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Renal cell cancer is the most common type of kidney cancer in adults, and clear cell renal cell carcinoma (ccRCC) is the most diagnosed type. T cell immunoglobulin and mucin-domain-containing-3 (TIM-3) belongs to immunological checkpoints that are key regulators of the immune response. One of the known TIM-3 ligands is galectin-9 (<i>LGALS9</i>). A limited number of studies have shown an association between <i>TIM-3</i> polymorphisms and cancer risk in the Asian population; however, there is no study on the role of <i>LGALS9</i> polymorphisms in cancer. The present study aimed to analyze the influence of <i>TIM-3</i> and <i>LGALS9</i> polymorphisms on susceptibility to ccRCC and patient overall survival (OS), with over ten years of observations. Using TaqMan probes, ARMS–PCR, and RFPL-PCR, we genotyped two <i>TIM-3</i> single-nucleotide polymorphisms (SNPs): rs1036199 and rs10057302, and four <i>LGALS9</i> SNPs: rs361497, rs3751093, rs4239242, and rs4794976. We found that the presence of the rs10057302 A allele (AC + AA genotypes) as well as the rs4794976 T allele (GT + TT genotypes) decreased susceptibility to ccRCC by two-fold compared to corresponding homozygotes. A subgroup analysis showed the association of some SNPs with clinical features. Moreover, <i>TIM-3</i> rs1036199 significantly influenced OS. Our results indicate that variations within <i>TIM-3</i> and <i>LGALS9</i> genes are associated with ccRCC risk and OS.