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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)1,2,3,4 and type 2 diabetes5,6,7. Despite evidence for a role of the associated interval in neighbouring gene regulation8,9,10, 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.

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Figure 1: Functional annotation of the 9p21 interval.
Figure 2: Linkage disequilibrium analysis of the 9p21 interval.
Figure 3: In vivo effects of the ECAD9 variants.
Figure 4: Long-range interaction with the enhancer locus.

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Acknowledgements

We thank X. Wang, K. Trevarthen and M. Nakano for experimental assistance. We thank the Scripps Genomic Medicine Clinical team for sample collection. This work was partially supported by National Center for Research Resources grants 1U54RR025204, 1UL1RR025774 and 1UL1RR031980-01 and National Institutes of Health grants HL065445, DK39949, DK018477, DK074868, L65445, CA97134, DK74686, NS34934 and 1R21CA152613-01, the Department of Defence grant BC075019 and the Prostate Cancer Foundation. M.G.R. is an Investigator with the Howard Hughes Medical Institute.

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Contributions

O.H., D.N., B.R., E.J.T., K.A.F. and M.G.R. designed the experiments. D.N., X.S., N.G.R., N.H. and X.-D.F. carried out the experiments. O.H., D.N., X.S., B.T., K.A.F. and M.G.R. contributed to analysing the data. O.H., D.N., K.A.F. and M.G.R. wrote the manuscript.

Corresponding authors

Correspondence to Eric J. Topol, Michael G. Rosenfeld or Kelly A. Frazer.

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Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-6 with legends, Supplementary Tables 1-16, Supplementary Methods and additional references. (PDF 4253 kb)

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Harismendy, O., Notani, D., Song, X. et al. 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature 470, 264–268 (2011). https://doi.org/10.1038/nature09753

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