Pathological Change and Whole Transcriptome Alternation Caused by ePTFE Implantation in Myocardium

Figures

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  Figure 1. ePTFE implantation induces myocardial tissue injury. (a) HE staining displayed myocardial tissue swelling (red arrows), cell degeneration (green arrows), and inflammatory infiltrates (black arrows) in the ePTFE and sham groups; Masson's trichrome staining exhibited fibrosis in myocardial tissues (blue staining with yellow arrows). Scale bar = 50 μm. (b) The degree of fibrosis in individual groups of rabbits. ∗P < 0.05.

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  Figure 2. Bioinformatic analyses of DEmRNAs. The distribution of DEmRNAs in the (a) ePTFE-control comparison or the (b) sham-control comparison was analyzed by a volcano plot. Vertical lines indicate 2-fold changes in upregulation or downregulation, and the horizontal line represents P = 0.05; red dots refer to upregulated mRNAs, and blue points refer to downregulated mRNAs. (c) The numbers of specific and overlapped DEmRNAs from the ePTFE-control and sham-control comparisons are presented by Venn diagrams. (d) The expression patterns of the corresponding DEmRNAs are exhibited by heatmaps. Red color indicates high expression and blue indicates low expression.

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  Figure 3. The features of lncRNAs. (a) Venn diagrams displayed lncRNA transcripts from CPC, CNCI, Pfam, and PLEK. (b) The numbers of different types of lncRNAs. (c) The length distribution of lncRNAs. (d) The number of exons per lncRNA.

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  Figure 4. Bioinformatic analysis of DElncRNAs. The distribution of DElncRNAs in the (a) ePTFE-control comparison or the (b) sham-control comparison was analyzed by a volcano plot. Vertical lines indicate 2-fold changes in upregulation or downregulation, and the horizontal line represents P = 0.05; red dots refer to upregulated mRNAs, and blue points refer to downregulated mRNAs. (c) The numbers of specific and overlapped DElncRNAs from the ePTFE-control and sham-control comparisons are presented by Venn diagrams. (d) The expression patterns of the corresponding DElncRNAs are exhibited by heatmaps. Red color indicates high expression and blue indicates low expression.

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  Figure 5. Circos plot displays the distribution of DEmRNAs and DElncRNAs on chromosomes. The distribution of DEmRNAs and DElncRNAs from the (a) ePTFE-control and (b) sham-control comparisons is exhibited by the Circos plot. The outermost circle is the distribution diagram of chromosomes. The second circle is the distribution of DElncRNAs on chromosomes, and the third circle is the histogram of DElncRNAs at different positions. The fourth circle is the distribution of DEmRNAs on chromosomes, and the innermost circle is the histogram of DEmRNAs at different positions. The higher the column, the higher the number of different genes. The red and green indicate the upregulated and downregulated genes, respectively.

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  Figure 6. Quantitative RT-PCR validates the altered levels of some DEmRNAs and lncRNAs. The expression levels of selected (a) DEmRNAs and (b) DElncRNAs in myocardial tissues form the ePTFE and sham groups were validated by RT-qPCR. Their expression levels were compared with the data from RNA-seq.

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  Figure 7. GO enrichment analysis of DEmRNAs in the ePTFE-control comparison. (a) The upregulated DEmRNAs. (b) The downregulated DEmRNAs. Data are the top 6 terms (according to P value) in the GO terms of BP, CC, and MF.

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  Figure 8. KEGG level 2 analysis of DEmRNAs in the ePTFE-control comparison. (a) The upregulated DEmRNAs. (b) The downregulated DEmRNAs.

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  Figure 9. KEGG level 3 analysis of DEmRNAs in the ePTFE-control comparison. (a) The upregulated DEmRNAs. (b) The downregulated DEmRNAs. Data are presented as the sized bubbles as the number of enriched mRNAs in the top 20 pathways. The colors indicate variable P values and positions indicate enrichment factors.

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  Figure 10. A diagram illustrates the key molecular signal pathways affected by ePTFE implantation. Bold lines indicate direct interaction, and dotted lines indicate indirect interaction. The upregulated genes are highlighted in red while the downregulated genes are shown in green. Yellow indicates both upregulated and downregulated genes.

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  Figure 11. lncRNA-mRNA cis-regulation network. The lncRNA-mRNA cis-regulation networks were established based on the GO term of immune response and extracellular matrix (marked with black star).

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  Figure 12. lncRNA-mRNA trans-regulation network. The lncRNA-mRNA trans-regulation networks were established based on the GO term of (a) immune response and (b) extracellular matrix.