Journal Article

RNA sequencing reveals the emerging role of bronchoalveolar lavage fluid exosome lncRNAs in acute lung injury

Wan, Bing, Wang, Li, Gao, Yizhou, Wang, Jinqiang, Li, Jinghang, Song, Yuanyuan, Huang, Mao, Wang, Xiaowei, Zhang, Xiuwei, Song, Meijuan, Shen, Xiaowei

2022

Overview

Bronchoalveolar lavage fluid (BALF) exosomes possess different properties in different diseases, which are mediated through microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), among others. By sequencing the differentially expressed lncRNAs in BALF exosomes, we seek potential targets for the diagnosis and treatment of acute lung injury (ALI). Considering that human and rat genes are about 80% similar, ALI was induced using lipopolysaccharide in six male Wistar rats, with six rats as control (all weighing 200 ± 20 g and aged 6-8 weeks). BALF exosomes were obtained 24 h after ALI. The exosomes in BALF were extracted by ultracentrifugation. The differential expression of BALF exosomal lncRNAs in BALF was analyzed by RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the functions of differentially expressed lncRNAs, which were confirmed by reverse transcription-polymerase chain reaction. Compared with the control group, the ALI group displayed a higher wet/dry ratio, tumor necrosis factor-α levels, and interleukin-6 levels (all < 0.001). The airway injection of exosomes in rats led to significant infiltration by neutrophils. A total of 2,958 differentially expressed exosomal lncRNAs were identified, including 2,524 upregulated and 434 downregulated ones. Five lncRNAs confirmed the reliability of the sequencing data. The top three GO functions were phagocytic vesicle membrane, regulation of receptor biosynthesis process, and I-SMAD binding. Salmonella infection, Toll-like receptor signaling pathway, and osteoclast differentiation were the most enriched KEGG pathways. The lncRNA-miRNA interaction network of the five confirmed lncRNAs could be predicted using miRDB. BALF-derived exosomes play an important role in ALI development and help identify potential therapeutic targets related to ALI.

• Publisher: PeerJ. Ltd,PeerJ, Inc,PeerJ Inc
• Subject: Acute lung injury / Acute Lung Injury - genetics / Acute respiratory distress syndrome / Alveoli / Analysis / Animals / Asthma / Biochemistry / Biomarkers / Bronchoalveolar Lavage Fluid / Bronchus / Cell Biology / Cytokines / Diagnosis / Edema / Enzymes / Exosomes / Exosomes - genetics / Experiments / Gene Regulatory Networks / Genomes / Genomics / Histology / Humans / Interleukin 6 / Intubation / Lavage / Leukocytes (neutrophilic) / Lipids / Lipopolysaccharides / Long noncoding RNA / Lungs / Male / Medical research / Metastases / MicroRNA / MicroRNAs / MicroRNAs - genetics / miRNA / Molecular Biology / Non-coding RNA / Osteoclastogenesis / Phagocytes / Physiological aspects / Polymerase chain reaction / Pore size / Proteins / Rats / Rats, Wistar / Reproducibility of Results / Respiratory Medicine / Reverse transcription / RNA sequencing / RNA, Long Noncoding - genetics / Sequence Analysis, RNA / Signal transduction / Smad protein / Therapeutic targets / Toll-like receptors / Tumor necrosis factor-TNF / Tumor necrosis factor-α / Ultracentrifugation