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Identification of benzo(a)pyrene-related toxicological targets and their role in chronic obstructive pulmonary disease pathogenesis: a comprehensive bioinformatics and machine learning approach.

作者信息

Deng Jiehua, Wei Lixia, Chen Yongyu, Li Xiaofeng, Zhang Hui, Wei Xuan, Feng Xin, Qiu Xue, Liang Bin, Zhang Jianquan

机构信息

Department of Respiratory and Critical Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, 3025 Shennan Zhong Lu, Shenzhen City, Guangdong Province, 518033, China.

Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.

出版信息

BMC Pharmacol Toxicol. 2025 Feb 17;26(1):33. doi: 10.1186/s40360-025-00842-1.


DOI:10.1186/s40360-025-00842-1
PMID:39962573
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11834632/
Abstract

BACKGROUND: Chronic obstructive pulmonary disease (COPD) pathogenesis is influenced by environmental factors, including Benzo(a)pyrene (BaP) exposure. This study aims to identify BaP-related toxicological targets and elucidate their roles in COPD development. METHODS: A comprehensive bioinformatics approach was employed, including the retrieval of BaP-related targets from the Comparative Toxicogenomics Database (CTD) and Super-PRED database, identification of differentially expressed genes (DEGs) from the GSE76925 dataset, and protein-protein interaction (PPI) network analysis. Functional enrichment and immune infiltration analyses were conducted using GO, KEGG, and ssGSEA algorithms. Feature genes related to BaP exposure were identified using SVM-RFE, Lasso, and RF machine learning methods. A nomogram was constructed and validated for COPD risk prediction. Molecular docking was performed to evaluate the binding affinity of BaP with proteins encoded by the feature genes. RESULTS: We identified 72 differentially expressed BaP-related toxicological targets in COPD. Functional enrichment analysis highlighted pathways related to oxidative stress and inflammation. Immune infiltration analysis revealed significant increases in B cells, DC, iDC, macrophages, T cells, T helper cells, Tcm, and TFH in COPD patients compared to controls. Correlation analysis showed strong links between oxidative stress, inflammation pathway scores, and the infiltration of immune cells, including aDC, macrophages, T cells, Th1 cells, and Th2 cells. Seven feature genes (ACE, APOE, CDK1, CTNNB1, GATA6, IRF1, SLC1A3) were identified across machine learning methods. A nomogram based on these genes showed high diagnostic accuracy and clinical utility. Molecular docking revealed the highest binding affinity of BaP with CDK1, suggestive of its pivotal role in BaP-induced COPD pathogenesis. CONCLUSIONS: The study elucidates the molecular mechanisms of BaP-induced COPD, specifically highlighting the role of oxidative stress and inflammation pathways in promoting immune cell infiltration. The identified feature genes may serve as potential biomarkers and therapeutic targets. Additionally, the constructed nomogram demonstrates high accuracy in predicting COPD risk, providing a valuable tool for clinical application in BaP-exposed individuals.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/87f54086cd37/40360_2025_842_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/33d79183e48f/40360_2025_842_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/e71fb46a6d5b/40360_2025_842_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/c234729e1f4d/40360_2025_842_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/7ef6c746fc1e/40360_2025_842_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/5cb8a5659716/40360_2025_842_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/679b7d51ba33/40360_2025_842_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/1d20c535af40/40360_2025_842_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/614b9e586e73/40360_2025_842_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/87f54086cd37/40360_2025_842_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/33d79183e48f/40360_2025_842_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/e71fb46a6d5b/40360_2025_842_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/c234729e1f4d/40360_2025_842_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/7ef6c746fc1e/40360_2025_842_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/5cb8a5659716/40360_2025_842_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/679b7d51ba33/40360_2025_842_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/1d20c535af40/40360_2025_842_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/614b9e586e73/40360_2025_842_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/748d/11834632/87f54086cd37/40360_2025_842_Fig9_HTML.jpg

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[2]
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本文引用的文献

[1]
Development and validation of a nomogram for predicting COPD: A nationwide population-based study in South Korea.

Medicine (Baltimore). 2024-9-27

[2]
Benzo[a]pyrene evokes epithelial-mesenchymal transition and pulmonary fibrosis through AhR-mediated Nrf2-p62 signaling.

J Hazard Mater. 2024-7-15

[3]
CDK1 and CCNA2 play important roles in oral squamous cell carcinoma.

Medicine (Baltimore). 2024-4-19

[4]
Citrus peel extract protects against diesel exhaust particle-induced chronic obstructive pulmonary disease-like lung lesions and oxidative stress.

Food Funct. 2023-10-30

[5]
Unraveling the protective role of Nrf2 in molluscs: Insights into mitochondrial and apoptosis pathways in the defense against Bap-induced oxidative stress.

Aquat Toxicol. 2023-11

[6]
Contribution of cuproptosis and Cu metabolism-associated genes to chronic obstructive pulmonary disease.

J Cell Mol Med. 2023-12

[7]
Wogonin alleviates BaP-induced DNA damage and oxidative stress in human airway epithelial cells by dual inhibiting CYP1A1 activity and expression.

Environ Toxicol. 2023-11

[8]
GRP/GRPR enhances alcohol-associated liver injury through the IRF1-mediated Caspase-1 inflammasome and NOX2-dependent ROS pathway.

Hepatology. 2024-2-1

[9]
A Single-Cell Atlas of Small Airway Disease in Chronic Obstructive Pulmonary Disease: A Cross-Sectional Study.

Am J Respir Crit Care Med. 2023-8-15

[10]
GATA6 coordinates cross-talk between BMP10 and oxidative stress axis in pulmonary arterial hypertension.

Sci Rep. 2023-4-22

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