Comprehensive Analysis of the Profiles of Differentially Expressed mRNAs, lncRNAs, and circRNAs in Phosgene-Induced Acute Lung Injury

Abstract

Phosgene exposure can cause acute lung injury (ALI), for which there is no currently available effective treatment. Mesenchymal stem cells (MSCs) which have been proven to have therapeutic potential and be helpful in the treatment of various diseases, but the mechanisms underlying the function of MSCs against phosgene-induced ALI are still poorly explored. In this study, we compared the expression profiles of mRNAs, lncRNAs, and circRNAs in the lung tissues from rats of three groups-air control (group A), phosgene-exposed (group B), and phosgene + MSCs (group C). The results showed that 389 mRNAs, 198 lncRNAs, and 56 circRNAs were differently expressed between groups A and B; 130 mRNAs, 107 lncRNAs, and 35 circRNAs between groups A and C; and 41 mRNAs, 88 lncRNAs, and 18 circRNAs between groups B and C. GO and KEGG analyses indicated that the differentially expressed RNAs were mainly involved in signal transduction, immune system processes, and cancers. In addition, we used a database to predict target microRNAs (miRNAs) interacting with circRNAs and the R network software package to construct a circRNA-targeted miRNA gene network map. Our study showed new insights into changes in the RNA expression in ALI, contributing to explore the mechanisms underlying the therapeutic potential of MSCs in phosgene-induced ALI.

Figure 1

Differentially expressed circRNAs in the lung tissues of three groups of rats. (a) A box and whisker plot of circRNAs showing the distribution of RNA intensities in all samples. (b) Heat maps of correlation coefficients for all samples. (c) Volcano plots showing variation in the circRNA expression. The vertical lines correspond to the 2-fold change, and the horizontal line represents a P value of 0.05. (d) Type and proportion of circRNAs. (e) Hierarchical clustering of all differentially expressed circRNAs in the lung tissues of rats in groups A and B. (f) Hierarchical clustering of all differentially expressed circRNAs in the lung tissues of rats in groups B and C. (g) Differentially expressed genes were analyzed using DEGseq software based on the fragments per kilobase of the transcript per million mapped reads (FPKM) method (≥2-fold change with P <0.05). The number of differentially expressed circRNAs was observed.

Figure 2

Differentially expressed lncRNAs in the lung tissues of rats in the three groups. (a) A box and whisker plot of lncRNAs showing the distributions of RNA intensities in all samples. (b) Heat map of correlation coefficients for all samples. (c) Volcano plots showing variation in the lncRNA expression. The vertical lines correspond to 2-fold change, and the horizontal line represents a P value of 0.05. (d) Type and proportion of lncRNAs. (e) Hierarchical clustering of all differentially expressed lncRNAs in the lung tissues of rats in groups A and B. (f) Hierarchical clustering of all differentially expressed lncRNAs in the lung tissues of rats in groups B and C. (g) Differentially expressed genes were analyzed using DEGseq software based on the FPKM method (≥2-fold change with P <0.05). The number of differentially expressed lncRNAs was observed.

Figure 3

Differentially expressed mRNAs in the lung tissues of rats in the three groups. (a) A box and whisker plot of mRNAs showing the distributions of RNA intensities in all samples. (b) Heat map of correlation coefficients for all samples. (c) Volcano plots showing variation in the mRNA expression. The vertical lines correspond to 2-fold change, and the horizontal line represents a P value of 0.05. (d) Hierarchical clustering of all differentially expressed mRNAs in the lung tissues of rats in groups A and B. (e) Hierarchical clustering of all differentially expressed mRNAs in the lung tissues of rats in groups B and C. (f) Differentially expressed genes were analyzed using DEGseq software based on the FPKM method (≥2-fold change with P <0.05). The number of differentially expressed mRNAs was observed.

Figure 4

GO analyses of differentially expressed mRNAs, lncRNA targets, and circRNA genes between groups A and B. (a) Enrichment of biological processes, cellular components, and molecular functions in differentially expressed mRNAs. (b) Enrichment of biological processes, cellular components, and molecular functions in differentially expressed lncRNAs. (c) Enrichment of biological processes, cellular components, and molecular functions in differentially expressed circRNAs.

Figure 5

GO analyses of differentially expressed mRNAs, lncRNA targets, and circRNA genes between groups B and C. (a) Enrichment of biological processes, cellular components, and molecular functions in differentially expressed mRNAs. (b) Enrichment of biological processes, cellular components, and molecular functions in differentially expressed lncRNAs. (c) Enrichment of biological processes, cellular components, and molecular functions in differentially expressed circRNAs.

Figure 6

KEGG pathway classification of identified genes. The abscissa represents the annotated genes in the KEGG database; the ordinate represents categories in the KEGG database. (a) KEGG pathway classification of mRNAs that were differently expressed between groups A and B. (b) KEGG pathway classification of lncRNAs that were differently expressed between groups A and B. (c) KEGG pathway classification of circRNAs that were differently expressed between groups A and B.

Figure 7

KEGG pathway classification of identified genes. The abscissa represents the annotated genes in the KEGG database; the ordinate represents categories in the KEGG database. (a) KEGG pathway classification of mRNAs that were differently expressed between groups B and C. (b) KEGG pathway classification of lncRNAs that were differently expressed between groups B and C. (c) KEGG pathway classification of circRNAs that were differently expressed between groups B and C.

Figure 8

Construction of a circRNA–miRNA coexpression network for groups A and B. Red circle and green triangle represent circRNA and miRNA, respectively.

Figure 9

Construction of a circRNA–miRNA coexpression network for groups B and C. Red circle and green triangle represent circRNA and miRNA, respectively.