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Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding.

Reschen ME, Gaulton KJ, Lin D, Soilleux EJ, Morris AJ, Smyth SS, O'Callaghan CA - PLoS Genet. (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

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.

No MeSH data available.


Related in: MedlinePlus

Characterization of the dynamic chromatin landscape resulting from oxLDL exposure.(A) Representative chromatin profile at the CD36 locus showing a dynamic chromatin cluster comprising three dynamic chromatin sites; the lower panel close-up view shows the relevant FAIRE-seq signals for macrophages, foam cells and the normalized dynamic signal (foam cell minus macrophage signal). Dynamic sites are highlighted in red boxes and are known DNAse hypersensitivity sites in other cell types in the ENCODE database; one site shows conservation in vertebrates. (B) Heatmap of open chromatin profile at all dynamic chromatin sites, split into panels showing sites with increased or decreased FAIRE-seq signal. Each line represents a 5kb window centered on an individual site. Sites are clustered into groups with similar signal patterns. (C) Dynamic chromatin sites are enriched for non-coding regulatory elements found in 9 other cell types (* p < 0.05, ** p < 0.005, TFBS—transcription factor binding site). (D) Dynamic chromatin clusters are enriched for gene sets involved in foam cell formation and lipid handling.
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pgen.1005061.g003: Characterization of the dynamic chromatin landscape resulting from oxLDL exposure.(A) Representative chromatin profile at the CD36 locus showing a dynamic chromatin cluster comprising three dynamic chromatin sites; the lower panel close-up view shows the relevant FAIRE-seq signals for macrophages, foam cells and the normalized dynamic signal (foam cell minus macrophage signal). Dynamic sites are highlighted in red boxes and are known DNAse hypersensitivity sites in other cell types in the ENCODE database; one site shows conservation in vertebrates. (B) Heatmap of open chromatin profile at all dynamic chromatin sites, split into panels showing sites with increased or decreased FAIRE-seq signal. Each line represents a 5kb window centered on an individual site. Sites are clustered into groups with similar signal patterns. (C) Dynamic chromatin sites are enriched for non-coding regulatory elements found in 9 other cell types (* p < 0.05, ** p < 0.005, TFBS—transcription factor binding site). (D) Dynamic chromatin clusters are enriched for gene sets involved in foam cell formation and lipid handling.

Mentions: All genomic sites with significant oxLDL-induced changes in chromatin profile were identified and termed dynamic chromatin sites (Fig. 3A). OxLDL changed the chromatin profile at around 10% of all open chromatin sites (13,516 sites of which 12,754 (94%) were non-promoter sites (defined as 1kb from a known RefSeq TSS)(S7 Table). 7,276 (54%) of these 13,516 sites had a more nucleosome-depleted profile and 6,240 had a more nucleosome-bound profile in foam cells (Fig. 3B). The size distribution of the dynamic chromatin sites demonstrates that changes at most non-promoter sites involve displacement of a single nucleosome, whereas those at promoter sites may involve displacement of one or two nucleosomes (S3 Fig). Overall, only a fraction of macrophage open chromatin sites, the majority distal to known promoter regions, are changed in response to oxLDL.


Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding.

Reschen ME, Gaulton KJ, Lin D, Soilleux EJ, Morris AJ, Smyth SS, O'Callaghan CA - PLoS Genet. (2015)

Characterization of the dynamic chromatin landscape resulting from oxLDL exposure.(A) Representative chromatin profile at the CD36 locus showing a dynamic chromatin cluster comprising three dynamic chromatin sites; the lower panel close-up view shows the relevant FAIRE-seq signals for macrophages, foam cells and the normalized dynamic signal (foam cell minus macrophage signal). Dynamic sites are highlighted in red boxes and are known DNAse hypersensitivity sites in other cell types in the ENCODE database; one site shows conservation in vertebrates. (B) Heatmap of open chromatin profile at all dynamic chromatin sites, split into panels showing sites with increased or decreased FAIRE-seq signal. Each line represents a 5kb window centered on an individual site. Sites are clustered into groups with similar signal patterns. (C) Dynamic chromatin sites are enriched for non-coding regulatory elements found in 9 other cell types (* p < 0.05, ** p < 0.005, TFBS—transcription factor binding site). (D) Dynamic chromatin clusters are enriched for gene sets involved in foam cell formation and lipid handling.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4383549&req=5

pgen.1005061.g003: Characterization of the dynamic chromatin landscape resulting from oxLDL exposure.(A) Representative chromatin profile at the CD36 locus showing a dynamic chromatin cluster comprising three dynamic chromatin sites; the lower panel close-up view shows the relevant FAIRE-seq signals for macrophages, foam cells and the normalized dynamic signal (foam cell minus macrophage signal). Dynamic sites are highlighted in red boxes and are known DNAse hypersensitivity sites in other cell types in the ENCODE database; one site shows conservation in vertebrates. (B) Heatmap of open chromatin profile at all dynamic chromatin sites, split into panels showing sites with increased or decreased FAIRE-seq signal. Each line represents a 5kb window centered on an individual site. Sites are clustered into groups with similar signal patterns. (C) Dynamic chromatin sites are enriched for non-coding regulatory elements found in 9 other cell types (* p < 0.05, ** p < 0.005, TFBS—transcription factor binding site). (D) Dynamic chromatin clusters are enriched for gene sets involved in foam cell formation and lipid handling.
Mentions: All genomic sites with significant oxLDL-induced changes in chromatin profile were identified and termed dynamic chromatin sites (Fig. 3A). OxLDL changed the chromatin profile at around 10% of all open chromatin sites (13,516 sites of which 12,754 (94%) were non-promoter sites (defined as 1kb from a known RefSeq TSS)(S7 Table). 7,276 (54%) of these 13,516 sites had a more nucleosome-depleted profile and 6,240 had a more nucleosome-bound profile in foam cells (Fig. 3B). The size distribution of the dynamic chromatin sites demonstrates that changes at most non-promoter sites involve displacement of a single nucleosome, whereas those at promoter sites may involve displacement of one or two nucleosomes (S3 Fig). Overall, only a fraction of macrophage open chromatin sites, the majority distal to known promoter regions, are changed in response to oxLDL.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

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.

No MeSH data available.


Related in: MedlinePlus