Transcriptomic Analysis of Cardiac Tissues in a Rodent Model of Coronary Microembolization

Abstract

Purpose: Coronary microembolization (CME) can result in cardiac dysfunction, severe arrhythmias, and a reduced coronary flow reserve. Impairment of mitochondrial energy metabolism has been implicated in the progression and pathogenesis of CME; however, its role remains largely undetermined. This study aimed to explore alterations in mitochondria-related genes in CME.

Methods: A rat model of CME was successfully established by injecting plastic microspheres into the left ventricle. The cardiac tissues of the two groups were sequenced and mitochondrial functions were assessed.

Results: Using RNA-Seq, together with GO and KEGG enrichment analyses, we identified 3822 differentially expressed genes (DEGs) in CME rats compared to control rats, and 101 DEGs were mitochondria-related genes. Notably, 36 DEGs were up-regulated and 65 DEGs were down-regulated (CME vs control). In particular, the oxidative phosphorylation (OXPHOS) and mitochondrial electron transport were obviously down-regulated in the CME group. Functional analysis revealed that CME mice exhibited marked reductions in ATP and mitochondrial membrane potential (MMP), by contrast, the production of reactive oxygen species (ROS) was much higher in CME mice than in controls. Protein-protein interaction (PPI) and quantitative PCR (qPCR) validation suggested that eight hub genes including Cmpk2, Isg15, Acsl1, Etfb, Ndufa8, Adhfe1, Gabarapl1 and Acot13 were down-regulated in CME, whereas Aldh18a1 and Hspa5 were up-regulated.

Conclusion: Our findings suggest that dysfunctions in mitochondrial activity and metabolism are important mechanisms for CME, and mitochondria-related DEGs may be potential therapeutic targets for CME.

Keywords: CME; DEGs; OXPHOS; RNA-Sequence; energy metabolism; rat model.

Figure 1

HE staining of myocardial tissues from CME and control groups, arrows indicate the microspheres.

Figure 2

The representative images of ultrastructural changes in mice microvascular from CME and control groups observed under TEM.

Figure 3

The images of ultrastructural changes in mice cardiomyocyte from CME and control groups observed under TEM.

Figure 4

(A). Number of upregulated and downregulated genes in CME rats. (B). Volcano plot of ten mitochondrial-related DEGs, blue dots indicate the downregulated genes, red dots suggest the upregulated genes. (C). A PCA plot for six samples enrolled in RNA-Seq analyses.

Figure 5

Identification of DEGs in CME, GO enrichment analysis of 101 mitochondria-related DEGs are shown in three functional groups: (A). Biological processes of DEGs; (B). Cellular component of DEGs; (C). Molecular function of DEGs.

Figure 6

Enrichment analysis of different DEGs in control and CME group. (A). KEGG pathway enrichment analysis; (B). GSEA functional enrichment analysis of OXPHOS signaling pathway.

Figure 7

Heatmap of 101 mitochondria-related DEGs in two groups. c: control group, m: CME group.

Figure 8

PPI network of mitochondria-related DEGs by using cytoHubba software, the inner circle shows the top 10 high scoring hub genes in CME progression.

Figure 9

Results of qPCR for the mRNA levels of Aldh18a1, Cmpk2, Isg15, Acsl1, Etfb, Hspa5, Ndufa8, Adhfe1, Gabarapl1 and Acot13 in CME and control groups.

Figure 10

Analysis of mitochondrial functions in CME and control groups. (A). MMP analysis; (B). determining the ATP level; (C). ROS analysis.