Integrative DNA methylome and transcriptome analysis identify potential genes on the influence of dilated cardiomyopathy-associated heart failure

Figures

• 

  Fig. 1. Cardiac function and pathological manifestations in DCM-HF. A Basic clinical information of the patients. B Echocardiographic functional assessment of hearts from healthy donors and heart transplant recipients with dilated cardiomyopathy-associated heart failure (DCM), including ejection fraction (EF) and left ventricular end-diastolic dimension (LVIDd). Data are presented as means ± SEM (n = 5 samples per group), **P < 0.01; ***P < 0.001. C Masson’s trichrome staining of atrial tissues from donor and recipient hearts. Scale bar = 100 μm

• 

  Fig. 2. RNA-sequencing analysis of atrial tissues from the Donor and Recipient groups. A General workflow used in this study. B Principal Component Analysis (PCA) of mRNA expression profiles in the hearts of donors and recipients. C Volcano plots depicting the distribution of differentially expressed genes (DEGs). D Heatmaps of 681 DEGs with |log2FC|> 1 and FDR < 0.05. (E) Gene Set Enrichment Analysis (GSEA) of expressed genes in Recipient versus Donor. F-G Kyoto Encyclopedia of Genes and Genomes (KEGG) (F, upper) and Gene Ontology (GO)-Biological Process (BP) enrichment (G, lower) of the significantly up- and downregulated DEGs

• 

  Fig. 3. Screening of candidate differentially expressed genes (DEGs) implicated in the pathogenesis of heart failure. A and B The Protein–protein Interaction (PPI) network (A, upper) and the Disease-gene Associations (DISEASES) prediction (B, lower) among the DEGs constructed using the STRING online tool. C Heatmaps of 12 DEGs associated with heart diseases

• 

  Fig. 4. Whole-Genome Bisulfite Sequencing (WGBS) analysis of atrial tissues from the Donor and Recipient groups. A Violin plots showing the global DNA methylation levels of CpG sites in recipient hearts compared to donors. (n = 5 samples per group, ***P < 0.001). B Methylation levels across various genomic functional regions in Recipient versus Donor. C Methylation patterns of the gene body, 2 kb upstream of the transcription start site (TSS) and 2 kb downstream of the transcription end site (TES) in each group. D The ratio of hypermethylated and hypomethylated Differentially Methylated Regions (DMRs) in Recipient versus Donor. E Proportions of DMRs located in different genomic features. F The distribution of DMRs across the whole-genome. G and H GO-BP enrichment (G, left) and KEGG analysis (H, right) of DMR-related Genes (DMGs)

• 

  Fig. 5. Correlation studies of DMRs-related Genes (DMGs) and Differentially Expressed Genes (DEGs). A Heatmaps showing DNA methylation levels of DMRs in promoter regions of Recipient and Donor group. B KEGG enrichment of DMGs in promoter regions. C Venn diagrams displaying the overlap between DEGs and DMGs in promoter regions. D Heatmap depicting the mRNA expression levels of 46 overlapped genes. E GO-BP enrichment of the overlapped genes. (F) 10 screened candidate key genes involved in enriched GO-BP terms. G and H Protein–protein Interaction (PPI) network (G, left) and the GO-BP enrichment (H, right) for the overlapped genes

• 

  Fig. 6. Validation of candidate genes associated with heart failure. A Feature plots of expression distribution for selected genes through Single cell RNA-sequencing (ScRNA-seq) analysis of the human heart cells. B Methylation levels in the promoter regions of the candidate genes. C RT-qPCR validation of the mRNA expression levels in Recipient and Donor groups. D Top20 identified transcription factors within the promoter regions of candidate genes using HOMER. E Candidate transcription factors associated with DCM-HF