Combining Bulk and Single-Cell RNA Sequencing Data to Identify RNA methylation and Autophagy-Related Signatures in Patients with Chronic Obstructive Pulmonary Disease

Abstract

AbstractBackgroundChronic Obstructive Pulmonary Disease (COPD) is a heterogeneous lung condition associated with RNA methylation and autophagy. However, the specific autophagy-related genes and RNA methylation regulators involved in COPD development remain unknown.MethodsWe analyzed COPD and non-COPD patients datasets obtained from the Gene Expression Omnibus database, including Tissue Sequencing Transcriptome (bulk-seq) and single-cell sequencing (scRNA-seq) data. Differentially expressed genes (DEGs) were identified through differential genetic analysis using non-COPD bulk-seq data as the control group and COPD samples were used as the experimental group. Animal experiments were conducted to validate the expression of key genes. COPD model mice were exposed to smoke for four months, and lung function and histopathological changes were assessed. The mRNA and protein expression levels ofFTO, IGF2BP2, DDIT3, DNAJB1, andYTHDF3were measured using RT-qPCR and Western blotting, respectively.ResultsWe identifiedFTO, IGF2BP2, andYTHDF3as key methylation genes, along with autophagy hub genesDDIT3andDNAJB1. Animal experiments showed significantly increased mRNA and protein levels ofFTO, YTHDF3and DNAJB1 and significantly decreased levels ofIGF2BP2in lung tissue of COPD mice compared to the control group.ConclusionOur findings suggest thatDDIT3andDNAJB1as autophagy hub genes, along withFTO, IGF2BP2andYTHDF3as RNA methylation genes, may play crucial roles in the development of COPD. These findings, supported by bulk-seq and scRNA-seq data, contribute novel genetic evidence for understanding the epigenetics of COPD.