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Yang S, Wang X, Huan R, Deng M, Kong Z, Xiong Y, Luo T, Jin Z, Liu J, Chu L, Han G, Zhang J, Tan Y. Machine learning unveils immune-related signature in multicenter glioma studies. iScience 2024; 27:109317. [PMID: 38500821 PMCID: PMC10946333 DOI: 10.1016/j.isci.2024.109317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 01/11/2024] [Accepted: 02/17/2024] [Indexed: 03/20/2024] Open
Abstract
In glioma molecular subtyping, existing biomarkers are limited, prompting the development of new ones. We present a multicenter study-derived consensus immune-related and prognostic gene signature (CIPS) using an optimal risk score model and 101 algorithms. CIPS, an independent risk factor, showed stable and powerful predictive performance for overall and progression-free survival, surpassing traditional clinical variables. The risk score correlated significantly with the immune microenvironment, indicating potential sensitivity to immunotherapy. High-risk groups exhibited distinct chemotherapy drug sensitivity. Seven signature genes, including IGFBP2 and TNFRSF12A, were validated by qRT-PCR, with higher expression in tumors and prognostic relevance. TNFRSF12A, upregulated in GBM, demonstrated inhibitory effects on glioma cell proliferation, migration, and invasion. CIPS emerges as a robust tool for enhancing individual glioma patient outcomes, while IGFBP2 and TNFRSF12A pose as promising tumor markers and therapeutic targets.
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Affiliation(s)
- Sha Yang
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China
| | - Xiang Wang
- Department of Neurosurgery, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Renzheng Huan
- Department of Neurosurgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Mei Deng
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Zhuo Kong
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Yunbiao Xiong
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Tao Luo
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Zheng Jin
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Jian Liu
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Liangzhao Chu
- Department of Neurosurgery, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Guoqiang Han
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Jiqin Zhang
- Department of Anesthesiology, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Ying Tan
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, China
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Yun D, Wang X, Wang W, Ren X, Li J, Wang X, Liang J, Liu J, Fan J, Ren X, Zhang H, Shang G, Sun J, Chen L, Li T, Zhang C, Yu S, Yang X. A Novel Prognostic Signature Based on Glioma Essential Ferroptosis-Related Genes Predicts Clinical Outcomes and Indicates Treatment in Glioma. Front Oncol 2022; 12:897702. [PMID: 35756689 PMCID: PMC9232254 DOI: 10.3389/fonc.2022.897702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/05/2022] [Indexed: 12/11/2022] Open
Abstract
Background Ferroptosis is a form of programmed cell death (PCD) that has been implicated in cancer progression, although the specific mechanism is not known. Here, we used the latest DepMap release CRISPR data to identify the essential ferroptosis-related genes (FRGs) in glioma and their role in patient outcomes. Methods RNA-seq and clinical information on glioma cases were obtained from the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA). FRGs were obtained from the FerrDb database. CRISPR-screened essential genes (CSEGs) in glioma cell lines were downloaded from the DepMap portal. A series of bioinformatic and machine learning approaches were combined to establish FRG signatures to predict overall survival (OS) in glioma patients. In addition, pathways analysis was used to identify the functional roles of FRGs. Somatic mutation, immune cell infiltration, and immune checkpoint gene expression were analyzed within the risk subgroups. Finally, compounds for reversing high-risk gene signatures were predicted using the GDSC and L1000 datasets. Results Seven FRGs (ISCU, NFS1, MTOR, EIF2S1, HSPA5, AURKA, RPL8) were included in the model and the model was found to have good prognostic value (p < 0.001) in both training and validation groups. The risk score was found to be an independent prognostic factor and the model had good efficacy. Subgroup analysis using clinical parameters demonstrated the general applicability of the model. The nomogram indicated that the model could effectively predict 12-, 36-, and 60-months OS and progression-free interval (PFI). The results showed the presence of more aggressive phenotypes (lower numbers of IDH mutations, higher numbers of EGFR and PTEN mutations, greater infiltration of immune suppressive cells, and higher expression of immune checkpoint inhibitors) in the high-risk group. The signaling pathways enriched closely related to the cell cycle and DNA damage repair. Drug predictions showed that patients with higher risk scores may benefit from treatment with RTK pathway inhibitors, including compounds that inhibit RTKs directly or indirectly by targeting downstream PI3K or MAPK pathways. Conclusion In summary, the proposed cancer essential FRG signature predicts survival and treatment response in glioma.
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Affiliation(s)
- Debo Yun
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China.,Department of Neurosurgery, Nanchong Central Hospital, Nanchong, China
| | - Xuya Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Wenbo Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Xiao Ren
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Jiabo Li
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Xisen Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Jianshen Liang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Jie Liu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Jikang Fan
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Xiude Ren
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Hao Zhang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Guanjie Shang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Jingzhang Sun
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Lei Chen
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Tao Li
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Chen Zhang
- Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Shengping Yu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China
| | - Xuejun Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin, China.,Department of Neurosurgery, Beijing Tsinghua Changgung Hospital, Beijing, China
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