Patent Application
20120269833
The present invention is directed to T cell receptors (TCR) recognizing antigenic peptides derived from tumor-associated antigen FMNL1/KW13 or the murine homolog FRL and being capable of inducing peptide specific killing of a target cell. The present invention is further directed to antigenic peptides derived from tumor-associated antigen FMNL1/KW13, to an antigen specific T cell, comprising said TCR, to a nucleic acid coding for said TCR and to the use of the antigen specific T cells for the manufacture of a medicament for the treatment of malignancies characterized by overexpression of FMNL1/KW13. The present invention is further disclosing a method of generating antigen specific allorestrictive T cells.
The present invention concerns the field of immunotherapies in B cell neoplasms, in particular B cell lymphoma, including acute and chronic lymphocytic leukemias.
The incidence of B cell neoplasms is increasing, especially in Western Countries (NCI, SEER). Most cases of low grade lymphoma are diagnosed at advanced stages where no curative standard therapy is available. In chronic lymphocytic leukemia (CLL), there is still no established curative therapy available at any time point of diagnosis. In contrast, patients with high grade lymphoma or acute lymphoblastic leukemia benefit from intensive and potentially curative chemotherapy regimens. However, long-term prognosis is unfavourable for adult patients with recurrent disease. Thus, novel therapies are needed.
Immunotherapy has been shown to be highly successful in low grade lymphoma including CLL. There are target specific therapies using monoclonal antibodies which are directed against surface antigens as CD20 (Rituximab) and CD52 (Alemtuzumab) (1,2). However, tumor escape occurs due to down regulation of the target antigen from the cell surface. T cells are able to recognize peptides associated to MHC molecules derived from extra- and intracellular antigens. T cells are currently applied associated to allogeneic stem cell transplantation and responsible for a Graft versus leukemia effect (GvL effect) which has been shown to be present in different B cell neoplasms (3-5). However, one major disadvantage of this approach is Graft versus host disease (GvHD) due to transferred T cells non-specifically recognizing allogeneic MHC molecules. Using allorestricted peptide-specific T cells it might be possible to circumvent central tolerance against tumor-associated self-peptides and simultaneously dissociate beneficial graft versus leukemia effect from detrimental graft versus host disease (6,7).
Krackhardt et al., “Identification of tumor associated antigens in chronic lymphocytic leukaemia by SEREX”, Blood Sep 2002, vol. 100, no. 6, pages 2123-2131, describe the identification of KW13/FMNL1. Here, peptide-specific autologous T cells were generated recognizing one single FMNL1-derived peptide (TLLHYLVKV; SEQ ID NO: 21). However, it turned out that these T cells did not recognize tumor cells as described in the paper. Thus, it is likely that the specific peptide is not an epitope presented on the surface of CLL cells. Moreover, the specific peptide has not been listed. In addition, no specific TCR has been described.
The identification of an antigenic epitope, however is of fundamental importance to use a specific antigen as target for a therapeutic approach as tumor cells can be only targeted if the specific peptide is presented on the surface of a cell. Given a protein length of 1100 amino acids, there are 1091 different nonapeptides which can be used for pulsing and most of them may not bind to the restriction element and/or are not produced by the immune proteasome, thus they are mostly not presented on the surface of a tumor cell.
Mayr et al., “Transduction of CLL cells by CD40 ligand enhances an antigen-specific immune recognition by autologous T cells”, Blood Nov 2005, vol. 106, no. 9, compare the functional reactivity of T cell lines generated by stimulation with CD40OL-AAV-transduced CLL cells, GFP-AAV-transduced CLL cells as well as native CLL cells and CLL cells stimulated by CD40-Ligand. Their read-out is an ELISPOT-assay where they use peptide-pulsed APC using different peptides for pulsing. They claim that they have generated antigen-specific T cells. However, several important controls are missing in order to prove the significance of the peptides used for detection of specific antigen recognition, as for example peptides and well characterized T cells for positive and negative controls, peptide dilution and tetramer-staining of T cell lines. As CD40L-activated CLL cells may prime for many antigens and peptide-pulsed CLL cells can express many other antigens, peptide-specificity is not shown in the manuscript. Moreover, no specific peptide is mentioned concerning KW13. The authors merely mention “KW13” in the methods section. KW13 is actually not a peptide but the whole FMNL1 protein. In addition, no specific TCR has been discovered and described.
Thus regarding Mayr et al., no precise peptide has been described concerning KW13/FMNL1, no peptide-specificity has been proven, no epitope has been discovered, no specific TCR was shown. This is exactly the critical development which has been undertaken in our last work and which motivates us for the patent claims.
It one object of the present invention to generate allorestrictive T cells that bear TCR that have the capacity to recognize their MHC-peptide ligands on tumor cells. Furthermore, it is an object of the invention to provide a T cell based pharmaceutical composition that can be used for treating a patient suffering from lymphoma without a risk of graft-versus-host-disease (GVHD).
These objects are achieved by the subject-matter of the independent claims. Preferred embodiments are set forth in the dependent claims.
The inventors have generated allorestricted peptide-specific T cells with specificity against a defined peptide derived from the tumor associated antigen FMNL1/KW13. For example, it could be demonstrated (I) the identification of specific T cell receptor chains which are allo-HLA-A2 restricted and specific for our selected peptide RLPERMTTL (SEQ ID NO: 2) as well as the murine homolog RLPERMNTL (SEQ ID NO: 5) derived from the murine FMNL1 homologous protein and (II) that the selected peptide RLPERMTTL (SEQ ID NO: 2) derived from FMNL1/KW13 is a natural presented epitope overexpressed on malignant tissue shown by specific cytotoxicity against lymphoma cell lines, other malignant cell lines and primary tumor material of patients with chronic lymphocytic leukaemia and acute lymphoblastic leukemia. These T cells will be helpful for the development of immunotherapies against malignant lymphoma.
In healthy tissue, FMNL1/KW13 is almost exceptionally expressed in leukocytes. FMNL1/KW13-specific allorestricted T cells, therefore, are also useful in the development of immunotherapeutic strategies against rheumatoid diseases.
Using the present approach, allorestricted peptide-specific T cells with specificity against the selected peptides which also show specific cytotoxicity against malignant cell lines derived from lymphoma, renal cell carcinoma, melanoma, breast cancer, as well as cells from patients with chronic lymphocytic leukaemia, acute lymphoblastic leukaemia cells and also activated lymphocytes could be generated. In contrast, healthy tissue cell lines as fetal fibroblasts and fetal kidney cells were not recognized (
According to a first aspect, the invention provides a T cell receptor (TCR) recognizing antigenic peptides derived from tumor-associated antigen FMNL1/KW13 or murine FRL and capable of inducing peptide specific killing of a target cell.
More precise information regarding tumor-associated antigen FMNL1/KW13 may be found in (8), including accession no., suggested function etc.
The term “TCR” as used in the present invention has the common meaning, which usually is attributed to that term in the pertinent field of technology. Thus, a rearranged T cell receptor (TCR) comprises a complex of two chains (α-chain and (β-chain) containing a CDR3-region of rearranged TCR VDJ genes mainly involved in the recognition of antigenic determinants (epitopes) represented in the MHC context. More detailed information can be found in Immunobiology, The Immune System in Health and Disease, Charles A. Janeway, et al, 5 ed. 2001, and other standard literature.
An “antigenic peptide” as used herein is defined as comprising at least one antigenic determinant, i.e. an epitope. The latter is a part of a macromolecule that is being recognized by the immune system, in the present case specifically by cytotoxic T cells.
Accordingly, the TCR of the present invention specifically recognizes one of the epitopes of any of SEQ ID NO: 1-5 and/or peptides/proteins containing same. It is noted that the epitope according to SEQ ID NO: 2 turned out to be most preferred in the present invention since it is a natural presented epitope overexpressed on malignant tissue and the TCR recognizing same effectively induced a specific cytotoxicity against lymphoma cell lines. The present invention also provides a homologous peptide to epitope of SEQ ID NO: 2, i.e. the murine homolog derived from FRL.
It is noted that the invention is not restricted to the precise amino acid sequences as defined herein, but also include variants of the sequences, for example deletions, insertions and/or substitutions in the sequence, which cause for so-called “silent” changes.
Preferably, such amino acid substitutions are the result of substitutions which substitute one amino acid with a similar amino acid with similar structural and/or chemical properties, i.e. conservative amino acid substitutions.
Amino acid substitutions can be performed on the basis of similarity in polarity, charges, solubility, hydrophobic, hydrophilic, and/or amphipathic (amphiphilic) nature of the involved residues. Examples for hydrophobic amino acids are alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. Polar, neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine. Positively (basic) charged amino acids include arginine, lysine and histidine. And negatively charged amino acids include aspartic acid and glutamic acid.
The allowed degree of variation can be experimentally determined via methodically applied insertions, deletions or substitutions of amino acids in a peptide and testing the resulting variants for their biological activity as an epitope. In case of variation of the TCR-CDR3 region specificity and function of the modified TCR can be experimentally investigated by TCR expression in transduced cells or by purified TCRs analyzed with surface plasmon resonance (e.g., BIACORE™)
An example of such a variant is the sequence of the murine homolog of SEQ ID NO: 2. Whereas the human sequence is RLPERMTTL (SEQ ID NO: 2), the murine homolog is RLPERMNTL (SEQ ID NO: 5). This variant showed also a very good recognition by TCR.
According to a further preferred embodiment, the TCR contains one or more of the amino acids of SEQ ID NO: 9-14.
In a second aspect, the present invention provides an antigenic peptide derived from tumor-associated antigen FMNL1/KW13 being selected from one of SEQ ID NO: 1-5.
However, also the epitopes of SEQ ID NO: 6-8 are contemplated herein.
According to a third aspect, the present invention provides an antigen specific T cell, comprising a TCR as defined above.
Said T cell preferably is a T cell with effector cell characteristics, more preferably a cytokine producing T cell, a cytotoxic T cell or regulatory T cell, preferably CD4+ or CD8+ T cells. Most preferably, the T cell is an autologous T cell.
In a fourth aspect, the invention provides a nucleic acid coding for a part of a TCR (CDR3-region) as defined above. Respective sequences are provided as SEQ ID NO: 15-20.
An additional aspect is directed to a vector, which comprises the nucleic acid coding for said TCR. This vector is preferably an expression vector which contains a nucleic acid according to the invention and one or more regulatory nucleic acid sequences. Preferably, this vector is a plasmid or a retroviral vector.
The invention further comprises a PBMC, which has been transformed with the vector as defined above. This can be done according to established methods such as those described in Engels et al., 2005 (9).
In a still further aspect, the present invention provides a pharmaceutical composition, which comprises the T cells or PBMCs as explained above and a pharmaceutically acceptable carrier.
Those active components of the present invention are preferably used in such a pharmaceutical composition in doses mixed with an acceptable carrier or carrier material, that the disease can be treated or at least alleviated. Such a composition can (in addition to the active component and the carrier) include filling material, salts, buffer, stabilizers, solubilizers and other materials, which are known state of the art.
The term “pharmaceutically acceptable” defines a non-toxic material, which does not interfere with effectiveness of the biological activity of the active component. The choice of the carrier is dependent on the application.
The pharmaceutical composition can contain additional components which enhance the activity of the active component or which supplement the treatment. Such additional components and/or factors can be part of the pharmaceutical composition to achieve synergistic effects or to minimize adverse or unwanted effects.
Techniques for the formulation or preparation and application/medication of active components of the present invention are published in “Remington's Pharmaceutical Sciences”, Mack Publishing Co., Easton, Pa., latest edition. An appropriate application is a parenteral application, for example intramuscular, subcutaneous, intramedular injections as well as intrathecal, direct intraventricular, intravenous, intranodal, intraperitoneal or intratumoral injections. The intravenous injection is the preferred treatment of a patient.
According to a preferred embodiment, the pharmaceutical composition is an infusion or an injection or a vaccine.
According to a further aspect, the present invention is directed to the use of the antigen specific T cells or PBMCs as explained above for the manufacture of a medicament for the treatment of malignancies characterized by overexpression of FMNL1/KW13, preferably chronic lymphocytic leukemia (CLL), or rheumatoid diseases.
In a further aspect, the invention provides a method of generating antigen specific allorestrictive T cells comprising the steps of
The APCs are preferably selected from dendritic cells, activated B cells, monocytes, macrophages, activated T cells, hematological malignancies with antigen presenting capacities and/or EBV-transformed lymphoblastoid cell lines.
Dendritic cells (DC) are in particular preferred. Mature dendritic cells (DCs) express both MHC class I and class II molecules at high levels, along with a wide variety of co-stimulatory molecules, which provide them with the full capacity to prime naïve T cells that have not encountered antigen previously. They also have all the necessary genes/proteins that allow them to process and present antigens form intracellular proteins in their MHC class I and class II molecules. Thus, they are optimal antigen presenting cells (APCs) to use as stimulating cells for induction of both CD4 and CD8 T cells responses.
The selection step d) is preferably performed by means of measuring the cytokine release of the T cells or other measures of T cell activation. For example, the activated T cells can be cloned as individual cells and following expansion, the T cell clones can be analyzed for their MHC-peptide specificity and those with the desired specificity can be selected for further use (10). Alternatively, soluble MHC-peptide ligands in various forms, such as tetramers, can be marked with a fluorescent label and incubated with the activated T cells. Those T cells bearing TCR that interact with the tetramers can then be detected by flow cytometry and sorted on the basis of their fluorescence (11). Furthermore, T cells can be stimulated for short periods of time with tumor cells to which they should react and their interferon gamma secretion detected by capture reagents, for example as published (12).
According to a preferred embodiment, the method of the invention further comprises the step of expanding the T cells selected in d) ex vivo. This can be done by co-culturing the selected T cells with APC generated in the same manner as used for their initial priming, adding new APC to the T cell cultures every 7-10 days and providing the cells with fresh culture medium on a regular basis that contains supplementary cytokines, dependent upon the type of T cell that one is expanding.
The present invention in the following is illustrated by the Figures and Examples presented below, which in no way should be construed to be limiting the scope of the invention.
Allorestricted peptide-specific T cells should be directed against tumor associated antigens with specific characteristics. These antigens should have a most possibly restricted expression to the tumor cell to avoid side effects and should play an important role for vitality and growth of the tumor cell to reduce the risk of target down regulation. We previously identified 14 novel tumor associated antigens using the SEREX (serological identification by recombinant expression cloning) approach in CLL (8). These antigens have been extensively tested for their potential use as target antigens and we selected a few of them for our on-going studies. FMNL1/KW13 (AF432213) is a formin related protein in leukocytes and has been first described using the SEREX approach in CLL (8). We investigated the mRNA expression of FMNL1/KW13 using quantitative RT-PCR. We observed expression of FMNL1 in healthy tissue mostly in PBMC and to a much lesser extent in bone marrow and thymus. However, we have not seen major expression in any healthy tissue (
Peptides derived from FMNL1 were selected using prediction algorithms for HLA-binding, proteasomal cleavage sites and TAP transportation (13-16). We are also investigating predicted peptide-antigen candidates of the B cell receptor α-chain (Table 1).
T2 cells which are defective in transporters associated with antigen-processing (TAP) can be efficiently loaded with exogenous HLA-A*0201 binding peptides and were pulsed with selected peptides at different concentrations. Mainly concentrations of 10 μM and 1 μM were used for pulsing. Peripheral blood mononuclear cells (PBMC) from HLA-A2-negative donors were isolated by Ficoll density gradient. T cells were negatively isolated using magnetic bead depletion (Dynal). T cells were then cultured with peptide-pulsed irradiated T2 cells at ratios of 1:10 to 1:100. Cytokines as IL-7 (5 ng/ml), IL-15 (5 ng/ml) and IL-2 (50 U/ml) were added. Restimulations were performed after 5-7 days using again peptide-pulsed T2 cells. Cultured T cells were stained with HLA-tetrameric complexes and anti-CD8 monoclonal antibodies and were sorted using a flow cytometry sorter. Sorted T cells were cloned by limiting dilution as well as cultured in oligoclonal T cell lines. These clones and unstimulated T cell lines were non-specifically restimulated with allogeneic feeder cells (PBMC pools) and OKT3. T cells were analyzed for their specificity using 51Cr release assays, ELISA and tetramer staining
Using this approach we were able to generate allorestricted peptide-specific T cells with specificity against the selected peptide KW13-PP2. These T cells also show specific cytotoxicity against malignant cell lines, chronic lymphocytic leukaemia cells, acute lymphoblastic leukaemia cells and also activated lymphocytes (
The inventors are currently investigating the T cell receptor (TCR) repertoire of the generated T cell lines and clones. One example is the oligoclonal T cell line PP2-PC1, presenting two a-chains and three β-chains which are involved in peptide-specific killing of allorestricted T cells (Table 2). Subcloning of this T cell line has been performed to identify the specific TCR chain responsible for peptide-specific killing. Clone SC22 shows a singular α-(Vα14J41) and β-chain (Vβ14J2.5) which is already represented in the T cell line PP2-PC1, demonstrating the fundamental functional role of these two CDR3-regions in allorestricted FMNL1-PP2-specificity (Table 3).
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| Number | Date | Country | Kind |
|---|---|---|---|
| 06012680.2 | Jun 2006 | EP | regional |
The instant application is a divisional application that claims the benefit of U.S. patent application Ser. No. 12/304,918, filed Dec. 15, 2008, which itself was a National Stage Application filed under 35 USC §371 of PCT International Patent Application Serial No. PCT/EP2007/056029, filed Jun. 8, 2007. The disclosure of each of these applications is incorporated herein by reference in its entirety
| Number | Date | Country | |
|---|---|---|---|
| Parent | 12304918 | Oct 2009 | US |
| Child | 13544226 | US |
