Functional Analysis of a Carotid Intima-Media Thickness Locus Implicates BCAR1 and Suggests a Causal Variant

Freya Boardman-Pretty; Andrew J P Smith; Jackie Cooper; Jutta Palmen; Lasse Folkersen; Anders Hamsten; Alberico L Catapano; Olle Melander; Jacqueline F Price; Meena Kumari; John E Deanfield; Mika Kivimäki; Karl Gertow; Andrea Baragetti; Giuseppe Danilo Norata; Steve E Humphries

doi:10.1161/CIRCGENETICS.115.001062

Functional Analysis of a Carotid Intima-Media Thickness Locus Implicates BCAR1 and Suggests a Causal Variant

Circ Cardiovasc Genet. 2015 Oct;8(5):696-706. doi: 10.1161/CIRCGENETICS.115.001062. Epub 2015 Aug 14.

Authors

Freya Boardman-Pretty¹, Andrew J P Smith², Jackie Cooper², Jutta Palmen², Lasse Folkersen², Anders Hamsten², Alberico L Catapano², Olle Melander², Jacqueline F Price², Meena Kumari², John E Deanfield², Mika Kivimäki², Karl Gertow², Andrea Baragetti², Giuseppe Danilo Norata², Steve E Humphries²

Affiliations

¹ From the Centre for Cardiovascular Genetics, Institute of Cardiovascular Sciences (F.B.-P., A.J.P.S., J.C., J.P., S.E.H.), National Centre for Cardiovascular Prevention and Outcomes Institute of Cardiovascular Science (J.E.D.), Department of Epidemiology and Public Health (M. Kumari, M. Kivimäki), University College London, London, United Kingdom; Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark (L.F.); Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden (L.F., A.H., K.G.); Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, University of Milan, Milan, Italy (A.L.C., A.B., G.D.N.); IRCCS Multimedica, Milan, Italy (A.L.C.); Department of Clinical Sciences, Lund University, Malmö, Sweden (O.M.); The Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, United Kingdom (J.F.P.); Institute for Social and Economic Research, University of Essex, Colchester, United Kingdom (M. Kumari); and SISA Center for the Study of Atherosclerosis, Bassini Hospital, Cinisello Balsamo, Italy (G.D.N., A.B.) f.boardman-pretty.10@ucl.ac.uk.
² From the Centre for Cardiovascular Genetics, Institute of Cardiovascular Sciences (F.B.-P., A.J.P.S., J.C., J.P., S.E.H.), National Centre for Cardiovascular Prevention and Outcomes Institute of Cardiovascular Science (J.E.D.), Department of Epidemiology and Public Health (M. Kumari, M. Kivimäki), University College London, London, United Kingdom; Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark (L.F.); Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden (L.F., A.H., K.G.); Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, University of Milan, Milan, Italy (A.L.C., A.B., G.D.N.); IRCCS Multimedica, Milan, Italy (A.L.C.); Department of Clinical Sciences, Lund University, Malmö, Sweden (O.M.); The Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, United Kingdom (J.F.P.); Institute for Social and Economic Research, University of Essex, Colchester, United Kingdom (M. Kumari); and SISA Center for the Study of Atherosclerosis, Bassini Hospital, Cinisello Balsamo, Italy (G.D.N., A.B.).

PMID: 26276885
DOI: 10.1161/CIRCGENETICS.115.001062

Abstract

Background: Carotid intima-media thickness (IMT) is a marker of subclinical atherosclerosis that can predict cardiovascular disease events over traditional risk factors. This study examined the BCAR1-CFDP1-TMEM170A locus on chromosome 16, associated with carotid IMT and coronary artery disease in the IMT and IMT-Progression as Predictors of Vascular Events (IMPROVE) cohort, to identify the functional variant.

Methods and results: In analysis of the locus lead single nucleotide polymorphism (SNP; rs4888378, intronic in CFDP1) in Progressione della Lesione Intimale Carotidea (PLIC), the protective AA genotype was associated with slower IMT progression in women (P=0.04) but not in men. Meta-analysis of 5 cohort studies also supported a protective effect of the A allele on common carotid IMT in women only (women: β=-0.0047, P=1.63 × 10(-4); men: β=-0.0029, P=0.0678). Two hundred fourteen noncoding variants in strong linkage disequilibrium (r(2) ≥ 0.8) with rs4888378 were identified from 1000 Genome Project. ENCODE regulatory chromatin marks were used to create a shortlist of 6 possible regulatory variants. Electrophoretic mobility shift assays on the shortlist detected allele-specific protein binding to the lead SNP rs4888378; multiplexed competitor electrophoretic mobility shift assays implicated FOXA as the protein. Luciferase reporter assays on rs4888378 showed a significant 35% to 92% (P=0.0057; P=4.0 × 10(-22)) decrease in gene expression with the A allele. Expression quantitative trait loci analysis confirmed previously reported associations of rs4888378 with BCAR1 in vascular tissues.

Conclusions: Molecular studies suggest the lead SNP as a potentially causal SNP at the BCAR1-CFDP1-TMEM170A locus, and expression quantitative trait loci studies implicate BCAR1 as the causal gene. This variant showed stronger effects on common carotid IMT in women, raising questions about the mechanism of the causal SNP on atherosclerosis.

Keywords: atherosclerosis; carotid intima-media thickness; coronary artery disease; genetics; polymorphism, single nucleotide.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.

MeSH terms

Aged
Atherosclerosis / genetics*
Carotid Intima-Media Thickness*
Cell Line, Tumor
Chromosomes, Human, Pair 16
Cohort Studies
Computational Biology
Coronary Artery Disease / genetics*
Crk-Associated Substrate Protein / genetics*
DNA / metabolism
DNA-Binding Proteins / metabolism
Disease Progression
Female
Gene Expression
Genes, Reporter
Humans
Male
Middle Aged
Polymorphism, Single Nucleotide
Prospective Studies
Quantitative Trait Loci
Risk Factors
Sex Factors

Substances

BCAR1 protein, human
Crk-Associated Substrate Protein
DNA-Binding Proteins
DNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding