Proteomic analysis to identification of hypoxia related markers in spinal tuberculosis: a study based on weighted gene co-expression network analysis and machine learning

BMC Medical Genomics

Research

Liyi Chen¹  Yuanlin Yao¹  Tianyou Chen¹  Chong Liu¹  Xinli Zhan¹  Wuhua Chen¹  Jiahui Qin¹  Siling Wu¹  Lu Liu¹  Zhen Ye¹  Hao Guo¹  Tuo Liang¹  Chenxing Zhou¹  Jie Jiang¹  Shengsheng Huang¹  Jichong Zhu¹  Binguang Fan¹  Fengzhi Ma¹  Shaofeng Wu¹ 

[1] The First Affiliated Hospital of Guangxi Medical University, Nanning, China;

关键词: Spinal tuberculosis;    WGCNA;    Machine learning;    ssGSEA;    Pharmaco-transcriptomic analysis;   

DOI  :  10.1186/s12920-023-01566-z

 received in 2022-08-23, accepted in 2023-05-31,  发布年份 2023

来源: Springer

【 摘 要 】

ObjectiveThis article aims at exploring the role of hypoxia-related genes and immune cells in spinal tuberculosis and tuberculosis involving other organs.MethodsIn this study, label-free quantitative proteomics analysis was performed on the intervertebral discs (fibrous cartilaginous tissues) obtained from five spinal tuberculosis (TB) patients. Key proteins associated with hypoxia were identified using molecular complex detection (MCODE), weighted gene co-expression network analysis(WGCNA), least absolute shrinkage and selection operator (LASSO), and support vector machine recursive feature Elimination (SVM-REF) methods, and their diagnostic and predictive values were assessed. Immune cell correlation analysis was then performed using the Single Sample Gene Set Enrichment Analysis (ssGSEA) method. In addition, a pharmaco-transcriptomic analysis was also performed to identify targets for treatment.ResultsThe three genes, namely proteasome 20 S subunit beta 9 (PSMB9), signal transducer and activator of transcription 1 (STAT1), and transporter 1 (TAP1), were identified in the present study. The expression of these genes was found to be particularly high in patients with spinal TB and other extrapulmonary TB, as well as in TB and multidrug-resistant TB (p-value < 0.05). They revealed high diagnostic and predictive values and were closely related to the expression of multiple immune cells (p-value < 0.05). It was inferred that the expression of PSMB9, STAT 1, and TAP1 could be regulated by different medicinal chemicals.ConclusionPSMB9, STAT1, and TAP1, might play a key role in the pathogenesis of TB, including spinal TB, and the protein product of the genes can be served as diagnostic markers and potential therapeutic target for TB.

【 授权许可】

CC BY   
© The Author(s) 2023

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