Identification of rs28362336 as a risk SNP for generalized myasthenia gravis and its impact on HCG27 regulation

Myasthenia gravis (MG) is an antibody-mediated autoimmune disease of the neuromuscular junctions. Accumulating amounts of evidence have indicated that single nucleotide polymorphisms (SNPs) and long noncoding RNAs (lncRNAs) play critical roles in the pathogenesis of MG; however, research on MG-related lncRNA SNPs remains limited. Therefore, our study focused on MG-related lncRNA SNPs to explore their association with genetic susceptibility to MG. We screened regulatory SNPs using MG GWAS data and conducted a case‒control study including 161 patients and 161 controls. After SNaPshot genotyping, LASSO regression and random forest were used to identify SNP-related risk factors. We performed eQTL analysis and ChIP-PCR to identify the functional role and underlying mechanism of rs28362336. qRT-PCR was performed to measure HCG27 expression in MG patients and to further assess HCG27 expression in generalized MG (gMG) patients. Finally, fluorescence in situ hybridization was used to determine the subcellular localization of HCG27 in CD4 + T cells, and the effects of HCG27 overexpression or knockdown were evaluated by Western blot analysis and CCK-8 assays. Significant SNPs were identified on chromosomes 1, 6, 11, 17, and 18. Although no differences in genotype or allele frequency were observed between the cases and controls overall, subtype analysis revealed that HCG27 rs9263872(TT), rs9263875(GG), and rs28362336(GG) were associated with gMG risk. The rs9263875 G allele was associated with gMG, whereas the HCG9 rs3823381 T allele was associated with ocular MG (oMG). Machine learning analysis further revealed that rs28362336 is a risk factor of MG. Bioinformatics and ChIP-PCR revealed H3K4me1, H3K27ac, and Pol II enrichment at the rs28362336 locus, suggesting enhancer activity upstream of HCG27. HCG27 expression was increased in MG patients, particularly in gMG harboring the rs28362336 GG genotype. Finally, HCG27 promoted CD4 + T cell proliferation and inhibited apoptosis. This study revealed the associations of HCG27-related SNPs with gMG and the potential regulatory role of rs28362336 in HCG27 expression. Moreover, the upregulation of HCG27 in MG patients and its proliferation-promoting effect in CD4 + T cells suggest that HCG27 may contribute to MG pathogenesis.