Whole exome sequencing analysis reveals TRPV3 as a risk factor for cardioembolic stroke/subtitle

Summary

Genetic studies suggest that hundreds of genes associated with stroke remain unidentified. Exome sequencing proves useful for finding new genes associated with stroke. We aimed to find new genetic risk factors for cardioembolic stroke by analysing exome sequence data using new strategies. For discovery, we analysed 42 cardioembolic stroke cases and controls with extreme phenotypes (cohort 1), and for replication, 32 cardioembolic stroke cases and controls (cohort 2) using the SeqCapExome capture kit. We then analysed the replicated genes in two new cohorts that comprised 834 cardioembolic strokes and controls (cohort 3) and 64,373 cardioembolic strokes and controls (cohort 4). Transcriptomic in-silico functional analyses were also performed. We found 26 coding regions with a higher frequency of mutations in cardioembolic strokes after correcting for the number of mutations found in the whole exome of every patient. The TRPV3 gene was associated with cardioembolic stroke after replication of exome sequencing analysis (p-value-discovery: 0.018, p-value-replication: 0.014). The analysis of the TRPV3 gene using polymorphisms in cohort 3 and 4 revealed two polymorphisms associated with cardioembolic stroke in both cohorts, the most significant polymorphism being rs151091899 (p-value: 3.1 × 10⁻⁰⁵; odds ratio: 5.4) in cohort 3. The genotype of one polymorphism of TRPV3 was associated with a differential expression of genes linked to cardiac malformations. In conclusion, new strategies using exome sequence data have revealed TRPV3 as a new gene associated with cardioembolic stroke. This strategy among others might be useful in finding new genes associated with complex genetic diseases.

Keywords

Genetics - cerebrovascular disease/stroke - ischaemic stroke

• References

• 1 Traylor M, Farrall M, Holliday EG. et al. International Stroke Genetics Consortium. Genetic risk factors for ischaemic stroke and its subtypes (the META-STROKE collaboration): a meta-analysis of genome-wide association studies. Lancet Neurol 2012; 11: 951-962
• 2 Woo D, Falcone GJ, Devan WJ. et al. International Stroke Genetics Consortium. Meta-analysis of genome-wide association studies identifies 1q22 as a susceptibility locus for intracerebralhemorrhage. Am J Hum Genet 2014; 94: 511-521.
• 3 Traylor M, Mäkelä KM, Kilarski LL. et al. A Novel MMP12 Locus Is Associated with Large Artery Atherosclerotic Stroke Using a Genome-Wide Age-at-Onset Informed Approach. PLoS Genet 2014; 10: e1004469.
• 4 Holliday EG, Maguire JM, Evans TJ. et al. Australian Stroke Genetics Collaborative; International Stroke Genetics Consortium; Wellcome Trust Case Control Consortium 2. Common variants at 6p21.1 are associated with large artery atherosclerotic stroke. Nat Genet 2012; 44: 1147-1151.
• 5 Kilarski LL, Achterberg S, Devan WJ. et al. GARNET Collaborative Research Group, Wellcome Trust Case Control Consortium 2, Australian Stroke Genetic Collaborative, the METASTROKEConsortium, and the International Stroke Genetics Consortium. Meta-analysis in more than 17,900 cases of ischaemic stroke reveals a novel association at 12q24.12. Neurology 2014; 83: 678-685.
• 6 Bevan S, Traylor M, Adib-Samii P. et al. Genetic heritability of ischaemic stroke and the contribution of previously reported candidate gene and genome wide associations. Stroke 2012; 43: 3161-3167.
• 7 Kim DS, Crosslin DR, Auer PL. et al. on behalf of the NHLBI Exome Sequencing Project. Rare coding variation in paraoxonase-1 is associated with ischaemic stroke in the NHLBI Exome Sequencing Project. J Lipid Res 2014; 55: 1173-1178.
• 8 Auer PL, Nalls M, Meschia JF. et al. National Heart, Lung, and Blood Institute Exome Sequencing Project. Rare and Coding Region Genetic Variants Associated With Risk of Ischaemic Stroke: The NHLBI Exome Sequence Project. JAMA Neurol 2015; 72: 781-788.
• 9 Adams HP, Bendixen BH, Kappelle 3rd LJ. et al. Classification of subtype of acute ischaemic stroke: definitions for use in a multicenter clinical trial. TOAST. Trial of Org 10172 in Acute Stroke Treatment. Stroke 1993; 24: 35-41.
• 10 Anderson CA, Pettersson FH, Clarke GM. et al. Data quality control in genetic case-control association studies. Nat Protoc 2010; 05: 1564-1573.
• 11 Adams DR, Sincan M, Fuentes Fajardo K. et al. Analysis of DNA sequence variants detected by high-throughput sequencing. HumMutat 2012; 33: 599-608.
• 12 Mercader JM, Saus E, Agüera Z. et al. Association of NTRK3 and its interaction with NGF suggest an altered cross-regulation of the neurotrophinsignaling pathway in eating disorders. Hum Mol Genet 2008; 17: 1234-1244.
• 13 Adzhubei IA, Schmidt S, Peshkin L. et al. A method and server for predicting damaging missense mutations. Nat Methods 2010; 07: 248-249.
• 14 Ichida F. Left ventricular noncompaction. Circ J 2009; 73: 19-26.
• 15 Moric-Janiszewska E. Markiewicz-Łoskot G. Genetic heterogeneity of left-ventricular noncompaction cardiomyopathy. Clin Cardiol 2008; 31: 201-204.
• 16 Fernandez-Cadenas I, Andreu AL, Gamez J. et al. Splicing mosaic of the myop-hosphorylase gene due to a silent mutation in McArdle disease. Neurology 2003; 61: 1432-1434.
• 17 Cole JW, Stine OC, Liu X. et al. Rare variants in ischaemic stroke: an exome pilot study. PLoS One 2012; 07: e35591.
• 18 Lin H, Sinner MF, Brody JA. et al. CHARGE Atrial Fibrillation Working Group. Targeted sequencing in candidate genes for atrial fibrillation: the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Targeted Sequencing Study. Heart Rhythm 2014; 11: 452-457.
• 19 Thodeti CK, Paruchuri S, Meszaros JG. A TRP to cardiac fibroblast differentiation. Channels 2013; 07: 211-214.
• 20 Nakayama H, Wilkin BJ, Bodi I. et al. Calcineurin-dependent cardiomyopathy is activated by TRPC in the adult mouse heart. FASEB J 2006; 20: 1660-1670.
• 21 Onohara N, Nishida M, Inoue R. et al. TRPC3 and TRPC6 are essential for angiotensin II-induced cardiac hypertrophy. EMBO J 2006; 25: 5305-5316.
• 22 Greiser M, Lederer WJ. Schotten U. Alterations of atrial Ca(2+) handling as cause and consequence of atrial fibrillation. Cardiovasc Res 2011; 89: 722-733.
• 23 Earley S, Heppner TJ, Nelson MT. et al. TRPV4 forms a novel Ca2+ signaling complex with ryanodine receptors and BKCa channels. Circ Res 2005; 97: 1270-1279.