A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide‐Induced Acute Lung Injury in Mice

Non-coding RNAs have remarkable roles in acute lung injury (ALI) initiation. Nevertheless, the significance of long non-coding RNAs (lncRNAs) in ALI is still unknown. Herein, we purposed to identify potential key genes in ALI and create a competitive endogenous RNA (ceRNA) modulatory network to unco...

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Autores principales:	Xianxian Jia, Jinhui Huang, Bo Wu, Miao Yang, Wei Xu
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	acute lung injury high-throughput RNA sequencing lncRNA lncRNA-miRNA-mRNA network competing endogenous RNA Genetics QH426-470
Acceso en línea:	https://doaj.org/article/c1273291f72e465999bd71ec3f4b1aa2
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spelling	oai:doaj.org-article:c1273291f72e465999bd71ec3f4b1aa22021-12-01T18:05:30ZA Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide‐Induced Acute Lung Injury in Mice1664-802110.3389/fgene.2021.745715https://doaj.org/article/c1273291f72e465999bd71ec3f4b1aa22021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.745715/fullhttps://doaj.org/toc/1664-8021Non-coding RNAs have remarkable roles in acute lung injury (ALI) initiation. Nevertheless, the significance of long non-coding RNAs (lncRNAs) in ALI is still unknown. Herein, we purposed to identify potential key genes in ALI and create a competitive endogenous RNA (ceRNA) modulatory network to uncover possible molecular mechanisms that affect lung injury. We generated a lipopolysaccharide-triggered ALI mouse model, whose lung tissue was subjected to RNA sequencing, and then we conducted bioinformatics analysis to select genes showing differential expression (DE) and to build a lncRNA-miRNA (microRNA)- mRNA (messenger RNA) modulatory network. Besides, GO along with KEGG assessments were conducted to identify major biological processes and pathways, respectively, involved in ALI. Then, RT-qPCR assay was employed to verify levels of major RNAs. A protein-protein interaction (PPI) network was created using the Search Tool for the Retrieval of Interacting Genes (STRING) database, and the hub genes were obtained with the Molecular Complex Detection plugin. Finally, a key ceRNA subnetwork was built from major genes and their docking sites. Overall, a total of 8,610 lncRNAs were identified in the normal and LPS groups. Based on the 308 DE lncRNAs [p-value < 0.05, \|log2 (fold change) \| > 1] and 3,357 DE mRNAs [p-value < 0.05, \|log2 (fold change) \| > 1], lncRNA-miRNA and miRNA-mRNA pairs were predicted using miRanda. The lncRNA-miRNA-mRNA network was created from 175 lncRNAs, 22 miRNAs, and 209 mRNAs in ALI. The RT-qPCR data keep in step with the RNA sequencing data. GO along with KEGG analyses illustrated that DE mRNAs in this network were mainly bound up with the inflammatory response, developmental process, cell differentiation, cell proliferation, apoptosis, and the NF-kappa B, PI3K-Akt, HIF-1, MAPK, Jak-STAT, and Notch signaling pathways. A PPI network on the basis of the 209 genes was established, and three hub genes (Nkx2-1, Tbx2, and Atf5) were obtained from the network. Additionally, a lncRNA-miRNA-hub gene subnetwork was built from 15 lncRNAs, 3 miRNAs, and 3 mRNAs. Herein, novel ideas are presented to expand our knowledge on the regulation mechanisms of lncRNA-related ceRNAs in the pathogenesis of ALI.Xianxian JiaJinhui HuangBo WuMiao YangWei XuFrontiers Media S.A.articleacute lung injuryhigh-throughput RNA sequencinglncRNAlncRNA-miRNA-mRNA networkcompeting endogenous RNAGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	acute lung injury high-throughput RNA sequencing lncRNA lncRNA-miRNA-mRNA network competing endogenous RNA Genetics QH426-470
spellingShingle	acute lung injury high-throughput RNA sequencing lncRNA lncRNA-miRNA-mRNA network competing endogenous RNA Genetics QH426-470 Xianxian Jia Jinhui Huang Bo Wu Miao Yang Wei Xu A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide‐Induced Acute Lung Injury in Mice
description	Non-coding RNAs have remarkable roles in acute lung injury (ALI) initiation. Nevertheless, the significance of long non-coding RNAs (lncRNAs) in ALI is still unknown. Herein, we purposed to identify potential key genes in ALI and create a competitive endogenous RNA (ceRNA) modulatory network to uncover possible molecular mechanisms that affect lung injury. We generated a lipopolysaccharide-triggered ALI mouse model, whose lung tissue was subjected to RNA sequencing, and then we conducted bioinformatics analysis to select genes showing differential expression (DE) and to build a lncRNA-miRNA (microRNA)- mRNA (messenger RNA) modulatory network. Besides, GO along with KEGG assessments were conducted to identify major biological processes and pathways, respectively, involved in ALI. Then, RT-qPCR assay was employed to verify levels of major RNAs. A protein-protein interaction (PPI) network was created using the Search Tool for the Retrieval of Interacting Genes (STRING) database, and the hub genes were obtained with the Molecular Complex Detection plugin. Finally, a key ceRNA subnetwork was built from major genes and their docking sites. Overall, a total of 8,610 lncRNAs were identified in the normal and LPS groups. Based on the 308 DE lncRNAs [p-value < 0.05, \|log2 (fold change) \| > 1] and 3,357 DE mRNAs [p-value < 0.05, \|log2 (fold change) \| > 1], lncRNA-miRNA and miRNA-mRNA pairs were predicted using miRanda. The lncRNA-miRNA-mRNA network was created from 175 lncRNAs, 22 miRNAs, and 209 mRNAs in ALI. The RT-qPCR data keep in step with the RNA sequencing data. GO along with KEGG analyses illustrated that DE mRNAs in this network were mainly bound up with the inflammatory response, developmental process, cell differentiation, cell proliferation, apoptosis, and the NF-kappa B, PI3K-Akt, HIF-1, MAPK, Jak-STAT, and Notch signaling pathways. A PPI network on the basis of the 209 genes was established, and three hub genes (Nkx2-1, Tbx2, and Atf5) were obtained from the network. Additionally, a lncRNA-miRNA-hub gene subnetwork was built from 15 lncRNAs, 3 miRNAs, and 3 mRNAs. Herein, novel ideas are presented to expand our knowledge on the regulation mechanisms of lncRNA-related ceRNAs in the pathogenesis of ALI.
format	article
author	Xianxian Jia Jinhui Huang Bo Wu Miao Yang Wei Xu
author_facet	Xianxian Jia Jinhui Huang Bo Wu Miao Yang Wei Xu
author_sort	Xianxian Jia
title	A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide‐Induced Acute Lung Injury in Mice
title_short	A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide‐Induced Acute Lung Injury in Mice
title_full	A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide‐Induced Acute Lung Injury in Mice
title_fullStr	A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide‐Induced Acute Lung Injury in Mice
title_full_unstemmed	A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide‐Induced Acute Lung Injury in Mice
title_sort	competitive endogenous rna network based on differentially expressed lncrna in lipopolysaccharide‐induced acute lung injury in mice
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/c1273291f72e465999bd71ec3f4b1aa2
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A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide‐Induced Acute Lung Injury in Mice

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