Identification of Lncrna-Mrna Networks in Hepg2 Cells upon Knockout and Copper Accumulation.

BACKGROUND

Hepatolenticular degeneration (HLD) is an inherited disorder caused by the mutation in the adenosine triphosphatase copper transporting β gene (). W aimed to explore the genetic changes in HLD using bioinformatics analysis.

METHODS

The study was conducted in Nepal, in 2019. The GSE107323 dataset was downloaded and the differentially expressed lncRNAs (DElncRNAs) as well as differentially expressed genes (DEGs) induced by knockout (KO) and copper toxicity were clustered using Mfuzz clustering analysis. LncRNAs and genes with high coexpression (correlation coefficient > 0.9) and pathways involving the DEGs were used to construct the lncRNA-gene-pathway network.

RESULTS

KO and KO + copper induced 51 overlapping DEGs and 687 overlapping DElncRNAs, respectively. Mfuzz analysis identified four clusters, including two clusters of consistently upregulated and downregulated DEGs/DElncRNAs. The lncRNA-gene-pathway network consisted of 13 DElncRNAs, 10 DEGs, and two pathways, including "hsa04630: Jak-STAT signaling pathway" and "hsa04920: Adipocytokine signaling pathway". Eight downregulated genes, including erythropoietin (), insulin receptor substrate 1 (), and PPARG coactivator 1 alpha (), and two upregulated genes (cardiotrophin-like cytokine factor 1 and cyclin D3) were involved in the two pathways. These genes were targeted by multiple lncRNAs, including and .

CONCLUSION

Collectively, the differentially expressed lncRNA-mRNA axes play crucial roles in HLD pathogenesis through mediating cell proliferation and inflammation. Moreover, the , , or genes were potent therapeutic targets for HLD.