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Wu M, Wang T, Ji N, Lu T, Yuan R, Wu L, Zhang J, Li M, Cao P, Zhao J, Li G, Li J, Li Y, Tang Y, Gao Z, Wang X, Cheng W, Ge M, Cui G, Li R, Wu A, You Y, Zhang W, Wang Q, Chen J. Multi-omics and pharmacological characterization of patient-derived glioma cell lines. Nat Commun 2024; 15:6740. [PMID: 39112531 PMCID: PMC11306361 DOI: 10.1038/s41467-024-51214-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
Glioblastoma (GBM) is the most common brain tumor and remains incurable. Primary GBM cultures are widely used tools for drug screening, but there is a lack of genomic and pharmacological characterization for these primary GBM cultures. Here, we collect 50 patient-derived glioma cell (PDGC) lines and characterize them by whole genome sequencing, RNA sequencing, and drug response screening. We identify three molecular subtypes among PDGCs: mesenchymal (MES), proneural (PN), and oxidative phosphorylation (OXPHOS). Drug response profiling reveals that PN subtype PDGCs are sensitive to tyrosine kinase inhibitors, whereas OXPHOS subtype PDGCs are sensitive to histone deacetylase inhibitors, oxidative phosphorylation inhibitors, and HMG-CoA reductase inhibitors. PN and OXPHOS subtype PDGCs stably form tumors in vivo upon intracranial transplantation into immunodeficient mice, whereas most MES subtype PDGCs fail to form tumors in vivo. In addition, PDGCs cultured by serum-free medium, especially long-passage PDGCs, carry MYC/MYCN amplification, which is rare in GBM patients. Our study provides a valuable resource for understanding primary glioma cell cultures and clinical translation and highlights the problems of serum-free PDGC culture systems that cannot be ignored.
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Affiliation(s)
- Min Wu
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, China
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Tingting Wang
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
- Changping Laboratory, Beijing, China
- Chinese Institute for Brain Research, Beijing, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Nan Ji
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ting Lu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ran Yuan
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, China
| | - Lingxiang Wu
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Junxia Zhang
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mengyuan Li
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
- Changping Laboratory, Beijing, China
| | - Penghui Cao
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiarui Zhao
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
| | - Guanzhang Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jianyu Li
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Li
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
| | - Yujie Tang
- Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengliang Gao
- Fundamental Research Center, Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Medicine, Tongji University, Shanghai, China
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
- Department of Anesthesiology, Gongli Hospital of Shanghai Pudong New Area, Shanghai, China
| | - Xiuxing Wang
- National Health Commission Key Laboratory of Antibody Techniques, Department of Cell Biology, Jiangsu Provincial Key Laboratory of Human Functional Genomics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Wen Cheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ming Ge
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Gang Cui
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Rui Li
- Department of Neurosurgery, China-Japan Friendship Hospital, No. 2 Yinghua East Road, Chaoyang District, Beijing, China
| | - Anhua Wu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yongping You
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Wei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.
| | - Qianghu Wang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.
| | - Jian Chen
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China.
- Changping Laboratory, Beijing, China.
- Chinese Institute for Brain Research, Beijing, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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