Construction of Adipogenic ceRNA Network Based on lncRNA Expression Profile of Adipogenic Differentiation of Human MSC Cells

Abstract

The Long non-coding RNA (lncRNA) expression profile data of ten samples including human Mesenchymal Stem Cell (MSC) adipogenic differentiation 0, 3, and 6 days from the GEO database, and then perform gene ID conversion, BLAST comparison, and annotation marking. Finally, group A (treatment group on day 3 of differentiation and control group on day 0 of differentiation) obtained a total of 1180 mRNA and 185 lncRNA; group B (treatment group on day 6 of differentiation and control group on day 0 of differentiation). A total of 1376 mRNA and 206 lncRNA were obtained. Finally, we processed the differential lncRNAs and mRNAs obtained in the two groups, and obtained 113 shared differential lncRNAs to further predict the targeted miRNA, a total of 815 lncRNA-miRNA pairs. The targeted mRNA was further predicted, and the grouped differential mRNAs were combined to obtain 64 differential mRNAs. In the end, we obtained 216 ceRNAs containing 26 lncRNAs, 27 miRNAs and 64 mRNAs. We found that the mRNAs in the ceRNA network were mainly enriched with 45 Gene Ontology (GO) terms, mainly including glucose homeostasis mechanism and insulin stimulation response. 69 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were mainly enriched. It mainly includes many pathways related to lipid metabolism such as Adenosine 5′-monophosphate (AMP)-activated protein kinase (AMPK), Rap1, cAMP, mitogen-activated protein kinase (MAPK), Ras, hypoxia inducible factor-1 (HIF-1), PI3K-Akt, insulin signaling and so on. In the end, we identified 216 ceRNA regulatory relationships related to obesity research. Our research provides a clearer direction for understanding the molecular mechanism of obesity, the screening and determination of drug targets biomarkers in the future.

Transcriptomic Changes and Regulatory Networks Associated with Resistance to Mastitis in Xinjiang Brown Cattle

“…Huang et al established a ceRNA network and reported that some differentially expressed non-coding RNAs might be involved in the regulation of muscle traits. Liang et al [48] identified 216 ceRNAs, including 26 lncRNAs, 27 miRNAs, and 64 mRNAs, in human mesenchymal stem cell (MSC) adipose differentiation at 0, 3, and 6 d. The mRNAs in the ceRNA network were found to be mainly associated with glucose homeostasis and the response to insulin stimulation, as well as many lipid metabolism-related pathways, such as Ras, hypoxia-inducible factor-1 (HIF-1), PI3K-Akt, and insulin signaling. Chen et al constructed a ceRNA network using RNA-seq data and annotated potential candidate miRNAs and circRNAs involved in udder development in sheep, providing further insights into the influence of miRNAs and circRNAs on udder development in this species [49].…”

Characterization of DNA methylation as well as mico-RNA expression and screening of epigenetic markers in adipogenesis

“…For example, lncRNA H19 targets LCoR by interacting with the miR-188 sponge, thereby affecting the osteogenic and adipogenic differentiation process of mouse BMSCs. LncRNA ADNCR inhibits adipogenesis and differentiation by targeting miR-204 [ 40 ]. Therefore, potential ceRNA networks have been predicted for the above four central genes.…”