Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma
Abstract Despite advances in diagnostic and therapeutic strategies, the prognosis of lung squamous cell carcinoma (LUSC) patients remains poor, and the potential of microbiome-based prognostic biomarkers and therapeutic targets remains largely unexplored. LUSC patient data from The Cancer Genome Atl...
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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/s41598-025-88120-2 |
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| author | Fan Yang Xiaodong Jia Zihuan Ma Siyao Liu Chunzi Liu Dan Chen Xiuju Wang Niansong Qian Hui Ma |
| author_facet | Fan Yang Xiaodong Jia Zihuan Ma Siyao Liu Chunzi Liu Dan Chen Xiuju Wang Niansong Qian Hui Ma |
| author_sort | Fan Yang |
| collection | DOAJ |
| description | Abstract Despite advances in diagnostic and therapeutic strategies, the prognosis of lung squamous cell carcinoma (LUSC) patients remains poor, and the potential of microbiome-based prognostic biomarkers and therapeutic targets remains largely unexplored. LUSC patient data from The Cancer Genome Atlas (TCGA), including microbial genus level abundance data and RNA sequencing (RNA-Seq) data, were used as a training dataset. Two other independent datasets GSE19188 and GSE157009 serve as validation datasets. A microbiome-based risk score (RS) model was constructed by univariate Cox regression analysis combined with the least absolute contraction and selection operator (LASSO) regression. 18 microbial genera were found to be significantly associated with RFS in LUSC patients. The microbial signature built with these microbial genera, exhibited robust predictive accuracy in both the training and validation datasets. Furthermore, hub mRNA between high- and low-risk groups were selected by XGBOOST and intersect with mRNAs screened by univariate Cox regression analysis, finally identifying four mRNA significantly associated with LUSC prognosis. This study reveals a complex interplay between the lung microbiome and genetic biomarkers, and identifies specific microbial-based and mRNA associated with prognosis in LUSC. These findings provide a basis for future studies aimed to elucidate the mechanisms underlying these associations and provide potential biomarkers for guiding treatment decisions and improving patient outcomes. |
| format | Article |
| id | doaj-art-3d7b629d39ef4724a4b5f84d355cd56a |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-3d7b629d39ef4724a4b5f84d355cd56a2025-02-09T12:29:21ZengNature PortfolioScientific Reports2045-23222025-02-0115111210.1038/s41598-025-88120-2Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinomaFan Yang0Xiaodong Jia1Zihuan Ma2Siyao Liu3Chunzi Liu4Dan Chen5Xiuju Wang6Niansong Qian7Hui Ma8Senior Department of Oncology, The Fifth Medical Center of Chinese PLA General HospitalSenior Department of Oncology, The Fifth Medical Center of Chinese PLA General HospitalBeijing ChosenMed Clinical Laboratory Co. Ltd, Jinghai Industrial Park, Economic and Technological Development AreaBeijing ChosenMed Clinical Laboratory Co. Ltd, Jinghai Industrial Park, Economic and Technological Development AreaSenior Department of Oncology, The Fifth Medical Center of Chinese PLA General HospitalSenior Department of Oncology, The Fifth Medical Center of Chinese PLA General HospitalSenior Department of Oncology, The Fifth Medical Center of Chinese PLA General HospitalSenior Department of Thoracic Oncology, Respiratory and Critical Care Medicine, The Eighth Medical Center of People’s Liberation Army General HospitalNursing Department of Chinese, PLA General HospitalAbstract Despite advances in diagnostic and therapeutic strategies, the prognosis of lung squamous cell carcinoma (LUSC) patients remains poor, and the potential of microbiome-based prognostic biomarkers and therapeutic targets remains largely unexplored. LUSC patient data from The Cancer Genome Atlas (TCGA), including microbial genus level abundance data and RNA sequencing (RNA-Seq) data, were used as a training dataset. Two other independent datasets GSE19188 and GSE157009 serve as validation datasets. A microbiome-based risk score (RS) model was constructed by univariate Cox regression analysis combined with the least absolute contraction and selection operator (LASSO) regression. 18 microbial genera were found to be significantly associated with RFS in LUSC patients. The microbial signature built with these microbial genera, exhibited robust predictive accuracy in both the training and validation datasets. Furthermore, hub mRNA between high- and low-risk groups were selected by XGBOOST and intersect with mRNAs screened by univariate Cox regression analysis, finally identifying four mRNA significantly associated with LUSC prognosis. This study reveals a complex interplay between the lung microbiome and genetic biomarkers, and identifies specific microbial-based and mRNA associated with prognosis in LUSC. These findings provide a basis for future studies aimed to elucidate the mechanisms underlying these associations and provide potential biomarkers for guiding treatment decisions and improving patient outcomes.https://doi.org/10.1038/s41598-025-88120-2Lung squamous cell carcinomaMicrobiomePrognosisRisk score model |
| spellingShingle | Fan Yang Xiaodong Jia Zihuan Ma Siyao Liu Chunzi Liu Dan Chen Xiuju Wang Niansong Qian Hui Ma Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma Scientific Reports Lung squamous cell carcinoma Microbiome Prognosis Risk score model |
| title | Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma |
| title_full | Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma |
| title_fullStr | Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma |
| title_full_unstemmed | Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma |
| title_short | Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma |
| title_sort | exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma |
| topic | Lung squamous cell carcinoma Microbiome Prognosis Risk score model |
| url | https://doi.org/10.1038/s41598-025-88120-2 |
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