Genetic Alterations on Chromosomes 21q, 6q and 15q and Methods of Use Thereof for the Diagnosis and Treatment of Type I Diabetes

Abstract

Compositions and methods for the detection and treatment of T1D are provided.

1 . A method for detecting the presence or absence of at least one genetic alteration in a target nucleic acid isolated from a patient for assessing susceptibility for developing type 1 diabetes (T1D), said method comprising:
 a) providing a target nucleic acid from a patient sample, said target nucleic acid having a predetermined sequence in the normal population;   b) assessing said target nucleic acid for the presence of a single nucleotide polymorphism which is indicative of an increased or decreased susceptibility of developing T1D, wherein genetic alteration is at least one single nucleotide polymorphism (SNP) set forth in Tables 1, 2, 4 or 5.   
     
     
         2 . The method as claimed in  claim 1 , wherein said genetic alteration is selected from the group consisting of inversion, deletion, duplication, and insertion of at least one nucleotide in said sequence. 
     
     
         3 . The method of  claim 1 , wherein said target nucleic acid is assessed for genetic alterations via a method selected from the group consisting of size analysis, hybridization of allele specific probes, allele-specific primer extension, oligomer ligation, DNA sequencing, single-stranded conformation polymorphism, and quantitative PCR. 
     
     
         4 . The method as claimed in  claim 1 , wherein said genetic alteration is a single nucleotide polymorphism (SNP) set forth in Table 2. 
     
     
         5 . The method as claimed in  claim 1 , wherein said genetic alteration is present in a linkage disequilibrium block provided in Table 3. 
     
     
         6 . The method of  claim 1 , wherein said SNP is present in a nucleic acid selected from the group consisting of UBASH3A, GLIS3, RASGRP1, BACH2, and EDG7 encoding nucleic acids. 
     
     
         7 . The method of  claim 6  wherein said SNP is selected from the group consisting of rs9976767 present on chromosome 21 at position 42709459 within the UBASH3A gene, rs3757247 present on chromosome 6 at position 91014184 in the BACH2 gene and rs7171171 present on chromosome 15 at position 36694333. 
     
     
         8 . A method for determining the presence or absence of at least one specific nucleotide in a target nucleic acid for the diagnosis of T1D, said method comprising the steps of:
 a) providing a detectable amount of a target nucleic acid polymer isolated from a chromosomal region known to be associated with diabetes,   b) hybridizing said detectable amount of the nucleic acid polymer with one or more oligonucleotide primers, wherein each primer has a nucleotide sequence that is complementary to a sequence in the target nucleic acid polymer,   c) exposing the hybridized nucleic acid polymer to a polymerization agent in a mixture containing at least one deoxynucleotide, said deoxynucleotide comprising a detectable label,   d) analyzing the polymerization mixture of step (c) for the presence or absence of the primer extension product containing the labeled deoxynucleotide, whereby the identity of the specific nucleotide at the defined site is determined; and   e) assessing said target nucleic acid for the presence of a genetic alteration at said at least one single nucleotide loci, the presence of the polymorphism being associated with an altered risk of developing T1D.   
     
     
         9 . A kit for practicing the method of  claim 8 . 
     
     
         10 . A nucleic acid comprising at least one SNP identified in Tables 1, 2, 4 and 5. 
     
     
         11 . A nucleic acid comprising at least one linkage disequilibrium block provided in Table 3, said nucleic acid comprising a genetic alteration indicative of an altered risk of developing T1D. 
     
     
         12 . A microarray comprising the at least one nucleic acid of  claim 10  or  claim 11 , said nucleic acid optionally being between 10 and 50 nucleotides in length. 
     
     
         13 . A method of management for T1D comprising:
 a) identifying a patient who is at an increased risk of developing T1D by detecting at least one of the polymorphisms in Tables 1, 2, 4, or 5;   b) administering to said patient a therapeutic agent in a therapeutically effective amount to manage T1D.   
     
     
         14 . The method of  claim 10 , wherein said therapeutic agent modulates signaling or glucose regulating function mediated via a gene product selected from the group consisting of UBASH3A, GLIS3, RASGRP1, BACH2, and EDG7. 
     
     
         15 . The method according to  claim 14 , wherein said therapeutic agent is selected from the group consisting of a small molecule, an antibody, a protein, an oligonucleotide, or an siRNA molecule. 
     
     
         16 . The method of  claim 14 , wherein said agent is at least one siRNA provided provided in Tables 6-10 in a pharmaceutically acceptable carrier. 
     
     
         17 . The method of  claim 14 , wherein said therapeutic agent is delivered to an inflammatory cell. 
     
     
         18 . The method of  claim 14 , wherein said therapeutic agent modulates natural killer cell activity. 
     
     
         19 . The method of  claim 14 , wherein said therapeutic agent modulates signaling in an insulin-producing beta cell. 
     
     
         20 . A single nucleotide polymorphism associated with an altered risk of developing T1D selected from the group consisting rs9976767 present on chromosome 21 at position 42709459 within the UBASH3A gene, rs3757247 present on chromosome 6 at position 91014184 in the BACH2 gene and gene and rs7171171 present on chromosome 15 at position 36694333 within the RASGRP1 gene. 
     
     
         21 . A method for identifying agents which modulate beta cell destruction leading to T1D comprising:
 a) providing a test subject having cells expressing a SNP selected from the group consisting those set forth in Tables 1, 2 , 4 or 5;   b) providing a test subject having cells which express the cognate sequence lacking the SNPs of step a);   c) contacting the cells of steps a) and b) with an agent; and   d) determining whether said agent alters beta cell destruction of the cells of step a) relative to those of step b), thereby identifying agents which modulate autoimmune beta cell destruction.   
     
     
         22 . An siRNA composition which is effective to down regulate expression of a gene target selected from the group consisting of UBASH3A, GLIS3, RASGRP1, BACH2, and EDG7, having a sequence provided in Tables 6-10 in a pharmaceutically acceptable carrier for delivery to a patient. 
     
     
         23 . A method of treating T1D in a patient in need thereof, comprising administration of an effective amount of the composition of  claim 22 . 
     
     
         24 . The method of  claim 22  wherein said siRNA modulates a parameter selected from the group consisting of insulin secretion, glucagon secretion and glucosamine induced beta cell apoptosis and the degree of said modification is determined. 
     
     
         25 . A method for identifying agents which modulate the diabetic phenotype:
 a) providing cells expressing a single nucleotide polymorphism selected from the group consisting of those set forth in Table 1, 2, 4 and 5;   b) providing cells which express the cognate sequences which lack the polymorphisms of step a);   c) contacting the cells of steps a) and b) with a test agent and   d) analyzing whether said agent alters an diabetic associated parameter in cells contacted in step a) relative to those of step b), thereby identifying agents which modulate the diabetic phenotype.   
     
     
         26 . The method of  claim 25 , wherein said parameter is selected from the group consisting of insulin secretion, glucagon secretion and glucosamine induced beta cell apoptosis.