H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

BACKGROUND: H3K27ac histone acetylome changes contribute to the phenotypic response in heart diseases, particularly in end-stage heart failure. However, such epigenetic alterations have not been systematically investigated in remodeled non-failing human hearts. Therefore, valuable insight into cardiac dysfunction in early remodeling is lacking. This study aimed to reveal the acetylation changes of chromatin regions in response to myocardial remodeling and their correlations to transcriptional changes of neighboring genes. RESULTS: We detected chromatin regions with differential acetylation activity (DARs; Padj. < 0.05) between remodeled non-failing patient hearts and healthy donor hearts. The acetylation level of the chromatin region correlated with its RNA polymerase II occupancy level and the mRNA expression level of its adjacent gene per sample. Annotated genes from DARs were enriched in disease-related pathways, including fibrosis and cell metabolism regulation. DARs that change in the same direction have a tendency to cluster together, suggesting the well-reorganized chromatin architecture that facilitates the interactions of regulatory domains in response to myocardial remodeling. We further show the differences between the acetylation level and the mRNA expression level of cell-type-specific markers for cardiomyocytes and 11 non-myocyte cell types. Notably, we identified transcriptome factor (TF) binding motifs that were enriched in DARs and defined TFs that were predicted to bind to these motifs. We further showed 64 genes coding for these TFs that were differentially expressed in remodeled myocardium when compared with controls. CONCLUSIONS: Our study reveals extensive novel insight on myocardial remodeling at the DNA regulatory level. Differences between the acetylation level and the transcriptional level of cell-type-specific markers suggest additional mechanism(s) between acetylome and transcriptome. By integrating these two layers of epigenetic profiles, we further provide promising TF-encoding genes that could serve as master regulators of myocardial remodeling. Combined, our findings highlight the important role of chromatin regulatory signatures in understanding disease etiology

Erratum : Exome-wide association study reveals novel susceptibility genes to sporadic dilated cardiomyopathy (PLoS ONE (2017) 12: 3 (e0172995) DOI: 10.1371/journal.pone.0172995)

Publisher Copyright: © 2020 Esslinger 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.Based on experiments conducted since this article's [1] publication, the authors have concluded that the protein-protein interaction results reported in Fig 4 are not reliable. In experiments done after the article was published, the authors observed signals for the negative control indicating that there was unspecific binding to the sepharose beads (S1 File). Furthermore, efforts to replicate the experiment using the transfection/co-immunoprecipitation protocol detailed in the article did not confirm the published results: a specific proteinprotein interaction was not observed in co-immunoprecipitation experiments using native neonate cardiomyocyte extracts (S2 File). Given these findings, the result and conclusion statements referring to a physical interaction between BAG3 and HSPB7 are not supported. Specifically: · The penultimate sentence of the ZBTB17-HSPB7 locus subsection of the Results: "Using GST pull-down experiment and co-immunoprecipitation we also observed that recombinant BAG3 interacts with HSPB7 (Fig 4)." · The fifth sentence of the second paragraph of the Discussion section: "In addition, our in vitro experiments demonstrate a physical interaction of BAG3 with HSPB7 (Fig 4) suggesting functional relationships between the 2 proteins that may be relevant for their genetic implication in DCM pathophysiology." · The seventh sentence of the second paragraph of the Discussion section: "The interaction signal of BAG3 Arg151 and Cys151 isoforms with HSPB7 was similar (data not shown), suggesting no direct effect of the polymorphism on HSPB7 binding." A member of PLOS ONE's Editorial Board confirmed that the main conclusions of the article stand are not substantively affected by this issue. The authors apologize for the errors in the published article. Supporting information S1 File. Results of co-immunoprecipitation experiment conducted in HEK cells, showing non-specific binding cells over-expressing BAG and HSPB7. (PPTX) S2 File. Experimental results of co-immunoprecipitations in native rat neonate cardiomyocytes. (PPTX)

Exome-wide association study reveals novel susceptibility genes to sporadic dilated cardiomyopathy

Aims: Dilated cardiomyopathy (DCM) is an important cause of heart failure with a strong familial component. We performed an exome-wide array-based association study (EWAS) to assess the contribution of missense variants to sporadic DCM. Methods and results: 116,855 single nucleotide variants (SNVs) were analyzed in 2796 DCM patients and 6877 control subjects from 6 populations of European ancestry. We confirmed two previously identified associations with SNVs in BAG3 and ZBTB17 and discovered six novel DCM-associated loci (Q-value<0.01). The lead-SNVs at novel loci are common and located in TTN, SLC39A8, MLIP, FLNC, ALPK3 and FHOD3. In silico fine mapping identified HSPB7 as the most likely candidate at the ZBTB17 locus. Rare variant analysis (MAF<0.01) demonstrated significant association for TTN variants only (P = 0.0085). All candidate genes but one (SLC39A8) exhibit preferential expression in striated muscle tissues and mutations in TTN, BAG3, FLNC and FHOD3 are known to cause familial cardiomyopathy. We also investigated a panel of 48 known cardiomyopathy genes. Collectively, rare (n = 228, P = 0.0033) or common (n = 36, P = 0.019) variants with elevated in silico severity scores were associated with DCM, indicating that the spectrum of genes contributing to sporadic DCM extends beyond those identified here. Conclusion: We identified eight loci independently associated with sporadic DCM. The functions of the best candidate genes at these loci suggest that proteostasis regulation might play a role in DCM pathophysiology

H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

Background: H3K27ac histone acetylome changes contribute to the phenotypic response in heart diseases, particularly in end-stage heart failure. However, such epigenetic alterations have not been systematically investigated in remodeled non-failing human hearts. Therefore, valuable insight into cardiac dysfunction in early remodeling is lacking. This study aimed to reveal the acetylation changes of chromatin regions in response to myocardial remodeling and their correlations to transcriptional changes of neighboring genes. Results: We detected chromatin regions with differential acetylation activity (DARs; P adj. < 0.05) between remodeled non-failing patient hearts and healthy donor hearts. The acetylation level of the chromatin region correlated with its RNA polymerase II occupancy level and the mRNA expression level of its adjacent gene per sample. Annotated genes from DARs were enriched in disease-related pathways, including fibrosis and cell metabolism regulation. DARs that change in the same direction have a tendency to cluster together, suggesting the well-reorganized chromatin architecture that facilitates the interactions of regulatory domains in response to myocardial remodeling. We further show the differences between the acetylation level and the mRNA expression level of cell-type-specific markers for cardiomyocytes and 11 non-myocyte cell types. Notably, we identified transcriptome factor (TF) binding motifs that were enriched in DARs and defined TFs that were predicted to bind to these motifs. We further showed 64 genes coding for these TFs that were differentially expressed in remodeled myocardium when compared with controls. Conclusions: Our study reveals extensive novel insight on myocardial remodeling at the DNA regulatory level. Differences between the acetylation level and the transcriptional level of cell-type-specific markers suggest additional mechanism(s) between acetylome and transcriptome. By integrating these two layers of epigenetic profiles, we further provide promising TF-encoding genes that could serve as master regulators of myocardial remodeling. Combined, our findings highlight the important role of chromatin regulatory signatures in understanding disease etiology

Gene-level association analysis of genes identified in the SNP-level analysis

<p>Gene-level association analysis of genes identified in the SNP-level analysis</p

Additional file 3 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

Additional file 3. Supplementary Figure 3. Correlation plots between H3K27ac ChIP-seq (red) with RNAPII ChIP-seq (blue) and RNA-seq datasets (blue), respectively. Correlations in four control samples (from a to d) used in this study. Gene expression rank is based on RPKM values

Variants associated with DCM.

<p>Variants associated with DCM.</p