Transcriptome sequencing of lncRNAs, circRNAs, miRNAs, mRNAs and interaction network constructing in acute exacerbation of idiopathic pulmonary fibrosis [microarray]

Background: Acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF) is the most common cause of acute respiratory deterioration and death in IPF patients, with an elusive etiology and pathogenesis. Roles of noncoding RNAs in AE-IPF have been proposed, however, it was rare to find studies have systematically investigated the crosstalk among various transcripts until now. The construction of RNA functional networks such as lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA interaction networks could therefore facilitate our understanding of RNA interactions in AE-IPF. The study aimed to identify the expression differences of RNA transcripts in RNA sequencing from AE-IPF patients and stable IPF (S-IPF), and further to construct the potential RNA networks. Methods: Five AE-IPF patients and five S-IPF were recruited in this study to perform RNA sequencing and miRNA sequencing. The differentially expression profiles of lncRNAs, circRNAs, miRNAs and mRNAs between AE-IPF and S-IPF patients were identified for further analyses. Gene Oncology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of were performed. The competing endogenous RNAs (ceRNAs) network of lncRNA/circRNA-miRNA-mRNA was constructed, and the core regulatory molecules in the ceRNA network were analyzed. Results: A total of 69 lncRNAs, 150 circRNAs, 27 miRNAs and 56 mRNAs were differentially expressed between AE-IPF and S-IPF. GO and KEGG analysis show that differentially expression mRNAs are significantly associated with tight junction and Hepatitis C, etc. In the ceRNA network, all nodes are directly or indirectly involved in the progression of AE-IPF. 1 lncRNAs, 6 circRNAs, 1 miRNAs, and 5 mRNAs constituted a hsa-miR-150-5p core sub-network. Based on the analysis of ceRNA sub-network, NR_120628/hsa-miR-150-5p/E2F3 and has-circ-0053515/hsa-miR-150-5p/E2F3 were considered to be the key ceRNA axis. Conclusions: In conclusion, this study reveals NR_120628/hsa-miR-150-5p/E2F3 and has-circ-0053515/hsa-miR-150-5p/E2F3 may be the key ceRNA axis in the regulation of AE-IPF, providing clues for future studies on their roles for AE-IPF. Our findings will help to explore the pathological mechanism of AE-IPF from a transcriptomic perspective and provide enlightenment for the biomarker and therapeutic targets of AE-IPF. This study complied with the Declaration of Helsinki and was approved by the Ethics Committee of the Affiliated Hospital of Liaoning University of Traditional Chinese Medicine with the approval number 20200055FS(KT)-028-02. All participants provided written informed consent prior to research participation. Ten participants (5 patients with AE-IPF and 5 patients with IPF) were recruited from the Affiliated Hospital of Liaoning University of Traditional Chinese Medicine (Shenyang, China) as the sequencing cohort. All the subjects aged between 45 to 80 years old. The diagnosis of AE-IPF was comfirmed by clinical symptoms of significant exacerbation of acute dyspneachest within a month and high resolution computed tomography of new GGO and/or consolidation shadows in both lungs on the background of UIP type changes. All AE-IPF patients met the international working group criteria for AE-IPF. The diagnosis of IPF was mainly according to UIP of HRCT which mentioned by the ATS/ERS/JRS/ALAT criteria for IPF [1]. Individuals with other respiratory or rheumatic immune diseases were all excluded from the study. Fresh peripheral whole blood samples (4-8mL) were drawn from each subject and centrifuged to get plasma. Samples were frozen on liquid nitrogen and then all frozen samples were transported in frozen conditions using dry ice.