Integrated Methylome and Transcriptome Analysis in Chronic Chagas Cardiomyopathy Uncovers Alterations in Heart Development

Figure 1.. DNA methylation analysis. Volcano plots displaying differentially variable positions (DVPs) in the comparisons between (A) chronic Chagas cardiomyopathy (CCC) patients versus asymptomatic (ASY) individuals and (B) severe CCC (Kuschnir 3, K3) versus ASY. The x-axis represents the difference in methylation variability as the logarithm of the var ratio, while the y-axis shows the significance level (−log10(P-value)). C, Gene ontology (GO) enrichment analysis for DVPs showing the top 15 most significant terms. The scale indicates the number of DVPs associated with each term. D, GO enrichment analysis of differentially methylated positions (DMPs) identified through meta-analysis. Points correspond to enriched pathways from the comparison of severe CCC versus ASY and the CCC versus ASY comparison. FDR, Benjamini–Hochberg false discovery rate; Var Ratio, ratio of the absolute deviation of methylation values.

Figure 2.. Gene expression and expression quantitative trait methylation (eQTM) analyses. A, Box plots showing the gene expression levels of the differentially expressed genes GATA5, ALPK2, and TRBV11-2 from the comparison between Kuschnir 3 (K3) and asymptomatic (ASY) patients. B, Gene ontology (GO) enrichment analysis eQTM genes obtained from the comparison between K3 and ASY patients. The scale represents the number of significant genes included in each biological pathway. C, Scatter plot illustrating the significant correlation between cg03945807 methylation levels in the x-axis and GATA5 gene expression in the y-axis. Each dot represents an individual, separated by group classification. TMM, trimmed mean of M-values of gene expression; RPKM, reads per kilobase per million mapped reads; β, DNA methylation beta values.

Figure 3.. Results from the transcription factor (TF) analysis. A, Table presenting the TF binding site enrichment analysis for differentially variably methylated positions (DVPs) in the comparison between Kuschnir 3 (K3) and asymptomatic (ASY) individuals. The “target sequences with motifs” column represents the proportion of DVPs overlapping a given binding site, while the “background sequences” column indicates the proportion of all analyzed CpGs overlapping that motif. COUP-TFII was highlighted in bold due to its relevance in the manuscript discussion. B, Two-sided barplot displaying the top 15 TFs with increased activity and the top 5 with decreased activity, scaled by −log10(P-value). GATA5 was highlighted in bold given its relevance in the discussion. C, Volcano plot of all analyzed transcription factors, with those overlapping findings from Brochet et al. specifically highlighted. The x-axis represents the activity score and the y-axis the −log10(P-value). D, Scatter plot showing the correlation between TF activity levels identified in this study and those obtained from heart tissue data from Brochet et al. The mean transcription factor activity score from both studies is…