Lipid-Induced Epigenomic Changes in Human Macrophages Identify a Coronary Artery Disease-Associated Variant that Regulates PPAP2B Expression through Altered C/EBP-Beta Binding

Authors

Michael E. Reschen, University of Oxford, UK
Kyle J. Gaulton, University of Oxford, UK
Da Lin, University of Oxford, UK
Elizabeth J. Soilleux, University of Oxford, UK
Andrew J. Morris, University of KentuckyFollow
Susan S. Smyth, University of KentuckyFollow
Christopher A. O'Callaghan, University of Oxford, UK

Abstract

Genome-wide association studies (GWAS) have identified over 40 loci that affect risk of coronary artery disease (CAD) and the causal mechanisms at the majority of loci are unknown. Recent studies have suggested that many causal GWAS variants influence disease through altered transcriptional regulation in disease-relevant cell types. We explored changes in transcriptional regulation during a key pathophysiological event in CAD, the environmental lipid-induced transformation of macrophages to lipid-laden foam cells. We used a combination of open chromatin mapping with formaldehyde-assisted isolation of regulatory elements (FAIRE-seq) and enhancer and transcription factor mapping using chromatin immuno-precipitation (ChIP-seq) in primary human macrophages before and after exposure to atherogenic oxidized low-density lipoprotein (oxLDL), with resultant foam cell formation. OxLDL-induced foam cell formation was associated with changes in a subset of open chromatin and active enhancer sites that strongly correlated with expression changes of nearby genes. OxLDL-regulated enhancers were enriched for several transcription factors including C/EBP-beta, which has no previously documented role in foam cell formation. OxLDL exposure up-regulated C/EBP-beta expression and increased genomic binding events, most prominently around genes involved in inflammatory response pathways. Variants at CAD-associated loci were significantly and specifically enriched in the subset of chromatin sites altered by oxLDL exposure, including rs72664324 in an oxLDL-induced enhancer at the PPAP2B locus. OxLDL increased C/EBP beta binding to this site and C/EBP beta binding and enhancer activity were stronger with the protective A allele of rs72664324. In addition, expression of the PPAP2B protein product LPP3 was present in foam cells in human atherosclerotic plaques and oxLDL exposure up-regulated LPP3 in macrophages resulting in increased degradation of pro-inflammatory mediators. Our results demonstrate a genetic mechanism contributing to CAD risk at the PPAP2B locus and highlight the value of studying epigenetic changes in disease processes involving pathogenic environmental stimuli.

Document Type

Article

Publication Date

4-2-2015

Notes/Citation Information

Published in PLOS Genetics, v. 11, no. 4, article e1005061, p. 1-33.

© 2015 Reschen et al.

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Digital Object Identifier (DOI)

http://dx.doi.org/10.1371/journal.pgen.1005061

Funding Information

This work was supported by the Wellcome Trust (097089/Z/11/Z), the Medical Research Council (G116/165) and the National Institute for Health Research Oxford Comprehensive Biomedical Research Centre Program. We thank the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Wellcome Trust grant reference 090532/Z/09/Z and MRC Hub grant G0900747 91070) for the generation of the sequencing data. This study was supported by grants from the NIH, American Heart Association and Department of Veterans Affairs and conducted in part using resources provided by the Lexington Veterans Affairs Medical Center. The recruitment of participants from the Oxford Biobank was supported by the NIHR Oxford Biomedical Research Centre and the National NIHR Bioresource. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Repository Citation

Reschen, Michael E.; Gaulton, Kyle J.; Lin, Da; Soilleux, Elizabeth J.; Morris, Andrew J.; Smyth, Susan S.; and O'Callaghan, Christopher A., "Lipid-Induced Epigenomic Changes in Human Macrophages Identify a Coronary Artery Disease-Associated Variant that Regulates PPAP2B Expression through Altered C/EBP-Beta Binding" (2015). Gill Heart & Vascular Institute Faculty Publications. 6.
https://uknowledge.uky.edu/heart_facpub/6