Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype

Abstract

Rationale: Identifying genetic markers for heterogeneous complex diseases such as heart failure is challenging, and requires prohibitively large cohort sizes in genome-wide association studies (GWAS) in order to meet the stringent threshold of genome-wide statistical significance. On the other hand, chromatin quantitative trait loci (QTL), elucidated by direct epigenetic profiling of specific human tissues, may contribute towards prioritising sub-threshold variants for disease-association. Objective: Here, we captured non-coding genetic variants by performing epigenetic profiling for enhancer H3K27ac ChIP-seq in 70 human control and end-stage failing hearts. Methods and Results: We have mapped a comprehensive catalogue of 47,321 putative human heart enhancers and promoters. 3,897 differential acetylation peaks (FDR 5%) pointed to pathways altered in heart failure (HF). To identify cardiac histone acetylation QTLs (haQTLs), we regressed out confounding factors including HF disease status, and employed the G-SCI test1 to call out 1,680 haQTLs (FDR 10%). RNA-seq performed on the same heart samples proved a subset of haQTLs to have significant association also to gene expression (expression QTLs), either in cis (180), or through long range interactions (81), identified by Hi-C and HiChIP performed on a subset of hearts. Furthermore, a concordant relationship between the gain or disruption of transcription factor (TF) binding motifs, inferred from alternative alleles at the haQTLs, implied a surprising direct association between these specific TF and local histone acetylation in human hearts. Finally, 62 unique loci were identified by colocalisation of haQTLs with the sub-threshold loci of heart-related GWAS datasets. Conclusions: Disease and phenotype-association for 62 unique loci are now implicated. These loci may indeed mediated their effect through modification of enhancer H3K27-acetylation enrichment and their corresponding gene expression differences.

Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association

“…Recent large-scale studies profiling the H3K27ac histone modification in human hearts have uncovered candidate enhancers associated with heart failure 14,16 . However, because these studies either examined heterogeneous bulk heart tissue 14,16 or focused solely on enriched cardiomyocytes 15 , it remains unclear what role, if any, additional cardiac cell types and cCREs may contribute to heart failure pathogenesis.…”

“…Recent large-scale studies profiling the H3K27ac histone modification in human hearts have uncovered candidate enhancers associated with heart failure 14,16 . However, because these studies either examined heterogeneous bulk heart tissue 14,16 or focused solely on enriched cardiomyocytes 15 , it remains unclear what role, if any, additional cardiac cell types and cCREs may contribute to heart failure pathogenesis. Using our cell atlas of cardiac cCREs, we revealed the cell type specificity of candidate enhancers showing differential H3K27ac signal strength between human hearts from healthy donors and donors with dilated cardiomyopathy (heart failure) 14 (Figure 4, Supplemental Figure VII).…”

“…in a broad spectrum of human tissues including in bulk heart tissues and in purified cardiomyocytes [2][3][4][12][13][14][15] . These maps have provided important insights into dynamic gene regulation during heart failure [14][15][16] and begun to shed light on the function of non-coding cardiovascular disease variants 7,12,15 . However, major limitations of these studies including their focus on particular chambers/regions of the heart and failure to interrogate cis-regulatory elements across all distinct cardiac cell types, have restricted their utility in understanding how specific gene regulatory mechanisms may impact distinct cell types and regions of human hearts in health and disease.…”

“…However, major limitations of these studies including their focus on particular chambers/regions of the heart and failure to interrogate cis-regulatory elements across all distinct cardiac cell types, have restricted their utility in understanding how specific gene regulatory mechanisms may impact distinct cell types and regions of human hearts in health and disease. Although recent single cell genomic tools provide the opportunity to interrogate cis-regulatory elements at single cell resolution [16][17][18][19][20] , their application to mammalian hearts has been limited to a few adult and fetal mouse hearts 20,21 . Thus, to comprehensively investigate cis-regulatory elements in the specific cell types of the human heart, we profiled chromatin accessibility in ~80,000 heart cells using single nucleus ATAC-seq (snATAC-seq) 17,18 and created a comprehensive cardiac cell atlas of cCREs annotated by cell type and putative target genes.…”

Cardiac cell type–specific gene regulatory programs and disease risk association

“…cCREs have been annotated in the human genome with the use of chromatin immunoprecipitation sequencing (ChIP-seq), deoxyribonuclease sequencing (DNase-seq), assay for transposaseaccessible chromatin using sequencing (ATAC-seq), global run-on sequencing, etc. in a broad spectrum of human tissues including in bulk heart tissues and in purified cardiomyocytes (2)(3)(4)(5)(13)(14)(15)(16)(17)(18). These maps have provided important insights into dynamic gene regulation during heart failure (15,16,18) and begun to shed light on the function of noncoding cardiovascular disease variants (8,13,16,18,19).…”