Integrative analysis of the transcriptome and targetome identifies the regulatory network of miR-16: An inhibitory role against the activation of hepatic stellate cells

Abstract

Hepatic stellate cell (HSC) activation is the critical event of liver fibrosis. Abnormality of miR-16 expression induces their activation. However, the action model of miR-16 remains to be elucidated because of its multiple-targeted manner.Here, we report that miR-16 restoration exerted a wide-range impact on transcriptome (2,082 differentially expressed transcripts) of activated HSCs. Integrative analysis of both targetome (1,195 targets) and transcriptome uncovered the miR-16 regulatory network based upon bio-molecular interaction databases (BIND, BioGrid, Tranfac, and KEGG), cross database searching with iterative algorithm, Dijkstra's algorithm with greedy method, etc. Eight targets in the targetome (Map2k1, Bmpr1b, Nf1, Pik3r3, Ppp2r1a, Prkca, Smad2, and Sos2) served as key regulatory network nodes that mediate miR-16 action. A set of TFs (Sp1, Jun, Crebl, Arnt, Fos, and Nf1) was recognized to be the functional layer of key nodes, which mapped the signal of miR-16 to transcriptome. In result, the comprehensive action of miR-16 abrogated transcriptomic characteristics that determined the phenotypes of activated HSCs, including active proliferation, ECM deposition, and apoptosis resistance. Therefore, a multi-layer regulatory network based upon the integration of targetome and transcriptome may underlie the global action of miR-16, which suggesting it plays an inhibitory role in HSC activation.

Suppression of microRNA-16 protects against acute myocardial infarction by reversing beta2-adrenergic receptor down-regulation in rats

“…Studies showed that miR-16 targets the 3′ UTR of vascular endothelial growth factor (VEGF) to regulate angiogenesis [35, 36]. In addition to bcl-2 and VEGF, TGF-β, PI3K-Akt and p53 are considered to be the potential targets of miR-16 [37]. In this study, we identified β 2 -AR as a direct target gene of miR-16, and did not investigate other potential targets.…”

Cancer driver mutations in endometriosis: Variations on the major theme of fibrogenesis

“…However, one study reports that forced miR-16 expression suppressed the activation of HSCs, which is the critical event in liver fibrogenesis, likely through negative cell-cycle regulation, enhanced fibrolysis, and increased apoptosis. 283 Subsequent integrative analysis identified the regulatory network of miR-16…”

“…and found that PPP2R1A is a target of miR-16 and that PP2R1A constitutes a key regulatory network node that mediates the miR-16 action in proliferation, ECM deposition, and survival. 283 Interestingly, treatment of endometriotic cells with peritoneal fluid from women with endometriosis reduced the expression of miR-16. 284,285 Thus, there is a possibility that miR-16 downregulation may induce PPP2R1A activation, facilitating the progression of fibrogenesis in endometriosis.…”

MicroRNAs as biomarkers and regulators of nonalcoholic fatty liver disease

“…19 However, our team found that there was a decrease in miR-16 level with the activation of hepatic stellate cells (HSCs), while its upregulation increased apoptosis and inhibited the activation of HSCs and finally, reduced hepatic fibrosis. 39,40 Other miRNAs miR-197 and miR-99 levels in VAT samples are significantly correlated with pericellular fibrosis in NASH patients. 41 Other studies have confirmed that the levels of miR-150, miR-182, miR-183, miR-224 and miR-31 are increased, while those of miR-17, miR-219a, miR-378i and miR-590 are decreased in liver biopsy specimens of patients with severe fibrosis or cirrhosis (F3-F4) compared to individuals without fibrosis (F0).…”

“…Increased miR-16 expression induces the apoptosis of HSCs and inhibits their activation, and thus improves liver fibrosis. 39,40 MiR-182 expressions are decreased in fibrotic samples of the liver, and FOXO3 is identified as its potential target gene. 42 Hepatic miR-146a is the most significantly downregulated miRNA in mice with NASH induced by MCD diet.…”