RNA Sequencing and Bioinformatics Analysis Implicate the Regulatory Role of a Long Noncoding RNA-mRNA Network in Hepatic Stellate Cell Activation

Guo, Can-Jie; Xiao, Xiao; Sheng, Li; Chen, Lili; Zhong, Wei; Li, Hai; Hua, Jing; Ma, Xiong

doi:10.1159/000479898

Cited by 23 publications

(23 citation statements)

References 34 publications

(31 reference statements)

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“…When comparing activated and quiescent HSCs, the lncRNAs NONRATT021402.2, NONRATT016788.2, and NONRATT012636.2 were upregulated, and the lncRNAs NONRATT024061.2, NONRATT019720.2, and NONRATT007863.2 were downregulated [41]. Furthermore, the upregulation of lncRNA NONRATT013819.2 and lysyl oxidase (Lox) mRNA in HSCs and fibrotic livers was associated with the ECM-related signalling pathway [41]. These results showing potentially vital functions for NONRATT013819.2 and Lox in ECM remodelling during HSC activation indicate that an abnormally regulated lncRNA-mRNA network might supply new hepatic fibrosis treatment measures.…”

Section: Lncrnas Are Widely Expressed In Animal Modelsmentioning

confidence: 99%

“…DE lncRNAs-mRNAs were observed between activated and quiescent mouse HSCs. Twenty-four DE lncRNAs (12 upregulated and 12 downregulated) and 529 DE mRNAs (155 upregulated and 374 downregulated) were found to be dysregulated in activated mouse HSCs [41]. When comparing activated and quiescent HSCs, the lncRNAs NONRATT021402.2, NONRATT016788.2, and NONRATT012636.2 were upregulated, and the lncRNAs NONRATT024061.2, NONRATT019720.2, and NONRATT007863.2 were downregulated [41].…”

Section: Lncrnas Are Widely Expressed In Animal Modelsmentioning

confidence: 99%

“…Twenty-four DE lncRNAs (12 upregulated and 12 downregulated) and 529 DE mRNAs (155 upregulated and 374 downregulated) were found to be dysregulated in activated mouse HSCs [41]. When comparing activated and quiescent HSCs, the lncRNAs NONRATT021402.2, NONRATT016788.2, and NONRATT012636.2 were upregulated, and the lncRNAs NONRATT024061.2, NONRATT019720.2, and NONRATT007863.2 were downregulated [41]. Furthermore, the upregulation of lncRNA NONRATT013819.2 and lysyl oxidase (Lox) mRNA in HSCs and fibrotic livers was associated with the ECM-related signalling pathway [41].…”

Section: Lncrnas Are Widely Expressed In Animal Modelsmentioning

confidence: 99%

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The Roles and Mechanisms of lncRNAs in Liver Fibrosis

Yang

Fan

et al. 2020

IJMS

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Many studies have revealed that circulating long noncoding RNAs (lncRNAs) regulate gene and protein expression in the process of hepatic fibrosis. Liver fibrosis is a reversible wound healing response followed by excessive extracellular matrix accumulation. In the development of liver fibrosis, some lncRNAs regulate diverse cellular processes by acting as competing endogenous RNAs (ceRNAs) and binding proteins. Previous investigations demonstrated that overexpression of lncRNAs such as H19, maternally expressed gene 3 (MEG3), growth arrest-specific transcript 5 (GAS5), Gm5091, NR_002155.1, and HIF 1alpha-antisense RNA 1 (HIF1A-AS1) can inhibit the progression of liver fibrosis. Furthermore, the upregulation of several lncRNAs [e.g., nuclear paraspeckle assembly transcript 1 (NEAT1), hox transcript antisense RNA (Hotair), and liver-enriched fibrosis-associated lncRNA1 (lnc-LFAR1)] has been reported to promote liver fibrosis. This review will focus on the functions and mechanisms of lncRNAs, the lncRNA transcriptome profile of liver fibrosis, and the main lncRNAs involved in the signalling pathways that regulate hepatic fibrosis. This review provides insight into the screening of therapeutic and diagnostic markers of liver fibrosis.

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Section: Lncrnas Are Widely Expressed In Animal Modelsmentioning

confidence: 99%

Section: Lncrnas Are Widely Expressed In Animal Modelsmentioning

confidence: 99%

Section: Lncrnas Are Widely Expressed In Animal Modelsmentioning

confidence: 99%

See 1 more Smart Citation

The Roles and Mechanisms of lncRNAs in Liver Fibrosis

Yang

Fan

et al. 2020

IJMS

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“…A comparative analysis of lncRNA and mRNA was carried out to observe the difference in transcript length, exon number, and expression level between lncRNA and mRNA, and it was verified whether the predicted lncRNA is in line with the general characteristics. 11…”

Section: Feature Comparisons Of Transcripts In Crcmentioning

confidence: 99%

RNA sequencing and bioinformatics analysis of the long noncoding RNA–mRNA network in colorectal cancer

Zhang

Jia

et al. 2018

J of Cellular Biochemistry

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Long noncoding RNA (lncRNA) plays an important regulatory role in tumorigenesis. This study aims to analyze the lncRNA-messenger RNA (mRNA) expression network and potential roles in colorectal cancer (CRC). The LncRNA expression profile was analyzed in CRC tissue by RNA sequencing and the functions of differentially expressed genes were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The lncRNA-mRNA network was predicted with bioinformatics. From the result, we identified 485 differential expression lncRNAs and 2383 mRNAs in CRC, GO, and KEGG analyses showed that the changes in lncRNAs were mainly associated with metabolism and transcription regulation that were different from mRNA function. Additionally, based on the predicted coexpression network, we identified that NONHSAT074176.2, downregulated in CRC tissue and cell lines, was a hub lncRNA in the development of CRC. Our results describe the lncRNA-mRNA network in detail and indicate that lncRNA NONHSAT074176.2 may be useful as a candidate diagnostic biomarker and may be a promising therapeutic target for CRC.

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“…Genome-wide RNA sequencing (RNA-seq) was widely used in basic research to identify key lncRNAs that regulate diseases [ 18 , 19 ]. It has been reported that 12 lncRNAs and 155 mRNAs were identified to be upregulated in activated rat HSCs by RNA-seq analysis, and in addition, the potential role of upregulated lncRNA NONRATTO13819.2 and Lox in extracellular matrix (ECM) remodeling during activation [ 20 ]. Some 3600 lncRNAs were identified in human HSC myofibroblasts in combination with RNA-seq and chromatin immunoprecipitation sequencing (ChIP-seq).…”

Section: Introductionmentioning

confidence: 99%

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

Ren

et al. 2018

IJMS

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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.

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RNA Sequencing and Bioinformatics Analysis Implicate the Regulatory Role of a Long Noncoding RNA-mRNA Network in Hepatic Stellate Cell Activation

Cited by 23 publications

References 34 publications

The Roles and Mechanisms of lncRNAs in Liver Fibrosis

The Roles and Mechanisms of lncRNAs in Liver Fibrosis

RNA sequencing and bioinformatics analysis of the long noncoding RNA–mRNA network in colorectal cancer

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

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