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Wang X, Chan S, Chen J, Xu Y, Dai L, Han Q, Wang Z, Zuo X, Yang Y, Zhao H, Wang M, Wang C, Li Z, Zhang H, Chen W. Robust machine-learning based prognostic index using cytotoxic T lymphocyte evasion genes highlights potential therapeutic targets in colorectal cancer. Cancer Cell Int 2024; 24:52. [PMID: 38297270 PMCID: PMC10829178 DOI: 10.1186/s12935-024-03239-y] [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: 12/04/2023] [Accepted: 01/24/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND A minute fraction of patients stands to derive substantial benefits from immunotherapy, primarily attributable to immune evasion. Our objective was to formulate a predictive signature rooted in genes associated with cytotoxic T lymphocyte evasion (CERGs), with the aim of predicting outcomes and discerning immunotherapeutic response in colorectal cancer (CRC). METHODS 101 machine learning algorithm combinations were applied to calculate the CERGs prognostic index (CERPI) under the cross-validation framework, and patients with CRC were separated into high- and low-CERPI groups. Relationship between immune cell infiltration levels, immune-related scores, malignant phenotypes and CERPI were further analyzed. Various machine learning methods were used to identify key genes related to both patient survival and immunotherapy benefits. Expression of HOXC6, G0S2, and MX2 was evaluated and the effects of HOXC6 and G0S2 on the viability and migration of a CRC cell line were in-vitro verified. RESULTS The CERPI demonstrated robust prognostic efficacy in predicting the overall survival of CRC patients, establishing itself as an independent predictor of patient outcomes. The low-CERPI group exhibited elevated levels of immune cell infiltration and lower scores for tumor immune dysfunction and exclusion, indicative of a greater potential benefit from immunotherapy. Moreover, there was a positive correlation between CERPI levels and malignant tumor phenotypes, suggesting that heightened CERPI expression contributes to both the occurrence and progression of tumors. Thirteen key genes were identified, and their expression patterns were scrutinized through the analysis of single-cell datasets. Notably, HOXC6, G0S2, and MX2 exhibited upregulation in both CRC cell lines and tissues. Subsequent knockdown experiments targeting G0S2 and HOXC6 resulted in a significant suppression of CRC cell viability and migration. CONCLUSION We developed the CERPI for effectively predicting survival and response to immunotherapy in patients, and these results may provide guidance for CRC diagnosis and precise treatment.
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Affiliation(s)
- Xu Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Shixin Chan
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Jiajie Chen
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Yuanmin Xu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Longfei Dai
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Qijun Han
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Zhenglin Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Xiaomin Zuo
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Yang Yang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Hu Zhao
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Ming Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Chen Wang
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Zichen Li
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Huabing Zhang
- Department of Biochemistry and Molecular Biology, Metabolic Disease Research Center, School of Basic Medicine, Anhui Medical University, Hefei, 230032, Anhui, China.
- The First Affiliated Chuzhou Hospital of Anhui Medical University, Chuzhou, 239000, Anhui, China.
| | - Wei Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China.
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Wang M, Xu X, Li J, Gao Z, Ding Y, Chen X, Xiang Q, Shen L. Integrated bioinformatics and experiment revealed that cuproptosis is the potential common pathogenesis of three kinds of primary cardiomyopathy. Aging (Albany NY) 2023; 15:14210-14241. [PMID: 38085668 PMCID: PMC10756114 DOI: 10.18632/aging.205298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/06/2023] [Indexed: 12/21/2023]
Abstract
Cuproptosis is a recently reported new mode of programmed cell death which might be a potential co-pathogenesis of three kinds of primary cardiomyopathy. However, no investigation has reported a clear relevance between primary cardiomyopathy and cuproptosis. In this study, the differential cuproptosis-related genes (CRGs) shared by three kinds of primary cardiomyopathy were identified in training sets. As a result, four CRGs shared by three kinds of primary cardiomyopathy were acquired and they were mainly related to biological processes such as cell death and immuno-inflammatory response through differential analysis, correlation analysis, GSEA, GSVA and immune cell infiltration analysis. Then, three key CRGs (K-CRGs) with high diagnostic value were identified by LASSO regression. The results of nomogram, machine learning, ROC analysis, calibration curve and decision curve indicated that the K-CRGs exhibited outstanding performance in the diagnosis of three kinds of primary cardiomyopathy. After that, in each disease, two molecular subtypes clusters were distinguished. There were many differences between different clusters in the biological processes associated with cell death and immunoinflammation and K-CRGs had excellent molecular subtype identification efficacy. Eventually, results from validation datasets and in vitro experiments verified the role of K-CRGs in diagnosis of primary cardiomyopathy, identification of primary cardiomyopathic molecular subtypes and pathogenesis of cuproptosis. In conclusion, this study found that cuproptosis might be the potential common pathogenesis of three kinds of primary cardiomyopathy and K-CRGs might be promising biomarkers for the diagnosis and molecular subtypes identification of primary cardiomyopathy.
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Affiliation(s)
- Mengxi Wang
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaozhuo Xu
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jianghong Li
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ziwei Gao
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yuhan Ding
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaohu Chen
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Qian Xiang
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Le Shen
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
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