title: Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding.
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.
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Reschen
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Kyle J
authors.initials: KJ
authors.lastname: Gaulton
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Da
authors.initials: D
authors.lastname: Lin
authors.affiliation: Nuffield Department of Clinical Laboratory Sciences, University of Oxford and Department of Cellular Pathology, John Radcliffe Hospital, Oxford, United Kingdom.
authors.forename: Elizabeth J
authors.initials: EJ
authors.lastname: Soilleux
authors.affiliation: Division of Cardiovascular Medicine, The Gill Heart Institute, University of Kentucky, Lexington, Kentucky, United States of America; Department of Veterans Affairs Medical Center, Lexington, Kentucky, United States of America.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Morris
authors.affiliation: Division of Cardiovascular Medicine, The Gill Heart Institute, University of Kentucky, Lexington, Kentucky, United States of America; Department of Veterans Affairs Medical Center, Lexington, Kentucky, United States of America.
authors.forename: Susan S
authors.initials: SS
authors.lastname: Smyth
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: O'Callaghan
mesh_terms: D022782:CCAAT-Enhancer-Binding Protein-beta / Q000378:metabolism*; D002478:Cells, Cultured; D003324:Coronary Artery Disease / Q000235:genetics*; D044127:Epigenesis, Genetic; D005487:Foam Cells / Q000187:drug effects / Q000378:metabolism*; D056426:Genetic Loci; D006801:Humans; D008077:Lipoproteins, LDL / Q000494:pharmacology; D010711:Phosphatidate Phosphatase / Q000235:genetics / Q000378:metabolism*; D058226:Plaque, Atherosclerotic / Q000235:genetics / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding
chemical_list: D022782:CCAAT-Enhancer-Binding Protein-beta; C545012:CEBPB protein, human; D008077:Lipoproteins, LDL; C521833:PLPP3 protein, human; D010711:Phosphatidate Phosphatase
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