELISPOT assays and / or intracellular cytokine staining.

30. 30. The method of any one of claims 24 to 29, wherein the reservoir comprises a plurality of peptides selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:

531.

31. The method of any one of claims 24 to 30, further comprising the steps of identifying at least one mutation specific to said tumor sample in comparison with normal corresponding tissue from said individual patient, and selecting a peptide associated with said mutation for inclusion in said vaccine or for creating a cell therapy.

32. 32. The method of claim 31 , wherein the at least one mutation is identified using whole genome sequencing.

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