Screening of specific microRNAs and bioinformatics analysis on cardiomyocytes in rat with heart failure

Objective To investigate microRNAs (miRNAs) expression profiling of cardiomyocytes in rats with heart failure, and predict miRNAs-regulated target genes and their functions. Methods Total of 18 male SD rats weighing 200-220 g were randomly divided into 2 groups: the control group (CON) and the heart failure group (HF). The rats in HF group were injected by adriamycin via tail vein to induce heart failure, meanwhile in CON group, rats were received an equal volume of 0.9% sodium chloride intravenously. The cardiomyocytes isolated from the rat hearts in two groups and cultured overnight. After that, total RNA was extracted and then subjected to miRNA microarray to screen differentially expressed miRNAs. The reults of microarray were further verified by quantitative real-time PCR (qRT-PCR). The target genes regulated by differentially expressed miRNAs were predicted by the software of Targetscan and miRanda. Bioinformatics analysis was performed to predict the miRNAs-regulated target genes and analyze the enriched gene ontology (GO) and signaling pathway (KEGG Pathway). Results The results of miRNA microarray showed that a total of 37 miRNAs were differentially expressed in HF group as compared to CON group, among which 22 miRNAs were up-regulated and 15 miRNAs were down-regulated (P<0.01, FDR<0.05). The expression of miR-133b-5p (t=14.56, P<0.01), miR-6216 (t=9.32, P<0.01) and let-7e-5p (t=13.92, P<0.01) which were detected by qRT-PCR exhibited the similar tendency of up or down regulation to those shown in microarray results. Bioinformatics analysis indicated that miRNAs-regulated target genes were significantly enriched in 31 GOs (P<0.01, FDR<0.05) and 12 signal pathways (P<0.05, FDR<0.05), among which ubiquitin-proteasome system, MAPK signaling pathway and Toll like siganling pathway exhibited a higher enrichment. Conclusion MiRNA expression profile on cardiomyocytes in rat with adriamycin-induced heart failure was significantly changed. These differentially expressed miRNAs might participate in the process of heart failing by regulating their target genes in rat cardiomyocytes. Key words: Heart failure; Cardiomyocytes; MiRNA expressional profiling; Bioinformatics analysis; Quantitative real-time PCR; Target genes; Gene ontology (GO); KEGG pathway