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

Jayashree Shanker; Prathima Arvind; Srikarthika Jambunathan; Jiny Nair; Vijay V. Kakkar

doi:10.1160/TH13-08-0706

Thrombosis and Haemostasis, Table of Contents

Thromb Haemost 2014; 111(05): 960-969
DOI: 10.1160/TH13-08-0706

Cardiovascular Biology and Cell Signalling

Schattauer GmbH

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

Authors

Jayashree Shanker^*

¹Mary and Garry Weston Functional Genomics Unit, Thrombosis Research Institute, Bangalore, India
Prathima Arvind^*

¹Mary and Garry Weston Functional Genomics Unit, Thrombosis Research Institute, Bangalore, India
Srikarthika Jambunathan

¹Mary and Garry Weston Functional Genomics Unit, Thrombosis Research Institute, Bangalore, India
Jiny Nair

¹Mary and Garry Weston Functional Genomics Unit, Thrombosis Research Institute, Bangalore, India
Vijay V. Kakkar

²Chairman and Managing Trustee, Thrombosis Research Institute, Bangalore, India

³Thrombosis Research Institute, London, UK

Abstract

Summary

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, MTAP 1, MTAP 2, p16^INK4a , p14^ARF , p15^INK4b 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 p16^INK4a , p14^ARF and p15^INK4b as well as plasma CDKN2A levels were lower in cases than controls. GG genotype was associated with higher EU741058 expression and lower p16^INK4a expression. HuAoSMCs transfected with siRNA-1 showed lower NR_003529, p16^INK4a and p14^ARF expression. 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.

Keywords

Coronary artery disease - 9p21.3 locus - association study - gene expression - Asian Indians

Full Text

References

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