Tagging single nucleotide polymorphisms in the IRF1 and IRF8 genes and tuberculosis susceptibility

Abstract

Genes encoding IRF1 and IRF8 protein have been proposed as candidate tuberculosis susceptibility genes. In order to elucidate whether the IRF1 and IRF8 variants were associated with tuberculosis susceptibility, we conducted a case-control study consisting of 495 controls and 452 ethnically matched cases with tuberculosis in a Chinese population. Seven haplotype tagging single-nucleotide polymorphisms (tagSNPs) (rs2057656; rs2706381; rs2070724; rs2070721; rs2549008; rs2549007; rs2706386) from HapMap database were analyzed, which provided an almost complete coverage of the genetic variations in the IRF1 gene. Fifteen tagSNPs (rs12924316; rs182511; rs305080; rs2292980; rs925994; rs424971; rs16939967; rs11117415; rs4843860; rs9926411; rs8064189; rs12929551; rs10514611; rs1044873; rs6638) were observed in the IRF8 gene. All these tagSNPs were genotyped by SNPstream genotyping and SNaPshot typing. None of the seven tagSNPs was individually associated with tuberculosis in the IRF1 gene. In the IRF8 gene, interestingly, we found that three tagSNPs (rs925994 and rs11117415 located in the intron region; rs10514611 located in the 3'UTR) were associated with risk of tuberculosis after Bonferroni correction. Per allele OR was 1.75 (95% CI 1.35 ~ 2.27, P = 0.002), 4.75 (95% CI 2.16 ~ 10.43, P = 0.002) and 3.39 (95% CI 1.60 ~ 7.20, P = 0.015) respectively. Luciferase reporter gene assay showed that the construct that contained the non-risk allele C of rs10514611 showed significantly higher luciferase activity than did the risk T allele (P<0.01), which implied rs10514611 was a potential functional SNP site. Our results indicated that the IRF8 gene might participate in genetic susceptibility to tuberculosis in a Chinese population.

Figure 1. Linkage disequilibrium (LD) statistic (r²) for the IRF1 gene.

(Genomic organization of the IRF1 gene, including the position of individual non-coding (open boxes) and coding (closed boxes) exons; the darker shading indicates stronger LD between SNPs).

Figure 2. Linkage disequilibrium statistic (r²) for the IRF8 gene.

(Genomic organization of the IRF8 gene, including the position of individual non-coding (open boxes) and coding (closed boxes) exons; the darker shading indicates stronger LD between SNPs).

Figure 3. The regulation of luciferase activity by the IRF8 3′-UTR is dependent on miR-330.

(HeLa cells were transfected with the pRL-TK containing Renilla luciferase gene and the indicated vectors or precursors. Bars indicated the Firefly luciferase activities normalized to Renilla luciferase activities of the cotransfected pRL-PK vector. **P<0.01).