Extended haplotypes based on rare single nucleotide polymorphisms of TNFA and HLA DRB1 associated with rheumatoid arthritis

Rheumatoid arthritis (RA) is a multifactorial disease, with genetic component based on intergenic interactions leading to the formation of gene networks. The current trend in RA immunogenetic studies is to assess the gene-to-gene interactions. Among possible genetic factors contributing to RA development, the genes of main histocompatibility complex (HLA class II) play a fundamental role. TNFA gene is among possible candidate genes providing susceptibility to this disorder and contributing to its immune pathogenesis. The special location of this gene suggests arrangement of extended TNFA – HLA haplotypes. This work analyzed the distribution features of two-locus SNP haplotypes (TNFA and HLA DRB1) for their association with rheumatoid arthritis in Russians. The following methods were used: DNA isolation, PCR-based genotyping, RFLP analysis with electrophoretic detection. Calculation of two-locus haplotypes frequencies and linkage disequilibrium (D’; χ2; p) was carried out using the EM algorithm in the Arlequin ver 3.5 program. Comparison of paired samples was carried out using standard immunogenetic criteria. The significance level was < 0.05. Analysis of the data showed that the two-locus haplotypes -1031T/C and -863C/A TNFA were not associated with predisposal for rheumatoid arthritis in Russian population sample. The haplotypes associated with predisposition for RA were TNFA -863*a – HLA DRB1*03, TNFA -1031*t – HLA DRB1*04, TNFA -1031*t – HLA DRB1*04. Meanwhile, TNFA -1031*t – HLA DRB1*15; TNFA -1031*t -HLA DRB1*11 proved to be protective haplotypes. Our study showed that, in addition to individual HLA II alleles, the predisposal or resistance to rheumatoid arthritis may be promoted by haplotypes of rare SNPs at positions -1031, -863 C/A of TNFA gene, and HLA DRB1.