CHIMERIC ANTIGEN RECEPTORS AND METHODS OF USE

Abstract

The invention relates to a chimeric antigen-receptor polypeptide heterodimer comprising two polypeptides, wherein the first contains an extracellular part of the major histocompatibility complex I alpha chain and the second contains a 32-microglobulin domain, or the first contains an extracellular part of the major histocompatibility complex II alpha chain and the second contains a major histocompatibility complex II beta chain. One of the polypeptides further contains a transmembrane domain, a hinge region and an intracellular domain of the T cell receptor alpha chain and the other one contains a transmembrane domain, a hinge region and an intracellular domain of the T cell receptor beta chain, and additionally an antigen-peptide covalently linked to said extracellular MHC domain. The invention further relates to a method for the identification of a TCR recognizable peptide sequence making use of the heterodimer of the invention.

Claims

1. A method for the identification of a TCR recognizable peptide sequence, comprising: i. providing a plurality of mammalian cells, wherein each of said plurality of mammalian cells expresses a member of a library; each member of said library encodes a transgenic antigen receptor; said transgenic antigen receptor comprises: an extracellular domain of MHC1 or MHC2, an oligopeptide comprised within said extracellular domain, wherein the oligopeptide is different for each member of the library, and wherein the oligopeptide is presented in a way suitable for the recognition by a T cell receptor, a transmembrane domain of a T-cell receptor (TCR), and an intracellular domain of a TCR; said transgenic antigen receptor is functionally linked to a reporter protein, whereby binding of a cognate T cell receptor to said transgenic antigen receptor results in the activation of said reporter gene, ii. contacting said plurality of mammalian cells with a preparation of T-lymphocytes, iii. separating cells showing a detectable reporter protein from said plurality of mammalian cells according to the detectable level of said reporter protein, yielding activated cells, iv. isolating DNA from said activated cells, and v. sequencing of said oligopeptide sequence comprised in said transgenic antigen-receptor.

2. A method for the identification of a TCR recognizable peptide sequence, comprising: i. providing a mammalian cell, wherein said mammalian cell expresses a transgenic antigen receptor; said transgenic antigen receptor molecule comprises an extracellular domain of MHC1 or MHC2 comprising an oligopeptide presented in a way suitable for the recognition by a T cell receptor, a transmembrane domain of a T-cell receptor (TCR), and an intracellular domain of a TCR, said transgenic antigen receptor is functionally linked to a reporter protein, whereby binding of a cognate T cell receptor to said transgenic antigen receptor results in the activation of said reporter gene, ii. contacting said mammalian cell with a preparation of T-lymphocytes, thereby activating said reporter gene yielding an activated mammalian cell, iii. isolating DNA from said activated mammalian cell, and iv. sequencing of said oligopeptide sequence encoded in said transgenic chimeric antigen-receptor.

3. The method according to claim 1, wherein said transgenic antigen receptor is a chimeric antigen-receptor polypeptide heterodimer comprising a first polypeptide and a second polypeptide, wherein a. said first polypeptide comprises an extracellular part of the major histocompatibility complex I (MHC class I) alpha chain and said second polypeptide comprises a ?2-microglobulin domain, or b. said first polypeptide comprises an extracellular part of the major histocompatibility complex II (MHC class II) alpha chain and said second polypeptide comprises an extracellular part of the major histocompatibility complex II (MHC class II) beta chain, wherein at least one of said first and said second polypeptide chain additionally comprises an oligopeptide, covalently linked to said extracellular MHC domain; one of said first polypeptide and said second polypeptide further comprises a hinge region, a transmembrane domain and an intracellular domain or intracellular tail of the T cell receptor alpha chain and the other one of said first polypeptide and said second polypeptide comprises a hinge region, a transmembrane domain and an intracellular domain of the T cell receptor beta chain.

4. A chimeric antigen-receptor polypeptide heterodimer comprising a first polypeptide and a second polypeptide, wherein a. said first polypeptide comprises an extracellular part of the major histocompatibility complex I (MHC class I) alpha chain and said second polypeptide comprises a ?2-microglobulin domain, or b. said first polypeptide comprises an extracellular part of the major histocompatibility complex II (MHC class II) alpha chain and said second polypeptide comprises an extracellular part of the major histocompatibility complex II (MHC class II) beta chain, one of said first polypeptide and said second polypeptide further comprises a hinge region, a transmembrane domain and an intracellular domain or intracellular tail of the T cell receptor alpha chain and the other one of said first polypeptide and said second polypeptide comprises a hinge region, a transmembrane domain and an intracellular domain of the T cell receptor beta chain; and wherein optionally, at least one of said first and said second polypeptide chain additionally comprises an oligopeptide that can be recognized by a T cell receptor, said oligopeptide being covalently linked to said extracellular MHC domain.

5. The chimeric antigen-receptor polypeptide heterodimer according to claim 4, wherein the extracellular part of the MHC molecule comprises i. each of a MHC class I alpha1, alpha2 and alpha3 domain forming part of said first polypeptide, or ii. an MHC class II alpha1 and an MHC class II alpha2 domain forming part of said first polypeptide, and an MHC class II beta1 and an MHC class II beta2 domain forming part of said second polypeptide, and/or iii. wherein the extracellular part of the MHC molecule is selected from the members of the human major histocompatibility complex gene family HLA as set forth in the IMGT HLA data base.

6. The chimeric antigen-receptor polypeptide heterodimer according to claim 4, wherein said oligopeptide sequence a. is inserted after amino acid 1, 2, 3, 4 or 5 of the MHC alpha1 domain sequence and/or b. said oligopeptide is 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30 or 40 amino acids in length.

7. The chimeric antigen-receptor polypeptide heterodimer according to claim 4, comprising a first polypeptide with an amino acid sequence having at least >80%, 85%, 90%, 92%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO 007 and a second polypeptide with an amino acid sequence having at least >80%, 85%, 90%, 92%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO 008.

8. A nucleic acid molecule encoding the chimeric antigen-receptor polypeptide heterodimer according to claim 4.

9. A cell, particularly a mammalian cell, more particularly a mammalian T-lymphocyte, comprising i. the chimeric antigen-receptor polypeptide heterodimer according to claim 4, and ii. an effector function functionally linked to said chimeric antigen-receptor polypeptide heterodimer; particularly wherein the effector function is: i. a reporter protein, and/or ii. a protein, or a plurality of proteins, capable of inducing cell death, particularly apoptosis, in cells bound to the chimeric antigen-receptor polypeptide; more particularly wherein the reporter protein is selected from: iii. a fluorescent protein, or iv. a luciferase protein, or v. an antibiotic resistance gene, or vi. a Cre recombinase, or vii. a CAS-9 nuclease, or viii. a CAS-9 chimeric transcriptional suppressor or activator.

10. A method for obtaining a preparation of T-lymphocytes having a reduced reactivity against an antigen, comprising the steps of: i. providing a preparation of T-lymphocytes obtained from a patient, ii. contacting said preparation of T-lymphocytes with a preparation of mammalian cells according to claim 9, said cells comprising a chimeric antigen-receptor polypeptide heterodimer, wherein said mammalian cell is characterized in that the effector function induces cell death, particularly apoptosis, in cells bound to the chimeric antigen-receptor polypeptide heterodimer.

11. A mammalian cell according to claim 9 for use in the treatment or prevention of autoimmune disease or immune dysfunction, particularly T cell mediated autoimmune disease, including but not limited to transplant rejection, type 1 diabetes, multiple sclerosis, rheumatoid arthritis, Crohn's disease and inflammatory bowel syndrome.

12. A method for detecting a patient's immune response to an antigenic peptide. comprising the steps of: i. providing the mammalian cell according to claim 9, wherein said cell comprises a reporter protein functionally linked to said chimeric antigen-receptor polypeptide heterodimer, ii. providing a blood sample of said patient ex-vivo, iii. contacting said mammalian cell with said blood sample, and iv. detecting said reporter protein in said mammalian cell;

13. The method of claim 12, further comprising the steps of i. separating the mammalian cells according to the expression of the reporter protein, ii. isolating DNA from said separated mammalian cells, and iii. sequencing of the antigen-peptide, encoded in the chimeric antigen-receptor polypeptide heterodimer.

Description

SHORT DESCRIPTION OF THE FIGURES

[0124] FIG. 1 shows structure and antigen-specific reactivity of the MCR2 sensor (chimeric antigen-receptor polypeptide heterodimer with extracellular parts from MHC II). (a) Schematic representation of the MCR2 and its interaction with the peptide-specific TCR. (b) Surface expression of the MCR2(gp61) on BEKO thymoma cells (c) Time course of MCR2(gp61) (left panel) or MCR2(OVA) (right panel) down-regulation in BEKO cells co-cultured with gp61-specific Smarta or OVA-specific OT-II TCR transgenic CD4+ T-cells. Values show MCR2 levels depicted as percentage of mean fluorescence intensity at the start of co-culture. (d) Time course of peptide-specific NFAT activation (GFP expression) in H18.3.13 cells transduced with MCR2(gp61) or MCR2(OVA) co-cultured with Smarta or OT-II CD4+ T-cells. Histogram shows examples of NFAT activation measurements in MCR2(gp61)+ cells at indicated time points. (e) Sensitivity of peptide-specific reporter cells. MCR2(gp61)+H18.3.13 cells were diluted in MCR2(OVA)+H18.3.13 cells and NFAT activation was measured in untreated cells (triangles) or after co-cultured with Smarta CD4+ T-cells (squares). The graph shows a linear (R>0.99) correlation between the percentage of GFP+H18.3.13 cells and the percentage of cells carrying the MCR2(gp61) (f) Minimal frequency of peptide-specific T-cells able to trigger robust NFAT activation in MCR2+ reporter cells. Splenocytes from Smarta and OT-II transgenic mice were mixed at different ratios and used to stimulate MCR2(gp61)+ or MCR2(OVA)+H18.3.13 cells. The graph shows percentage of GFP+ cells among MCR2(gp61)+H18.3.13 or MCR2(OVA)+H18.3.13 cells as a function of the percentage of peptide-specific CD4+ T-cells, after 8 h of co-culture. (g) The minimal number of peptide-specific T cells able to trigger a response in reporter cells. NFAT activation in MCR2(gp61)+(left) and MCR2(OVA)+(right) H18.3.13 cells following overnight co-culture with different numbers of Smarta or OT-II CD4+ T-cells. h) Kinetics of LCMV-specific CD4+ T-cell expansion in the blood of infected mice (n=3) detected by the activation of MCR2(gp61)+H18.3.13 cells. Percentage of GFP+ reporter cells after overnight co-culture with blood taken at different days post infection is shown. Blood from a na?ve Smarta mouse was used as a positive control.

[0125] FIG. 2 shows screening for gp61 mimotopes. (a) A scheme of RAG-mediated peptide randomization based on which the MCR2(gp61-RSS) mimotope library was generated (see materials and methods), RSSrecombination signal sequence. (b) Examples of altered gp61 sequences found in the library (new amino acids are shown in grey). (c) 16.2c11 cells carrying the NFAT-FT reporter were transduced with the MCR2(gp61-RSS) library or with MCR2(OVA) or MCR2(gp61) as controls and co-cultured with Smarta or OT-II CD4+ T-cells hybridomas. Single MCR2(gp61-RSS)+ cells showing NFAT activation (blue-FT fluorescence) after 9h co-culture with the gp61-specific Smarta hybridoma (top right panel) were sorted and expanded. (d) Activation of MCR2(gp61)+, MCR2(gp61S)+ and MCR2(gp61N)+16.2c11 cells co-cultured with the Smarta hybridoma. (e) Sequences of the original gp61 and two new gp61 mimotopes found in the MCR2(gp61-RSS) library. (f) CFSE dilution in Smarta CD4+ T-cells after a 3-day co-culture with dendritic cells pulsed with gp61 mimotopes at different concentrations (histograms) and cytokine production at a concentration of 100 nM (dot plots).

[0126] FIG. 3 shows search for new LCMV epitopes. (a, b) CD4+ T-cells from mice infected with LCMV were purified from the spleens 5 and 8 days p.i. and fused with BW5147 cells carrying an NFAT-GFP reporter. Reactivity of the resulting hybridomas was determined by GFP expression after co-culture with LCMV- or gp61-pulsed dendritic cells. Histograms (a) show examples of different types of reactivity (LCMV-open or gp61-filled dark grey) and the table (b) a summary of the data (c) A scheme of the cloning strategy for the construction of libraries enriched for naturally occurring peptides (NPLs). ORFopen reading frame dictating the natural protein sequence (d) MCR2(LCMV-NPL)+16.2c11 reporter cells were co-cultured with LCMV-reactive hybridomas (H2, H3, H14 and H30) of unknown peptide-specificity. Activated reporter cells were sorted, expanded and co-cultured again with the corresponding hybridomas. To achieve enough enrichment this procedure was repeated three times. Dot plots show example NFAT-activation after two or three rounds of co-culture. (e) After the 3rd round of enrichment, single cells were sorted, expanded and their reactivity verified by co-culture with hybridomas (histogram shows example NFAT reactivity). The table on the right shows frequencies of reactive clones. Peptide sequences from the MCR2 constructs, representing the dominant NP311 epitope and the new NP547 epitope are shown below.

[0127] FIG. 4 shows a function test of the MCR1 (chimeric antigen-receptor polypeptide heterodimer with extracellular parts from MHC I; gp33/H2-Kb) molecule transduced into the H18.3.13 reporter cell line. (A) After an over-night culture in wells coated with ?MHC-I antibodies NFAT activation was induced in the MCR1-transduced, but not in control cells.

[0128] FIG. 5 shows a) Activation of MCR2(LCMV-NPL)+16.2c11 cells after one, two and three rounds of enrichment by co-culture with hybridomas H3 and H4. b) Examples of activation of MCR2+ 16.2c11 clones derived from the screening of a random peptide MCR2 library with the hybridoma H9 after the final co-culture. Examples of sequences recovered from the library before and after enrichment for H9-reactive peptides are shown.

[0129] FIG. 6 shows peptide-specific reactivity and sensitivity of the MCR2 sensor. a) Time course of peptide-specific NFAT activation (GFP reporter expression) in MCR2(OVA)+H18.3.13 cells co-cultured with OT-II CD4+ T-cells or Smarta CD4+ T-cells as controls. Histogram shows examples of NFAT-activation measurements in MCR2(OVA)+ cells at indicated time points b) Sensitivity of peptide-specific reporter cells. MCR2(OVA)+H18.3.13 cells were diluted in MCR2(gp61)+H18.3.13 cells and NFAT activation was measured after co-culture with OT-II CD4+ T-cells. The graph shows a linear (R>0.99) correlation between the percentage of GFP+H18.3.13 cells and the percentage of cells carrying the MCR2(OVA).

EXAMPLES

Example 1: Screening of T-Cell Epitopes in Mammalian Cells Using the Disclosed Chimeric Antigen-Receptor Polypeptide Heterodimer

[0130] Current methods to identify cognate T-cell epitopes are based in principle on two major approaches. The first approach relies on detecting physical MHC-TCR interactions by staining T-cells with MHC-tetramers or by staining phage, yeast or insect cells displaying peptide-MHC complexes with recombinant TCRs. The second approach relies on measuring T-cell activation in co-cultures with dendritic cells (DCs) presenting peptide pools or positional scanning combinatorial peptide libraries. Screening of MHC-tetramer libraries is effective for defining the fine-specificity of recognition of known or predicted antigens, but because not all peptide-MHC tetramers bind with equal strength, low affinity interactions may be easily missed (e.g. 400 times more OVA-I-A.sup.b tetramers than gp66-I-A.sup.b tetramers are needed, for similar staining of OVA-specific OT-II and gp61-specific Smarta2 T-cells, respectively). Similar affinity constraints apply to current peptide-MHC display methods, were soluble TCRs are used. Furthermore, MHC molecules have to be mutagenized to allow efficient surface expression on phages or yeast cells. Screening of positional scanning combinatorial peptide libraries takes advantage of the cross-reactivity of the TCR and uses peptide pools to define motifs that lead to T-cell activation. While T-cell epitopes resembling naturally occurring peptides have been found with this method, the identified peptides often have no clear homology to known proteins and one need to resort to bioinformatics approaches.

[0131] The inventors disclose herein the development of an universal system that allows direct, unbiased, sensitive and efficient epitope screening in mammalian cells. Such a method should: i) provide a complex mixture of APCs, each presenting peptides of one, unique, naturally occurring sequence; ii) provide efficient means to identify and separate APCs presenting cognate peptides; iii) offer a possibility to iteratively repeat the procedure and iv) allow easy recovery of peptide sequences by cloning. To generate APCs fulfilling the first criteria, the inventors followed the approaches used to produce single-peptide mice and to construct different peptide-MHC display systems. By means of recombinant DNA technology a peptide was attached directly to the MHC molecule, making a stable complex and preventing other peptides from binding. A library of such peptide-MHC complexes transfected into MHC-deficient cells yields a pool of cells each presenting a unique peptide (for details see Materials and Methods). Ideally, identification of APCs carrying cognate peptides for particular T-cells would involve an easily measurable signal once their peptide-MHC complexes were bound by the TCRs of the specific T-cells. Therefore the peptide-MHC fusion molecule was linked to the TCR complex, which is tailor-made for sensing low-affinity interactions. Direct zeta chain (CD247) fusions have been successfully used to construct various chimeric antigen receptors. However, to create a molecular sensor resembling the native TCR complex as close as possible, the peptide MHC complexes were fused to truncated TCR? and TCR? chains consisting of the hinge region, trans-membrane (TM) and intracellular (IC) domains. Connecting the peptide-MHC to the whole TCR signaling machinery provides more physiological signals. This MHC-TCR chimera is referred to as the MCR in the context of this specification. Such a molecule, upon transfection into TCR-deficient T-cell hybridomas, allows direct monitoring of peptide-MHC engagement by the TCRs of specific T-cells using an NFAT-EGFP reporter system (FIG. 1a). Co-culture of cells carrying a library of peptide-MCR molecules with antigen-specific T cell clones or hybridomas allows direct identification of cognate peptide specificities of T-cells by massively parallel, functional screening in mammalian cells.

[0132] Therefore the MCR was designed and cloned for the screening of cognate peptides of MHC class II-restricted T-cells, hence MCR2. MCR2 consists of two chains: the ?-chain, composed of the extracellular domains of the I-A.sup.b MHC class II ?-chain linked to a truncated TCR?; and the ?-chain composed of a peptide (the dominant LCMV-derived epitope, gp61) and the extracellular domains of the I-A.sup.b MHC class II ?-chain linked to a truncated TCR? (FIG. 1a). A second MCR2 was also cloned carrying the OVA-peptide and the two were designated MCR2(gp61) and MCR2(OVA), respectively. After transduction of the MCRs into a MHC-II.sup.? TCR.sup.? BEKO thymoma cell line, their expression was verified by staining with anti-MHC-II antibodies. As depicted in FIG. 1b, the MCR2 was efficiently expressed on the cell surface, indicating that it assembled with CD3 components of the TCR complex. To verify its specificity, BEKO cells expressing MCR2(gp61) or MCR2(OVA) were co-cultured, with purified Smarta2 or OT-II CD4.sup.+ T-cells. A very fast, peptide-specific MCR2 down-regulation from the surface was observed, with kinetics identical to conventional TCRs. MCR2(gp61) was down-regulated in co-cultures with Smarta2 T-cells and not in the presence of OT-II T-cells (FIG. 1c, left panel). The reverse was true for the MCR2(OVA), highlighting the specificity of the MCR2 system (FIG. 1c, right panel). We further assessed the ability of the MCR2 to trigger NFAT activation by transducing it into a TCR-deficient T-cell hybridoma carrying the NFAT-EGFP reporter (H18.3.13). Again, NFAT response was only triggered when MCR2-carrying hybridomas were co-cultured with peptide-specific T-cells (FIG. 1d). The response was robust and easily measurable already after 2h (FIG. 1d most right panel).

[0133] The inventors tested the sensitivity of the MCR system by mixing MCR2(gp61).sup.+ and MCR2(OVA).sup.+ reporter cells at different ratios and measuring NFAT-activation after co-culture with Smarta2 or OT-II CD4.sup.+ T-cells. As shown in FIG. 1e, it was possible to directly detect specific NFAT-reporter expression in cells present at frequencies above 1/10000. Importantly, a linear correlation between the percentage of detected NFAT-EGFP expressing cells and the percentage of cells carrying the T-cell/idotype-specific MCR2 was observed, indicating that specific cells present at frequencies lower than 1/10000 are still NFAT-EGFP.sup.+, even if they cannot be distinguished from the background. The lowest frequency of peptide specific T-cells in a heterogeneous population, that was able to trigger robust NFAT-activation in MCR2.sup.+ cells was also determined. Sorted CD4.sup.+ T-cells (FIG. 1f, top panel) or unsorted splenocytes (FIG. 1f, bottom panel) from Smarta2 and OT-II mice were mixed at different ratios and used to stimulate MCR2(gp61).sup.+ or MCR2(OVA).sup.+ cells. Even with only 1% peptide-specific CD4.sup.+ T-cells, 50% of the maximal NFAT-activation was triggered in MCR2.sup.+ cells, when T-cells were provided in excess. Remarkably, as shown in FIG. 1g (left panel), even a single Smarta2 CD4.sup.+ T-cell was able to trigger significant NFAT-EGFP activation in MCR2(gp61).sup.+ cells, while in the case of MCR2(OVA).sup.+ cells, 5 cells were required, probably due to a lower interaction affinity (FIG. 1g right panel). These results indicate that the MCR-technology can be used as a sensitive diagnostic tool for monitoring T cell specificities in the blood taken from patients. Indeed MCR2(gp61).sup.+ reporter cells can be used to efficiently track antigen-specific CD4.sup.+ T-cell expansion in the blood of LCMV-infected animals (FIG. 1h). These results demonstrate the great sensitivity of the MCR-method.

[0134] To use the disclosed invention for finding rare specific peptides in a complex library, multiple iterative cycles of co-culture and sorting of NFAT-EGFP.sup.+ reporter cells are necessary. Because efficient detection of NFAT-activation in subsequent rounds of stimulation depends on fast disappearance of NFAT-reporter signals triggered in previous rounds, the very stable EGFP was replaced with the slow Fluorescent Timer (sFT). This mutant of mCherry changes color with time, enabling the distinction of recent (blue-mCherry) and past NFAT-activation (red-mCherry) and therefore allows for much shorter intervals between subsequent rounds of stimulation.

[0135] First the disclosed invention was applied to search for mimotopes of gp61 in the MCR2(gp61-RSS) library, generated by randomizing center residues of gp61 through RAG-mediated rearrangement (FIG. 2a and M&M). Randomly picked clones consistently contained unique mutants of the gp61-sequence (FIG. 2a). After transducing this library into NFAT-sFT carrying reporter cells (16.2c11), MCR2.sup.+ cells were sorted, expanded and co-cultured with gp61-specific or OVA-specific T-cell hybridomas (FIG. 2b). Around 10% of the MCR2(gp61-RSS/I-A.sup.b).sup.+16.2c11 cells showed blue NFAT-reporter activation when co-cultured with gp61-specific hybridomas. These cells were sorted as single cells, expanded and rescreened (FIG. 2c). All of the 24 tested clones responded to re-stimulation with gp61-specific hybridomas. PCR-amplification and sequencing of the peptide parts of the MCRs from these clones revealed two new mimotopes and the original gp61 peptide (FIG. 2c). The lysine at position 9 of gp61 was mutated to serine (gp61S) or to asparagine (gp61N), indicating that it is not absolutely required for Smarta2 T-cell activation. However, the level of NFAT-activation suggested that Smarta2 TCR binds the new mimotopes (in particular gp61S) with lower affinity (histogram in FIG. 2c). In co-cultures of T-cells with dendritic cells, both mimotopes induced robust Smarta2 T-cell responses. Interestingly, while gp61N induced proliferation and Th1-like cytokine production similarly to the original peptide, the suboptimal gp61S was much less efficient in driving proliferation, but induced a strong Th2-like cytokine response (FIG. 2d).

[0136] Finally, a screen for novel LCMV epitopes with the help of CD4.sup.+ T-cell hybridomas derived from LCMV-infected animals 5 and 8 days post infection was performed (FIGS. 3a and b). The hybridomas carried an NFAT-EGFP reporter that allowed verification of their reactivity against LCMV and pick gp61-nonreactive hybridomas for further analysis (FIG. 3b). Five such hybridomas (H30, H14, H2 responding strongly and H4, H3 responding weekly) were used to screen 16.2c11 reporter cells transduced with a library of MCR2 molecules carrying all possible, overlapping peptides of the LCMV glycoprotein (GP) and nuclear protein (NP). This genuine peptide library (GPL) was generated by cloning random pieces of cDNA encoding GP and NP into the MCR2 vector (FIG. 3c) and has a significant advantage over random or combinatorial peptide libraries, as many (?) of the recovered peptides represent native proteins. Indeed, for 4 out of 5 hybridomas, the LCMV-specific target peptides were directly identified. Three of the hybridomas (H30, H14 and H2) recognized a known dominant LCMV-epitope NP311 and H3 reacted with a new epitope NP547 (FIG. 3d). The fifth hybridoma (H4) did not yield any enrichment for reactive reporter cells even after 3 iterative rounds of screening. TCR surface expression was tested on this hybridoma and was found to be TCR-negative. The TCR was probably lost during expansion after the initial LCMV-specificity screening. This result further verifies the TCR-specificity of the disclosed method. One additional hybridoma (H9) was used to screen a MCR2 library carrying random peptides and found several strongly reactive epitopes, but they did not resemble any LCMV peptides. This further supports the strategy of using GPLs rather than random peptide libraries for T-cell epitope screening.

[0137] Herein a new molecular sensor is disclosed, which allows for sensing of peptide-MHC-TCR interactions on the APC side with great specificity, sensitivity and fast kinetics. Using this reporter, a novel approach for unbiased, functional screening of T-cell epitopes was established. It combines the versatility of expression cloning with the sensitivity and high-throughput capabilities of fluorescence activated cell sorting and allows for efficient iterative screening of peptide libraries in mammalian cells. All this provides significant advantages over the methods known in the art. First, thanks to the multivalent interaction between the MCRs and TCRs, high and low affinity binding generate similar NFAT-reporter signals (FIG. 1d) and therefore low affinity ligands are less likely to be missed. Indeed, even though LCMV epitopes have been extensively studied, a novel epitopeNP547 could be identified. Second, engineering of individual recombinant TCRs or mutagenesis of the MHC are not required, as the peptides are screened in the context of native TCR and MHC molecules expressed on the surface of mammalian cells. Third, as exemplified by the LCMV virus peptide screen, the MCR-technology facilitates efficient screening of libraries highly enriched for peptides derived from the pathogen/cell/tissue targeted by the T-cell of interest.

[0138] The MCR-based approach provides a versatile, easy to use and powerful way of identifying antigenic specificities of T-cells. As such, it may impact several fields of basic and clinical research. Defining specificities of regulatory and effector tumour-infiltrating T-cells enables the discovery of novel tumour-antigens. Defining the specificities of auto-reactive tissue-infiltrating T-cells aids in the development of antigen-specific therapies for autoimmune diseases. In this respect, MCR may also allow for efficient redirecting of T-cell effector functions towards peptide-specific T-cells, enabling the purging of the repertoire from undesired specificities. Furthermore, screening of mimotope libraries will lead to the discovery of high affinity peptide variants and the development of sensitive flow cytometry based tests for antigenic reactivity of T-cells circulating in the blood of patients.

[0139] Materials and Methods

[0140] Mice

[0141] C57/Bl6, mice were purchased from Charles River. Smarta2 and OT-II mice were bred at the ETH mouse facility.

[0142] Cell Lines

[0143] Beko is a spontaneous thymoma cell line derived from TCR?-deficient mice. The H18.3.13 reporter cell line was generated by retrovirally transducing the NFAT-EGFP reporter (carrying four copies of the minimal human IL-2 promoter, each containing 3 NFAT binding sites ACGCCTTCTGTATGAAACAGTTTTTCCTCC (SEQ ID NO 001), inserted upstream of the EGFP coding sequence) into a TCR.sup.? B6 T-cell hybridoma. The 16.2c11 reporter cell line was generated by transfecting the 16.2 T-cell hybridoma with the NFAT-sFT reporter construct and a vector encoding the murine eco-tropic retrovirus receptor Slc7a1.

[0144] Hybridoma Generation

[0145] Sorted T-cells or thymocytes were activated with plastic-bound anti-CD3E and anti-CD28 antibodies in the presence of mouse IL-2 for 2-3 days. Equal numbers of activated T-cells and the TCR?.sup.??.sup.? BW5147 fusion partner were fused using PEG-1500, and plated at limiting dilution in the presence of 100 mM hypoxanthine, 400 nM aminopterin, and 16 mM thymidine (HAT).

[0146] Cloning of the MCR2

[0147] The MCR2 ? and ? chains were cloned by standard techniques and contain the following parts:

[0148] MCR2 ? chain: the MHC-II I-A.sup.b ? chain residues 1-208 linked to the TCR? chain constant region residues 87-137 by the GGSGGSAQ (SEQ ID NO 002) linker.

[0149] MCR2 ? chain: the MHC-II I-A.sup.b ? chain residues 1-217 linked to the TCR? chain constant region (C1) residues 123-173 by the AQSGGSGGSAQ (SEQ ID NO 003) linker. In the MCR2(gp61) residues DS at positions 29 and 30 of the MHC-II part were replaced by the amino acid sequence

TABLE-US-00001 SGLNGPDIYKGVYQFKSVGSGGSGGSGDS(SEQIDNO004; containingthegp61peptide).

[0150] In MCR2(OVA) the same residues were replaced by the amino acid sequence

TABLE-US-00002 SISQAVHAAHAEINEAGRGSGGSGGSGDS(SEQIDNO005; containingtheOVApeptide).

[0151] Retroviral Transduction of Reporter Cell Lines and Sorted Thymocytes

[0152] MCR? and MCR? were cloned into the pMYiresGFP retroviral vector, so that MCR? replaced GFP. Throughout the study we used this vector (pMY-MCR?iresMCR?) to generate MCRs containing various peptides and referred to them as MCR (peptide/MHC haplotype). Retrovirus containing supernatants were produced in the ecotropic Phoenix packaging cell line and used to infect reporter cell lines and sorted cells.

[0153] RAG-Mediated Generation of Mimotope Libraries

[0154] To generate the gp61 mimotope library, the MCR2(gp61-RSS-EGFP-RSS/I-A.sup.b) construct was built by inserting a stuffer fragment containing EGFP and the RAG recombination signal sequences (RSS) into the middle of the gp61 peptide in the MCR2(gp61) construct (FIG. 2a). This construct was transduced into sorted CD4.sup.?CD8.sup.? double-negative (DN) thymocytes cultured on Tst-4/DLL1.sup.32. After a week of culture (during which DN cells develop into CD4.sup.+CD8.sup.+ double-positive (DP) cells and recombine their TCR genes, as well as the RSS-EGFP-RSS stuffer, by RAG-mediated rearrangement) cells expressing low levels of EGFP were sorted and cDNA was made. The peptide-encoding part of the recombined MCR2(gp61-RSS-EGFP-RSS/I-A.sup.b) construct was PCR amplified from the cDNA and cloned into the empty MCR2(I-A.sup.b) vector, generating the MCR2(gp61-RSS/I-A.sup.b) mimotope library.

[0155] Genuine and Random Peptide Library Generation and Screening

[0156] To generate the MCR2-LCMV genuine overlapping peptide library DNA encoding the GP and NP proteins was digested for a limited amount of time (Takara DNA fragmentation Kit). The fragments were ligated with linkers homologous to vector sequences flanking the cloning site, PCR amplified, cloned into the pMY-MCR2 vector by Gibsson assembly and transfected into bacteria generating over 2.Math.10.sup.6 clones. 16.2c11 cells were transduced with this library and 0.5*10.sup.6 MCR.sup.low and 2.2*10.sup.4 MCR.sup.hi cells were sorted.

[0157] The MCR2 random peptide library was made by cloning an oligonucleotide (GGTNNNNNNTWCNNNNNNBCCNNNSCCNNNNNNKCCNNNGGA) (SEQ ID NO 006) into the MCR2-vector using the strategy described above. This oligonucleotide encoded random amino acids at positions facing the TCR, while anchor residues were partially fixed to ensure good presentation. The complexity was 5.5*10.sup.6 bacterial clones and after transduction 11.5*10.sup.6 individual MCR2+ cells were sorted.

[0158] MCR Down-Regulation Assay

[0159] If not stated otherwise, MCR2.sup.+ Beko cells were co-cultured with a 5-fold excess of sorted CD4.sup.+ T-cells from indicated donor mice.

[0160] Stimulation of MCR.sup.+ H18.3.13 or 16.2c11 Cells

[0161] If not stated otherwise, MCR2.sup.+ cells were co-cultured with a 5-fold excess of sorted CD4.sup.+ T-cells or CD4.sup.+ T-cell hybridomas from indicated donor mice for 8-12h.

Example 2: Chimeric Antigen-Receptor Polypeptide Heterodimer

[0162]

TABLE-US-00003 Firstpolypeptide,alphachain(SEQIDNO007): MPRSRALILGVLALTTMLSLCGGEDDIEADHVGTYGISVYQSPGDIGQYT FEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVL TKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLR NSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEP VLKHWEPEGGSGGSAQSDVPCDATLTEKSFETDMNLNFQNLSVMGLRILL LKVAGFNLLMTLRLWSS

[0163] Amino acids 1-208 are derived from MHC2 alpha. Amino acids 209-216 are a linker sequence. Amino acids 217-267 are derived from TCR alpha.

TABLE-US-00004 Secondpolypeptide,betachain(SEQIDNO008): MALQIPSLLLSAAVVVLMVLSSPRTEGGSGGSGGSGDSERHFVYQFMGEC YFTNGTQRIRYVTRYIYNREEYVRYDSDVGEHRAVTELGRPDAEYWNSQP EILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVISLSRTEALNHHNT LVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMT PRRGEVYTCHVEHPSLKSPITVEWRAQSGGSGGSAQGRADCGITSASYQQ GVLSATILYEILLGKATLYAVLVSTLVVMAMVKRKNS

[0164] Amino acids 1 to 26 are a leader peptide. Between amino acids 27 and 28 is the insertion site of oligopeptides to be displayed. Amino acids 29 to 36 are a linker sequence. Amino acids 37 to 228 are derived from MHC2 beta. Amino acids 229 to 236 are a linker sequence. Amino acids 237 to 287 are derived from TCRbeta.

[0165] Peptides to be inserted in SEQ ID NO 008 between amino acids 27 and 28 (GG):

TABLE-US-00005 Gp61(SEQIDNO009): ILNGPDIYKGVYQFKSV OVA(SEQIDNO010): ISQAVHAAHAEINEAGR