Key Anti-Fibrosis Associated Long Noncoding RNAs Identified in Human Hepatic Stellate Cell via Transcriptome Sequencing Analysis

Abstract

Hepatic fibrosis is the main pathological basis for chronic cirrhosis, and activated hepatic stellate cells (HSCs) are the primary cells involved in liver fibrosis. Our study analyzed anti-fibrosis long noncoding RNAs (lncRNAs) in activated human HSCs (hHSCs). We performed RNA sequencing (RNA-seq) and bioinformatics analysis to determine whether lncRNA expression profile changes between hHSCs activation and quiescence. Eight differentially expressed (DE) lncRNAs and three pairs of co-expression lncRNAs-mRNAs were verified by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). A total of 34146 DE lncRNAs were identified in this study. Via gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, we found several DE lncRNAs regulated hHSC activation by participating in DNA bending/packaging complex, growth factor binding and the Hippo signaling pathway (p < 0.05). With lncRNA–mRNA co-expression analysis, three lncRNAs were identified to be associated with connective tissue growth factor (CTGF), fibroblast growth factor 2 (FGF2) and netrin-4 (NTN4). The quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) results of the eight DE lncRNAs and three pairs of co-expression lncRNAs–mRNAs were consistent with the RNA-seq data and previous reports. Several lncRNAs may serve as potential targets to reverse the progression of liver fibrosis. This study provides a first insight into lncRNA expression profile changes associated with activated human HSCs.

The Roles and Mechanisms of lncRNAs in Liver Fibrosis

“…Eight DE lncRNAs and three pairs of coexpressed lncRNAs-mRNAs were confirmed and enriched in growth factor binding terms, such as connective tissue growth factor (CTGF), netrin-4 (NTN4), and fibroblast growth factor 2 (FGF2), and the coexpressed lncRNAs may be involved in liver injury activation and human HSCs [38]. GO (gene ontology) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were enriched mainly in human HSC activation due to participation in growth factor binding, the DNA packaging/bending complex, and the Hippo signalling pathway [38]. Three lncRNAs were found to be closely related to CTGF, FGF2, and NTN4 by lncRNA-mRNA coexpression analysis [38].…”

“…A total of 139 lncRNA loci were induced and 242 lncRNA loci were found to be repressed by TGF-β signalling activation [37]. Furthermore, the first insights into lncRNA expression pattern changes in activated human HSCs have been reported [38]. A total of 34,146 differentially expressed (DE) lncRNAs were described during human HSC quiescence and activation, and the expression changes of only 1685 DE mRNAs and 3763 DE lncRNAs were statistically significant when activated hHSCs were compared to quiescent hHSCs [38].…”

“…Furthermore, the first insights into lncRNA expression pattern changes in activated human HSCs have been reported [38]. A total of 34,146 differentially expressed (DE) lncRNAs were described during human HSC quiescence and activation, and the expression changes of only 1685 DE mRNAs and 3763 DE lncRNAs were statistically significant when activated hHSCs were compared to quiescent hHSCs [38]. Moreover, the lncRNA expression patterns of fibrotic and normal liver samples in NASH patients have been investigated [27].…”

“…Among those identified lncRNAs, some lncRNAs were firmly linked to numerous proteins and collagen genes that regulate the ECM during fibrotic scar formation, according to coexpression analyses [37]. Eight DE lncRNAs and three pairs of coexpressed lncRNAs-mRNAs were confirmed and enriched in growth factor binding terms, such as connective tissue growth factor (CTGF), netrin-4 (NTN4), and fibroblast growth factor 2 (FGF2), and the coexpressed lncRNAs may be involved in liver injury activation and human HSCs [38]. GO (gene ontology) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were enriched mainly in human HSC activation due to participation in growth factor binding, the DNA packaging/bending complex, and the Hippo signalling pathway [38].…”

“…GO (gene ontology) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were enriched mainly in human HSC activation due to participation in growth factor binding, the DNA packaging/bending complex, and the Hippo signalling pathway [38]. Three lncRNAs were found to be closely related to CTGF, FGF2, and NTN4 by lncRNA-mRNA coexpression analysis [38]. Furthermore, through experimental verification, 77 NASH-related target mRNAs were found to take part in 137 pathways, such as tumour necrosis factor (TNF) and TGFβ1 signalling, insulin resistance, and ECM maintenance [27].…”