Integrating bulk and single-cell RNA sequencing data: unveiling RNA methylation and autophagy-related signatures in chronic obstructive pulmonary disease patients
Abstract Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous lung disease influenced by epigenetic modifications, particularly RNA methylation. Emerging evidence also suggests that autophagy plays a crucial role in immune cell infiltration and is implicated in COPD progression. This stud...
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| Format: | Article |
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Nature Portfolio
2025-02-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-87437-2 |
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| author | Shi-Xia Liao Lan-Ying Zhang Ling-Mei Shi Huai-Yu Hu Yan-Hui Gu Ting-Hua Wang Yao Ouyang Peng-Peng Sun |
| author_facet | Shi-Xia Liao Lan-Ying Zhang Ling-Mei Shi Huai-Yu Hu Yan-Hui Gu Ting-Hua Wang Yao Ouyang Peng-Peng Sun |
| author_sort | Shi-Xia Liao |
| collection | DOAJ |
| description | Abstract Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous lung disease influenced by epigenetic modifications, particularly RNA methylation. Emerging evidence also suggests that autophagy plays a crucial role in immune cell infiltration and is implicated in COPD progression. This study aimed to investigate key RNA methylation regulators and explore the roles of RNA methylation and autophagy in COPD pathogenesis. We analyzed tissue-based bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) datasets from COPD and non-COPD patients, sourced from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified between COPD and non-COPD samples, and protein–protein interaction networks were constructed. Univariate logistic regression identified shared genes between DEGs and RNA methylation gene sets. Functional enrichment analyses, including Gene Ontology (GO), gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA), were performed. Weighted gene co-expression network analysis (WGCNA) and immune infiltration analysis were conducted. Integration with scRNA-seq data further elucidated changes in immune cell composition, and cell communication analysis assessed interactions between macrophages and other immune cells. AddModuleScore analysis quantified RNA methylation and autophagy effects. Finally, a COPD mouse model was used to validate the expression of critical RNA methylation genes (FTO and IGF2BP2) in lung macrophages via RT-qPCR and flow cytometry. As revealed, we identified 13 RNA methylation-related genes enriched in translation and methylation processes. GSEA and GSVA revealed significant enrichment of these genes in immune and autophagy pathways. WGCNA analysis pinpointed key hub genes linking RNA methylation and autophagy. Integrated scRNA-seq analysis demonstrated a marked reduction of macrophages in COPD, with FTO and IGF2BP2 emerging as critical RNA methylation regulators. Macrophages with elevated RNA methylation and autophagy scores had increased interactions with other immune cells. In COPD mouse models, decreased expression of FTO and IGF2BP2 in lung macrophages was validated. Taken together, this study highlights the significant roles of RNA methylation in relation to autophagy pathways in the context of COPD. We identified key RNA methylation-related hub genes, such as FTO and IGF2BP2, which were found to have decreased expression in COPD macrophages. These findings provide novel genetic insights into the epigenetic mechanisms of COPD and suggest potential avenues for developing diagnostic and therapeutic strategies. |
| format | Article |
| id | doaj-art-9e567425443944809376fc53e6591fa3 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-9e567425443944809376fc53e6591fa32025-02-02T12:20:02ZengNature PortfolioScientific Reports2045-23222025-02-0115112010.1038/s41598-025-87437-2Integrating bulk and single-cell RNA sequencing data: unveiling RNA methylation and autophagy-related signatures in chronic obstructive pulmonary disease patientsShi-Xia Liao0Lan-Ying Zhang1Ling-Mei Shi2Huai-Yu Hu3Yan-Hui Gu4Ting-Hua Wang5Yao Ouyang6Peng-Peng Sun7Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical UniversityDepartment of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical UniversityDepartment of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical UniversityShenQi Ethnic Medicine College of Guizhou Medical UniversityDepartment of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical UniversityInstitute of Neurological Disease, West China Hospital, Sichuan UniversityDepartment of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical UniversityDepartment of Osteopathy, Affiliated Hospital of Zunyi Medical UniversityAbstract Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous lung disease influenced by epigenetic modifications, particularly RNA methylation. Emerging evidence also suggests that autophagy plays a crucial role in immune cell infiltration and is implicated in COPD progression. This study aimed to investigate key RNA methylation regulators and explore the roles of RNA methylation and autophagy in COPD pathogenesis. We analyzed tissue-based bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) datasets from COPD and non-COPD patients, sourced from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified between COPD and non-COPD samples, and protein–protein interaction networks were constructed. Univariate logistic regression identified shared genes between DEGs and RNA methylation gene sets. Functional enrichment analyses, including Gene Ontology (GO), gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA), were performed. Weighted gene co-expression network analysis (WGCNA) and immune infiltration analysis were conducted. Integration with scRNA-seq data further elucidated changes in immune cell composition, and cell communication analysis assessed interactions between macrophages and other immune cells. AddModuleScore analysis quantified RNA methylation and autophagy effects. Finally, a COPD mouse model was used to validate the expression of critical RNA methylation genes (FTO and IGF2BP2) in lung macrophages via RT-qPCR and flow cytometry. As revealed, we identified 13 RNA methylation-related genes enriched in translation and methylation processes. GSEA and GSVA revealed significant enrichment of these genes in immune and autophagy pathways. WGCNA analysis pinpointed key hub genes linking RNA methylation and autophagy. Integrated scRNA-seq analysis demonstrated a marked reduction of macrophages in COPD, with FTO and IGF2BP2 emerging as critical RNA methylation regulators. Macrophages with elevated RNA methylation and autophagy scores had increased interactions with other immune cells. In COPD mouse models, decreased expression of FTO and IGF2BP2 in lung macrophages was validated. Taken together, this study highlights the significant roles of RNA methylation in relation to autophagy pathways in the context of COPD. We identified key RNA methylation-related hub genes, such as FTO and IGF2BP2, which were found to have decreased expression in COPD macrophages. These findings provide novel genetic insights into the epigenetic mechanisms of COPD and suggest potential avenues for developing diagnostic and therapeutic strategies.https://doi.org/10.1038/s41598-025-87437-2COPDRNA methylationAutophagyMacrophagesSingle cell RNA sequencing |
| spellingShingle | Shi-Xia Liao Lan-Ying Zhang Ling-Mei Shi Huai-Yu Hu Yan-Hui Gu Ting-Hua Wang Yao Ouyang Peng-Peng Sun Integrating bulk and single-cell RNA sequencing data: unveiling RNA methylation and autophagy-related signatures in chronic obstructive pulmonary disease patients Scientific Reports COPD RNA methylation Autophagy Macrophages Single cell RNA sequencing |
| title | Integrating bulk and single-cell RNA sequencing data: unveiling RNA methylation and autophagy-related signatures in chronic obstructive pulmonary disease patients |
| title_full | Integrating bulk and single-cell RNA sequencing data: unveiling RNA methylation and autophagy-related signatures in chronic obstructive pulmonary disease patients |
| title_fullStr | Integrating bulk and single-cell RNA sequencing data: unveiling RNA methylation and autophagy-related signatures in chronic obstructive pulmonary disease patients |
| title_full_unstemmed | Integrating bulk and single-cell RNA sequencing data: unveiling RNA methylation and autophagy-related signatures in chronic obstructive pulmonary disease patients |
| title_short | Integrating bulk and single-cell RNA sequencing data: unveiling RNA methylation and autophagy-related signatures in chronic obstructive pulmonary disease patients |
| title_sort | integrating bulk and single cell rna sequencing data unveiling rna methylation and autophagy related signatures in chronic obstructive pulmonary disease patients |
| topic | COPD RNA methylation Autophagy Macrophages Single cell RNA sequencing |
| url | https://doi.org/10.1038/s41598-025-87437-2 |
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