Patent Application
20180099033
The Sequence Listing for this application is labeled “SEQ-LIST-5-28-15.TXT”, which was created on May 28, 2015, and is 26 KB. The entire content is incorporated herein by reference in its entirety.
The present invention relates to novel tumor-associated antigens, which elicit independently from a presentation via MHC a CD8 positive T-cell response. GM-CSF-Receptor alpha chain (CSF2RA) and Tyrosinase-related protein 2 (TRP-2) were found to be targets of CD8 positive reactive T-cell clones which could detect the proteins on the surface of HLA I negative melanoma cells. Thus, the invention provides proteins, protein fragments and polypeptides of the novel antigens for use in medicine, for example for the treatment, diagnosis and prevention of a tumor disease. Furthermore provided are nucleic acids expressing the antigens of the invention, binding agents specific for the antigens of the invention, such as T-cell receptor chains and isolated T cells which are reactive against the antigens of the invention or which express the T-cell receptors of the invention. The invention further pertains to pharmaceutical compositions, especially vaccine compositions, comprising the antigens, nucleic acids, binding agents or T cells in accordance with the invention, and methods for the generation of T cells specifically reactive to the antigens of the invention in an MHC-independent manner.
Cancer is still the main cause of death albeit the development of many treatment strategies including extensive radiation and chemotherapy. Furthermore, it is known that tumor rejection mechanisms are mediated by autologous immune cells, especially T-cells, which are able to differentiate between cancerous cells and healthy cells by the detection of tumor-associated antigen (TAA)-fragments via major histocompatibility complex (MHC) presentation. Antigens which are specifically expressed in tumor cells and not in healthy tissue can be categorized into four types: (I) mutated antigens develop during tumorigenesis by point mutations or translocations within the tumor cells. Those antigens are strictly tumor-specific. (II) cancer/germline antigens are usually expressed solely within the germ cells of an adult organism and not in healthy somatic tissue. In cancer cells, however, due to the loss of epigenetic regulation, germ-cell specific genes can be activated. (III) differentiation antigens are expressed in tumors and their healthy progenitor cells. CTL responses against such antigens often result in auto-immune reactions. (IV) overexpressed TAA show only minor expression in healthy cells whereas in a tumor those antigens are strongly activated. Human tumors usually express antigens of different categories and might even process and present distinct peptides from each of these proteins via their respective HLA class I and class II molecules.
MHC molecules in humans are normally referred to as HLA (human leukocyte antigen) molecules. There are two principal classes of HLA molecules: class I and class II. CD8-positive T cells are usually cytotoxic (therefore named cytotoxic T cells=CTL), recognize peptides of 9 to 10 amino acids which are intracellularly processed from proteins of any subcellular localization and which are presented on the cellular surface by HLA class I molecules. In the field of human cancer immunology, the last two decades have seen intensive efforts to characterise cancer-associated and cancer-specific antigens. Also, effort has been devoted to the analysis of antibodies to human tumor antigens. Such antibodies can be used for diagnostic and therapeutic purposes, for instance in combination with an anti-cancer agent. In addition, promising approaches of vaccine therapies are currently developed based on MHC-class I antigenic fragments, there is still no satisfactory immune therapy available for most cancer types.
To date only few examples are known for HLA/MHC-independent recognition of TAA via CD4- or CD8-positive T cells. Barnd and co-workers, 1989 PNAS, described the recognition of epithelial mucin on breast and ovarian cancer cells. A HLA-independent recognition was further found for nickel-reactive CD8-positive T-cells in two patients suffering from contact dermatitis (Moulon et al., J Invest Dermatol 2003), for a melanoma-reactive T-cell clone without identifying the responsible antigen (Somasundaram et al., J Transl Med 2005) and for a kidney cell carcinoma-reactive T-cell clone (Wang et al., J Immunol 2008); the antigen of the latter was recently published (Hanada et al., Blood 2011).
Although a high number of HLA-restricted TAAs out of all four of the above mentioned categories were identified in the past, still no satisfactory treatment based on a therapeutic vaccination and adoptive transfer of antigen-specific T cells is available. This is in part due to problems with respect to reproducibility of the results in clinical studies or to the observation of an only insufficient clinical effect of the vaccine. A problem often encountered in cancer immunotherapy is further an impairment of the immunogenicity in cancer tissue. This so-called “immune escape” can be understood on the basis of phenotype differences encountered in neoplastic cells. For example, tumor cells show decreased ability to process and present antigens, have a decreased ability to stimulate autologous T cells, show complete down-regulation of immunogenic proteins associated with transformed cells and/or no or low expression of leukocyte adhesion molecules or other accessory molecules and selective down-regulation of certain MHC class I and class II alleles. The latter may affect all class I/II antigens, or only part of them. Partial HLA loss of function or expression can be caused by loss of single HLA alleles, HLA haplotypes or complete HLA class I loss due to bi-allelic β2m gene loss (Aptsiauri et al., Cancer Immunol Immunother 2008; Bernal M. et al. Cancer Immunol Immunother 61:1359-71, 2012). Tumors that have lost the expression of HLA are thus resistant to any treatment based on HLA-dependent T cells. Indeed, impairment of HLA function is one of the key “immune escape” mechanisms of tumor cells and thus limits the application of T-cell mediated immune therapy.
In view of the above described background art, the objective of the present invention is to provide novel tumor associated antigens (TAA) which allow for the development of novel treatments of cancer, and specifically novel treatments that circumvent the problem of immune escape in cancer cells.
In a first aspect of the present invention, the above objective is solved by providing a protein, protein fragment or polypeptide comprising at least 8 contiguous amino acids from the amino acid sequence of the GM-CSF-receptor alpha chain (CSF2RA) (SEQ ID NO: 1) or the tyrosinase-related protein 2 (TRP-2) (SEQ ID NO: 2), wherein said protein, protein fragment or polypeptide is capable of inducing a T-cell response and/or binding a cognate T-cell receptor.
In another embodiment of the invention, the protein, protein fragment or polypeptide comprises the amino acid sequence of a complex epitope of the native TRP-2 or CSF2RA proteins. A complex epitope in connection with the herein described invention is a binding site for an immunological binding agent, such as a T-cell receptor (TCR) or antibody, which is composed of two or more amino acid sequences which are in close spatial proximity in the native three-dimensional folded proteins, but which do not constitute one contiguous sequence within the linear amino acid sequence of the antigen. A complex epitope, for example, can be composed of stretches of the amino acid sequences of two spatially closely folded secondary structures within the antigen, or between two separate amino acid chains of contacting subunits of a multi protein complex.
The inventors surprisingly identified the proteins tyrosinase-related protein 2 (TRP-2) and GM-CSF receptor alpha chain (CSF2RA) as molecules expressed in melanoma (TRP-2) and other malignant cell types (CSF2RA), which are recognized by T cells in an HLA-independent manner. Thus, T cells against the antigens of the invention provide the surprising advantage to lyse tumors cells that are either completely negative for HLA class I expression, or at least show an impairment of HLA expression and/or function. Normally such cells would escape the patient's natural or a therapeutically induced immune rejection.
The protein, protein fragment or polypeptide of the invention in an additional embodiment comprises at least 10, preferably 15, 20, 50, and most preferably 100 contiguous amino acids from the amino acid sequence of GM-CSF-Receptor alpha chain (CSF2RA) (SEQ ID NO: 1) or tyrosinase-related protein 2 (TRP-2) (SEQ ID NO: 2), wherein said protein, protein fragment or polypeptide is capable of inducing a T-cell response and/or binding a cognate T cell receptor.
In the context of the present invention the terms “protein” or “polypeptide” are used interchangeably and denote a polymer composed of amino acid monomers joined by peptide bonds. A “peptide bond” is a covalent bond between two amino acids in which the α-amino group of one amino acid is bonded to the α-carboxyl group of the other amino acid. All amino acid or polypeptide sequences, unless otherwise designated, are written from the amino terminus (N-terminus) to the carboxy terminus (C-terminus). The terms “protein”, “protein fragment” and “polypeptide” refer to a molecular chain of amino acids, and do not refer to a specific length of the product and if required can be modified in vivo or in vitro, for example by glycosylation, amidation, carboxylation or phosphorylation. Thus, inter alia peptides, oligopeptides and proteins are included within the definition of polypeptide.
Of course, functional derivatives and fragments of the polypeptide, summarized under the term “protein fragment”, are also included in the present invention. Functional derivatives are meant to include polypeptides which differ in one or more amino acids in the overall sequence, which have deletions, substitutions, inversions, insertions or additions. Amino acid substitutions which can be expected not to essentially alter biological and immunological activities, have been described. Amino acid replacements between related amino acids or replacements which have occurred frequently in evolution are inter alia Ser/Ala, Ser/Gly, Asp/Gly, Asp/Asn, Ile/Val.
In addition, the term “functional derivatives” of these polypeptides also implies the addition salts of the polypeptides, amides of the polypeptides and specifically the C-terminal amides, esters and specifically the C-terminal esters and N-acyl derivatives specifically N-terminal acyl derivatives and N-acetyl derivatives.
In accordance with the present invention, the protein, protein fragment or polypeptide is in a preferred embodiment a protein, protein fragment or polypeptide comprising an amino acid sequence with at least 50%, 60%, 70%, 80%, 90%, 95%, most preferably 99% and even more preferably 100% sequence identity to the amino acid sequence of the proteins GM-CSF receptor alpha chain (CSF2RA) or tyrosinase-related protein 2 (TRP-2), specifically to the amino acid sequences as shown in SEQ ID NO: 1 or 2.
In preferred embodiments protein fragments of the herein described antigens are immunogenic fragments, which still have the ability to induce an immunogenic response, preferably independent of MHC class I and/or II.
In preferred embodiments of the invention the protein, protein fragment or polypeptide consists of the amino acid sequence shown in SEQ ID NO: 1 or 2.
The polypeptides according to the invention can be produced either synthetically or by recombinant DNA technology. Methods for producing synthetic polypeptides are well known in the art.
With the aid of the proteins, protein fragments or polypeptides in accordance with the invention cytotoxic and helper T cells can be generated, which develop an antigen-specific, MHC-independent cytotoxic activity against tumor cells expressing proteins, protein fragments or polypeptides of the invention and destroy them. Therefore, these polypeptides open up the possibility of an effective tumor therapy, in the course of which the suppression of an immune reaction, which is often observed in tumor patients, can be reversed.
The invention also relates to a fusion protein composed of one of the aforementioned proteins, protein fragments or polypeptides and of a second protein or polypeptide. Such fusion proteins are suitable for use as a diagnostic or therapeutic or prophylactic agent or generally for a detection and/or manipulation of T cells that recognize TRP-2 or CSF2RA, specifically independent of their presentation via MHC. For example, fusion proteins could be envisioned that consist of a carrier protein such as, for example, HSA, collagen or other proteins and one or more of the polypeptides of the invention. The polynucleotides coding for this fusion protein are also the subject matter of the present invention.
Further provided is the protein, protein fragment or polypeptide in accordance with the present invention, which is characterized by the presence of a signal peptide which mediates the cellular transport of the molecule, when expressed in a cell, to the outside of the cellular membrane. Signal peptides are known to the person of skill in the art. More preferably the protein, protein fragment or polypeptide in accordance with the present invention comprises a domain capable of anchoring the molecule of the invention to the cellular membrane. Such a domain could be a membrane anchor or a transmembrane domain.
In one embodiment the protein, protein fragment or polypeptide according to the invention is characterized in that it is capable of inducing a major histocompatibility complex (MHC) independent T-cell response, preferably a MHC class I independent T-cell response, or a MHC class I and II independent T-cell response; and/or the protein, protein fragment or polypeptide is characterized in that it is capable of binding a cognate T-cell receptor expressed by a MHC class I independent T cell or a MHC class I and II independent T cell.
Due to the surprising finding of the independence of the recognition of the molecules of the invention from HLA/MHC expression, it is one further preferred embodiment that the protein, protein fragment or polypeptide in accordance with the invention is not presented by MHC class I, or MHC class I and II. The protein, protein fragment or polypeptide of the invention is preferably expressed on the cellular surface without undergoing a fragmentation as it is known for the presentation of MHC-restricted antigens. Thus, the present invention shall in a preferred embodiment pertain to such a protein, protein fragment or polypeptide which, when expressed in an HLA/MHC-negative cell, still is able to induce a T-cell response.
In the context of the various embodiments described herein, a protein, protein fragment or polypeptide shall not be excluded from the scope of the invention just because in addition to its capability to mediate a HLA-independent T-cell response, it still can be processed and presented by the MHC/HLA pathway. Only in specific embodiments of the invention a protein, a protein fragment or polypeptide shall be excluded, when it consists of an MHC/HLA class I and/or II binding epitope.
One particularly preferred embodiment of the present invention relates to the protein, protein fragment or polypeptide according to the description herein before, for use in medicine, specifically for use in a method of treatment of the human or animal body by surgery or therapy, or diagnostic methods practised on the human or animal body.
Further provided according to the present invention is the protein, protein fragment or polypeptide as described herein, for use in the prevention, diagnosis or treatment of a proliferative disease, preferably wherein the proliferative disease is a tumor disease. A preferred tumor disease according to the invention is a tumor disease that is devoid of a functional MHC class I complex, or that is devoid of functional WIC class I and II complexes, specifically such tumors which do not express MHC class I, or do not express MHC class I and II. Hence, the protein, protein fragment or polypeptide as described herein are specifically for use in the prevention, diagnosis or treatment of a tumor which exhibit immune escape by alteration of the MHC class I and/or II presentation complex.
As used herein, the term “tumor” or “tumor disease” means both benign and malignant tumors or neoplasms and includes melanomas, lymphomas, leukemias, and sarcomas, illustrative examples of tumor tissues are cutaneous such as malignant melanomas and mycosis fungoides; hematologic tumors such as leukemias, for example, acute lymphoblastic, acute myelocytic, or chronic myelocytic leukemia; lymphomas such as Hodgkin's disease or malignant lymphoma; gynecologic tumors such as ovarian and uterine tumors; urologic tumors such as those of the prostate, bladder, or testis; soft tissue sarcomas, osseus, or non-osseous sarcomas, breast tumors; tumors of the pituitary, thyroid, and adrenal cortex; gastrointestinal tumors such as those of the esophagus, stomach, intestine, and colon; pancreatic and hepatic tumors; laryngeal papillomas/carcinomas and lung tumors.
In preferred embodiments the tumor to be treated, diagnosed or prevented is characterized by the expression of CSF2RA (SEQ ID NO: 1) and/or TRP-2 (SEQ ID NO: 2). Or tumors expressing homologs of the aforementioned antigens, wherein a homolog is characterized the sequence identity of at least 75, preferably 80, 90, or 95% compared to a sequence as shown in SEQ ID NOs: 1 or 2, respectively.
Furthermore, such tumors are preferred in accordance with the various embodiments of the invention which underwent, or are at risk of undergoing, immune escape mechanisms by altering the expression and/or function of the HLA complexes (either class I or II or both) within the tumor cell.
Preferred tumors of the present invention with respect of TRP-2 are tumors of the skin, preferably melanoma, or tumors of the central nervous system, preferably glioblastoma.
On the other hand preferred tumors (or malignancies) of the present invention with respect to CSF2RA are tumors of the skin, such as melanoma, hematological malignancies expressing CSF2RA, such as leukemia, and solid tumors expressing CSFRA, such as lung cancer, pancreatic cancer, colorectal cancer and ovarian cancer. Specifically preferred in another embodiment is that the malignancy which expresses CSF2RA does not express CSF2RB, or expressed CSF2RB to a significantly lower level than CSF2RA.
In a preferred embodiment of the present invention, the above described protein, protein fragment or polypeptide of the invention for use in medicine, or proteins used within the herein described specific methods, are the full length proteins of CSF2RA and/or TRP-2, possible with minor amino acid changes of preferably not more than 50, 40, 30, 20, preferably 10, most preferably 5 amino acid residues compared to the sequences shown in SEQ ID NO: 1 or 2, respectively. Such sequence changes can be additions, deletions, substitutions, inversions, insertions or chemical modification of one or more amino acid residues.
In an additional aspect, the present invention further provides an isolated nucleic acid molecule, wherein said nucleic acid molecule (a) has a strand encoding for a protein, protein fragment or polypeptide according to the invention; (b) has a strand complementary to the strand in (a); or (c) has a strand that hybridizes under stringent conditions with a molecule as described in (a) or (b). Stringent conditions are known to the person of skill in the art, specifically from Sambrook et al, “Molecular Cloning”. In addition to that, the nucleic acid optionally has further sequences which are necessary for expressing the nucleic acid sequence corresponding to the protein, specifically for expression in a mammalian/human cell. The nucleic acid used can be contained in a vector suitable for allowing expression of the nucleic acid sequence corresponding to the peptide in a cell. However, the nucleic acids can also be used to transfect a presenting cell, which shall not be restricted to classical antigen-presenting cells such as dendritic cells, in such a way that they themselves produce the corresponding proteins on their cellular surface.
The nucleic acid molecules of the invention are preferably for use in medicine.
Also provided is a vector or a cell comprising a nucleic acid molecule described herein above, specifically wherein the vector is for use in medicine. Also a cell comprising a vector according to the invention is provided.
Another aspect of the present invention is the use of at least one protein, protein fragment or polypeptide in accordance with the invention or a nucleic acid in accordance with the invention for eliciting an immune reaction in connection with a tumor therapy or a treatment for preventing a tumor. Advantageous here is the fact that the frequently observed immune escape mechanisms and tolerance to TAA in a tumor disease can be overcome (or reversed) by the use of a protein, protein fragment or polypeptide, or nucleic acids in accordance with the invention. The use in accordance with the invention can also be employed in addition to established tumor therapies.
A preventive treatment in the context of the herein described invention is of benefit possibly mainly to persons who have an increased risk of developing a tumor, because, for example, they are hereditarily predisposed or because they have already had a tumor before. In another embodiment a preventive treatment is of benefit for a patient suffering from a tumor disease with increased risk of having developed or developing resistance to immune rejection, by e.g. immune escape via the alteration of the function and/or expression of HLA class I/II complexes.
Yet another aspect of the invention pertains to a binding agent, which binds to a protein, protein fragment or polypeptide as described herein above, preferably wherein the binding agent is specific for said protein, protein fragment or polypeptide. In preferred embodiments the binding agents as described herein are for use in medicine.
In one embodiment the binding agent according to the invention is an antibody, or a fragment thereof. The term “antibody” in its various grammatical forms is used herein to refer to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antibody combining site or a paratope. Such molecules are also referred to as “antigen binding fragments” of immunoglobulin molecules. Illustrative antibody molecules are intact immunoglobulin molecules, substantially intact immunoglobulin molecules and those portions of an immunoglobulin molecule that contain the paratope, including those portions known in the art as Fab, Fab′, F(ab′)2 and F(v). Antibodies of the present invention may be monoclonal or polyclonal. The term antibody is also intended to encompass single chain antibodies, chimeric, humanized or primatized (CDR-grafted) antibodies and the like, as well as chimeric or CDR-grafted single chain antibodies, comprising portions from two different species. Immunological adjuvants for vaccines comprising lecithin may be used to stimulate antibody production.
In another embodiment the binding agent of the invention is a T-cell receptor (TCR), or a fragment thereof. A TCR is a heterodimeric cell surface protein of the immunoglobulin superfamily which is associated with invariant proteins of the CD3 complex involved in mediating signal transduction. TCRs exist in αβ and γδ forms, which are structurally similar but have quite distinct anatomical locations and probably functions. The extracellular portion of native heterodimeric αβTCR consists of two polypeptides, each of which has a membrane-proximal constant domain, and a membrane-distal variable domain. Each of the constant and variable domains includes an intra-chain disulfide bond. The variable domains contain the highly polymorphic loops analogous to the complementarity determining regions (CDRs) of antibodies.
In one preferred embodiment the TCR of the invention is characterized to comprise a sequence according to any one of SEQ ID NO: 3 to 8, or having a sequence that is at least 75, preferably 80, 90, or 95% identical any one of SEQ ID NO: 3 to 8. Also comprised are T cells which express TCRs having a sequence according to any one of SEQ ID NO: 3 to 8, or having a sequence that is at least 75, preferably 80, 90, or 95% identical to SEQ ID NO: 3 to 8.
An antigen binding agent of the invention, preferable a TCR or antibody, is in one embodiment characterized by the presence of any one of, or preferably all, CDR 1 to 3 sequences as depicted for the respective alpha or beta chains of the TCRs of the invention in the figures and table 1 below. In this embodiment it is also preferred that the TCR of the invention is a chimerized TCR, for example, by exchanging completely or in part the original human constant domain with a murine constant domain (see
One embodiment of the present invention pertains to an antigen binding polypeptide comprising at least one CDR sequences, preferably CDR3, more preferably CDR1, CDR2 and CDR3, of any one of the TCR as isolated in context of the present invention and as depicted in table 1 below.
The antigen binding polypeptide of the invention is preferably a TCR.
Thus also preferred is a T cell receptor alpha chain comprising any one, or all of, of the SEQ ID NO: 9 to 11, or 15 to 17, or 21 to 23.
Thus also preferred is a T cell receptor beta chain comprising any one, or all of, of the SEQ ID NO: 12 to 14, or 18 to 20, or 24 to 26.
Preferably a T-cell receptor of the invention, or a binding fragment thereof, has an alpha chain variable region comprising the CDR sequences of SEQ ID NO: 9, 10 and/or 11, and a beta chain variable region comprising the CDR sequences of SEQ ID NO: 12, 13 and/or 14. Such a TCR is a TCR specific for the antigen CSF2RA. Preferably this TCR is the TCR as isolated from the CTL 1A.1/506 as described herein in the examples. Such a receptor may in one embodiment comprise the at least variable region, preferably full length, sequence according to SEQ ID NO: 3 (alpha chain) and 4 (beta chain).
Preferably a T-cell receptor of the invention, or a binding fragment thereof, has an alpha chain variable region comprising the CDR sequences of SEQ ID NO: 21, 22 and/or 23, and a beta chain variable region comprising the CDR sequences of SEQ ID NO: 24, 25 and/or 26. Such a TCR is a TCR specific for the antigen CSF2RA. Preferably this TCR is the TCR as isolated from the CTL 1A3/46 as described herein in the examples. Such a receptor may in one embodiment comprise the at least variable region, preferably full length, sequence according to SEQ ID NO: 7 (alpha chain) and 8 (beta chain).
Preferably a T-cell receptor, or a binding fragment thereof, has an alpha chain variable region comprising the CDR sequences of SEQ ID NO: 15, 16 and/or 17, and a beta chain variable region comprising the CDR sequences of SEQ ID NO: 18, 19 and/or 20. Such a TCR is a TCR specific for the antigen TRP2. Preferably this TCR is the TCR as isolated from the CTL 2C/417 as described as described herein in the examples. Such a receptor may in one embodiment comprise the at least variable region, preferably full length, sequence according to SEQ ID NO: 5 (alpha chain) and 6 (beta chain).
Yet another embodiment of the invention pertains to a single chain TCR (scTCR) as a binding agent, preferably an αβ-scTCR. Single-chain TCRs (scTCRs) are artificial constructs consisting of a single amino acid strand. An scTCR can comprise a polypeptide of a variable region of a first TCR chain (e.g., an [alpha] chain) and a polypeptide of an entire (full-length) second TCR chain (e.g., a [beta] chain), or vice versa. Furthermore, the scTCR can optionally comprise one or more linkers which join the two or more polypeptides together. The linker can be, for instance, a peptide which joins together two single chains, as described herein.
Such a scTCR may be composed of any of the variable and/or constant region as provided herein.
Also provided is such a scTCR of the invention, which is fused to a human cytokine, such as IL-2, IL-7 or IL-15.
The binding agent according to the invention can also be provided in the form of a multimeric complex, comprising at least two scTCR molecules, wherein said scTCR molecules are each fused to at least one biotin moiety, and wherein said scTCRs are interconnected by biotin-strepavidin interaction to allow the formation of said multimeric complex. Also provided are multimeric complexes of a higher order comprising more than two scTCR of the invention.
In another preferred embodiment the binding agents of the invention is a bi-specific monoclonal antibody comprising the binding fragments of an antibody as described herein above, and the binding fragments of a second antibody which is, for example, specific for CD3.
Another aspect of the present invention pertains to a nucleic acid encoding a TCR or antigen binding agent as described herein.
In a further aspect, the objective of the present invention is solved by providing a T cell which is reactive against any one of the proteins, protein fragments or polypeptides according to the invention, specifically against CSF2RA or TRP-2. In a preferred embodiment, the T-cell of the invention is reactive against the protein, protein fragment or polypeptide according to the invention independent of the presentation of said protein, protein fragment or polypeptide by MHC class I and/or class II. An even more preferred embodiment of the invention provides a T cell comprising a T-cell receptor (TCR) which binds to a protein, protein fragment or polypeptide according to the invention, and wherein said binding is independent of the presentation of said polypeptide by MHC class I or MHC class I and II. The T cell of the invention is preferably CD8 and/or CD4 positive.
Further provided according to the present invention is the use of a protein, protein fragment or polypeptide as described above, a nucleic acid as described above, a vector or cell as described above, a binding agent as described above, a T cell as described above, a multimeric complex as described above, in the preparation of a medicament for treating cancer, or in the preparation of a diagnostic for diagnosing cancer. The cancer may be a mammalian cancer. In particular, the cancer may be human cancer. For example, the cancer may be breast cancer, prostate cancer, pancreatic cancer, colorectal cancer, lung cancer, malignant melanoma, leukaemia, lymphoma, ovarian cancer, cervical cancer or a biliary tract carcinoma. Specifically preferred cancers are melanoma, glioblastoma or leukemia. Said medicament may be a vaccine.
In another aspect the objective of the invention is further solved by an in-vitro method for generating MHC-independent T-cells, comprising the steps of
In this aspect, the MHC is preferably MHC class I and/or class II.
In one preferred embodiment of the method described above, said tumor cell and said PBMCs are autologous cells derived from one tumor patient. This embodiment has the advantage that MHC independent T cells can be generated for a tumor patient. Such T cells are usable for re-injection into the patient as a treatment-agent against the tumor the patient is suffering from.
The above described method in one preferred embodiment comprises as said first cell a cell that does not express MHC class I, or MHC class I and II, or that is at least impaired in MHC class I and/or II function and/or expression.
Yet a further preferred embodiment of the above described method is, when in step (iii) said ability of a T cell to recognize a cell expressing the protein, protein fragment or polypeptide used in (i) independent of the expression of MHC in said cell, is determined by testing the reactivity of said T cell against said cell expressing the protein, protein fragment or polypeptide, wherein
Also provided are T cells which are generated by a method according to the invention as described herein above. Preferably, the T cell of the invention is for use in medicine. Specifically, the T cell of the invention is for treating a patient suffering from a malignant disease by infusing said T cells into said patient, preferably wherein said T cells are derived from autologous PBMCs of said patient.
A further aspect pertains to a pharmaceutical composition, comprising a protein, protein fragment or polypeptide according to the invention, or a nucleic acid, a vector, a cell, a binding agent or an isolated T cell according to the invention. In a preferred embodiment the pharmaceutical composition is a vaccine.
Examples of pharmaceutically acceptable carriers or diluents useful in the present invention include stabilizers such as SPGA, carbohydrates (e.g. sorbitol, mannitol, starch, sucrose, glucose, dextran), proteins such as albumin or casein, protein containing agents such as bovine serum or skimmed milk and buffers (e.g. phosphate buffer).
Optionally, one or more compounds having adjuvant activity may be added to the vaccine. Suitable adjuvants are, for example, aluminium hydroxide, phosphate or oxide, oil-emulsions (e.g. of Bayol F<(R)> or Marcol 52<(R)>), saponins or vitamin-E solubilisate.
The vaccine according to the present invention can be given inter alia intravenously, intraperitoneally, intranasally, intradermally, subcutaneously or intramuscularly.
The useful effective amount to be administered will vary depending on the age and weight of the patient and mode of administration of the vaccine.
The vaccine can be employed to specifically obtain a T-cell response, but it is also possible that a B-cell response is elicited after vaccination. If so, the B-cell response leads to the formation of antibodies against the protein, protein fragment or polypeptide of the vaccine, which antibodies will be directed to the source of the antigen production, i.e. the tumor cells. This is an advantageous feature, because in this way the tumor cells are combatted by responses of both the cellular and the humoral arm of the immune system.
Both arms of immunological defence will even be more effectively triggered when the vaccine comprises the antigens of the invention in an antigen-presenting cell, independent of MHC expression. Antigen presentation can be achieved by using monocytes, macrophages, interdigitating cells, Langerhans cells and especially dendritic cells, loaded with one of the antigens of the invention.
It is also possible to use cells already transfected with a cloning vehicle harbouring the information for the antigens of the invention. These cells will act as antigen-presenting cells and will present the full-length antigens of the invention, or fragments thereof, on their surface in an MHC-independent manner. Thus, in the context of the present invention it is preferred to express the antigens of the invention such, that they are transported to the cellular surface of the antigen-presenting cell.
Instead of a vaccination with these cells, which next to the desired expression products also harbour many elements which are also expressed and which can negatively affect the desired immunogenic reaction of the cell, it is also possible that a vaccine is composed of liposomes which are loaded with the proteins, protein fragments and polypeptides of the invention, and which thus expose these antigens to the host immune system. Such liposomes, for instance, are filled with lymphokines. Such liposomes will trigger an immunological T-cell reaction.
By presenting the protein, protein fragment or peptide in the same way as it is also presented in vivo, an enhanced T-cell response will be evoked. Furthermore, by the natural adjuvant working of the relatively large antigen-presenting cells also a B-cell response is triggered. This B-cell response will a.o. lead to the formation of antibodies directed to the native antigen. This complex is especially found in tumor cells, where it has been shown that the antigens of the invention are presented naturally, which are thus able to elicit a T-cell response. It is this naturally occurring phenomenon which is enlarged by the vaccination with cells already presenting the proteins, protein fragments or peptides of the invention. By enlarging not only an enlarged T-cell response will be evoked, but also a B-cell response will be initiated which leads to antibodies directed against the MHC-independent peptide.
The vaccines according to the invention can be enriched by numerous compounds which have an enhancing effect on the initiation and the maintenance of both the T-cell and the B-cell response after vaccination.
In this way addition of cytokines to the vaccine will enhance the T-cell response. Suitable cytokines are for instance interleukins, such as IL-2, IL-4, IL-7, IL-15 or IL-12, GM-CSF, RANTES, tumor necrosis factor and interferons, such as IFN-α, -β, or -γ.
In a similar way, antibodies against T-cell surface antigens, such as CD2, CD3, CTLA-4, PD-1, CD27 and CD28 will enhance the immunogenic reaction.
Also the addition of helper epitopes to stimulate CD4<+> helper cells or CD8<+> killer cells augments the immunogenic reaction. Alternatively also helper epitopes from other antigens can be used, for instance from heat shock-derived proteins or cholera toxin.
Finally, the present invention relates to a method of treating a patient suffering from a tumor disease, comprising the administration of a therapeutically effective amount of at least one protein, protein fragment or polypeptide in accordance with the invention and/or at least one nucleic acid and/or at least one binding agent and/or at least one vector molecule and/or at least one T cell of the invention in an amount sufficient to achieve a therapeutic effect. Another aspect is a method of eliciting a tumor-specific CTL response comprising the administration of a response-eliciting amount of the MHC independent antigens in accordance with the invention (the proteins, protein fragments and polypeptides of the invention). Target malignancies are those expressing CSF2RA and TRP-2.
The present invention will now be further described in the following examples with reference to the accompanying figures and sequences, nevertheless, without being limited thereto. For the purposes of the present invention, all references as cited herein are incorporated by reference in their entireties. In the Figures and Sequences:
SEQ ID NO: 1 shows the amino acid sequence of CSF2RA:
SEQ ID NO: 2 shows the amino acid sequence of TRP-2 (isoform 1)
SEQ ID NO: 3 shows the TCR alpha chain sequence of CTL 1A.1/506
SEQ ID NO: 4 shows the TCR beta chain sequence of clone CTL 1A.1/506
SEQ ID NO: 5 shows the TCR alpha chain sequence of clone CTL 2C/417
SEQ ID NO: 6 shows the TCR beta chain sequence of clone CTL 2C/417
SEQ ID NO: 7 shows the TCR alpha chain sequence of clone CTL 1A3/46
SEQ ID NO: 8 shows the TCR beta chain sequence of clone CTL 1A3/46
SEQ ID NOs: 9 to 26 show the CDR sequences of the TCR of the invention.
Out of the melanoma patient MA-MEL-86 four different permanent tumor cell lines (MA-MEL-86A, -86B, -86C, -86F) were established from separate lymph node metastases. Both MA-MEL-86B and MA-MEL-86F did not express HLA I on their cellular surface due to a biallelic mutation in the β2-microglobulin gene. The tumor cell line MA-MEL-86C lost one MLA haplotype. In contrast thereto, the MA-MEL-86A line expressed all HLA I alleles, but showed as the only one out of the four tumor cell lines no expression of melanosomal differentiation antigens (
Tumor-reactive CD8 positive T cells were generated in so called mixed lymphocyte-tumor cell culture (MLTC) by weekly stimulation of lymphocytes taken from peripheral blood mononuclear cells, PBMCs, with autologous tumor cell lines MA-MEL-86A or MA-MEL-86C. Surprisingly, the inventors recognized that MLTC-responder lymphocytes in varying recognition patterns still recognized the HLA I negative variants MA-MEL-86B (
A cDNA library of the melanoma cell line MEL-86A constructed in the eukaryotic expression vector pcDNA3.1 was screened with responder lymphocytes of MLTC 1A.1. In a first step, cDNA pools consisting of 100 cDNA clones were co-transfected with HLA I alleles of the patient into 293T-cells. The transfectants were tested for recognition by the T cells. One of the pools was found to be responsive. Subsequently, a step-by-step cDNA cloning was performed. In this way CSF2RA was identified as a target of the MLTC 1A.1 (
On the other hand, all tested normal cell lines, amongst others melanocytes, granulocytes and monocytes, derived from peripheral blood, were not recognized by the CSF2RA-reactive T cells (see
Using flow cytometry the inventors furthermore showed that all CSF2RA-reactive T-cells were TCRαβ positive, CD3 positive and CD8 positive, and expressed the T cell receptor beta chain Vβ12 (TRBV10-3). The reactivity of these T cells could only be inhibited by antibodies against CD3 or CSF2RA, but not with antibodies against HLA I or II (see
cDNAs of the alpha and the beta chain of the TCR of the HLA-independent CSF2RA-reactive T-cell clone 1A.1/506 were cloned and sequenced (see
In panel test 40 cDNA clones which encode known melanoma-associated antigens, were transfected into 293T cells. The transfectants were subsequently tested for recognition by responder lymphocytes of MLTCs 1C and 2C. It was found that both MLTCs and CTL clones derived thereof could recognize the HLA I negative tumor cell lines MA-MEL-86B and -86F and targeted the melanosomal differentiation antigen TRP-2. They cross-reacted with any of the TRP-2-expressing melanoma cell lines available in the laboratory as well as with normal melanocytes, and—after transfection with TRP-2—also with non-melanocytic cells of mouse, hamster and monkey origin (see
Using flow cytometry the inventors furthermore showed that all TRP-2-reactive T cells were TCRαβ positive, CD3 positive and CD8 positive, and expressed the T-cell receptor beta chain (TRBV28). The reactivity of these T cells could only be inhibited by antibodies against CD3, but not by antibodies against HLA I or II.
The direct recognition of TRP-2 by CD8 positive T cells would require the cell surface expression of the antigen. Indeed the inventors could show cell surface expression with a TRP-2 reactive antibody (see
This result was further supported by the finding that a deletion of the transmembrane domain (TMD) of TRP-2 resulted in a loss of the recognition by the T cells, which could be reversed by the substitution with an unrelated TMD of HLA-A*24:01 (see
cDNAs of the alpha and the beta chain of the TCR of the HLA-independent TRP-2-reactive T-cell clone 2C/417 were cloned and their function was tested via transfer into CD8 positive T cells of PBMCs of a healthy donor (SEQ ID NO: 5 and 6;
The a- and b T cell receptor chain- (TCR-) cDNAs were isolated from the CSF2RA-specific CTL 1A.3/46 and cloned as a bicistronic construct into a retroviral vector (
Cell surface expression of the CSF2RA-specific TCR in human T cells transduced with the native (left) and the chimerized (right) constructs is shown in
In a response analysis of the CSF2RA-reactive CTL 1A.3/44 in comparison to CSF2RA-TCR-transduced allogeneic T cells CSF2RA-negative target cells (MA-MEL-86F and 293T) were not recognized while MA-MEL-86B cells expressing CSF2RA endogenously and 293T cells transfected with the antigen were recognized (
| Number | Date | Country | Kind |
|---|---|---|---|
| 12197289.7 | Dec 2012 | EP | regional |
This application is a Continuation Application of co-pending application Ser. No. 14/648,703, filed May 30, 2015; which is a National Stage Application of International Application Number PCT/EP2013/076760, filed Dec. 16, 2013; which claims priority to European Application No. 12197289.7, filed Dec. 14, 2012; all of which are incorporated herein by reference in their entirety.
| Number | Date | Country | |
|---|---|---|---|
| Parent | 14648703 | May 2015 | US |
| Child | 15826879 | US |
