Whole transcriptome analysis of the differential RNA profiles and associated competing endogenous RNA networks in LPS-induced acute lung injury (ALI)

Abstract

Acute lung injury (ALI) is a serious inflammation disease usually arises alveolar epithelial membrane dysfunction and even causes death. Therefore, the aims of this study are to screen the differentially expressed lncRNAs, circRNAs, miRNAs, and mRNAs in ALI based on the high-throughput sequencing. The lipopolysaccharide (LPS)-induced ALI mouse model was established, the injury of ALI mouse model was evaluated through histological analysis with hemotoxylin and eosin (H & E) staining assay, dry/wet ratio, infiltrated-immune cells, ET-1 mRNA expression and released-proinflammation factors. Then, expression data of lncRNAs, circRNAs, miRNAs and mRNAs in ALI were acquired using whole-transcriptome sequencing. The differential expression of lncRNAs (DE lncRNAs), circRNAs (DE circRNAs), miRNAs (DE miRNAs) and mRNAs (DE mRNAs) were identified, and the lncRNA-miRNA-mRNA network and circRNA-miRNA-mRNA network were constructed, and the biological function of target genes were annotated based on bioinformatics analysis. In the present study, the LPS-induced ALI mouse model was successfully established. The biological analysis results showed that total 201 DE lncRNAs, 172 DE circRNAs, 62 DE miRNAs, and 3081 DE mRNAs were identified in ALI. The 182 lncRNA-miRNA-mRNA networks and 32 circRNA-miRNA-mRNA networks were constructed were constructed based on the correlation between lncRNAs/circRNAs, miRNAs, mRNAs. The biological function analysis indicated that TNF signaling pathway, chemokine signaling pathway and so on involved in ALI. In the present study, the differential expression coding and non-coding RNAs (ncRNAs) in ALI were identified, and their regulatory networks were constructed. There might provide the potential biomarkers and underlying mechanism for ALI diagnosis and treatment.

Deregulated RNAs involved in sympathetic regulation of sepsis-induced acute lung injury based on whole transcriptome sequencing

“…Meanwhile, most RNAs were predicted to relate to inflammation (Fig. S 3 , S 4 , S 5 , S 6 ) in the ALI group compared with the Ctrl group, and some researchers have already reported [ 16 , 17 ]. To further explore the mechanism of action of sympathetic nerves in ALI, we only focus on the result between the SD + ALI group and the ALI group as follows.…”

“…We found many differentially expressed circRNAs, lncRNAs, miRNAs, and mRNAs in the ALI group, compared with the Ctrl group that regulated inflammatory signaling pathways indicated by GO and KEGG enrichment. Some previous studies have also used whole-transcriptome sequencing to assess the transcriptome changes in ALI and have proven that multiple circRNAs, lncRNAs, miRNAs, and mRNAs are significantly altered in ALI [ 16 , 17 ]. In the current study, we identified 629 DE circRNAs, 269 DE lncRNAs, 192 DE mRNAs, and 7 DE circRNAs in the SD + ALI group compared with the ALI group.…”

Microarray Profiling and Co-Expression Network Analysis of LncRNAs and mRNAs in Acute Respiratory Distress Syndrome Mouse Model

“…Our study implies that LncRNA is involved in ARDS development through the cell death signal pathway. Then, to confirm the reproducibility of LncRNA-mRNA co-expression network, we tested it by using Teng’s dada of ALI model [ 28 ]. As shown in Table S3 , 69 mRNA and 1 LncRNA (ENSMUST00000124853) in Teng’s research were consistent with our LncRNA-mRNA co-expression network.…”

Long Noncoding RNA: A Novel Insight into the Pathogenesis of Acute Lung Injury

“…Crucial roles of lncRNAs have been identified in the pathogenesis of ALI [ 14 , 15 ]. LncRNAs not only possess a key role in the pathogenesis of ALI but also retain great potentials for the diagnosis [ 16 ] and treatment of ALI [ 17 ]. In this review, we summarize the current knowledge of lncRNAs to provide a better understanding of their regulation and function in the development of ALI/ARDS.…”