Whole transcriptome sequencing identifies key lncRNAs,circRNAs, and mRNAs for exploring the pathogenesis and therapeutic target of mouse pneumoconiosis

The purpose of this study was to characterize the lncRNA, circRNA, and mRNA profile of silica-treated pneumoconiosis mice model and to analyze the changes in differential expression genes, biological processes, and signaling pathways based on the differently expressed genes. Lung tissues from 12 mice, 6 silicosis mice, and 6 normal saline were collected and analyzed for their lncRNA, circRNA, and mRNA profile profiles. After qualified library inspection, Illumina PE150 sequencing was performed after pooling according to the effective concentration of the library and data output requirements. Differentially expressed mRNAs/lncRNAs/circRNAs (DEMs) were identified between the different groups, the target miRNAs (co-pre-miRNAs) were obtained by intersecting the miRNAs predicted by DElncRNA and DEcircRNA, respectively, and the target mRNAs (co-mRNA) were obtained by intersecting the mRNAs predicted by target miRNA and DEGs. Then, the lncRNA/circRNA-miRNA-mRNA networks were constructed by Cytoscape. Next, the key mRNAs were obtained by protein-protein interaction (PPI) analysis, and the key lncRNAs/circRNAs were selected by correlation analysis. Moreover, the expression of the key lncRNAs, circRNAs and mRNAs on chromosome were studied by the “circlize” package. Furthermore, the TFs-miRNA-mRNA network was constructed and the function of DEGs were explored by Ingenuity Pathway Analysis (IPA). Finally, We used the Drug-Gene Interaction database to predict potential drugs that could interfere with key genes,which may help to find promising treatment. This study constructed the lncRNA/circRNA-miRNA-mRNA and TFs-miRNA-mRNA networks, which could deepen the potential molecular regulatory mechanism of pneumoconiosis/silicosis.