Genetic association of nuclear factor of activated T cells’ 3′UTR and structural polymorphisms with susceptibility to generalized vitiligo in Gujarat population

Abstract

Generalized vitiligo (GV) is an autoimmune skin depigmenting disease characterized by loss of functional melanocytes. Nuclear factor of activated T cells (NFATs) play a key role in regulatory T cells’ (Tregs) activation and function. Our previous studies have highlighted the role of reduced NFATs expression and activity in impaired Tregs suppressive capacity, leading to GV pathogenesis. 3′UTR region and structural single nucleotide polymorphisms(SNPs) could lead to reduced NFAT expression and activity. Therefore, we studied the association of NFATs 3′UTR [NFATC2 rs4811198 (T > G) &NFATC4 rs11848279 (A > G)] and structural [NFATC1 rs754093 (T > G) &NFATC2 rs12479626 (T > C)] SNPs in 427 GV patients and 415 controls from Gujarat population by Polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP). Additionally, we carried out genotype-phenotype correlation and in silico analysis to assess the effect of NFATs SNPs on NFATs expression and structure. NFATC2 rs4811198 (T > G) 3′ UTR &NFATC2 rs12479626 (T > C) structural SNPs were significantly associated with GV (p < 0.0001). Interestingly, for NFATC2 rs4811198 (T > G) SNP, there was a significant difference in the TT vs GG genotypes’ frequencies (p = 0.0034; Table 2), and for NFATC2 rs12479626 (T > C) SNP there was a significant difference between TT vs TC and CC genotypes’ frequencies (p < 0.0001 & p = 0.0002) between GV patients and controls. Furthermore, Odds ratio suggested that the susceptible alleles for NFATC2 rs4811198 (T > G) &NFATC2 rs12479626 (T > C) SNPs increased the risk of GV by 1.38 & 3.04 fold. However, the NFAT 3′ UTR [NFATC2 rs4811198 (T > G)] and structural [NFATC1 rs754093 (T > G)] SNPs were not significantly associated with GV. Interestingly, the genotype-phenotype correlation suggested that the susceptible ‘G’ allele of NFATC2 rs4811198 (T > G) &NFATC4 rs11848279 (A > G) 3′ UTR SNPs lead to reduced NFATC2 and NFATC4 expression (p < 0.0001). Furthermore, in silico analysis suggested that hsa-miR-3183 & hsa-miR-6720-3p miRNAs specifically bound to ‘G’ allele of NFATC2 rs4811198 SNP and has-miR-4652-3p miRNA specifically bound to ‘G’ allele of NFATC4 rs11848279 SNP. Overall, our study suggests that NFATC2 rs4811198 (T > G) 3′ UTR &NFATC2 rs12479626 (T > C) structural SNPs may be associated with GV susceptibility in Gujarat population. Moreover, the susceptible alleles for the 3′ UTR SNPs could lead to reduced NFATs levels, which may further possibly, affect the Treg suppressive function leading to GV.