Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction

Figures

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  Figure 1. Gene expression profiles of left ventricle tissues discriminate HFpEF proxy from Normal physiology. (A) Stack barplot showing uniquely mapped, multiple mapped and unmapped reads. The x axis shows the samples and the y axis the number of reads. (B) Bar plot showing the relative abundance of each biotype (y axis) in the samples (x axis). (C) Principal component analysis (PCA) score plot with the two principal components (PC1 and PC2) plotted on the x- and y-axis, respectively. Each data point represents one sample, which is colour-coded according to the condition and shaped according to the sequencing batch. Green and orange colours correspond to Normal physiology and HFpEF proxy, respectively. (D) Orthogonal projections to latent structures discriminant analysis (OPLS-DA) score plot for the groups HFpEF proxy (orange) and Normal physiology (green). (E) S-plot of the OPLS-DA data showing the magnitude of each gene’s contribution to the separation, p[1], in relationship to its significance, p(corr)[1]. Genes contributing to the highest magnitude of the separation for the respective groups are highlighted in red/orange. Shaded boxes indicate up-regulated genes in the HFpEF proxy…

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  Figure 2. Identification and annotation of the dysregulated genes in HFpEF proxy versus Normal physiology. (A) Bar plot showing number of differentially expressed genes between HFpEF proxy and Normal physiology predicted using NOISeq with false discovery rate (FDR) adjusted p-value < 0.05. The x axis represents significantly dysregulated genes and the y axis showing the fold change in log2 scale of the corresponding genes. Down-regulated genes in blue and up-regulated genes in orange. (B) Volcano plot of the differentially expressed genes. The x axis represents fold change in log2 scale of HFpEF proxy versus Normal physiology while the y axis indicates the differences of mean expression between HFpEF proxy and Normal physiology. Each point represents a gene, and significantly expressed genes are highlighted in green. Genes that are significantly expressed (FDR-adjusted p-value < 0.05) and with a difference of mean expression above 3.5 are labelled with gene symbols. (C) Similar to plot “A”, but FDR-adjusted p-value < 0.1. (D) Similar to plot “B” but FDR-adjusted p-value < 0.1. Genes that are significantly expressed and with a difference of mean expression above 3.7 are labelled with gene…

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  Figure 3. Functional classification of the differentially expressed genes. (A,B) GO annotations of biological process and molecular function, respectively, of the down-regulated genes in HFpEF proxy group. The horizontal bars show percentage of the down-regulated genes with the corresponding GO annotations (scale at bottom x axis), The orange lines represent significance of the corresponding GO annotations (scale at top x axis) as calculated by Enrichr53.

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  Figure 4. Predicted upstream regulators and gene expression of their regulomes. (A) Bar plot showing activation or inhibition scores of the upstream regulators. Transcription factors are highlighted in red. (B–F) Heat maps showing the expression profiles of the genes regulated by predicted transcription factors from A. Additional heat maps are shown in Supplementary Fig. S3. Samples in the HFpEF proxy group are coloured orange in Condition, and samples in the Normal physiology group are coloured green. The regulators genes were identified using IPA. Patient numbers and conditions are shown at the bottom of each heatmap.

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  Figure 5. Transcription factor regulatory effect network identified using Ingenuity Pathway Analysis (IPA). In the network nodes, the upper panel shows transcription factors, the middle panel shows differentially expressed genes, and the lower panel shows biological functions and diseases. For the network edges, a solid line indicates direct interaction, while a dashed line indicate indirect interaction. Node colours in upper and lower panels: predicted activation in orange; predicted inhibition in blue. Node colours in middle panel: downregulated in data set coloured green; upregulated in data set coloured red (not represented in this network). Edge colours; predicted activation in orange; predicted inhibition in blue, findings inconsistent with state of downstream node in yellow; effect not predicted in grey.

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  Figure 6. Schematic summary of the current study. Cardiac biopsies from CABG patients were submitted to RNA sequencing to detect differentially expressed genes between HFpEF and Normal. These differentially expressed genes were characterised using gene ontology and predicted transcription factor regulatory effect network.