Effects of Gypenoside XLIX on fatty liver cell gene expression in vitro: a genome-wide analysis

Fengming Liu; Qiu Wei; Yidan Liang; Qingmei Yang; Chunxi Huang; Qiuju Huang; Jiankang Qin; Lili Pang; Liuyan Xu; Juan Zhong

Effects of Gypenoside XLIX on fatty liver cell gene expression in vitro: a genome-wide analysis

Am J Transl Res. 2023 Feb 15;15(2):834-846. eCollection 2023.

Authors

Affiliations

¹ Department of Critical Care Medicine, The First People's Hospital of Nanning Nanning 530022, Guangxi, China.
² Department of Traditional Chinese Medicine, The First People's Hospital of Nanning Nanning 530022, Guangxi, China.

PMID: 36915770
PMCID: PMC10006792

Abstract

Objective: To perform Genome-wide analysis of Gypenoside XLIX (Gyp-XLIX) in the treatment of fatty liver cells.

Methods: The gene profiles of 3 normal liver cells, 3 fatty liver cells, and 3 fatty liver cells treated with Gyp-XLIX were detected by high-throughput sequencing to identify the differentially expressed genes (DEGs) in fatty liver treated by Gyp-XLIX. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to explore the biological functions of DEGs. By constructing lncRNA-mRNA co-expression network of DEGs, network node genes were mined. Possible target genes of differentially expressed lncRNA were predicted by cis regulation.

Results: 782 DEGs were screened out; that is, 172 genes were highly expressed in fatty liver cells, and the expression decreased to the level of normal liver cells after Gyp-XLIX treatment; 610 genes were under expressed in fatty liver cells, and the expression increased to the level of normal liver cells after Gyp-XLIX treatment. Functional analysis of KEGG and GO showed that DEGs process DNA-binding transcription factor activity and ion transmembrane transporter activity in the plasma membrane region. This mediates glycerophospholipid metabolism, bile secretion, fatty acid degradation and other signaling pathways. lncRNA analysis showed that the expression of 16 lncRNAs was low in fatty liver cells, and the expression was increased to the level of normal liver cells after Gyp-XLIX treatment. Target gene prediction showed that 16 differentially expressed lncRNAs had cis potential to regulate target genes, among which lncRNA RPARP-AS1 had a high degree of relationship with other genes. lncRNA-mRNA co-expression network results showed that lncRNA RPARP-AS1 may acted on NFKB2.

Conclusion: LncRNA was differentially expressed in fatty liver cells and Gyp-XLIX treated fatty liver cells, and lncRNA RPARP-AS1 may be a regulatory gene in Gyp-XLIX treated fatty liver.

Keywords: Gypenoside XLIX; LncRNA; fatty liver; genome-wide analysis; mRNA.