Abstract

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.

Highlights

  • Acute lung injury (ALI) is one of the main causes of acute respiratory failure (Pan et al, 2018)

  • The mechanism of lung injury varies according to its cause, epithelial and endothelial cell damage has been shown to be a critical factor in the onset and progress of ALI/acute respiratory distress syndrome (Tomashefski, 2000)

  • Unrecognized for a long time, long non-coding RNAs (lncRNA) has undergone a significant breakthrough given the emergence of highthroughput sequencing and is considered as a research hot point in the field of medicine

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Summary

Introduction

Acute lung injury (ALI) is one of the main causes of acute respiratory failure (Pan et al, 2018). The death rate of severe ALI was >40.0% (Pan et al, 2018). Approaches to ameliorate ventilator management have been widely used to provide supportive care for patients with ALI (Fan et al, 2005). Despite recent advances in comprehending the epidemiology along with the pathogenesis of the disease, clinical studies shows that some drug approaches are not effective in decreasing mortality rates in individuals with ALI (Raghavendran et al, 2008). Further research is urgently needed to unravel the molecular drivers of ALI development and to produce more effective treatments

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