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Wu S, Liang T, Jiang J, Zhu J, Chen T, Zhou C, Huang S, Yao Y, Guo H, Ye Z, Chen L, Chen W, Fan B, Qin J, Liu L, Wu S, Ma F, Zhan X, Liu C. 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 Med Genomics 2023; 16:142. [PMID: 37340462 DOI: 10.1186/s12920-023-01566-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/31/2023] [Indexed: 06/22/2023] Open
Abstract
OBJECTIVE This article aims at exploring the role of hypoxia-related genes and immune cells in spinal tuberculosis and tuberculosis involving other organs. METHODS In 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. RESULTS The 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. CONCLUSION PSMB9, 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.
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Affiliation(s)
- Shaofeng Wu
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Tuo Liang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jie Jiang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jichong Zhu
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Tianyou Chen
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chenxing Zhou
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shengsheng Huang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuanlin Yao
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hao Guo
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhen Ye
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Liyi Chen
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wuhua Chen
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Binguang Fan
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiahui Qin
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Lu Liu
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Siling Wu
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Fengzhi Ma
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xinli Zhan
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China.
| | - Chong Liu
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China.
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Jiang J, Zhan X, Qu H, Liang T, Li H, Chen L, Huang S, Sun X, Jiang W, Chen J, Chen T, Yao Y, Wu S, Zhu J, Liu C. Upregulated of ANXA3, SORL1, and Neutrophils May Be Key Factors in the Progressionof Ankylosing Spondylitis. Front Immunol 2022; 13:861459. [PMID: 35464477 PMCID: PMC9019158 DOI: 10.3389/fimmu.2022.861459] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/18/2022] [Indexed: 11/16/2022] Open
Abstract
Introduction The specific pathogenesis of ankylosing spondylitis (AS) remains unclear, and our study aimed to investigate the possible pathogenesis of AS. Materials and Methods Two datasets were downloaded from the GEO database to perform differentially expressed gene analysis, GO enrichment analysis, KEGG pathway analysis, DO enrichment analysis, GSEA analysis of differentially expressed genes, and construction of diagnostic genes using SVM and WGCNA along with Hypoxia-related genes. Also, drug sensitivity analysis was performed on diagnostic genes. To identify the differentially expressed immune genes in the AS and control groups, we analyzed the composition of immune cells between them. Then, we examined differentially expressed genes in three AS interspinous ligament specimens and three Degenerative lumbar spine specimens using high-throughput sequencing while the immune cells were examined using the neutrophil count data from routine blood tests of 1770 HLA-B27-positive samples and 7939 HLA-B27-negative samples. To assess the relationship between ANXA3 and SORL1 and disease activity, we took the neutrophil counts of the first 50 patients with above-average BASDAI scores and the last 50 patients with below-average BASDAI scores for statistical analysis. We used immunohistochemistry to verify the expression of ANXA3 and SORL1 in AS and in controls. Results ANXA3 and SORL1 were identified as new diagnostic genes for AS. These two genes showed a significant differential expression between AS and controls, along with showing a significant positive correlation with the neutrophil count. The results of high-throughput sequencing verified that these two gene deletions were indeed differentially expressed in AS versus controls. Data from a total of 9707 routine blood tests showed that the neutrophil count was significantly higher in AS patients than in controls (p < 0.001). Patients with AS with a high BASDAI score had a much higher neutrophil count than those with a low score, and the difference was statistically significant (p < 0.001). The results of immunohistochemistry showed that the expression of ANXA3 and SORL1 in AS was significantly higher than that in the control group. Conclusion Upregulated of ANXA3, SORL1, and neutrophils may be a key factor in the progression of Ankylosing spondylitis.
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Affiliation(s)
- Jie Jiang
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xinli Zhan
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Haishun Qu
- Department of Traditional Chinese Medicine, The People's Hospital of Guangxi Zhuang Autonmous Region, Nanning, China
| | - Tuo Liang
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hao Li
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Liyi Chen
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shengsheng Huang
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xuhua Sun
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wenyong Jiang
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiarui Chen
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Tianyou Chen
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuanlin Yao
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shaofeng Wu
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jichong Zhu
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chong Liu
- Department of Spinal Orthopedic Surgery, The First Clinical Affiliated Hospital of Guangxi Medical University, Nanning, China
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