title: 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response.
abstract: Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) in the 9p21 gene desert associated with coronary artery disease (CAD) and type 2 diabetes. Despite evidence for a role of the associated interval in neighbouring gene regulation, the biological underpinnings of these genetic associations with CAD or type 2 diabetes have not yet been explained. Here we identify 33 enhancers in 9p21; the interval is the second densest gene desert for predicted enhancers and six times denser than the whole genome (P < 6.55 × 10(-33)). The CAD risk alleles of SNPs rs10811656 and rs10757278 are located in one of these enhancers and disrupt a binding site for STAT1. Lymphoblastoid cell lines homozygous for the CAD risk haplotype show no binding of STAT1, and in lymphoblastoid cell lines homozygous for the CAD non-risk haplotype, binding of STAT1 inhibits CDKN2BAS (also known as CDKN2B-AS1) expression, which is reversed by short interfering RNA knockdown of STAT1. Using a new, open-ended approach to detect long-distance interactions, we find that in human vascular endothelial cells the enhancer interval containing the CAD locus physically interacts with the CDKN2A/B locus, the MTAP gene and an interval downstream of IFNA21. In human vascular endothelial cells, interferon-γ activation strongly affects the structure of the chromatin and the transcriptional regulation in the 9p21 locus, including STAT1-binding, long-range enhancer interactions and altered expression of neighbouring genes. Our findings establish a link between CAD genetic susceptibility and the response to inflammatory signalling in a vascular cell type and thus demonstrate the utility of genome-wide association study findings in directing studies to novel genomic loci and biological processes important for disease aetiology.
authors.affiliation: Department of Pediatrics and Rady's Children's Hospital, University of California at San Diego, School of Medicine, La Jolla, California 92093, USA.
authors.forename: Olivier
authors.initials: O
authors.lastname: Harismendy
authors.forename: Dimple
authors.initials: D
authors.lastname: Notani
authors.forename: Xiaoyuan
authors.initials: X
authors.lastname: Song
authors.forename: Nazli G
authors.initials: NG
authors.lastname: Rahim
authors.forename: Bogdan
authors.initials: B
authors.lastname: Tanasa
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Heintzman
authors.forename: Bing
authors.initials: B
authors.lastname: Ren
authors.forename: Xiang-Dong
authors.initials: XD
authors.lastname: Fu
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Topol
authors.forename: Michael G
authors.initials: MG
authors.lastname: Rosenfeld
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Frazer
mesh_terms: D000483:Alleles; D002460:Cell Line; D002843:Chromatin / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D002899:Chromosomes, Human, Pair 9 / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D003324:Coronary Artery Disease / Q000235:genetics*; D050762:Cyclin-Dependent Kinase Inhibitor p15 / Q000235:genetics; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics; D042783:Endothelial Cells / Q000187:drug effects / Q000378:metabolism; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D005786:Gene Expression Regulation / Q000187:drug effects / Q000235:genetics; D055785:Gene Knockdown Techniques; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D006239:Haplotypes / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D016898:Interferon-alpha / Q000235:genetics; D007371:Interferon-gamma / Q000494:pharmacology*; D015810:Linkage Disequilibrium; D008297:Male; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011485:Protein Binding / Q000187:drug effects; D011683:Purine-Nucleoside Phosphorylase / Q000235:genetics; D050794:STAT1 Transcription Factor / Q000096:biosynthesis / Q000172:deficiency / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000187:drug effects*; D044465:White People / Q000235:genetics
chemical_list: C493966:CDKN2B protein, human; D002843:Chromatin; D050762:Cyclin-Dependent Kinase Inhibitor p15; C554326:IFNA21 protein, human; D016898:Interferon-alpha; D050794:STAT1 Transcription Factor; C494079:STAT1 protein, human; D007371:Interferon-gamma; D011683:Purine-Nucleoside Phosphorylase; C021784:5'-methylthioadenosine phosphorylase