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Oxidative stress-associated genes TPPP3 and VEGFA in COPD revealed by bulk and single-cell sequencing analysis
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  • Published: 31 January 2026

Oxidative stress-associated genes TPPP3 and VEGFA in COPD revealed by bulk and single-cell sequencing analysis

  • Wenglam Choi1,
  • Yueren Wu1,
  • Wenjing Chen1,
  • Yuting Shi1,
  • Weihang Luo1,
  • Xinyuan Wu1,
  • Zhenhui Ruan1 &
  • …
  • Jingcheng Dong1,2 

Scientific Reports , Article number:  (2026) Cite this article

We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Bioinformatics
  • Biomarkers
  • Chronic obstructive pulmonary disease
  • Mechanisms of disease

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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Authors and Affiliations

  1. Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China

    Wenglam Choi, Yueren Wu, Wenjing Chen, Yuting Shi, Weihang Luo, Xinyuan Wu, Zhenhui Ruan & Jingcheng Dong

  2. Institutes of Integrative Medicine, Fudan University, Shanghai, 200040, China

    Jingcheng Dong

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Contributions

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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Correspondence to Jingcheng Dong.

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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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  • Received: 11 October 2024

  • Accepted: 21 January 2026

  • Published: 31 January 2026

  • DOI: https://doi.org/10.1038/s41598-026-37375-4

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Keywords

  • Chronic obstructive pulmonary disease
  • Oxidative stress
  • Bioinformatics
  • Single-cell analysis
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