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Niu B, Liang C, Lu Y, Zhao M, Chen Q, Zhang Y, Zheng L, Chou KC. Glioma stages prediction based on machine learning algorithm combined with protein-protein interaction networks. Genomics 2019; 112:837-847. [PMID: 31150762 DOI: 10.1016/j.ygeno.2019.05.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 05/25/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Glioma is the most lethal nervous system cancer. Recent studies have made great efforts to study the occurrence and development of glioma, but the molecular mechanisms are still unclear. This study was designed to reveal the molecular mechanisms of glioma based on protein-protein interaction network combined with machine learning methods. Key differentially expressed genes (DEGs) were screened and selected by using the protein-protein interaction (PPI) networks. RESULTS As a result, 19 genes between grade I and grade II, 21 genes between grade II and grade III, and 20 genes between grade III and grade IV. Then, five machine learning methods were employed to predict the gliomas stages based on the selected key genes. After comparison, Complement Naive Bayes classifier was employed to build the prediction model for grade II-III with accuracy 72.8%. And Random forest was employed to build the prediction model for grade I-II and grade III-VI with accuracy 97.1% and 83.2%, respectively. Finally, the selected genes were analyzed by PPI networks, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and the results improve our understanding of the biological functions of select DEGs involved in glioma growth. We expect that the key genes expressed have a guiding significance for the occurrence of gliomas or, at the very least, that they are useful for tumor researchers. CONCLUSION Machine learning combined with PPI networks, GO and KEGG analyses of selected DEGs improve our understanding of the biological functions involved in glioma growth.
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Affiliation(s)
- Bing Niu
- School of Life Sciences, Shanghai University, Shanghai 200444, China; Gordon Life Science Institute, Boston, MA 02478, USA.
| | - Chaofeng Liang
- Department of Neurosurgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yi Lu
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Manman Zhao
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Qin Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Yuhui Zhang
- Renji Hospital, Medical School, Shanghai Jiaotong University, 160 Pujian Rd, New Pudong District, Shanghai 200127, China; Changhai Hospital, Second Military Medical University, Shanghai 200433, China.
| | - Linfeng Zheng
- Department of Radiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China; Department of Radiology, Shanghai First People's Hospital, Baoshan Branch, Shanghai 200940, China.
| | - Kuo-Chen Chou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China; Gordon Life Science Institute, Boston, MA 02478, USA.
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Qi XT, Zhan JS, Xiao LM, Li L, Xu HX, Fu ZB, Zhang YH, Zhang J, Jia XH, Ge G, Chai RC, Gao K, Yu ACH. The Unwanted Cell Migration in the Brain: Glioma Metastasis. Neurochem Res 2017; 42:1847-1863. [PMID: 28478595 DOI: 10.1007/s11064-017-2272-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/12/2017] [Accepted: 04/17/2017] [Indexed: 12/19/2022]
Abstract
Cell migration is identified as a highly orchestrated process. It is a fundamental and essential phenomenon underlying tissue morphogenesis, wound healing, and immune response. Under dysregulation, it contributes to cancer metastasis. Brain is considered to be the most complex organ in human body containing many types of neural cells with astrocytes playing crucial roles in monitoring both physiological and pathological functions. Astrocytoma originates from astrocytes and its most malignant type is glioblastoma multiforme (WHO Grade IV astrocytoma), which is capable to infiltrate widely into the neighboring brain tissues making a complete resection of tumors impossible. Very recently, we have reviewed the mechanisms for astrocytes in migration. Given the fact that astrocytoma shares many histological features with astrocytes, we therefore attempt to review the mechanisms for glioma cells in migration and compare them to normal astrocytes, hoping to obtain a better insight into the dysregulation of migratory mechanisms contributing to their metastasis in the brain.
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Affiliation(s)
- Xue Tao Qi
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
| | - Jiang Shan Zhan
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
| | - Li Ming Xiao
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
| | - Lina Li
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China.
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China.
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China.
- Hai Kang Life (Beijing) Corporation Ltd., Sino-I Campus No.1, Beijing Economic-Technological Development Area, Beijing, 100176, China.
- Hai Kang Life Corporation Ltd., Hong Kong Science Park, Shatin, New Territories, Hong Kong, China.
| | - Han Xiao Xu
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
- Department of Human Anatomy, Guizhou Medical University, Guian New Area, Guiyang, Guizhou, 550025, China
| | - Zi Bing Fu
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
| | - Yan Hao Zhang
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
| | - Jing Zhang
- Department of Pathology, Peking University Health Science Center and Peking University Third Hospital, Beijing, 100191, China
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, 98104, USA
| | - Xi Hua Jia
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
- Hai Kang Life (Beijing) Corporation Ltd., Sino-I Campus No.1, Beijing Economic-Technological Development Area, Beijing, 100176, China
- Hai Kang Life Corporation Ltd., Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Guo Ge
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
- Department of Human Anatomy, Guizhou Medical University, Guian New Area, Guiyang, Guizhou, 550025, China
| | - Rui Chao Chai
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
- Hai Kang Life (Beijing) Corporation Ltd., Sino-I Campus No.1, Beijing Economic-Technological Development Area, Beijing, 100176, China
- Hai Kang Life Corporation Ltd., Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Kai Gao
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Albert Cheung Hoi Yu
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China.
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China.
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China.
- Hai Kang Life (Beijing) Corporation Ltd., Sino-I Campus No.1, Beijing Economic-Technological Development Area, Beijing, 100176, China.
- Hai Kang Life Corporation Ltd., Hong Kong Science Park, Shatin, New Territories, Hong Kong, China.
- Laboratory of Translational Medicine, Institute of Systems Biomedicine, Peking University, Beijing, 100191, China.
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Qiu Y, Li WH, Zhang HQ, Liu Y, Tian XX, Fang WG. P2X7 mediates ATP-driven invasiveness in prostate cancer cells. PLoS One 2014; 9:e114371. [PMID: 25486274 PMCID: PMC4259308 DOI: 10.1371/journal.pone.0114371] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 11/06/2014] [Indexed: 12/18/2022] Open
Abstract
The ATP-gated P2X7 has been shown to play an important role in invasiveness and metastasis of some tumors. However, the possible links and underlying mechanisms between P2X7 and prostate cancer have not been elucidated. Here, we demonstrated that P2X7 was highly expressed in some prostate cancer cells. Down-regulation of P2X7 by siRNA significantly attenuated ATP- or BzATP-driven migration and invasion of prostate cancer cells in vitro, and inhibited tumor invasiveness and metastases in nude mice. In addition, silencing of P2X7 remarkably attenuated ATP- or BzATP- driven expression changes of EMT/invasion-related genes Snail, E-cadherin, Claudin-1, IL-8 and MMP-3, and weakened the phosphorylation of PI3K/AKT and ERK1/2 in vitro. Similar effects were observed in nude mice. These data indicate that P2X7 stimulates cell invasion and metastasis in prostate cancer cells via some EMT/invasion-related genes, as well as PI3K/AKT and ERK1/2 signaling pathways. P2X7 could be a promising therapeutic target for prostate cancer.
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Affiliation(s)
- Ying Qiu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Wei-hua Li
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Hong-quan Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing, 100191, China
| | - Yan Liu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xin-Xia Tian
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- * E-mail: (WGF); (XXT)
| | - Wei-Gang Fang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- * E-mail: (WGF); (XXT)
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