miRNA Regulatory Networks Associated with Peripheral Vascular Diseases

Abstract

A growing body of evidence indicates a crucial role of miRNA regulatory function in a variety of mechanisms that contribute to the development of diseases. In our previous work, alterations in miRNA expression levels and targeted genes were shown in peripheral blood mononuclear cells (PBMCs) from patients with lower extremity artery disease (LEAD), abdominal aortic aneurysm (AAA), and chronic venous disease (CVD) in comparison with healthy controls. In this paper, previously obtained miRNA expression profiles were compared between the LEAD, AAA, and CVD groups to find either similarities or differences within the studied diseases. Differentially expressed miRNAs were identified using the DESeq2 method implemented in the R programming software. Pairwise comparisons (LEAD vs. AAA, LEAD vs. CVD, and AAA vs. CVD) were performed and revealed 10, 8, and 17 differentially expressed miRNA transcripts, respectively. The functional analysis of the obtained miRNAs was conducted using the miRNet 2.0 online tool and disclosed associations with inflammation and cellular differentiation, motility, and death. The miRNet 2.0 tool was also used to identify regulatory interactions between dysregulated miRNAs and target genes in patients with LEAD, AAA, and CVD. The presented research provides new information about similarities and differences in the miRNA-dependent regulatory mechanisms involved in the pathogenesis of LEAD, AAA, and CVD.

Keywords: abdominal aortic aneurysm; chronic venous disease; lower extremity artery disease; miRNA; miRNA expression; next-generation sequencing.

Figure 1

The comparison of the sets of differentially expressed miRNA transcripts selected from pairwise comparative analysis performed among the LEAD, AAA, and CVD groups using DESeq2 method. (A) The comparison of the sets of miRNA transcripts selected from LEAD vs. CVD, LEAD vs. AAA, and AAA vs. CVD comparisons using the following selection criteria: p-value < 0.05, absolute log2 fold change > 1, and mean of normalized counts > 10. The number in the intersection fields of the Venn diagram represents the number of miRNA transcripts common to the comparisons. The frames below the Venn diagram include six miRNAs common for AAA vs. CVD and LEAD vs. CVD comparisons and one miRNA common for LEAD vs. CVD and LEAD vs. AAA comparisons. (B) Heatmap of the expression of 28 miRNA transcripts selected from LEAD vs. AAA, LEAD vs. CVD, and AAA vs. CVD comparisons and included in the Venn diagram in panel A. Hierarchical clustering was performed using the average method applied to Euclidean distances. AAA—abdominal aortic aneurysm, CVD—chronic venous disease, LEAD—lower extremity artery disease.

Figure 2

The functional network of miRNAs selected from pairwise comparisons among the LEAD, AAA, and CVD groups. (A) Network for miRNAs selected from the LEAD vs. AAA comparison. (B) Network for miRNAs selected from the LEAD vs. CVD comparison. (C) Network for miRNAs selected from the AAA vs. CVD comparison. Each panel presents the top 15 most enriched functional terms (with the lowest p-value of enrichment) of ‘miRNA Function’ category in the miRNet 2.0 tool as well as associated miRNAs. AAA—abdominal aortic aneurysm, CVD—chronic venous disease, LEAD—lower extremity artery disease.

Figure 3

The regulatory network containing miRNAs selected in the current study and genes selected from a previous study [47] regarding (A) LEAD vs. AAA comparison, (B) AAA vs. CVD comparison, and (C) LEAD vs. CVD comparison. AAA—abdominal aortic aneurysm, CVD—chronic venous disease, LEAD—lower extremity artery disease.