Epitopes Related To Coeliac Disease

Abstract

The invention herein disclosed is related to epitopes useful in methods of diagnosing, treating, and preventing coeliac disease. Therapeutic compositions which comprise at least one epitope are provided.

We claim: 
     
         1 . A method of preventing or treating coeliac disease comprising administering to an individual at least one agent selected from:
 (a) a peptide comprising at least one epitope comprising a sequence selected from the group consisting of SEQ ID NOs: 1-1927, and equivalents thereof; and   (b) an analogue of (a) which is capable of being recognised by a T cell receptor that recognises the peptide of (a) and which is not more than 50 amino acids in length.   
     
     
         2 . A method of  claim 1  wherein the agent is HLA-DQ2-restricted. 
     
     
         3 . A method of  claim 1  wherein the agent is HLA-DQ8-restricted. 
     
     
         4 . A method of  claim 1  wherein one agent is HLA-DQ2-restricted and a second agent is HLA-DQ8-restricted. 
     
     
         5 . A method of  claim 1  wherein the agent comprises a wheat epitope. 
     
     
         6 . A method of  claim 1  wherein the agent comprises an oat epitope. 
     
     
         7 . A method of  claim 1  wherein one agent comprises a wheat epitope and one agent comprises an oat epitope. 
     
     
         8 . A method of preventing or treating coeliac disease comprising administering to an individual a pharmaceutical composition comprising an agent as defined in  claim 1  and a pharmaceutically acceptable carrier or diluent. 
     
     
         9 . A method of preventing or treating coeliac disease comprising administering to an individual a pharmaceutical composition comprising an antagonist of a T cell which has a T cell receptor as defined in  claim 1 , and a pharmaceutically acceptable carrier or diluent. 
     
     
         10 . A method of preventing or treating coeliac disease comprising administering to an individual a composition for tolerising an individual to a gluten protein to suppress the production of a T cell or antibody response to an agent as defined in  claim 1 , which composition comprises an agent as defined in  claim 1 . 
     
     
         11 . A method of preventing or treating coeliac disease comprising:
 diagnosing coeliac disease in an individual by either:
 a) contacting a sample from the host with at least one agent selected from:
 i) a peptide comprising at least one epitope comprising a sequence selected from the group consisting of: SEQ ID NOS: 1-1927, and equivalents thereof and 
 ii) an analogue of i) which is capable of being recognised by a T cell receptor that recognises i) and which is not more than 50 amino acids in length; and determining in vitro whether T cells in the sample recognise the agent; recognition by the T cells indicating that the individual has, or is susceptible to, coeliac disease; or 
 
 b) administering an agent as defined in  claim 1  and determining in vivo whether T cells in the individual recognise the agent, recognition of the agent indicating that the individual has or is susceptible to coeliac disease; and 
   administering to an individual diagnosed as having, or being susceptible to, coeliac disease a therapeutic agent for preventing or treating coeliac disease.   
     
     
         12 . Use of an agent for the preparation of a medicament for treating or preventing coeliac disease, wherein the agent comprises:
 (a) a peptide comprising at least one epitope comprising a sequence selected from the group consisting of SEQ ID NOs: 14927 and equivalents thereof; and   (b) an analogue of (a) which is capable of being recognised by a T cell receptor that recognises the peptide of (a) and which is not more than 50 amino acids in length.   
     
     
         13 . A use of  claim 12  wherein the agent is HLA-DQ2-restricted. 
     
     
         14 . A use of  claim 12  wherein the agent is HLA-DQ8-restricted. 
     
     
         15 . A use of  claim 12  wherein one agent is HLA-DQ2-restricted and a second agent is HLA-DQ8-restricted. 
     
     
         16 . A use of  claim 12  wherein the agent comprises a wheat epitope. 
     
     
         17 . A use of  claim 12  wherein the agent comprises an oat epitope. 
     
     
         18 . A use of  claim 12  wherein one agent comprises a wheat epitope and one agent comprises an oat epitope. 
     
     
         19 . A use of  claim 12  wherein the agent is present within a pharmaceutical composition comprising a pharmaceutically acceptable carrier or diluent. 
     
     
         20 . A use of  claim 12  wherein the agent is present within a pharmaceutical composition comprising an antagonist of a T cell which has a T cell receptor as defined in  claim 12 , and a pharmaceutically acceptable carrier or diluent. 
     
     
         21 . A use of  claim 12  wherein the agent is present within a composition for tolerising an individual to a gluten protein to suppress the production of a T cell or antibody response to an agent as defined in  claim 1 . 
     
     
         22 . An agent as defined in  claim 1 , optionally in association with a carrier, for use in a method of treating or preventing coeliac disease by tolerising T cells which recognise the agent. 
     
     
         23 . An antagonist of a T cell which has a T cell receptor as defined in  claim 1 , optionally in association with a carrier, for use in a method of treating or preventing coeliac disease by antagonising such T cells. 
     
     
         24 . An agent as defined in  claim 1  or an analogue that binds an antibody that binds to an epitope of an agent as defined in  claim 1  for use in a method of treating or preventing coeliac disease in an individual by tolerising the individual to prevent the production of such an antibody. 
     
     
         25 . A protein that comprises a sequence which is able to bind to a T cell receptor, which T cell receptor recognises an agent as defined in  claim 1 , and which sequence is able to cause antagonism of a T cell that carries such a T cell receptor. 
     
     
         26 . An agent as defined in  claim 1  or an antagonist as defined in  claim 9 . 
     
     
         27 . A pharmaceutical composition comprising an agent as defined in  claim 1  or an antagonist as defined in  claim 9  and a pharmaceutically acceptable carrier or diluent. 
     
     
         28 . A composition for tolerising an individual to a gluten protein to suppress the production of a T cell or antibody response to an agent as defined in  claim 1 , which composition comprises an agent as defined in  claim 1 . 
     
     
         29 . A composition for antagonising a T cell response to an agent as defined in  claim 1 , which composition comprises an antagonist as defined in  claim 9 . 
     
     
         30 . A mutant gluten protein whose wild-type sequence can be modified by a transglutaminase to a sequence which is an agent as defined in  claim 1 , which mutant gluten protein comprises a mutation which prevents its modification by a transglutaminase to a sequence which is an agent as defined in  claim 1 ; or a fragment of such a mutant gluten protein which is at least 7 amino acids long and which comprises the mutation. 
     
     
         31 . A polynucleotide that comprises a coding sequence that encodes a protein or fragment as defined in  claim 25  or  30 . 
     
     
         32 . A polynucleotide according to  claim 31  that additionally comprises one or more regulatory sequences operably linked to the coding sequence, which regulatory sequences are capable of securing the expression of the coding sequence in a cell. 
     
     
         33 . A polynucleotide according to  claim 32  wherein the regulatory sequence(s) allow expression of the coding sequence in a prokaryotic or mammalian cell. 
     
     
         34 . A polynucleotide according to any one of  claims 31  to  33  which is a vector or which is in the form of a vector. 
     
     
         35 . A cell comprising a polynucleotide as defined in any one of  claims 31  to  34  or which has been transformed with such a polynucleotide. 
     
     
         36 . A cell according to  claim 35  which is a prokaryotic cell or a mammalian cell. 
     
     
         37 . A mammal that expresses a T cell receptor as defined in  claim 1 . 
     
     
         38 . A method of diagnosing coeliac disease, or susceptibility to coeliac disease, in an individual comprising:
 (a) contacting a sample from the host with at least one agent selected from:
 i) a peptide comprising at least one epitope comprising a sequence selected from the group consisting of: SEQ ID NOS: 1-1927, and equivalents thereof; and 
 ii) an analogue of (i) which is capable of being recognised by a T cell receptor that recognises (i) and which is not more than 50 amino acids in length; and 
   (b) determining in vitro whether T cells in the sample recognise the agent; recognition by the T cells indicating that the individual has, or is susceptible to, coeliac disease.   
     
     
         39 . Use of an agent as defined in  claim 38  for the preparation of a diagnostic means for use in a method of diagnosing coeliac disease, or susceptibility to coeliac disease, in an individual, said method comprising determining whether T cells of the individual recognise the agent, recognition by the T cells indicating that the individual has, or is susceptible to, coeliac disease. 
     
     
         40 . A method or use according to  claim 38  or  39  wherein the agent is an analogue (iii) which comprises (i) or (ii) bound to (a) an HLA molecule, or (b) a fragment of an HLA molecule capable of binding (i) or (ii). 
     
     
         41 . A method or use according to  claim 40  wherein the HLA molecule or fragment is in a complex comprising four HLA molecules or fragments of HLA molecules. 
     
     
         42 . Use according to any one of  claims 39 - 41  wherein the method comprises administering the agent to the skin of an individual and detecting the presence of inflammation at the site of administration, the detection of inflammation indicating that the T cells of the individual recognise the agent. 
     
     
         43 . A method according to  claim 39 ,  41  or  42  wherein the sample is blood sample. 
     
     
         44 . A method according to  claim 38 ,  40 ,  41  or  43  wherein the T cells are not restimulated in antigen specific manner in vitro before the said determining. 
     
     
         45 . A method or use according to any one  claims 38 - 44  in which the recognition of the agent by the T cells is determined by detecting the secretion of a cytokine from the T cells. 
     
     
         46 . A method or use according to  claim 45  in which the cytokine is IFN-γ. 
     
     
         47 . A method or use according to  claim 45  or  claim 46  in which the cytokine is detected by allowing the cytokine to bind to an immobilised antibody specific to the cytokine and then detecting the presence of the antibody/cytokine complex. 
     
     
         48 . A method or use according to any one of  claims 38  to  44  wherein said determining is done by measuring whether the agent binds the T cell receptor. 
     
     
         49 . A method for identifying an analogue as defined in a  claim 38 ,  40  or  41  comprising determining whether a candidate substance is recognised by a T cell receptor that recognises an epitope comprising sequence as defined in  claim 38 , recognition of the substance indicating that the substance is an analogue. 
     
     
         50 . A method of diagnosing coeliac disease, or susceptibility to coeliac disease, in an individual comprising determining the presence of an antibody that binds to an epitope of an epitope comprising sequence as defined in  claim 38  in a sample from the individual, the presence of the antibody indicating that the individual has, or is susceptible to, coeliac disease. 
     
     
         51 . A method of determining whether a composition is capable of causing coeliac disease comprising determining whether a protein capable of being modified by a transglutaminase to an oligopeptide sequence as defined in  claim 38  is present in the composition, the presence of the protein indicating that the composition is capable of causing coeliac disease. 
     
     
         52 . A method according to  claim 51  wherein the said determining is done by contacting the composition with an antibody specific for the sequence which is capable of being modified to the oligopeptide sequence, binding of the antibody to a protein in the composition indicating the composition is capable of causing coeliac disease. 
     
     
         53 . A method of identifying an antagonist of a T cell, which T cell recognises an agent as defined in  claim 1 , comprising contacting a candidate substance with the T cell and detecting whether the substance causes a decrease in the ability of the T cell to undergo an antigen specific response, the detecting of any such decrease in said ability indicating that the substance is an antagonist. 
     
     
         54 . A kit for carrying out a method or use according to any one of  claims 38  to  48  comprising an agent as defined in  claim 38 ,  40  or  41  and a means to detect the recognition of the peptide by the T cell. 
     
     
         55 . A kit according to  claim 54  wherein the means to detect recognition comprises an antibody to IFN-γ. 
     
     
         56 . A kit according to  claim 55  wherein the antibody is immobilised on a solid support and optionally the kit also comprises a means to detect the antibody/IFN-γ complex. 
     
     
         57 . Use of an agent or antagonist as defined in  claim 56  or a wild type sequence as defined in  claim 30  to produce an antibody specific to the agent, antagonist or wild type sequence. 
     
     
         58 . Use of a mutation in an epitope of a gluten protein, which epitope is as defined in  claim 38 , to decrease the ability of the gluten protein to cause coeliac disease. 
     
     
         59 . Method of identifying a product which is therapeutic for coeliac disease comprising administering a candidate substance to a mammal as defined in  claim 37  which has, or which is susceptible to, coeliac disease and determining whether substance prevents or treats coeliac disease in the mammal, the prevention or treatment of coeliac disease indicating that the substance is a therapeutic product. 
     
     
         60 . A therapeutic product as identified in the method of  claim 59  for use in a method of preventing or treating coeliac disease. 
     
     
         61 . A method of diagnosing coeliac disease, or susceptibility to coeliac disease in an individual comprising administering an agent as defined in  claim 38  and determining in vivo whether cells in the individual recognise the agent, recognition of the agent indicating that the individual has or is susceptible to coeliac disease. 
     
     
         62 . A cell according to  claim 35  which is a cell of a graminaceous monocotyledonous species. 
     
     
         63 . A cell according to  claim 62  which is a cell of wheat, maize, oats, rye, rice, barley, triticale, sorghum, or sugar cane. 
     
     
         64 . A process for the production of a protein encoded by a coding sequence as defined in  claim 31  which process comprises:
 (a) cultivating a cell according to any one of  claim 35 ,  36 ,  62  or  63  under conditions that allow the expression of the protein; and optionally 
 (b) recovering the expressed protein. 
 
     
     
         65 . A method of obtaining a transgenic plant cell comprising:
 (a) transforming a plant cell with a vector according to  claim 34  to give a transgenic plant cell.   
     
     
         66 . A method of obtaining a first-generation transgenic plant comprising:
 (b) regenerating a transgenic plant cell transformed with a vector according to  claim 34  to give a transgenic plant.   
     
     
         67 . A method of obtaining a transgenic plant seed comprising:
 (c) obtaining a transgenic seed from a transgenic plant obtainable by step (b) of  claim 66 .   
     
     
         68 . A method of obtaining a transgenic progeny plant comprising obtaining a second-generation transgenic progeny plant from a first-generation transgenic plant obtainable by a method according to  claim 66 , and optionally obtaining transgenic plants of one or more further generations from the second-generation progeny plant thus obtained. 
     
     
         69 . A method according to  claim 68  comprising:
 (d) obtaining a transgenic seed from a first-generation transgenic plant obtainable by the method according to  claim 67 , then obtaining a second-generation transgenic progeny plant from the transgenic seed; 
 and/or 
 (e) propagating clonally a first-generation transgenic plant obtainable by the method according to  claim 66  to give a second-generation progeny plant; 
 and/or 
 (f) crossing a first-generation transgenic plant obtainable by a method according to  claim 66  with another plant to give a second-generation progeny plant; 
 and optionally 
 (g) obtaining transgenic progeny plants of one or more further generations from the second-generation progeny plant thus obtained. 
 
     
     
         70 . A transgenic plant cell, plant, plant seed or progeny plant obtainable by a method according to any one of  claims 65  to  69 . 
     
     
         71 . A transgenic plant or plant seed comprising plant cells according to  claim 62  or  63 . 
     
     
         72 . A transgenic plant cell callus comprising plant cells according to  claim 62  or  63  obtainable from a transgenic plant cell, first-generation plant, plant seed or progeny as defined in any one of  claims 62 ,  63 , or  65  to  69 . 
     
     
         73 . A plant or callus according to any one of claims  claim 70  to  72  which is of a species as defined in  claim 62  or  63 . 
     
     
         74 . A method of obtaining a crop product comprising harvesting a crop product from a plant according to any one of  claims 70  to  73  and optionally further processing the harvested product. 
     
     
         75 . A method according to  claim 74  wherein the plant is a wheat plant and the harvested crop product is grain; optionally further processed into flour or another grain product. 
     
     
         76 . A crop product obtainable by a method according to  claim 74  or  75 . 
     
     
         77 . A food that comprises a protein as defined in any  claim 25  or  30 . 
     
     
         78 . A food according to  claim 77  in which a protein as defined in  claim 25  or  30  is used instead of wild-type gluten.