Patent Application
20240425847
This application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. The XML copy, created on Sep. 13, 2024, is named REPT-201USD2_SL.xml and is 52,876 bytes in size.
Most T-cells express αβT-cell receptors (TCRs) and recognize antigens in the form of peptides (epitopes) presented by the major histocompatibility complex (MHC) on other cells. The TCRs of cytotoxic T-lymphocytes recognise epitopes displayed by MHC class I molecules on the surface of almost every cell in the body. The TCRs of helper T cells recognise epitopes displayed by MHC class II molecules on the surface of antigen-presenting immune cells, including macrophages, dendritic cells and B-cells. Efficient recognition of the epitope by T cells involves additional T cell surface glycoproteins: CD8 on cytotoxic T-lymphocytes (CD8+ T cells), and CD4 on helper T cells (CD4+ T cells), which bind MHC class I and II molecules, respectively. The binding of a TCR to an epitope can result in signals being sent to the T lymphocyte's nucleus to induce a T cell response.
Unambiguous and efficient identification of antigenic specificities of T cells holds great promise for the development of efficient immune therapies and diagnostic tools. In particular:
However, TCRs bind MHC-peptide complexes with low affinity, which makes phage-and yeast-display methods inefficient. Alternative methods, like screening of positional scanning combinatorial peptide libraries, take advantage of the cross-reactivity of the TCR and use peptide pools to define motifs that lead to T-cell activation. Apart from similar affinity constrains, these cumbersome methods suffer from a high rate of false-positive results. Because random peptide sequences are interrogated, the identified peptide motifs are ambiguous or have no clear homology to native proteins.
The problem underlying the present invention is to provide the means for direct and sensitive, unbiased identification of antigenic peptide specificities of CD4+ and CD8+ T cells for use in vitro and in vivo. This problem is solved by the subject-matter of the independent claims.
Amino acid sequences are given from amino to carboxyl terminus. Capital letters for sequence positions refer to L-amino acids in the one-letter code (Stryer, Biochemistry, 3rd ed. p. 21). Lower case letters for amino acid sequence positions refer to the corresponding D- or (2R)-amino acids.
In the context of the present invention, the terms identity or sequence identity are used in their meaning known in the art of genetics and bioinformatics; they refer to a single quantitative parameter representing the result of a sequence comparison position by position. Methods of sequence comparison are known in the art; the BLAST algorithm available publicly is an example.
One such example for comparison of amino acid sequences is the BLASTP algorithm that uses default settings such as: Expect threshold: 10; Word size: 3; Max matches in a query range: 0; Matrix: BLOSUM62; Gap Costs: Existence 11, Extension 1; Compositional adjustments: Conditional compositional score matrix adjustment. In the absence of further details, these settings are used for determination of amino acid sequence identity values given below.
One such example for comparison of nucleic acid sequences is the BLASTN algorithm that uses the default settings: Expect threshold: 10; Word size: 28; Max matches in a query range: 0; Match/Mismatch Scores: 1.-2; Gap costs: Linear. In the absence of further details, these settings are used for determination of nucleic acid sequence identity values given below.
In the context of the present specification, the term major histocompatibility complex (MHC) is used in its meaning known in the art of cell biology and biochemistry; it refers to a cell surface molecule that displays a peptide, a fraction of a protein, in a way suitable for the recognition by a T cell receptor. Peptides recognised by the immune system are referred to as epitopes or antigenic peptides or oligopeptides in the context of the present specification.
There are two major classes of MHC molecules: class I and class II.
MHC class I occurs as a chain composed of three domains—α1, α2, α3. The α3 domain interacts with the non-MHC molecule β2-microglobulin. The peptide being displayed or presented is held by the peptide-binding groove, in the central region of the α1/α2 heterodimer. The α3 subunit contains a transmembrane domain, anchoring the MHC class I molecule to the cell membrane.
MHC class II is formed of two chains, α and β, each having two domains—α1 and α2 and β1 and β2, respectively. The peptide-binding groove (the structural element formed by the MHC class II molecule that presents or displays the peptide epitope) is formed by the heterodimer of α1 and β1. The α2 and β2 subunits contain transmembrane domains anchoring the MHC class II molecule to the cell membrane.
MHC class I and class II molecules comprise in their immature form a signal peptide like the majority of newly synthesized proteins that are destined towards the secretory pathway. The MHC signal peptide sequence is located upstream (5′) of the MHC α1 domain on the MHC mRNA molecule. After cleavage of the signal peptide the MHC molecule is referred to as the mature MHC molecule.
In the context of the present specification, the term β2-microglobulin domain is used in its meaning known in the art of cell biology and biochemistry; it refers to a non-MHC molecule that is part of the MHC class I heterodimer molecule. In other words, it constitutes the β chain of the MHC class I heterodimer.
In the context of the present specification, the term T cell receptor (TCR) is used in its meaning known in the art of cell biology and biochemistry; it refers to a molecule found on the surface of T cells that is able to recognize antigens bound to major histocompatibility complex molecules. TCRs are disulfide-linked membrane-anchored heterodimers consisting of highly variable α and β chains. Each chain is composed of two extracellular domains: Variable (V) region and a Constant (C) region. The Variable region binds to the peptide-MHC complex; the Constant region is proximal to the cell membrane, followed by a hinge region, transmembrane region and a short cytoplasmic tail.
In the context of the present specification, the term T cell receptor complex is used in its meaning known in the art of cell biology and immunology; it refers to an octameric complex of the heterodimeric TCRα/β, with two heterodimeric signaling modules CD3ε/δ and CD3γ/ε and the homodimer CD247ζ/ζ (also known as TCR ζ-chain or zeta-chain). Ionizable residues in the transmembrane domain of each subunit form a polar network of interactions that hold the complex together. Since the cytoplasmic tail of the TCRα/β is extremely short, making it unlikely to participate in signaling, these signaling molecules are vital in propagating the signal from the triggered TCR into the cell. The most common mechanism for activation and regulation of molecules beneath the plasma membrane is via phosphorylation/dephosphorylation by protein kinases. The intracellular parts of CD3 and CD247ζ contain immunoreceptor tyrosine-based activation motifs (ITAMs) that are targeted by the Src family of tyrosine-kinases.
In the context of the present specification, the term functionally linked refers to the linkage of the activity status of two different functions. For example a receptor polypeptide (function 1) may be functionally linked to a reporter gene and its promoter (function 2); then, if the receptor changes its activity status (e.g. activated), the promoter of the reporter gene will also change its activity status (e.g. activated) and the reporter gene is transcribed. One such non-limiting example is the nuclear factor of activated T cells (NFAT) signaling pathway known in the art. Activation of native TCRs (function 1) in T cells results in the activation of protein kinases and phosphatases that initiate nuclear import of the transcription factor NFAT leading to the expression of NFAT target genes (function 2). In other words the TCR is functionally linked to the expression of NFAT target genes.
In the context of the present specification, the term activation of the reporter gene refers to a change in the activity status of the reporter gene. One example of such a change in activity status is the activation of the promoter of a reporter gene. This results in the increased transcription/translation of the reporter gene. Another example is the cleavage of an inhibitor of the reporter protein which results in an increased amount of active reporter protein.
In the context of the present specification, the term transgenic is used in its meaning known in the art of cell biology; it refers to the introduction of a exogenous nucleic acid sequence into a living organism so that this organism displays a new property it does not possess endogenously.
In the context of the present specification, the term antigen receptor is used in its meaning known in the art of cell biology and immunology; it refers to surface receptors able to bind antigens or epitopes. Examples for antigen receptors are B-cell and T-cell receptors.
In the context of the present specification, the term chimeric antigen receptor refers to artificial engineered receptors comprising parts of antigen receptors. A non-limiting example is a hybrid receptor that comprise domains from T-cell or B-cell receptors fused to MHC domains and/or antigenic peptide sequences.
In the context of the present specification, the term oligopeptide or oligopeptide sequence exclusively refers to T-cell reactive oligopeptides that, when presented in the context of an MHC molecule on a cell, may elicit a T-cell response if recognized by a cognate T cell receptor. Where mention is made of an oligopeptide sequence being comprised in a (longer) polypeptide of the invention, the skilled person will understand that this refers to an oligopeptide sequence that can be recognized by a TCR when presented on an MHC molecule. The oligopeptide sequence comprises, in addition to the MHC-presented T cell reactive epitope, a linker of several amino acids, allowing the T cell reactive epitope to fit into the MHC molecule. Examples for linker length and sequence are given below.
According to a first aspect of the invention, a method for the identification of a TCR recognizable peptide sequence is provided, comprising the steps of:
In other words, the method of the invention allows assessing the antigenic potential of oligopeptides, or—to be more precise-the potential of a particular oligopeptide sequence to be a MHC-presented epitope triggering a cognate TCR response. To accomplish this assessment, a library of transgenic antigen receptors comprising potentially antigenic oligopeptides is required. A member of the library is expressed in each mammalian cell of the plurality of cells, wherein the oligopeptide sequence can be different for each member of the library. The oligopeptide is presented by the transgenic antigen receptor in a way that is suitable for the recognition by a T cell receptor. Binding of the antigenic oligopeptide by the provided T lymphocytes via their T cell receptor activates the reporter protein that is functionally linked to the transgenic antigen receptor. The mammalian cell is then separated according to the level of detectable reporter. DNA is isolated from the separated mammalian cell and the comprised oligopeptide DNA is sequenced. Every oligopeptide retrieved by this method is recognized by a T cell receptor.
The transgenic antigen receptor comprises an oligopeptide that is presented in a way suitable for the recognition by a T cell receptor, an extracellular domain of MHC1 or MHC2, a transmembrane domain of a T cell receptor and an intracellular domain of a T cell receptor. The oligopeptide and the different domains are covalently linked to form a single polypeptide chain (extracellular-transmembrane-intracelluar). In certain embodiments, the transgenic receptor additionally comprises a hinge region of a T cell receptor that is situated between the extracellular domain and the transmembrane domain.
In the context of the present specification, the terms expresses or expression are used in their meaning in the art of cell biology and molecular biology; they refer to the transcription and translation of a DNA sequence and the derived mRNA.
In certain embodiments the separation of cells with a detectable reporter protein from the plurality of mammalian cells according to the level of detectable reporter protein as described in step iii. is performed at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 times. This embodiment is particularly advantageous if libraries of high complexity are used.
According to an alternative aspect of the invention, a method for the identification of a TCR recognizable peptide sequence is provided. The method comprises:
In certain embodiments the transgenic antigen receptor additionally comprises a hinge region. In certain embodiments according to the first and second aspect of the invention the transgenic antigen receptor is a transgenic antigen receptor already known in the art. Examples of suitable transgenic antigen receptors known in the art are disclosed in Jyothi et al., Nat Biotechnol 20, 1215-1220 (2002); Geiger et al., Blood 98 (8) 2364-2371 (2001); U.S. Pat. No. 20,082,86312A1; Mekala et al., PNAS 102 (33), 11817-11822, (2005); Moisini et al., J Immunol (2008), 180:3601-3611; Scott et al., J Autimm 35, 390-397 (2010).
In certain embodiments of any of the above aspects of the invention, the transgenic antigen receptor is a chimeric antigen-receptor polypeptide heterodimer comprising a first polypeptide and a second polypeptide, and
At least one of the first and the second polypeptide chain additionally comprises an oligopeptide, covalently linked to the extracellular MHC domain, wherein the oligopeptide can be recognized by a T cell receptor.
In certain embodiments, the oligopeptide sequence further comprises a linker sequence 4 to 16 amino acids, particularly 6, 8, 10, 12 or 14 amino acids in length. In certain embodiments, the linker is predominantly composed of glycine and one of serine, threonine and alanine. In certain embodiments, the linker comprises glycine and serine only.
One of the first polypeptide and the 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 the first polypeptide and the second polypeptide comprises a hinge region, a transmembrane domain and an intracellular domain of the T cell receptor beta chain.
In certain embodiments the oligopeptide sequence and a glycine-serine linker are inserted between the last amino acid of the MHC signal/leader peptide and the first amino acid of the MHC α1 domain or β1 domain.
In certain embodiments the oligopeptide sequence and a linker sequence is inserted after amino acid 1, 2, 3, 4 or 5 of the MHC α1 domain sequence or β1 domain sequence. Attaching the peptide to the beta chain (β1 domain) will insert the peptide into the MHC in the most commonly found direction. Attaching it to the alpha chain will insert the peptide in a reverse orientation.
In certain embodiments the extracellular part of the MHC molecule is selected from the human major histocompatibility complex gene family HLA available to the person skilled in the art in specialist databases such as IMGT/HLA (http://www.ebi.ac.uk/ipd/imgt/hla/). Alternatively, the HLA sequence is derived from the RNA extracted from patient blood or tissue samples.
In certain embodiments the oligopeptide is 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30 or 40 amino acids (AA) in length. The majority of MHC class I peptides are 8-10 amino acids long whereas MHC class II can present much longer peptides, as the binding cleft is open, nevertheless the actual epitope ranges from 10 to 12 AA. In the herein disclosed method the peptides might be even longer than 20 (see
In certain embodiments the hinge region, the transmembrane and intracellular part of the transgenic antigen-receptor in the first and/or second polypeptide is not derived from the same TCR chain. In other words the hinge region or the transmembrane domain of the TCR α-chain could be connected to the transmembrane or intracellular domain of the TCR β-chain and vice versa.
In certain embodiments the chimeric antigen-receptor polypeptide heterodimer according to the second aspect of the invention, comprises 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.
According to a third aspect of the invention a chimeric antigen-receptor polypeptide heterodimer is provided comprising a first polypeptide and a second polypeptide. The first polypeptide is linked to the second polypeptide by one or several disulfide bonds, and
One of the first polypeptide and the second polypeptide further comprises a hinge region, transmembrane domain (and the intracellular domain or tail) of the T cell receptor (TCR) alpha chain and the other one of the first polypeptide and the second polypeptide comprises a hinge region, transmembrane domain (and the intracellular domain or tail) of the T cell receptor beta chain.
In other words the chimeric antigen-receptor polypeptide heterodimer is able to present an oligopeptide (epitope) in an MHC-context, in order for the oligopeptide (epitope) to be recognized and bound by its cognate TCR. The binding of its cognate TCR results in the activation of the intracellular domains of the CD3 and CD247 molecules associated with the chimeric antigen-receptor polypeptide heterodimer, which leads to the activation of NFAT.
In certain embodiments, the extracellular parts of the MHC molecule comprise
In certain embodiments, the first polypeptide comprises substantially the entire extracellular part of the major histocompatibility complex I (MHC class I) alpha chain. In certain embodiments, the first polypeptide is the extracellular part of the major histocompatibility complex I (MHC class I) alpha chain.
In certain embodiments, the second polypeptide comprises substantially the entire extracellular part of the major histocompatibility complex I (MHC class I) associated β2-microglobulin domain. In certain embodiments, the second polypeptide is the major histocompatibility complex I (MHC class I) associated β2-microglobulin domain.
In certain other embodiments, the first polypeptide comprises substantially the entire extracellular part of the major histocompatibility complex II (MHC class II) alpha chain. In certain embodiments, the first polypeptide is the extracellular part of the major histocompatibility complex II (MHC class II) alpha chain. In certain embodiments, the second polypeptide comprises substantially the entire major histocompatibility complex II (MHC class II) beta chain. In certain embodiments, the second polypeptide is the major histocompatibility complex II (MHC class II) beta chain.
In certain embodiments at least one of the first and the second polypeptide chain additionally comprises an antigen-peptide covalently linked to the extracellular MHC domain, wherein said oligopeptide can be recognized by a T cell receptor.
In certain embodiments the antigen-peptide sequence and a glycine-serine linker are inserted between the last amino acid of the MHC signal/leader peptide and the first amino acid of the MHC α1 domain or β1 domain.
In certain embodiments the antigen-peptide sequence and a linker sequence is inserted after amino acid 1, 2, 3, 4 or 5 of the MHC α1 domain sequence or β1 domain sequence.
In certain embodiments the extracellular part of the MHC molecule is selected from the human major histocompatibility complex gene family HLA available in specialist databases such as IMGT/HLA (http://www.ebi.ac.uk/ipd/imgt/hla/). Alternatively, the HLA sequence is derived from the RNA extracted from patient blood or tissue samples.
In certain embodiments the oligopeptide is 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30 or 40 amino acids in length. The majority of MHC class I peptides are 8-10 amino acids long whereas MHC class II can present much longer peptides, as the binding cleft is open, nevertheless the actual epitope is inside 10-12 AA. In the herein disclosed method the peptides might be even longer than 20 (see
In certain embodiments the hinge region, the transmembrane and intracellular part of the chimeric antigen-receptor polypeptide in the first and/or second polypeptide is not derived from the same TCR chain. In other words the hinge region or the transmembrane domain of the TCR α-chain could be connected to the transmembrane or intracellular domain of the TCR β-chain and vice versa.
According to a fourth aspect of the invention a nucleic acid molecule encoding the chimeric antigen-receptor polypeptide heterodimer according to the third aspect of the invention is provided, particularly a nucleic acid molecule having a promoter sequence operable in a mammalian host cell.
According to a fifth aspect of the invention a cell, particularly a mammalian cell, comprising or expressing the nucleic acid molecule according to the fourth aspect of the invention is provided.
According to a sixth aspect of the invention a cell, particularly a mammalian cell, more particularly a mammalian T-lymphocyte is provided, comprising
In certain embodiments the effector function is:
In certain embodiments the reporter protein is selected from:
According to a seventh aspect of the invention a method for obtaining a preparation of T-lymphocytes having a reduced reactivity against an antigen is provided. The method comprises:
In other words, specific T lymphocytes able to bind to the oligopeptide sequences provided within the chimeric antigen-receptor polypeptide heterodimer of the mammalian cell would undergo cell death, particularly apoptosis.
According to an eighth aspect of the invention a method for depletion of T lymphocytes having an activity against specific antigens for use in a patient in need thereof is provided. The method comprises the steps of:
In other words T lymphocytes able to bind to the oligopeptide sequence that is displayed in the chimeric antigen-receptor polypeptide heterodimer are selectively depleted. This can be used for example for the reduction or removal of autoreactive T lymphocytes in a patient with need thereof.
In certain embodiments this method is used to treat autoimmune diseases such as allergies. In certain embodiments this method is used for the prevention and treatment of organ rejection after transplantation.
According to a ninth aspect of the invention, a mammalian cell according to the fourth aspect of the invention is provided for use in the treatment or prevention of autoimmune disease, transplant rejection or immune dysfunction including but not limited to, type 1 diabetes, multiple sclerosis, rheumatoid arthritis, Crohn's disease and inflammatory bowel syndrome. In other words, the mammalian cell is used for the depletion of T-lymphocytes having an activity against specific, disease associated antigens.
According to a tenth aspect of the invention a method for detecting a patient's immune response to an oligopeptide is provided. The method comprises the steps of:
In other words if in the blood of an individual T lymphocytes able to bind to the used oligopeptide are enriched resulting in a strong reporter protein expression this indicates an immune response against the oligopeptide.
In certain embodiments the oligopeptide used in this method is derived from a virus, a bacterium, a fungus or a parasite.
In certain embodiments the method according to the ninth aspect of the invention further comprises the steps of
In other words a multitude of the mammalian cells according to the fourth aspect of the invention with different oligopeptides in the chimeric antigen-receptor polypeptide heterodimer is used. Each of these oligopeptides is derived from a certain pathogen, allergen, tumour or inflamed tissue (in the case of an autoimmune patient). This allows simultaneous testing for a multitude of different immune responses. One non-limiting example is the use as a diagnostic tool.
Wherever alternatives for single separable features such as, for example, a linker sequence, linker length, are laid out herein as “embodiments”, it is to be understood that such alternatives may be combined freely to form discrete embodiments of the invention disclosed herein. The person skilled in the art understands that isolated features of the invention mentioned as specific embodiments may be combined with any other features mentioned.
The invention is further illustrated by the following examples and figures, from which further embodiments and advantages can be drawn. These examples are meant to illustrate the invention but not to limit its scope.
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. 400times more OVA-I-Ab tetramers than gp66-I-Ab 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.
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 TCRα and TCRβ 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 (
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 α-chain, composed of the extracellular domains of the I-Ab MHC class II α-chain linked to a truncated TCRα; and the β-chain composed of a peptide (the dominant LCMV-derived epitope, gp61) and the extracellular domains of the I-Ab MHC class II β-chain linked to a truncated TCRB (
The inventors tested the sensitivity of the MCR system by mixing MCR2 (gp61)+ and MCR2 (OVA)+ reporter cells at different ratios and measuring NFAT-activation after co-culture with Smarta2 or OT-II CD4+ T-cells. As shown in
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+ 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.
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 (
Finally, a screen for novel LCMV epitopes with the help of CD4+ T-cell hybridomas derived from LCMV-infected animals 5 and 8 days post infection was performed (
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 (
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.
C57/BI6, mice were purchased from Charles River. Smarta2 and OT-II mice were bred at the ETH mouse facility.
Beko is a spontaneous thymoma cell line derived from TCRβ-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− 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.
Sorted T-cells or thymocytes were activated with plastic-bound anti-CD3ε and anti-CD28 antibodies in the presence of mouse IL-2 for 2-3 days. Equal numbers of activated T-cells and the TCRα−β− BW5147 fusion partner were fused using PEG-1500, and plated at limiting dilution in the presence of 100 mM hypoxanthine, 400nM aminopterin, and 16 mM thymidine (HAT).
The MCR2 α and β chains were cloned by standard techniques and contain the following parts: MCR2 α chain: the MHC-II I-Ab α chain residues 1-208 linked to the TCRα chain constant region residues 87-137 by the GGSGGSAQ (SEQ ID NO 002) linker.
MCR2 β chain: the MHC-II I-Ab β chain residues 1-217 linked to the TCRB 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
In MCR2 (OVA) the same residues were replaced by the amino acid sequence
MCRα and MCRβ were cloned into the pMYiresGFP retroviral vector, so that MCRβ replaced GFP. Throughout the study we used this vector (pMY-MCRαiresMCRβ) 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.
To generate the gp61 mimotope library, the MCR2(gp61-RSS-EGFP-RSS/I-Ab) 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 (
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*106 clones. 16.2c11 cells were transduced with this library and 0.5*106 MCRlow and 2.2*104 MCRhi cells were sorted.
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*106 bacterial clones and after transduction 11.5*106 individual MCR2+ cells were sorted.
If not stated otherwise, MCR2+ Beko cells were co-cultured with a 5-fold excess of sorted CD4+ T-cells from indicated donor mice.
If not stated otherwise, MCR2+ cells were co-cultured with a 5-fold excess of sorted CD4+ T-cells or CD4+ T-cell hybridomas from indicated donor mice for 8-12 h.
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.
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.
Peptides to be inserted in SEQ ID NO 008 between amino acids 27 and 28 (GG):
| Number | Date | Country | Kind |
|---|---|---|---|
| 14199148.9 | Dec 2014 | EP | regional |
This application is a divisional of U.S. patent application Ser. No. 17/098,226, filed on Nov. 13, 2020, which is a divisional of U.S. patent application Ser. No. 15/537,418, filed on Jun. 18, 2017, which is a U.S. national stage application, filed under 35 U.S.C. § 371, of International Application No. PCT/EP2015/080576, filed on Dec. 18, 2015, which application claims priority to and the benefit of European Patent Application No. 14199148.9, filed on Dec. 19, 2014, the entire disclosures of each of which are incorporated by reference herein for all purposes.
| Number | Date | Country | |
|---|---|---|---|
| Parent | 17098226 | Nov 2020 | US |
| Child | 18437678 | US | |
| Parent | 15537418 | Jun 2017 | US |
| Child | 17098226 | US |
