T cell receptor Vbeta-Dbeta-Jbeta sequence and methods for its detection

Abstract

In one embodiment, the present invention is directed to a first oligonucleotide comprising the sequence of or derived from 5′-CTAGGGCGGGCGGGACTCACCTAC-3′or the nucleic acid sequence complementary thereto. The first oligonucleotide can be used with a nucleic acid of between 15 and 30 nucleotides that does not comprise the sequence of the first oligonucleotide and is found in the region from Vβ to Jβ of the Vβ13.1 gene in Vβ13.1 T cells, wherein the sequences of the oligonucleotide and the nucleic acid are not found on the same strand of the Vβ13.1 gene pair, to amplify a portion of the Vβ13.1 gene. Alternatively, the first oligonucleotide can be used with a labeling moiety in methods of detecting a LGRAGLTY motif found in T cell receptors of Vβ13.1 T cells. This motif is associated with autoimmune diseases, such as multiple sclerosis (MS). Once the motif is detected, the autoimmune disease can be treated or its progress monitored. The autoimmune disease can be treated by administering one or more peptides comprising the LGRAGLTY motif.

What is claimed is:  
     
         1 . An oligonucleotide of about 15 to 30 nucleotides in length, comprising at least 10 contiguous nucleotides of SEQ ID NO: 1, or the nucleic acid complementary thereto.  
     
     
         2 . The oligonucleotide of  claim 1 , which comprises at least 15 contiguous nucleotides of SEQ ID NO: 1, or the nucleic acid complementary thereto.  
     
     
         3 . The oligonucleotide of  claim 1 , which comprises the sequence of SEQ ID NO: 1, or the nucleic acid complementary thereto.  
     
     
         4 . A primer pair, comprising: 
 (a) a first primer of about 15 to 30 nucleotides in length, comprising at least 10 contiguous nucleotides of SEQ ID NO: 1, or the nucleic acid complementary thereto; and    (b) a second primer comprising a nucleic acid of about 15 and 30 nucleotides in length that does not comprise the sequence of (a) and is found in the region from Vβ to Jβ of the Vβ13.1 gene in T cell receptor T cells,    wherein the sequences of said first and second primers are not found on the same strand of the T cell receptor gene.    
     
     
         5 . The primer pair of  claim 4 , wherein the Vβ13.1 gene sequence is SEQ ID NO: 2.  
     
     
         6 . An oligonucleotide probe comprising: 
 (a) an oligonucleotide of about 10 to 30 nucleotides in length, comprising at least 10 contiguous nucleotides of SEQ ID NO: 1, or the nucleic acid complementary thereto; and    (b) a labeling moiety.    
     
     
         7 . The oligonucleotide probe of  claim 6 , wherein the labeling moiety is selected from  32 P or digoxingenin.  
     
     
         8 . A method of detecting MBP83-99 Vβ13.1 T cells expressing a T cell receptor LGRAGLTY motif, comprising: 
 (a) obtaining a nucleic acid sample from MBP83-99 Vβ13.1 T cells;  
 (b) contacting the nucleic acid sample with a primer pair selected or derived from: 
 (i) a first oligonucleotide of about 15 to 30 nucleotides in length, comprising at least 10 contiguous nucleotides of SEQ ID NO: 1, or the nucleic acid complementary thereto; and  
 (ii) a second oligonucleotide of about 15 and 30 nucleotides in length that does not comprise the sequence of the first oligonucleotide and is found in the region from Vβ to Jβ of the Vβ13.1 gene in T cell receptor T cells,  
 wherein the sequences of the first and second oligonucleotides are not found on the same strand of the T cell receptor gene; and  
 
 (c) detecting the presence of the nucleic acid encoding the LGRAGLTY motif.  
 
     
     
         9 . The method of  claim 8 , wherein the Vβ13.1 gene sequence is SEQ ID NO: 2.  
     
     
         10 . The method according to  claim 8 , wherein a fragment of the nucleic acid sample is amplified by polymerase chain reaction (PCR).  
     
     
         11 . The method according to  claim 10 , wherein the detection step comprises probing with an oligonucleotide probe comprising: 
 i) an oligonucleotide, which comprises the sequence of SEQ ID NO: 1, or the nucleic acid complementary thereto; and,    ii) a labeling moiety.    
     
     
         12 . The method according to  claim 10 , wherein the detection step comprises autoradiography.  
     
     
         13 . A test kit comprising a first oligonucleotide of about 15-30 nucleotides in length: 
 said first oligonucleotide comprising at least 10 contiguous nucleotides of SEQ ID NO: 1, or the nucleic acid complementary thereto.    
     
     
         14 . The test kit of  claim 13 , further comprising: a second oligonucleotide of about 15 and 30 nucleotides in length that does not comprise the sequence of said first oligonucleotide and is found in the region from Vβ to Jβ of the Vβ13.1 gene in T cell receptor T cells, wherein the sequences of the first and second oligonucleotides are not found on the same strand of the T cell receptor gene.  
     
     
         15 . The test kit of  claim 14 , wherein the Vβ13.1 gene sequence is SEQ ID NO: 2.  
     
     
         16 . The test kit of  claim 13 , further comprising a labeling moiety, wherein the labeling moiety is selected from  32 P or digoxingenin.  
     
     
         17 . A peptide of from 8 to approximately 45 amino acids in length, comprising the sequence of SEQ ID NO: 3.  
     
     
         18 . The peptide of  claim 17  which is SEQ ID NO: 3.  
     
     
         19 . The peptide of  claim 17  which comprises amino acids 2-21 of SEQ ID NO: 32.  
     
     
         20 . The peptide of  claim 17  which consists of amino acids 2-21 of SEQ ID NO: 32.  
     
     
         21 . A method of treating an autoimmune disease, in a human comprising: 
 (a) obtaining MBP83-99 Vβ13.1 T cells from a human;    (b) obtaining a nucleic acid sample from MBP83-99 Vβ13.1 T cells;    (c) contacting the nucleic acid sample with a primer pair selected or derived from: 
 (i) a first oligonucleotide of about 15 to 30 nucleotides in length, comprising at least 10 contiguous nucleotides of SEQ ID NO: 1, or the nucleic acid complementary thereto; and  
 (iii) a second oligonucleotide of about 15 and 30 nucleotides in length that does not comprise the sequence of said first oligonucleotide and is found in the region from Vβ to Jβ of the Vβ13.1 gene in T cell receptor T cells,  
   wherein the sequences of said first and second oligonucleotides are not found on the same strand of the T cell receptor gene; and    (d) detecting the presence of the nucleic acid encoding the LGRAGLTY motif, and, if the nucleic acid is detected,    (e) administering a peptide of from 8 to approximately 45 amino acids in length, peptide to the human; wherein the peptide comprising the sequence of SEQ ID NO: 3.    
     
     
         22 . The method of  21 , wherein the Vβ13.1 gene sequence is SEQ ID NO: 2.  
     
     
         23 . The method of  claim 21 , wherein the administering step further comprises administering a T cell activation marker peptide.  
     
     
         24 . The method of  21  wherein the peptide consists of the sequence of SEQ ID NO: 3.  
     
     
         25 . The method of  21  wherein the peptide consists of amino acids 2-21 of SEQ ID NO: 32.  
     
     
         26 . A method of monitoring an autoimmune disease, comprising: 
 (A) obtaining MBP83-99 Vβ13.1 T cells from a human;    (B) detecting the presence of a nucleic acid encoding a LGRAGLTY motif by 
 (i) obtaining a nucleic acid sample from MBP83-99 Vβ13.1 T cells;  
 (ii) contacting the nucleic acid sample with a primer pair selected or derived from: 
 (a) a first oligonucleotide of about 15 to 30 nucleotides in length, comprising at least 10 contiguous nucleotides of SEQ ID NO: 1, or the nucleic acid complementary thereto; and  
 (b) a second oligonucleotide of about 15 and 30 nucleotides in length that does not comprise the sequence of said first oligonucleotide and is found in the region from Vβ to Jβ of the Vβ13.1 gene in T cell receptor T cells,  
 
 wherein the sequences of said first and second oligonucleotides are not found on the same strand of the T cell receptor gene; and 
 (c) detecting the presence of the nucleic acid encoding the LGRAGLTY motif; and, if the nucleic acid is detected,  
 
   (C) quantifying the amount of the nucleic acid.    
     
     
         27 . The method of  26 , wherein the Vβ13.1 gene sequence is SEQ ID NO: 2.