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.
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This work was supported by grants from the National Key Research and Development Program of China (2018YFD0501700), the National Key Technology Support Program (2015BAD03B04), the National Beef and Yak Industrial Technology System (CARS-37), the Agricultural Science and Technology Innovation and Transformation Project of Shaanxi Province (NYKJ-2018-LY09) and the Technical Innovation Engineering Project of Shaanxi Province (2016 KTCL02-15).
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CL and SHAR conceptualization, data curation, formal analysis, investigation, methodology, software, validation, writing—original draft, writing—review and editing. MARN and RK; YF conceptualization, data curation, formal analysis, methodology, software, validation, writing—review and editing. ZMM and AFS, Data curation, formal analysis, writing—review and editing. BMA and FMS Writing—review and editing. MAB software, methodology, visualization software. LZ: conceptualization, funding acquisition, project administration, resources, supervision, visualization, writing—review and editing.
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Liang, C., Raza, S.H.A., Naqvi, M.A.R. et al. Construction of Adipogenic ceRNA Network Based on lncRNA Expression Profile of Adipogenic Differentiation of Human MSC Cells. Biochem Genet 60, 543–557 (2022). https://doi.org/10.1007/s10528-021-10115-1
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DOI: https://doi.org/10.1007/s10528-021-10115-1