Genetic analysis of the 9p21.3 CAD risk locus in Asian Indians

Abstract

The 9p21.3 locus is the best replicated region to date for coronary artery disease (CAD). We investigated the association of 9p21.3 common variants with CAD, candidate gene expression including ANRIL, a non-coding RNA, followed by in vitro validation. Five variants, rs10757278, rs10757274, rs2383206, rs1333049 and rs4977574 were genotyped in 1,034 cases and 1,034 controls. Gene expression of C9orf5, MTAP1, MTAP 2, p16INK4a, p14ARF, p15INK4b and two ANRIL splice variants, NR_003529 and EU741058, were measured in 100 cases and 100 controls. Human aortic smooth muscle cells (HuAoSMCs) were transfected with siRNA targeting ANRIL exon 19 (siRNA-1) or exon 2 (siRNA-2) and consequent effect determined. rs2383206 showed the highest association with CAD (odds ratio [OR] 2.02, 95% confidence interval [CI] 1.56 -2.62) and an adjusted OR of 2.55, 1.33-2.88 along with rs10757278. Conventional risk factors (conventional RFs), rs2383206 and rs10757278 variants together yielded a higher c index (OR 0.790, 95% CI 0.770 -0.810) as compared to conventional RFs (OR 0.783, 95% CI 0.763-0.803) or genetic variants (OR 0.561, 95% CI 0.536-0.586) alone. GAAAA haplotype showed significant protective association with CAD compared to CGGGG risk haplotype (OR 0.45, 95% CI 0.27-0.77). Expression of p16INK4a, p14ARF and p15INK4b as well as plasma CDKN2A levels were lower in cases than controls. GG genotype was associated with higher EU741058 expression and lower p16INK4a expression. HuAoSMCs transfected with siRNA-1 showed lower NR_003529, p16INK4aand p14ARFexpression. Our study provides further evidence on the significance of 9p21.3 locus for CAD wherein the risk allele regulate the expression of ANRIL and adjacent tumour suppressor genes which in turn alter smooth muscle proliferation, a fundamental process in atherosclerosis.

ANRIL Promoter DNA Methylation: A Perinatal Marker for Later Adiposity

“…Interestingly the genetic associations seem independent of obesity (Broadbent et al, 2008). Disease associated genotype is also associated with ANRIL expression levels, and ANRIL expression also differs relative to disease (Zhao et al, 2015, Shanker et al, 2014, Bochenek et al, 2013). Previously Zhuang et al (2012) found that methylation in blood at a locus overlapping with the DMR discussed here, was higher in coronary artery disease compared to controls but methylation was not associated with genotype at rs10757274 (Zhuang et al, 2012).…”

9P21.3 locus; An Important Region in Coronary Artery Disease: A Panel Approach to Investigation of the Coronary Artery Disease Etiology

“…Association of three most frequently detected SNP, rs1333049, rs2383206 and rs10757278, in European populations was confirmed in a large meta-analysis of an East Asian population [126]. Among these variants, rs2383206 and rs10757278 displayed the closest association with CAD in an Indian population [127,128]. Investigation of CAD in a Saudi population identified four SNPs including rs564398, rs4977574, rs2891168, and rs1333042 associated with CAD/MI [129].…”

“…However, investigation of the rs10757274 and rs1333042 variants showed that the risk alleles of these SNP in a haplotype form did constitute a risk factor for CAD [137]. This demonstrated that some haplotype arrangements have protective effects against CAD, such as a GAAAA haplotype for five common variants, rs1333049, rs10757278, rs2383206, rs4977574 and rs10757274 [127]. The majority of SNP in the ANRIL gene were located in intronic regions, but recently two exonic variants were reported to be associated with MI.…”

Association of the rs10757274 SNP with coronary artery disease in a small group of a Pakistani population

“…Their study indicated the importance of this SNP due to its involvement in the expression of the EU741058 and p16INK4a genes, modulating the chances of CAD. The same SNP also showed its association with peripheral artery disease in a Han Chinese population (40). These findings are in agreement with our results, obtained without the consideration of covariates.…”

“…The family history was associated with the extent and severity of coronary atherosclerotic plaque formation in premature CAD (38). The effects of rs10757274 were investigated by Shanker et al (40). Their study indicated the importance of this SNP due to its involvement in the expression of the EU741058 and p16INK4a genes, modulating the chances of CAD.…”