Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by chronic airway inflammation and is closely linked to oxidative stress. This study aimed to identify and validate key oxidative stress-related genes and pathways involved in COPD using integrated bioinformatics and experimental approaches. Public COPD datasets were obtained from the Gene Expression Omnibus (GEO) database, and oxidative stress-related genes were retrieved from the GeneCards database. Differentially expressed genes (DEGs) were screened and analyzed for functional enrichment. Machine-learning algorithms, including Least Absolute Shrinkage and Selection Operator (LASSO) regression and Random Forest, were used to identify hub genes and evaluate diagnostic value by calculating the area under the receiver operating characteristic (ROC) curve (AUC). Single-cell RNA sequencing (scRNA-seq) data were analyzed to determine the distribution of hub genes across different cell types. Finally, a COPD combined oxidative stress cell model was established using human bronchial epithelial cells (BEAS-2B), and key gene expression was experimentally validated. We identified 76 overlapping genes associated with both COPD and oxidative stress, mainly enriched in necroptosis, JAK-STAT, MAPK, and related pathways. 12 hub genes were screened using machine-learning methods. Single-cell analysis showed that TPPP3 and VEGFA were predominantly expressed in epithelial cells. Experimental validation confirmed the bioinformatics predictions at the gene level. This study identified and validated 12 oxidative stress-related hub genes in COPD, highlighting TPPP3 and VEGFA as key genes enriched in epithelial cells and potentially involved in tissue remodeling. These findings not only provide insights for exploring new therapeutic strategies but may also serve as potential diagnostic biomarkers or candidate therapeutic targets for COPD.
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Data availability
The datasets and codes used or analyzed during the current study are available from the corresponding author or first author upon request.
Abbreviations
- COPD:
-
Chronic obstructive pulmonary disease
- ROS:
-
Reactive oxygen species
- DEGs:
-
Differentially expressed genes
- FC:
-
Fold change
- GO:
-
Gene ontology
- KEGG:
-
Kyoto encyclopedia of genes and genomes
- LASSO:
-
Least absolute shrinkage and selection operator
- ROC:
-
Receiver operating characteristic
- AUC:
-
Area under the curve
- scRNA-seq:
-
Single-cell RNA sequencing
- PCA:
-
Principal component analysis
- t-SNE:
-
T-distributed stochastic neighbor embedding
- UMAP:
-
Uniform manifold approximation and projection
- BP:
-
Biological process
- CC:
-
Cellular component
- MF:
-
Molecular function
- CSE:
-
Cigarette smoke extract
- PBS:
-
Phosphate buffered saline
- DCFH-DA:
-
2',7'-Dichlorodihydrofluorescein diacetate
- SOD:
-
Superoxide dismutase
- CAT:
-
Catalase
- IL-1β:
-
Interleukin-1β
- IL-6:
-
Interleukin-6
- TNF-α:
-
Tumor necrosis factor-α
- ELISA:
-
Enzyme-linked immunosorbent assay
- JAK-STAT:
-
Janus kinase-signal transducer and activator of transcription
- qRT-PCR:
-
Quantitative real-time PCR
- cDNA:
-
Complementary DNA
- qPCR:
-
Quantitative polymerase chain reaction
- SEM:
-
Standard error of the mean
- MDG:
-
Mean decrease gini
- SVA:
-
Surrogate variable analysis
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Funding
This study received financial support from the National Natural Science Foundation of China (No.81973631), The Science and Technology Commission of Shanghai Municipality (YDZX00003008), Basic research on kidney tonic formula for intervention in several airway inflammatory diseases (three projects)(2022QD056), 2023 Ground High Construction Project—First-class Integrative Medicine/Summit Discipline Construction—Cultivation of Provincial and Ministerial Key Laboratories of Integrative Medicine (DGF601013), and NDRC Equipment Reform Special Project-DK07 Basic Technology Platform for Scientific Research in the Disciplines of Integrative Medicine (DKF132001).
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Wenglam Choi conceived of the presented idea and performed the computations and, experimentation. Yueren Wu assisted with calculations and article writing as well as code handling. Wenjing Chen and Yuting Shi assisted in laboratory operations and data processing. Weihang Luo and Xinyuan Wu assisted experimental operation. Zhenhui Ruan collected references and data. Jingcheng Dong provided guidance and article correction. All authors discussed the results and contributed to the final manuscript.
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Choi, W., Wu, Y., Chen, W. et al. Oxidative stress-associated genes TPPP3 and VEGFA in COPD revealed by bulk and single-cell sequencing analysis. Sci Rep (2026). https://doi.org/10.1038/s41598-026-37375-4
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DOI: https://doi.org/10.1038/s41598-026-37375-4


