Haplotypes of polymorphic antigen processing genes for low molecular mass polypeptides (LMP2 and LMP7) are strongly associated with Type 1 diabetes in North India

Abstract

Objective: Type 1 diabetes (T1D) is a multifactorial autoimmune disorder where several genes have been implicated. Aberrant presentation of auto-antigens on the MHC molecules is the hallmark of autoimmune disorders. The antigen is processed into small peptides by low molecular mass polypeptides, LMP2 and LMP7 before they are presented on the MHC class-I molecules. We have studied the associations of the Single nucleotide polymorphisms (SNPs) in these antigen processing genes and their haplotypes which may be detrimental for the processing of the auto-antigens in T1D. Methods: 239 T1D subjects and 752 normal healthy controls from North India were studied for LMP2 codon 60 G/A (R/H), LMP7 codon 49 of C/A (Q/K) and LMP7 Intron 6 G/T polymorphisms using PCR-RFLP. HLA class-II alleles were studied using bead based Luminex assays. Haplotypes of LMP2 and LMP7 were constructed using SHEsis online software. χ2 test was used to study the significance of differences between patients and controls. Results: The G (R) allele (p<0.009) and homozygous GG (RR) genotype (p<0.01) of LMP2 codon 60, C (Q) allele (p<0.0098) and homozygous CC (QQ) (p<0.03) of LMP 7 codon 49 and LMP7 Intron 6 G allele (p<0.01) were significantly increased in T1D subjects compared to controls. Haplotype analysis showed that haplotypes GCG and ACT (LMP2 codon 60- LMP7codon 49- LMP7 intron 6) (p<5.9×10-13, p<1.9×10-8 respectively) were significantly increased and haplotypes GCT and ACG (p<1.9×10-12, p<1.9×10-13 respectively) were significantly reduced in T1D patients irrespective of the gender, age at onset of T1D and the predisposing HLA DRB1*03:01. Conclusion: Association of LMP2 and LMP7 haplotypes GCG and ACT with T1D may have a role in processing of auto-antigens to be presented by MHC class-I molecules to cytotoxic T cells in T1D.