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Wang Y, Suo J, Wang Z, Ran K, Tian Y, Han W, Liu Y, Peng X. The PTPRZ1-MET/STAT3/ISG20 axis in glioma stem-like cells modulates tumor-associated macrophage polarization. Cell Signal 2024; 120:111191. [PMID: 38685521 DOI: 10.1016/j.cellsig.2024.111191] [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: 03/13/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Recent studies have revealed that PTPRZ1-MET (ZM) fusion plays a pivotal role in the progression of glioma to glioblastoma multiforme (GBM), thus serving as a biomarker to distinguish between primary GBM and secondary GBM (sGBM). However, the mechanisms through which ZM fusion influences this progression remain to be elucidated. GBMs with ZM showed poorer prognoses and greater infiltration of tumor-associated macrophages (TAMs) than those without ZM. Glioma stem-like cells (GSCs) and TAMs play complex roles in glioma recurrence, glioma progression and therapy resistance. In this study, we analyzed RNA-seq data from sGBM patients' glioma tissues with or without ZM fusion, and found that stemness and macrophage markers were more highly expressed in sGBM patients harboring ZM than in those without ZM fusion. ZM enhanced the self-renewal and proliferation of GSCs, thereby accelerating glioma progression. In addition, ZM-positive GSCs facilitated the infiltration of TAMs and drove their polarization toward an immunosuppressive phenotype, which was primarily accomplished through the extracellular secretion of ISG20. Our research identified the MET-STAT3-ISG20 axis within GSCs, thus demonstrating the critical role of ZM in GBM initiation and progression. Our study demonstrated that, in contrast to ZM-positive differentiated glioma cells, ZM-positive GSCs upregulated ISG20 expression through the MET-STAT3-ISG20 axis. The extracellular secretion of ISG20 recruited and induced M2-like polarization in macrophages, thereby promoting tumor progression. Our results reveal a novel mechanism involved in ZM-positive GBM pathogenesis and identify potential therapeutic targets.
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Affiliation(s)
- Yuxin Wang
- Department of Molecular Biology and Biochemistry, Medical Primate Research Center, Neuroscience Center, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Jinghao Suo
- Department of Molecular Biology and Biochemistry, Medical Primate Research Center, Neuroscience Center, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Zhixing Wang
- Department of Molecular Biology and Biochemistry, Medical Primate Research Center, Neuroscience Center, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Kunnian Ran
- Department of Molecular Biology and Biochemistry, Medical Primate Research Center, Neuroscience Center, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yuan Tian
- Department of Molecular Biology and Biochemistry, Medical Primate Research Center, Neuroscience Center, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Wei Han
- Department of Molecular Biology and Biochemistry, Medical Primate Research Center, Neuroscience Center, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China.
| | - Yanwei Liu
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.
| | - Xiaozhong Peng
- Department of Molecular Biology and Biochemistry, Medical Primate Research Center, Neuroscience Center, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China.
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2
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Chiablaem K, Jinawath A, Nuanpirom J, Arora JK, Nasaree S, Thanomchard T, Singhto N, Chittavanich P, Suktitipat B, Charoensawan V, Chairoungdua A, Jinn-Chyuan Sheu J, Kiyotani K, Svasti J, Nakamura Y, Jinawath N. Identification of RNF213 as a Potential Suppressor of Local Invasion in Intrahepatic Cholangiocarcinoma. J Transl Med 2024; 104:102074. [PMID: 38723854 DOI: 10.1016/j.labinv.2024.102074] [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: 10/16/2023] [Revised: 04/08/2024] [Accepted: 04/30/2024] [Indexed: 06/14/2024] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a lethal cancer with poor survival especially when it spreads. The histopathology of its rare intraductal papillary neoplasm of the bile duct type (IPNB) characteristically shows cancer cells originating within the confined bile duct space. These cells eventually invade and infiltrate the nearby liver tissues, making it a good model to study the mechanism of local invasion, which is the earliest step of metastasis. To discover potential suppressor genes of local invasion in ICC, we analyzed the somatic mutation profiles and performed clonal evolution analyses of the 11 pairs of macrodissected locally invasive IPNB tissues (LI-IPNB) and IPNB tissues without local invasion from the same patients. We identified a protein-truncating variant in an E3 ubiquitin ligase, RNF213 (c.6967C>T; p.Gln2323X; chr17: 78,319,102 [hg19], exon 29), as the most common protein-truncating variant event in LI-IPNB samples (4/11 patients). Knockdown of RNF213 in HuCCT1 and YSCCC cells showed increased migration and invasion, and reduced vasculogenic mimicry but maintained normal proliferation. Transcriptomic analysis of the RNF213-knockdown vs control cells was then performed in the HuCCT1, YSCCC, and KKU-100 cells. Gene ontology enrichment analysis of the common differentially expressed genes revealed significantly altered cytokine and oxidoreductase-oxidizing metal ion activities, as confirmed by Western blotting. Gene Set Enrichment Analysis identified the most enriched pathways being oxidative phosphorylation, fatty acid metabolism, reactive oxygen species, adipogenesis, and angiogenesis. In sum, loss-of-function mutation of RNF213 is a common genetic alteration in LI-IPNB tissues. RNF213 knockdown leads to increased migration and invasion of ICC cells, potentially through malfunctions of the pathways related to inflammation and energy metabolisms.
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Affiliation(s)
- Khajeelak Chiablaem
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand; Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
| | - Artit Jinawath
- Molecular Histopathology Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Jiratchaya Nuanpirom
- Integrative Computational Bioscience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand
| | - Jantarika Kumar Arora
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sirawit Nasaree
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thanastha Thanomchard
- Ramathibodi Comprehensive Cancer Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nilubon Singhto
- Ramathibodi Comprehensive Cancer Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pamorn Chittavanich
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Bhoom Suktitipat
- Integrative Computational Bioscience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand; Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Varodom Charoensawan
- Integrative Computational Bioscience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand; Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Arthit Chairoungdua
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jim Jinn-Chyuan Sheu
- Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan; Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kazuma Kiyotani
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Jisnuson Svasti
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
| | - Yusuke Nakamura
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan; National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand; Integrative Computational Bioscience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand; Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bang Phli, Samut Prakan, Thailand.
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3
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Sharma V, Vinchure OS, Yadav G, Sarkar C, Kulshreshtha R. A novel interplay between PRC2 and miR-3189 regulates epithelial-mesenchymal transition (EMT) via modulating COL6A2 in glioblastoma. J Cell Physiol 2024. [PMID: 38860406 DOI: 10.1002/jcp.31326] [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: 09/25/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/12/2024]
Abstract
Recent studies have shed light on disrupted collagen signaling in Gliomas, yet the regulatory landscape remains largely unexplored. This study enquired into the role of polycomb repressive complex-2 (PRC2)-mediated H3K27me3 modification, a key epigenetic factor in glioma. Using in-house data, we identified miRNAs downregulated in glioblastoma (GBM) with the potential to regulate Collagen VI family genes. Notably, miR-3189 emerged as a prime PRC2 target. Its expression was significantly downregulated in Indian GBM patients as well as other glioma cohorts. Mechanistic insights, involving Luciferase assays, mutagenesis, and Western blot analysis, confirmed direct targeting of Collagen VI member COL6A2 by miR-3189-3p. Functional assays demonstrated that miR-3189-3p restrained GBM malignancy by inhibiting proliferation, migration, and epithelial-mesenchymal transition (EMT). Conversely, COL6A2 overexpressed in GBM patients, countered miR-3189, and promoted the malignant phenotype. Gene set enrichment analysis highlighted EMT enrichment in GBM patients with elevated COL6A2 expression, carrying prognostic implications. This study uncovers intricate interactions between two epigenetic regulators-H3K27me3 and miR-3189-working synergistically to modulate Collagen VI gene; thus, influencing the malignancy of GBM. Targeting this H3K27me3|miR-3189-3p|COL6A2 axis presents a potential therapeutic avenue against GBM.
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Affiliation(s)
- Vikas Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
- Centralized Core Research Facility, All India Institute of Medical Sciences, New Delhi, India
| | - Omkar Suhas Vinchure
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Garima Yadav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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4
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Zuckermann M, He C, Andrews J, Bagchi A, Sloan-Henry R, Bianski B, Xie J, Wang Y, Twarog N, Onar-Thomas A, Ernst KJ, Yang L, Li Y, Zhu X, Ocasio JK, Budd KM, Dalton J, Li X, Chepyala D, Zhang J, Xu K, Hover L, Roach JT, Chan KCH, Hofmann N, McKinnon PJ, Pfister SM, Shelat AA, Rankovic Z, Freeman BB, Chiang J, Jones DTW, Tinkle CL, Baker SJ. Capmatinib is an effective treatment for MET-fusion driven pediatric high-grade glioma and synergizes with radiotherapy. Mol Cancer 2024; 23:123. [PMID: 38849845 PMCID: PMC11157767 DOI: 10.1186/s12943-024-02027-6] [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: 11/04/2023] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Pediatric-type diffuse high-grade glioma (pHGG) is the most frequent malignant brain tumor in children and can be subclassified into multiple entities. Fusion genes activating the MET receptor tyrosine kinase often occur in infant-type hemispheric glioma (IHG) but also in other pHGG and are associated with devastating morbidity and mortality. METHODS To identify new treatment options, we established and characterized two novel orthotopic mouse models harboring distinct MET fusions. These included an immunocompetent, murine allograft model and patient-derived orthotopic xenografts (PDOX) from a MET-fusion IHG patient who failed conventional therapy and targeted therapy with cabozantinib. With these models, we analyzed the efficacy and pharmacokinetic properties of three MET inhibitors, capmatinib, crizotinib and cabozantinib, alone or combined with radiotherapy. RESULTS Capmatinib showed superior brain pharmacokinetic properties and greater in vitro and in vivo efficacy than cabozantinib or crizotinib in both models. The PDOX models recapitulated the poor efficacy of cabozantinib experienced by the patient. In contrast, capmatinib extended survival and induced long-term progression-free survival when combined with radiotherapy in two complementary mouse models. Capmatinib treatment increased radiation-induced DNA double-strand breaks and delayed their repair. CONCLUSIONS We comprehensively investigated the combination of MET inhibition and radiotherapy as a novel treatment option for MET-driven pHGG. Our seminal preclinical data package includes pharmacokinetic characterization, recapitulation of clinical outcomes, coinciding results from multiple complementing in vivo studies, and insights into molecular mechanism underlying increased efficacy. Taken together, we demonstrate the groundbreaking efficacy of capmatinib and radiation as a highly promising concept for future clinical trials.
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Affiliation(s)
- Marc Zuckermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, Germany.
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany.
| | - Chen He
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jared Andrews
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Aditi Bagchi
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Roketa Sloan-Henry
- Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Brandon Bianski
- Department of Radiation Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jia Xie
- Department of Radiation Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yingzhe Wang
- Preclinical Pharmacokinetics Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Nathaniel Twarog
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Arzu Onar-Thomas
- Department of Biostatistics, Departments of BiostatisticsSt. Jude Children's Research Hospital, Memphis, 262 Danny Thomas Place, TN, 38105, USA
| | - Kati J Ernst
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yong Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xiaoyan Zhu
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jennifer K Ocasio
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kaitlin M Budd
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - James Dalton
- Department of Pathology, Departments of PathologySt. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xiaoyu Li
- Department of Pathology, Departments of PathologySt. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Divyabharathi Chepyala
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Junyuan Zhang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ke Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Laura Hover
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jordan T Roach
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kenneth Chun-Ho Chan
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Nina Hofmann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Burgess B Freeman
- Preclinical Pharmacokinetics Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jason Chiang
- Department of Pathology, Departments of PathologySt. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Christopher L Tinkle
- Department of Radiation Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
- Center Of Excellence in Neuro-Oncology Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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5
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Pham LC, Weller L, Gann CN, Schumacher KM, Vlassak S, Swanson T, Highsmith K, O'Brien BJ, Nash S, Aaroe A, de Groot JF, Majd NK. Prolonged complete response to adjuvant tepotinib in a patient with newly diagnosed disseminated glioblastoma harboring mesenchymal-epithelial transition fusion. Oncologist 2024:oyae100. [PMID: 38815166 DOI: 10.1093/oncolo/oyae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/17/2024] [Indexed: 06/01/2024] Open
Abstract
The prognosis of patients with glioblastoma (GBM) remains poor despite current treatments. Targeted therapy in GBM has been the subject of intense investigation but has not been successful in clinical trials. The reasons for the failure of targeted therapy in GBM are multifold and include a lack of patient selection in trials, the failure to identify driver mutations, and poor blood-brain barrier penetration of investigational drugs. Here, we describe a case of a durable complete response in a newly diagnosed patient with GBM with leptomeningeal dissemination and PTPRZ1-MET fusion who was treated with tepotinib, a brain-penetrant MET inhibitor. This case of successful targeted therapy in a patient with GBM demonstrates that early molecular testing, identification of driver molecular alterations, and treatment with brain-penetrant small molecule inhibitors have the potential to change the outcome in select patients with GBM.
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Affiliation(s)
- Lily C Pham
- Department of Neurology, University of Maryland, Baltimore, MD, United States
| | - Lauryn Weller
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | | | | | - Todd Swanson
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Kaitlin Highsmith
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Barbara J O'Brien
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sebnem Nash
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ashley Aaroe
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - John F de Groot
- Department of Neuro-Oncology, University of California San Francisco, San Francisco, CA, United States
| | - Nazanin K Majd
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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6
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Ding Y, Jiang Y, Zeng H, Zhou M, Zhou X, Yu Z, Pan J, Geng X, Zhu Y, Zheng H, Huang S, Gong Y, Huang H, Xiong C, Huang D. Identification of a robust biomarker LAPTM4A for glioma based on comprehensive computational biology and experimental verification. Aging (Albany NY) 2024; 16:6954-6989. [PMID: 38613802 PMCID: PMC11087115 DOI: 10.18632/aging.205736] [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: 11/14/2023] [Accepted: 03/03/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND Glioma, a highly invasive and deadly form of human neoplasm, presents a pressing need for the exploration of potential therapeutic targets. While the lysosomal protein transmembrane 4A (LATPM4A) has been identified as a risk factor in pancreatic cancer patients, its role in glioma remains unexplored. METHODS The analysis of differentially expressed genes (DEG) was conducted from The Cancer Genome Atlas (TCGA) glioma dataset and the Genotype Tissue Expression (GTEx) dataset. Through weighted gene co-expression network analysis (WGCNA), the key glioma-related genes were identified. Among these, by using Kaplan-Meier (KM) analysis and univariate/multivariate COX methods, LAPTM4A emerged as the most influential gene. Moreover, the bioinformatics methods and experimental verification were employed to analyze its relationships with diagnosis, clinical parameters, epithelial-mesenchymal transition (EMT), metastasis, immune cell infiltration, immunotherapy, drug sensitivity, and ceRNA network. RESULTS Our findings revealed that LAPTM4A was up-regulated in gliomas and was associated with clinicopathological features, leading to poor prognosis. Furthermore, functional enrichment analysis demonstrated that LATPM4A played a role in the immune system and cancer progression. In vitro experiments indicated that LAPTM4A may influence metastasis through the EMT pathway in glioma. Additionally, we found that LAPTM4A was associated with the tumor microenvironment (TME) and immunotherapy. Notably, drug sensitivity analysis revealed that patients with high LAPTM4A expression were sensitive to doxorubicin, which contributed to a reduction in LAPTM4A expression. Finally, we uncovered the FGD5-AS1-hsa-miR-103a-3p-LAPTM4A axis as a facilitator of glioma progression. CONCLUSIONS In conclusion, our study identifies LATPM4A as a promising biomarker for prognosis and immune characteristics in glioma.
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Affiliation(s)
- Yongqi Ding
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yike Jiang
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hong Zeng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Minqin Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xuanrui Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Zichuan Yu
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xitong Geng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yanting Zhu
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hao Zheng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Shuhan Huang
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yiyang Gong
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Huabin Huang
- Department of Radiology, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Chengfeng Xiong
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Da Huang
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
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7
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Cubillos P, Ditzer N, Kolodziejczyk A, Schwenk G, Hoffmann J, Schütze TM, Derihaci RP, Birdir C, Köllner JE, Petzold A, Sarov M, Martin U, Long KR, Wimberger P, Albert M. The growth factor EPIREGULIN promotes basal progenitor cell proliferation in the developing neocortex. EMBO J 2024; 43:1388-1419. [PMID: 38514807 PMCID: PMC11021537 DOI: 10.1038/s44318-024-00068-7] [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: 09/13/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/23/2024] Open
Abstract
Neocortex expansion during evolution is linked to higher numbers of neurons, which are thought to result from increased proliferative capacity and neurogenic potential of basal progenitor cells during development. Here, we show that EREG, encoding the growth factor EPIREGULIN, is expressed in the human developing neocortex and in gorilla cerebral organoids, but not in the mouse neocortex. Addition of EPIREGULIN to the mouse neocortex increases proliferation of basal progenitor cells, whereas EREG ablation in human cortical organoids reduces proliferation in the subventricular zone. Treatment of cortical organoids with EPIREGULIN promotes a further increase in proliferation of gorilla but not of human basal progenitor cells. EPIREGULIN competes with the epidermal growth factor (EGF) to promote proliferation, and inhibition of the EGF receptor abrogates the EPIREGULIN-mediated increase in basal progenitor cells. Finally, we identify putative cis-regulatory elements that may contribute to the observed inter-species differences in EREG expression. Our findings suggest that species-specific regulation of EPIREGULIN expression may contribute to the increased neocortex size of primates by providing a tunable pro-proliferative signal to basal progenitor cells in the subventricular zone.
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Affiliation(s)
- Paula Cubillos
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Nora Ditzer
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Annika Kolodziejczyk
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Gustav Schwenk
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Janine Hoffmann
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Theresa M Schütze
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Razvan P Derihaci
- Department of Gynecology and Obstetrics, TU Dresden, 01307, Dresden, Germany
- National Center for Tumor Diseases, 01307, Dresden, Germany
| | - Cahit Birdir
- Department of Gynecology and Obstetrics, TU Dresden, 01307, Dresden, Germany
- Center for feto/neonatal Health, TU Dresden, 01307, Dresden, Germany
| | - Johannes Em Köllner
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Andreas Petzold
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, 30625, Hannover, Germany
- REBIRTH-Cluster of Excellence, Hannover, Germany
| | - Katherine R Long
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE1 1UL, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE1 1UL, United Kingdom
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, TU Dresden, 01307, Dresden, Germany
- National Center for Tumor Diseases, 01307, Dresden, Germany
| | - Mareike Albert
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany.
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8
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Crepaldi T, Gallo S, Comoglio PM. The MET Oncogene: Thirty Years of Insights into Molecular Mechanisms Driving Malignancy. Pharmaceuticals (Basel) 2024; 17:448. [PMID: 38675409 PMCID: PMC11054789 DOI: 10.3390/ph17040448] [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: 02/24/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The discovery and subsequent research on the MET oncogene's role in cancer onset and progression have illuminated crucial insights into the molecular mechanisms driving malignancy. The identification of MET as the hepatocyte growth factor (HGF) receptor has paved the path for characterizing the MET tyrosine kinase activation mechanism and its downstream signaling cascade. Over the past thirty years, research has established the importance of HGF/MET signaling in normal cellular processes, such as cell dissociation, migration, proliferation, and cell survival. Notably, genetic alterations that lead to the continuous activation of MET, known as constitutive activation, have been identified as oncogenic drivers in various cancers. The genetic lesions affecting MET, such as exon skipping, gene amplification, and gene rearrangements, provide valuable targets for therapeutic intervention. Moreover, the implications of MET as a resistance mechanism to targeted therapies emphasize the need for combination treatments that include MET inhibitors. The intriguing "flare effect" phenomenon, wherein MET inhibition can lead to post-treatment increases in cancer cell proliferation, underscores the dynamic nature of cancer therapeutics. In human tumors, increased protein expression often occurs without gene amplification. Various mechanisms may cause an overexpression: transcriptional upregulation induced by other oncogenes; environmental factors (such as hypoxia or radiation); or substances produced by the reactive stroma, such as inflammatory cytokines, pro-angiogenic factors, and even HGF itself. In conclusion, the journey to understanding MET's involvement in cancer onset and progression over the past three decades has not only deepened our knowledge, but has also paved the way for innovative therapeutic strategies. Selective pharmacological inactivation of MET stands as a promising avenue for achieving cancer remission, particularly in cases where MET alterations are the primary drivers of malignancy.
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Affiliation(s)
- Tiziana Crepaldi
- Department of Oncology, University of Turin, Regione Gonzole 10, 10143 Orbassano, Italy; (T.C.); (S.G.)
- Candiolo Cancer Institute, FPO-IRCCS, SP142, Km 3.95, 10060 Candiolo, Italy
| | - Simona Gallo
- Department of Oncology, University of Turin, Regione Gonzole 10, 10143 Orbassano, Italy; (T.C.); (S.G.)
- Candiolo Cancer Institute, FPO-IRCCS, SP142, Km 3.95, 10060 Candiolo, Italy
| | - Paolo Maria Comoglio
- IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano, Italy
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9
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Al-Ghabkari A, Huang B, Park M. Aberrant MET Receptor Tyrosine Kinase Signaling in Glioblastoma: Targeted Therapy and Future Directions. Cells 2024; 13:218. [PMID: 38334610 PMCID: PMC10854665 DOI: 10.3390/cells13030218] [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: 11/08/2023] [Revised: 11/27/2023] [Accepted: 01/12/2024] [Indexed: 02/10/2024] Open
Abstract
Brain tumors represent a heterogeneous group of neoplasms characterized by a high degree of aggressiveness and a poor prognosis. Despite recent therapeutic advances, the treatment of brain tumors, including glioblastoma (GBM), an aggressive primary brain tumor associated with poor prognosis and resistance to therapy, remains a significant challenge. Receptor tyrosine kinases (RTKs) are critical during development and in adulthood. Dysregulation of RTKs through activating mutations and gene amplification contributes to many human cancers and provides attractive therapeutic targets for treatment. Under physiological conditions, the Met RTK, the hepatocyte growth factor/scatter factor (HGF/SF) receptor, promotes fundamental signaling cascades that modulate epithelial-to-mesenchymal transition (EMT) involved in tissue repair and embryogenesis. In cancer, increased Met activity promotes tumor growth and metastasis by providing signals for proliferation, survival, and migration/invasion. Recent clinical genomic studies have unveiled multiple mechanisms by which MET is genetically altered in GBM, including focal amplification, chromosomal rearrangements generating gene fusions, and a splicing variant mutation (exon 14 skipping, METex14del). Notably, MET overexpression contributes to chemotherapy resistance in GBM by promoting the survival of cancer stem-like cells. This is linked to distinctive Met-induced pathways, such as the upregulation of DNA repair mechanisms, which can protect tumor cells from the cytotoxic effects of chemotherapy. The development of MET-targeted therapies represents a major step forward in the treatment of brain tumours. Preclinical studies have shown that MET-targeted therapies (monoclonal antibodies or small molecule inhibitors) can suppress growth and invasion, enhancing the efficacy of conventional therapies. Early-phase clinical trials have demonstrated promising results with MET-targeted therapies in improving overall survival for patients with recurrent GBM. However, challenges remain, including the need for patient stratification, the optimization of treatment regimens, and the identification of mechanisms of resistance. This review aims to highlight the current understanding of mechanisms underlying MET dysregulation in GBM. In addition, it will focus on the ongoing preclinical and clinical assessment of therapies targeting MET dysregulation in GBM.
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Affiliation(s)
- Abdulhameed Al-Ghabkari
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
| | - Bruce Huang
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
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10
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Georgescu MM. Translation into Clinical Practice of the G1-G7 Molecular Subgroup Classification of Glioblastoma: Comprehensive Demographic and Molecular Pathway Profiling. Cancers (Basel) 2024; 16:361. [PMID: 38254850 PMCID: PMC10814912 DOI: 10.3390/cancers16020361] [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: 11/21/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Glioblastoma is the most frequent and malignant primary neoplasm of the central nervous system. In a recent breakthrough study on a prospective Discovery cohort, I proposed the first all-inclusive molecular classification of glioblastoma into seven subgroups, G1-G7, based on MAPK pathway activation. New data from a WHO-grade-4 diffuse glioma prospective Validation cohort offers, in this study, an integrated demographic-molecular analysis of a 213-patient Combined cohort. Despite cohort differences in the median age and molecular subgroup distribution, all the prospectively-acquired cases from the Validation cohort mapped into one of the G1-G7 subgroups defined in the Discovery cohort. A younger age of onset, higher tumor mutation burden and expanded G1/EGFR-mutant and G3/NF1 glioblastoma subgroups characterized the glioblastomas from African American/Black relative to Caucasian/White patients. The three largest molecular subgroups were G1/EGFR, G3/NF1 and G7/Other. The fourth largest subgroup, G6/Multi-RTK, was detailed by describing a novel gene fusion ST7-MET, rare PTPRZ1-MET, LMNA-NTRK1 and GOPC-ROS1 fusions and their overexpression mechanisms in glioblastoma. The correlations between the MAPK pathway G1-G7 subgroups and the PI3-kinase/PTEN, TERT, cell cycle G1 phase and p53 pathways defined characteristic subgroup pathway profiles amenable to personalized targeted therapy. This analysis validated the first all-inclusive molecular classification of glioblastoma, showed significant demographic and molecular differences between subgroups, and provided the first ethnic molecular comparison of glioblastoma.
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11
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Sun D, Xing X, Wang Y, Hou H. MET fusions are targetable genomic variants in the treatment of advanced malignancies. Cell Commun Signal 2024; 22:20. [PMID: 38195556 PMCID: PMC10775437 DOI: 10.1186/s12964-023-01454-0] [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: 08/25/2023] [Accepted: 12/21/2023] [Indexed: 01/11/2024] Open
Abstract
Targeted therapy for malignancies has developed rapidly in recent years, benefiting patients harboring genetic mutations sensitive to relevant tyrosine kinase inhibitors (TKIs). With the development of targeted sequencing techniques, an increasing number of detectable genomic alterations in malignancies, including MET fusions, have been revealed. MET fusions, although rare among malignancies, might be functional driver genes that participate in activating downstream signaling pathways and promoting cell proliferation. Therefore, it is believed that MET fusions could be targetable genomic variants of MET, and inhibition of MET is considered an optionable therapeutic choice for patients harboring MET fusions. According to the summary presented in this review, we recommend MET-TKIs as suitable treatment agents for patients harboring primary MET fusions. For patients harboring acquired MET fusions after the development of resistance to TKIs targeting primary genomic alterations, such as sensitive EGFR mutations, treatment with a MET-TKI alone or in combination with TKIs targeting primary genomic alterations, such as EGFR-TKIs, is hypothesized to be a reasonable option for salvage treatment. In summary, MET fusions, despite their low incidence, should be taken into consideration when developing treatment strategies for cancer patients.
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Affiliation(s)
- Dantong Sun
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaoming Xing
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Yongjie Wang
- Department of Thoracic Surgery, The Affiliation Hospital of Qingdao University, No. 59 Haier Road, Qingdao, 266000, Shandong, China
| | - Helei Hou
- Department of Oncology, The Affiliated Hospital of Qingdao University, No. 7 Jiaxing Road, Qingdao, 266000, Shandong, China.
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12
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Li R, Chen Y, Yang B, Li Z, Wang S, He J, Zhou Z, Li X, Li J, Sun Y, Guo X, Wang X, Wu Y, Zhang W, Guo G. Integrated bioinformatics analysis and experimental validation identified CDCA families as prognostic biomarkers and sensitive indicators for rapamycin treatment of glioma. PLoS One 2024; 19:e0295346. [PMID: 38181024 PMCID: PMC10769025 DOI: 10.1371/journal.pone.0295346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/21/2023] [Indexed: 01/07/2024] Open
Abstract
The cell division cycle associated (CDCA) genes regulate the cell cycle; however, their relationship with prognosis in glioma has been poorly reported in the literature. The Cancer Genome Atlas (TCGA) was utilized to probe the CDCA family in relation to the adverse clinical features of glioma. Glioma single-cell atlas reveals specific expression of CDCA3, 4, 5, 8 in malignant cells and CDCA7 in neural progenitor cells (NPC)-like malignant cells. Glioma data from TCGA, the China Glioma Genome Atlas Project (CGGA) and the gene expression omnibus (GEO) database all demonstrated that CDCA2, 3, 4, 5, 7 and 8 are prognostic markers for glioma. Further analysis identified CDCA2, 5 and 8 as independent prognostic factors for glioma. Lasso regression-based risk models for CDCA families demonstrated that high-risk patients were characterized by high tumor mutational burden (TMB), low levels of microsatellite instability (MSI), and low tumor immune dysfunction and rejection (TIDE) scores. These pointed to immunotherapy for glioma as a potentially viable treatment option Further CDCA clustering suggested that the high CDCA subtype exhibited a high macrophage phenotype and was associated with a higher antigen presentation capacity and high levels of immune escape. In addition, hsa-mir-15b-5p was predicted to be common regulator of CDCA3 and CDCA4, which was validated in U87 and U251 cells. Importantly, we found that CDCAs may indicate response to drug treatment, especially rapamycin, in glioma. In summary, our results suggest that CDCAs have potential applications in clinical diagnosis and as drug sensitivity markers in glioma.
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Affiliation(s)
- Ren Li
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yang Chen
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Biao Yang
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ziao Li
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Shule Wang
- Department of General and Vascular Surgery, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jianhang He
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zihan Zhou
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xuepeng Li
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jiayu Li
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yanqi Sun
- Department of Emergency, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaolong Guo
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaogang Wang
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yongqiang Wu
- Department of Emergency, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Wenju Zhang
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Geng Guo
- Department of Emergency, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
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13
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Kim T, Lee A, Ahn S, Park JS, Jeun SS, Lee YS. Comprehensive Molecular Genetic Analysis in Glioma Patients by Next Generation Sequencing. Brain Tumor Res Treat 2024; 12:23-39. [PMID: 38317486 PMCID: PMC10864139 DOI: 10.14791/btrt.2023.0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/16/2023] [Accepted: 11/10/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Glioma is caused by multiple genomic alterations. The evolving classification of gliomas emphasizes the significance of molecular testing. Next generation sequencing (NGS) offers the assessment of parallel combinations of multiple genetic alterations and identifying actionable mutations that guide treatment. This study comprehensively analyzed glioma patients using multi-gene NGS panels, providing powerful insights to inform diagnostic classification and targeted therapies. METHODS We conducted a targeted panel-based NGS analysis on formalin-fixed and paraffin-embedded nucleic acids extracted from a total of 147 glioma patients. These samples underwent amplicon capture-based library preparation and sequenced using the Oncomine Comprehensive Assay platform. The resulting sequencing data were then analyzed using the bioinformatics tools. RESULTS A total of 301 mutations, were found in 132 out of 147 tumors (89.8%). These mutations were in 68 different genes. In 62 tumor samples (42.2%), copy number variations (CNVs) with gene amplifications occurred in 25 genes. Moreover, 25 tumor samples (17.0%) showed gene fusions in 6 genes and intragenic deletion in a gene. Our analysis identified actionable targets in several genes, including 11 with mutations, 8 with CNVs, and 3 with gene fusions and intragenic deletion. These findings could impact FDA-approved therapies, NCCN guideline-based treatments, and clinical trials. CONCLUSION We analyzed precisely diagnosing the classification of gliomas, detailing the frequency and co-occurrence of genetic alterations and identifying genetic alterations with potential therapeutic targets by NGS-based molecular analysis. The high-throughput NGS analysis is an efficient and powerful tool to comprehensively support molecular testing in neurooncology.
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Affiliation(s)
- Taeeun Kim
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahwon Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Stephan Ahn
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae Sung Park
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sin Soo Jeun
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Youn Soo Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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14
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Liu L, Liu Z, Liu Q, Wu W, Lin P, Liu X, Zhang Y, Wang D, Prager BC, Gimple RC, Yu J, Zhao W, Wu Q, Zhang W, Wu E, Chen X, Luo J, Rich JN, Xie Q, Jiang T, Chen R. LncRNA INHEG promotes glioma stem cell maintenance and tumorigenicity through regulating rRNA 2'-O-methylation. Nat Commun 2023; 14:7526. [PMID: 37980347 PMCID: PMC10657414 DOI: 10.1038/s41467-023-43113-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/31/2023] [Indexed: 11/20/2023] Open
Abstract
Glioblastoma (GBM) ranks among the most lethal of human cancers, containing glioma stem cells (GSCs) that display therapeutic resistance. Here, we report that the lncRNA INHEG is highly expressed in GSCs compared to differentiated glioma cells (DGCs) and promotes GSC self-renewal and tumorigenicity through control of rRNA 2'-O-methylation. INHEG induces the interaction between SUMO2 E3 ligase TAF15 and NOP58, a core component of snoRNP that guides rRNA methylation, to regulate NOP58 sumoylation and accelerate the C/D box snoRNP assembly. INHEG activation enhances rRNA 2'-O-methylation, thereby increasing the expression of oncogenic proteins including EGFR, IGF1R, CDK6 and PDGFRB in glioma cells. Taken together, this study identifies a lncRNA that connects snoRNP-guided rRNA 2'-O-methylation to upregulated protein translation in GSCs, supporting an axis for potential therapeutic targeting of gliomas.
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Affiliation(s)
- Lihui Liu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ziyang Liu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Qinghua Liu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Wei Wu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Peng Lin
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, China
| | - Xing Liu
- Beijing Neurosurgical Institute, 100050, Beijing, China
| | - Yuechuan Zhang
- Department of Department of Orthopedics, Peking Union Medical College Hospital, 100730, Beijing, China
| | - Dongpeng Wang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Briana C Prager
- Department of Pathology, Case Western Reserve University, Cleveland, 44106, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, 44195, USA
| | - Ryan C Gimple
- Department of Pathology, Case Western Reserve University, Cleveland, 44106, USA
| | - Jichuan Yu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, China
| | - Weixi Zhao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, China
| | - Qiulian Wu
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, 15261, USA
| | - Wei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100050, Beijing, China
| | - Erzhong Wu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiaomin Chen
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jianjun Luo
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jeremy N Rich
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, 15261, USA.
| | - Qi Xie
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, China.
| | - Tao Jiang
- Beijing Neurosurgical Institute, 100050, Beijing, China.
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100050, Beijing, China.
| | - Runsheng Chen
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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15
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Wang X, Yang J, Yang F, Mu K. The disulfidptosis-related signature predicts prognosis and immune features in glioma patients. Sci Rep 2023; 13:17988. [PMID: 37864127 PMCID: PMC10589205 DOI: 10.1038/s41598-023-45295-w] [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: 06/28/2023] [Accepted: 10/18/2023] [Indexed: 10/22/2023] Open
Abstract
Glioma is the most common primary malignant tumor in the central nervous system. Disulfidptosis is a recently identified programmed cell death in tumor cells overexpressing SLC7A11 under glucose starvation. Clinical prognostic significance of disulfidptosis has been reported in several tumors, and in this study, we explored the correlation of disulfidptosis with clinical prognosis, immune cell infiltration, and immunotherapy response in glioma. A total of 1592 glioma patients were included in this study, including 691 glioma patients from The Cancer Genomic Atlas (TCGA), 300 patients with from the Chinese Glioma Genomic Atlas (CGGA) array, 325 patients from CGGA sequencing, and 276 patients from Gene Expression Omnibus (GEO) GSE16011. R software (V4.2.2) and several R packages were applied to develop the risk score model and correlation calculation and visualization. Three disulfidptosis-related genes, LRPPRC, RPN1, and GYS1, were screened out and applied to establish the risk score model. Low-risk patients exhibit favorable prognosis, and the disulfidptosis-related signature significantly correlated with clinicopathological properties, molecular subtypes, and immunosuppressive microenvironment of glioma patients. We developed a disulfidptosis-related risk model to predict the prognosis and immune features in glioma patients, and this risk model may be applied as an independent prognostic factor for glioma.
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Affiliation(s)
- Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jijun Yang
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengjie Yang
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Ketao Mu
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Bassot A, Dragic H, Haddad SA, Moindrot L, Odouard S, Corlazzoli F, Marinari E, Bomane A, Brassens A, Marteyn A, Hibaoui Y, Petty TJ, Chalabi-Dchar M, Larrouquere L, Zdobnov EM, Legrand N, Tamburini J, Lincet H, Castets M, Yebra M, Migliorini D, Dutoit V, Walker PR, Preynat-Seauve O, Dietrich PY, Cosset É. Identification of a miRNA multi-targeting therapeutic strategy in glioblastoma. Cell Death Dis 2023; 14:630. [PMID: 37749143 PMCID: PMC10519979 DOI: 10.1038/s41419-023-06117-z] [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: 09/12/2022] [Revised: 08/14/2023] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
Glioblastoma (GBM) is a deadly and the most common primary brain tumor in adults. Due to their regulation of a high number of mRNA transcripts, microRNAs (miRNAs) are key molecules in the control of biological processes and are thereby promising therapeutic targets for GBM patients. In this regard, we recently reported miRNAs as strong modulators of GBM aggressiveness. Here, using an integrative and comprehensive analysis of the TCGA database and the transcriptome of GBM biopsies, we identified three critical and clinically relevant miRNAs for GBM, miR-17-3p, miR-222, and miR-340. In addition, we showed that the combinatorial modulation of three of these miRNAs efficiently inhibited several biological processes in patient-derived GBM cells of all these three GBM subtypes (Mesenchymal, Proneural, Classical), induced cell death, and delayed tumor growth in a mouse tumor model. Finally, in a doxycycline-inducible model, we observed a significant inhibition of GBM stem cell viability and a significant delay of orthotopic tumor growth. Collectively, our results reveal, for the first time, the potential of miR-17-3p, miR-222 and miR-340 multi-targeting as a promising therapeutic strategy for GBM patients.
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Affiliation(s)
- Arthur Bassot
- Department of CITI, Team GLIMMER Of lIght, Cancer Research Centre of Lyon - CRCL, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Helena Dragic
- Department of CITI, Team GLIMMER Of lIght, Cancer Research Centre of Lyon - CRCL, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Sarah Al Haddad
- Laboratory of Tumor Immunology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
| | - Laurine Moindrot
- Department of CITI, Team GLIMMER Of lIght, Cancer Research Centre of Lyon - CRCL, INSERM U1052, CNRS UMR 5286, Lyon, France
- Laboratory of Tumor Immunology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
| | - Soline Odouard
- Laboratory of Tumor Immunology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
| | - Francesca Corlazzoli
- Laboratory of Tumor Immunology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Leman (SCCL), Agora Cancer Research Center, Geneva and Lausanne, Switzerland
| | - Eliana Marinari
- Laboratory of Tumor Immunology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Leman (SCCL), Agora Cancer Research Center, Geneva and Lausanne, Switzerland
| | - Alexandra Bomane
- Department of CITI, Team Cell Death and Chilhood Cancers, Cancer Research Centre of Lyon - CRCL, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Augustin Brassens
- Department of CITI, Team GLIMMER Of lIght, Cancer Research Centre of Lyon - CRCL, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Antoine Marteyn
- Laboratory of Tumor Immunology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
| | - Youssef Hibaoui
- Service de Gynécologie Obstétrique, HFR Fribourg - Hôpital Cantonal, Fribourg, Switzerland
| | - Tom J Petty
- Swiss Institute of Bioinformatics, Geneva, Switzerland
- SOPHiA GENETICS, Rolle, Switzerland
| | - Mounira Chalabi-Dchar
- Department of CITI, Team Ribosome, Translation & Cancer, Cancer Research Centre of Lyon - CRCL, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Louis Larrouquere
- Department of CITI, Team GLIMMER Of lIght, Cancer Research Centre of Lyon - CRCL, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Noémie Legrand
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
| | - Jérôme Tamburini
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Leman (SCCL), Agora Cancer Research Center, Geneva and Lausanne, Switzerland
| | - Hubert Lincet
- Department of CITI, Team GLIMMER Of lIght, Cancer Research Centre of Lyon - CRCL, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Marie Castets
- Department of CITI, Team Cell Death and Chilhood Cancers, Cancer Research Centre of Lyon - CRCL, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Mayra Yebra
- Department of Surgery, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA
| | - Denis Migliorini
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Leman (SCCL), Agora Cancer Research Center, Geneva and Lausanne, Switzerland
| | - Valérie Dutoit
- Laboratory of Tumor Immunology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Leman (SCCL), Agora Cancer Research Center, Geneva and Lausanne, Switzerland
| | - Paul R Walker
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Leman (SCCL), Agora Cancer Research Center, Geneva and Lausanne, Switzerland
- Laboratory of Immunobiology of Brain Tumors, Center for Translational Research in OncoHematology, Geneva University Hospitals, and University of Geneva, Geneva, Switzerland
| | - Olivier Preynat-Seauve
- Department of Pathology and Immunology, Medical School, University of Geneva, Geneva, Switzerland
| | - Pierre-Yves Dietrich
- Laboratory of Tumor Immunology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Leman (SCCL), Agora Cancer Research Center, Geneva and Lausanne, Switzerland
| | - Érika Cosset
- Department of CITI, Team GLIMMER Of lIght, Cancer Research Centre of Lyon - CRCL, INSERM U1052, CNRS UMR 5286, Lyon, France.
- Laboratory of Tumor Immunology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland.
- Center for Translational Research in Onco-Hematology, Department of Oncology, University Hospital of Geneva, University of Geneva, Geneva, Switzerland.
- Team: GLIMMER Of lIght "GLIoblastoma MetabolisM, HetERogeneity, and OrganoIds"; Cancer Research Centre of Lyon - CRCL, INSERM U1052, CNRS UMR 5286, Lyon, France.
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Altintas DM, Comoglio PM. An Observatory for the MET Oncogene: A Guide for Targeted Therapies. Cancers (Basel) 2023; 15:4672. [PMID: 37760640 PMCID: PMC10526818 DOI: 10.3390/cancers15184672] [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: 08/31/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
The MET proto-oncogene encodes a pivotal tyrosine kinase receptor, binding the hepatocyte growth factor (HGF, also known as scatter factor, SF) and governing essential biological processes such as organogenesis, tissue repair, and angiogenesis. The pleiotropic physiological functions of MET explain its diverse role in cancer progression in a broad range of tumors; genetic/epigenetic alterations of MET drive tumor cell dissemination, metastasis, and acquired resistance to conventional and targeted therapies. Therefore, targeting MET emerged as a promising strategy, and many efforts were devoted to identifying the optimal way of hampering MET signaling. Despite encouraging results, however, the complexity of MET's functions in oncogenesis yields intriguing observations, fostering a humbler stance on our comprehension. This review explores recent discoveries concerning MET alterations in cancer, elucidating their biological repercussions, discussing therapeutic avenues, and outlining future directions. By contextualizing the research question and articulating the study's purpose, this work navigates MET biology's intricacies in cancer, offering a comprehensive perspective.
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Affiliation(s)
| | - Paolo M. Comoglio
- IFOM ETS—The AIRC Institute of Molecular Oncology, 20139 Milano, Italy;
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18
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Wang H, Wang X, Xu L, Zhang J. RARRES2 is Downregulated in Isocitrate Dehydrogenase 1 Mutant Glioma Patients and Served as an Unfavorable Prognostic Factor of Glioma. World Neurosurg 2023; 176:e610-e622. [PMID: 37271257 DOI: 10.1016/j.wneu.2023.05.109] [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: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Mutations in isocitrate dehydrogenase 1 (IDH1) induce extensive transcriptional alterations to promote glioma development. However, IDH1 mutation contributes the better clinical outcomes of glioma. Further understanding the transcriptional and DNA methylation changes mediated by IDH1 mutation will provide new therapeutic targets for glioma. METHODS Public glioma cohorts were collected and processed using R software. The transcriptional changes mediated by IDH1 mutation were determined and presented using heatmap. The differentially expressed genes in IDH1 mutant glioma were overlapped using TBtools. The prognostic effects of IDH1 regulated genes were determined by Kaplan-Meier survival analysis. RESULTS Retinoic acid receptor responder 2 (RARRES2) was upregulated in IDH1 wild type lower-grade glioma (LGG) patients, and higher expression levels of RARRES2 were associated with worse clinical outcomes of LGG. Moreover, IDH1 wild type LGG patients with higher expression levels of RARRES2 had even worse overall survival. Compared with LGG, RARRES2 was upregulated in grade IV glioma (glioblastoma multiforme, GBM). Also, RARRES2 represented an unfavorable prognostic factor of glioma. In GBM, RARRES2 was also associated with IDH1 mutation. In both LGG and GBM, IDH1 mutation induced extensive DNA hypermethylation, and more than half genes that were downregulated in IDH1 mutant glioma were contributed by DNA hypermethylation. RARRES2 was also hypermethylated in IDH1 mutant LGG or GBM patients. Furthermore, RARRES2 hypomethylation was an unfavorable prognostic factor in patients with LGG. CONCLUSIONS RARRES2 was downregulated by IDH1 mutation and served as an unfavorable prognostic factor in glioma.
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Affiliation(s)
- Haiwei Wang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Xinrui Wang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Ji Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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19
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Kothari S, Dusenbery AC, Doucette A, Zhang DY, Ballinger D, Desai A, Morrissette JJD, Bagley SJ, Nasrallah MP. RNA fusion transcript panel identifies diverse repertoire of fusions in adult glioma patients with therapeutic implications. Neurooncol Pract 2023; 10:370-380. [PMID: 37457221 PMCID: PMC10346416 DOI: 10.1093/nop/npad022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
Background Recurrent gliomas are therapeutically challenging diseases with few treatment options available. One area of potential therapeutic vulnerability is the presence of targetable oncogenic fusion proteins. Methods To better understand the clinical benefit of routinely testing for fusion proteins in adult glioma patients, we performed a retrospective review of 647 adult patients with glioma who underwent surgical resection at our center between August 2017 and May 2021 and whose tumors were analyzed with an in-house fusion transcript panel. Results Fifty-two patients (8%) were found to harbor a potentially targetable fusion with 11 (21%) of these patients receiving treatment with a fusion-targeted inhibitor. The targetable genes found to be involved in a fusion included FGFR3, MET, EGFR, NTRK1, NTRK2, BRAF, ROS1, and PIK3CA. Conclusions This analysis demonstrates that routine clinical testing for gene fusions identifies a diverse repertoire of potential therapeutic targets in adult patients with glioma and can offer rational therapeutic options for patients with recurrent disease.
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Affiliation(s)
- Shawn Kothari
- Division of Hematology/Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna C Dusenbery
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Abigail Doucette
- Division of Hematology/Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel Y Zhang
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dominique Ballinger
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arati Desai
- Electronic Phenotyping Core, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen J Bagley
- Division of Hematology/Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - MacLean P Nasrallah
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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20
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Bao Z, Li S, Wang L, Zhang B, Zhang P, Shi H, Qiu X, Jiang T. PTPRZ1-METFUsion GENe (ZM-FUGEN) trial: study protocol for a multicentric, randomized, open-label phase II/III trial. Chin Neurosurg J 2023; 9:21. [PMID: 37443050 DOI: 10.1186/s41016-023-00329-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 06/02/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND PTPRZ1-MET fusion was reported to associate with glioma progression from low-grade to high-grade glioma, which was a target by a MET inhibitor vebreltinib. However, little is known about the further efficacy of vebreltinib among more glioma patients. This trial aims to evaluate the safety and efficacy of vebreltinib enteric-coated capsules in the treatment of sGBM/IDH mutant glioblastoma patients with the ZM fusion gene. METHODS This multicentric, randomized, open-label, controlled trial plans to include 19 neurosurgical centers and recruit 84 sGBM or IDH mutant glioblastoma patients with the ZM fusion gene. This trial enrolls sGBM or IDH mutant glioblastoma patients with the inclusion criteria and without the exclusion criteria. It was registered with chinadrugtrials.org.cn (CTR20181664). The primary efficacy endpoint is overall survival (OS). The secondary endpoints are progression-free survival (PFS) and objective response rate (ORR). DISCUSSION If proven effective, this targeted multifaceted intervention protocol will be extended for more glioma patients as a protocol to evaluate the safety and efficacy of MET inhibitors. TRIAL REGISTRATION It was registered with chinadrugtrials.org.cn (CTR20181664).
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Affiliation(s)
- Zhaoshi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
| | - Shouwei Li
- Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Liang Wang
- Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Bisi Zhang
- Beijing Pearl Biotechnology Limited Liability Company, Beijing, China
| | - Peilong Zhang
- Beijing Pearl Biotechnology Limited Liability Company, Beijing, China
| | - Hepeng Shi
- Beijing Pearl Biotechnology Limited Liability Company, Beijing, China
| | - Xiaoguang Qiu
- Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China.
- Department of Radio-Therapy, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China.
| | - Tao Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
- Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China.
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China.
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, 100069, China.
- China National Clinical Research Center for Neurological Diseases, Beijing, 100050, China.
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21
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Lu J, Liang K, Zou R, Peng Y, Wang H, Huang R, Zeng Z, Feng Z, Fan Y, Zhang S, Ji Y, Pang X, Wang Y, Zhang H, Wang Z. Comprehensive analysis of the prognostic and immunological signature of eight Tripartitemotif (TRIM) family molecules in human gliomas. Aging (Albany NY) 2023; 15:5798-5825. [PMID: 37367937 PMCID: PMC10333093 DOI: 10.18632/aging.204841] [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: 02/13/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND TRIM family molecules have been identified as being involved in the tumor progression of various cancer types. Increasingly, experimental evidence indicates that some of TRIM family molecules are implicated in glioma tumorigenesis. However, the diverse genomic changes, prognostic values and immunological landscapes of TRIM family of molecules have yet to be fully determined in glioma. METHODS In our study, employing the comprehensive bioinformatics tools, we evaluated the unique functions of 8 TRIM members including TRIM5/17/21/22/24/28/34/47 in gliomas. RESULTS The expression levels of 7 TRIM members (TRIM5/21/22/24/28/34/47) were higher in glioma as well as its diverse cancer subtypes than in normal tissues, whereas the expression level of TRIM17 was the opposite, lower in the former than in the latter. In addition, survival analysis revealed that the high expression profiles of TRIM5/21/22/24/28/34/47 were associated with poor overall survival (OS), disease-specific survival (DSS) and progress-free interval (PFI) in glioma patients, whereas TRIM17 displayed adverse outcomes. Moreover, the 8 TRIM molecules expression as well as methylation profiles remarkably correlated with different WHO grades. And genetic alterations, including mutations and copy number alterations (CNAs), in the TRIM family were correlated with longer OS, DSS and progress-free survival (PFS) in glioma patients. Furthermore, through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results of these 8 molecules and their related genes, we found that these molecules may change the immune infiltration of the tumor microenvironment and regulate the expression of immune checkpoint molecules (ICMs), affecting the occurrence and development of gliomas. The correlation analyses between the 8 TRIM molecules and TMB (tumor mutational burden)/MSI (microsatellite instability)/ICMs discovered that as the expression level of TRIM5/21/22/24/28/34/47 increased, the TMB score also increased significantly, while TRIM17 showed an opposite outcome. Further, a 6-gene signature (TRIM 5/17/21/28/34/47) for predicting overall survival (OS) in gliomas was built by using the least absolute shrinkage and selection operator (LASSO) regression, and the survival and time-dependent ROC analyses all were found to perform well in testing and validation cohorts. Results of multivariate COX regression analysis showed that TRIM5/28 are both expected to become independent risk predictors to guide clinical treatment. CONCLUSION In general, the results indicate that TRIM5/17/21/22/24/28/34/47 might exert a crucial influence on gliomas tumorigenesis and might be putative prognostic markers and therapeutic targets for glioma patients.
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Affiliation(s)
- Jiajie Lu
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Kairong Liang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Renheng Zou
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yuecheng Peng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Haojian Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Rihong Huang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Zhaorong Zeng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Zejia Feng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Yongyang Fan
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Shizhen Zhang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yunxiang Ji
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Xiao Pang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yezhong Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Hongri Zhang
- Department of Neurosurgery, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, China
| | - Zhaotao Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
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Xia H, Zhang J, Chen T, Wang M, Chen D, Si T, Liu Y. Molecular characterization of MET fusions from a large real-world Chinese population: A multicenter study. Cancer Med 2023. [PMID: 37326363 PMCID: PMC10358190 DOI: 10.1002/cam4.6047] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/03/2023] [Accepted: 04/26/2023] [Indexed: 06/17/2023] Open
Abstract
PURPOSE MET is a notable driver gene in the diversity of aberrations with clinical relevance, including exon 14 skipping, copy number gain, point mutations, and gene fusions. Compared with the former two, MET fusions are severely under-reported, leaving a series of unanswered questions. In this study, we addressed this gap by characterizing MET fusions in a large, real-world Chinese cancer population. METHODS We retrospectively included patients with solid tumors who had DNA-based genome profiles acquired through targeted sequencing from August 2015 to May 2021. MET fusion-positive (MET+) patients were subsequently selected for clinical and molecular characterization. RESULTS We screened 79,803 patients across 27 tumor types and detected 155 putative MET fusions from 122 patients, resulting in an overall prevalence of 0.15%. Lung cancer comprised the majority of MET+ patients (92, 75.4%). Prevalence was markedly higher in liver cancer, biliary tract cancer, and renal cancer (range 0.52%-0.60%). It was lower in ovarian cancer (0.06%). A substantial proportion (48/58, 82.8%) of unique partners were reported for the first time. High heterogeneity was observed for partners, with ST7, HLA-DRB1, and KIF5B as the three most common partners. Mutational landscape analysis of lung adenocarcinoma (n = 32) revealed a high prevalence of TP53 in MET+ alterations, EGFR L858R, EGFR L861Q, and MET amplification. CONCLUSION To our knowledge, this is currently the largest study in characterizing MET fusions. Our findings warrant that further clinical validation and mechanistic study may translate into therapeutic avenues for MET+ cancer patients.
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Affiliation(s)
- Hui Xia
- Thoracic Surgery Department, The Fourth Medical Center of PLA General Hospital, Beijing, China
| | - Junhua Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Clinical Research Center for Radiation Oncology Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Tong Chen
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Mingzhao Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dongna Chen
- Department of Medical Oncology, Sanhuan Cancer Hospital of Chaoyang District, Beijing, China
| | - Tongguo Si
- Department of Interventional Treatment, Tianjin Medical University Cancer Hospital and Institute, Tianjin, China
| | - Yutao Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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23
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Sun Y, Li R, Chen Y, Yang B, Li X, Li Z, He J, Zhou Z, Li J, Guo X, Wang X, Wu Y, Zhang W, Guo G. The value of basement membrane-associated genes in the prognosis and immune regulation of glioma. Medicine (Baltimore) 2023; 102:e33935. [PMID: 37335645 DOI: 10.1097/md.0000000000033935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Gliomas have a high incidence rate in central nervous tumors. Although many breakthroughs have been made in the pathogenesis and treatment of glioma, the recurrence and metastasis rates of patients have not been improved based on the uniqueness of glioma. Glioma destroys the surrounding basement membrane (BM), leading to local infiltration, resulting in the corresponding clinical and neurological symptoms. Therefore, exploring the biological roles played by BM associated genes in glioma is particularly necessary for a comprehensive understanding of the biological processes of glioma and its treatment. Differential expression and univariate COX regression analyses were used to identify the basement membrane genes (BMGs) to be included in the model. LASSO regression was used to construct the BMG model. The Kaplan-Meier (KM) survival analysis model was used to assess the prognosis discrimination between training sets, validation sets, and clinical subgroups. Receiver-operating characteristic (ROC) analysis was used to test the prognostic efficacy of the model. Use calibration curves to verify the accuracy of nomograms. Gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and gene set enrichment analysis (GSEA) were used to analyze the function and pathway enrichment among the model groups. ESTIMATE and other 7 algorithms including CIBERSORT were used to evaluate the immune microenvironment. "pRRophetic" was used to evaluate drug sensitivity. This study demonstrated that high-risk genes (LAMB4, MMP1, MMP7) promote glioma progression and negatively correlate with patient prognosis. In the tumor microenvironment (TME), high-risk genes have increased scores of macrophages, neutrophils, immune checkpoints, chemokines, and chemokine receptors. This study suggests that BMGs, especially high-risk-related genes, are potential sites for glioma therapy, a new prospect for comprehensively understanding the molecular mechanism of glioma.
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Affiliation(s)
- Yanqi Sun
- Department of Emergency, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ren Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yang Chen
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Biao Yang
- Department of Emergency, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xuepeng Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ziao Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jianhang He
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zihan Zhou
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jiayu Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaolong Guo
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaogang Wang
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yongqiang Wu
- Department of Emergency, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Wenju Zhang
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Geng Guo
- Department of Emergency, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
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Shi Z, Wu Y, Zhuo Q, Zuo Y, Lin J, Shi H, Zhou H, Xu Z. Comprehensive analysis of oxidative stress-related lncRNA signatures in glioma reveals the discrepancy of prognostic and immune infiltration. Sci Rep 2023; 13:7731. [PMID: 37173373 PMCID: PMC10182081 DOI: 10.1038/s41598-023-34909-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/09/2023] [Indexed: 05/15/2023] Open
Abstract
Oxidative stress refers to the process of reactive oxide species (ROS) increase in human body due to various factors, which leads to oxidative damage in human tissues. Current studies have confirmed that sustained oxidative stress is one of the distinctive features throughout the development of tumors. Numerous reports have shown that lncRNAs can regulate the process of oxidative stress through multiple pathways. However, the relationship between glioma-associated oxidative stress and lncRNAs is not clearly investigated. RNA sequencing data of GBM (glioblastoma) and LGG (low grade glioma) and corresponding clinical data were retrieved from the TCGA database. Oxidative stress related lncRNAs (ORLs) were identified by Pearson correlation analysis. Prognostic models for 6-ORLs were structured in the training cohort by univariate Cox regression analysis, multivariate Cox regression analysis and LASSO regression analysis. We constructed the nomogram and verified its predictive efficacy by Calibration curves and DCA decision curves. The biological functions and pathways of 6-ORLs-related mRNAs were inferred by Gene Set Enrichment Analysis. Immune cell abundance and immune function associated with risk score (RS) were estimated by ssGSEA, CIBERSORT and MCPcounter synthetically. External validation of the signature was completed using the CGGA-325 and CGGA-693 datasets. 6-ORLs signature-AC083864.2, AC107294.1, AL035446.1, CRNDE, LINC02600, and SNAI3-AS1-were identified through our analysis as being predictive of glioma prognosis. Kaplan-Meier and ROC curves indicated that the signature has a dependable predictive efficacy in the TCGA training cohort, validation cohort and CGGA-325/CGGA-693 test cohort. The 6-ORLs signature were verified to be independent prognostic predictors by multivariate cox regression and stratified survival analysis. Nomogram built with risk scores had strong predictive efficacy for patients' overall survival (OS). The outcomes of the functional enrichment analysis revealing potential molecular regulatory mechanisms for the 6-ORLs. Patients in the high-risk subgroup presented a significant immune microenvironment of macrophage M0 and cancer-associated fibroblast infiltration which was associated with a poorer prognosis. Finally, the expression levels of 6-ORLs in U87/U251/T98/U138 and HA1800 cell lines were verified by RT-qPCR. The nomogram in this study has been made available as a web version for clinicians. This 6-ORLs risk signature has the capabilities to predict the prognosis of glioma patients, assist in evaluating immune infiltration, and assess the efficacy of various anti-tumor systemic therapy regimens.
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Affiliation(s)
- Zhenyi Shi
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China
| | - Yingying Wu
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China
| | - Qingchan Zhuo
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China
| | - Yufang Zuo
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China
| | - Jiong Lin
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China
| | - Huadi Shi
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China.
| | - Hechao Zhou
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China.
| | - Zumin Xu
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China.
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Wang T, Yao S, Li S, Fei X, Zhang M. A prognostic model based on the Augmin family genes for LGG patients. Sci Rep 2023; 13:7520. [PMID: 37161065 PMCID: PMC10170088 DOI: 10.1038/s41598-023-34779-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 05/08/2023] [Indexed: 05/11/2023] Open
Abstract
Gliomas are the most prevalent primary tumors in the central nervous system. Despite some breakthroughs in the treatment of glioma in recent years, survival rates remain low. Although genes of the Augmin family play a key role in microtubule nucleation, the role they play in gliomas is unclear. Transcriptome data were extracted from UCSC XENA and GTEx for low-grade glioma (LGG) and normal tissues, respectively. The protein interaction network associated with Augmin family genes was established using STRING and GeneMANIA databases. Enrichment analysis of gene-related functions and pathways was used to explore potential biological pathways and TIMER to assess immune cell infiltration. Regression analysis and Kaplan-Meier analysis were used to look at the clinical characteristics of the Augmin family genes and the association with the prognosis of patients with glioma. The results showed that the mRNA expression of Augmin family genes was significantly elevated in LGG tissues, except for HAUS7. Immunoregulation, cell cycle, apoptosis and other signaling pathways may be involved in the development and progression of LGG. Except for HAUS4 and HAUS7, the expression of all genes was positively correlated with immune cell infiltration. High expression of HAUS1, HAUS3, HAUS5, HAUS7, HAUS8 and low expression of HAUS4, HAUS6 in LGG was associated with poor prognosis. The risk models constructed based on the pivotal genes HAUS2, HAUS4 and HAUS8 were validated by nomogram and confirmed to be clinically useful for predicting the prognosis of LGG.
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Affiliation(s)
- Tao Wang
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Senbang Yao
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Siyu Li
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xichang Fei
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Mingjun Zhang
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
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Fang X, Wu F, Jiang C. A novel gene, TARDBP, and the protein it encodes can predict glioma patient prognosis and establish a prediction model. BMC Neurol 2023; 23:182. [PMID: 37147573 PMCID: PMC10163712 DOI: 10.1186/s12883-023-03224-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND TDP-43 (43-kD transactive response DNA-binding protein) is a DNA-/RNA-binding protein that plays an important role in several nervous system diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Whether it plays an important role in glioma patients is unknown. METHODS Datasets were downloaded from the Chinese Glioma Genome Atlas (CGGA) website ( http://www.cgga.org.cn/ ). Cox survival analysis was performed to determine the relationship between TARDBP gene expression and the overall survival of glioma patients. GO analyses were performed to determine the biological functions of the TARDBP gene. Finally, we used PRS type, age, grade, IDH mutation status, 1p/19q codeletion status, and expression value of the TARDBP gene to construct a prediction model. With this model, we can predict patients' 1-, 2-, 3-, 5-, and 10-year survival rates. RESULTS The TARDBP gene plays an important role in glioma patients. The expression of the TARDBP gene has a significant correlation with glioma patient survival. We also constructed an ideal prediction model. CONCLUSION Our findings suggest that the TARDBP gene and the protein it encodes play important roles in glioma patients. The expression of the TARDBP gene has a significant correlation with the overall survival of glioma patients.
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Affiliation(s)
- Xu Fang
- Department of Neurosurgery, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Fan Wu
- Department of Orthopaedics and Traumatology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chen Jiang
- Department of Neurosurgery Intensive Care Unit, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China.
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Papadimitriou E, Kanellopoulou VK. Protein Tyrosine Phosphatase Receptor Zeta 1 as a Potential Target in Cancer Therapy and Diagnosis. Int J Mol Sci 2023; 24:ijms24098093. [PMID: 37175798 PMCID: PMC10178973 DOI: 10.3390/ijms24098093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Protein tyrosine phosphatase receptor zeta 1 (PTPRZ1) is a type V transmembrane tyrosine phosphatase that is highly expressed during embryonic development, while its expression during adulthood is limited. PTPRZ1 is highly detected in the central nervous system, affecting oligodendrocytes' survival and maturation. In gliomas, PTPRZ1 expression is significantly upregulated and is being studied as a potential cancer driver and as a target for therapy. PTPRZ1 expression is also increased in other cancer types, but there are no data on the potential functional significance of this finding. On the other hand, low PTPRZ1 expression seems to be related to a worse prognosis in some cancer types, suggesting that in some cases, it may act as a tumor-suppressor gene. These discrepancies may be due to our limited understanding of PTPRZ1 signaling and tumor microenvironments. In this review, we present evidence on the role of PTPRZ1 in angiogenesis and cancer and discuss the phenomenal differences among the different types of cancer, depending on the regulation of its tyrosine phosphatase activity or ligand binding. Clarifying the involved signaling pathways will lead to its efficient exploitation as a novel therapeutic target or as a biomarker, and the development of proper therapeutic approaches.
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Affiliation(s)
- Evangelia Papadimitriou
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | - Vasiliki K Kanellopoulou
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, 26504 Patras, Greece
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28
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Qi C, Lei L, Hu J, Ou S. Establishment and validation of a novel integrin-based prognostic gene signature that sub-classifies gliomas and effectively predicts immunosuppressive microenvironment. Cell Cycle 2023; 22:1259-1283. [PMID: 37096960 DOI: 10.1080/15384101.2023.2205204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
The integrin family members play a key role in cancer immunomodulation and prognosis. We comprehensively analyzed the expression patterns and clinical significance of integrin family-related genes in gliomas. A total of 2293 gliomas from the Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA) and Gliovis platform were enrolled for analyses. Twenty-six integrin coding genes showed different expression patterns between glioma and normal brain tissues. We screened an integrin family-related gene signature (ITGA5, ITGA9, ITGAE, ITGB7 and ITGB8) that showed independent prognostic value and sub-classified gliomas into different prognostic and molecular clusters, further composed an integrin-based risk score model associated with glioma malignant clinical features, overall survival (OS), and immune microenvironment alterations. Besides, glioma patients with high-risk scores showed chemotherapeutic resistance and more immune cells infiltration as well as high immune checkpoints expression. Concurrently, we also revealed that high-risk score group presented resistance to T cell-mediated cancer killing process and lower rates of response to immune checkpoint blockade (ICB) treatment. In conclusion, our study identified a valuable integrin gene signature that predicted gliomas OS effectively, and sub-classified them into different phenotypes and accompanied with immunological changes, possibly acted as a biomarker for ICB treatment.
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Affiliation(s)
- Chunxiao Qi
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
- Department of Neurosurgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, P.R. China
| | - Lei Lei
- Department of Rheumatology and Immunology, Dalian Municipal Central Hospital Affiliated of Dalian Medical University, Dalian, Liaoning, P.R. China
| | - Jinqu Hu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Shaowu Ou
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
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Wei Y, Li G, Feng J, Wu F, Zhao Z, Bao Z, Zhang W, Su X, Li J, Qi X, Duan Z, Zhang Y, Vega SF, Jakola AS, Sun Y, Carén H, Jiang T, Fan X. Stalled oligodendrocyte differentiation in IDH-mutant gliomas. Genome Med 2023; 15:24. [PMID: 37055795 PMCID: PMC10103394 DOI: 10.1186/s13073-023-01175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Roughly 50% of adult gliomas harbor isocitrate dehydrogenase (IDH) mutations. According to the 2021 WHO classification guideline, these gliomas are diagnosed as astrocytomas, harboring no 1p19q co-deletion, or oligodendrogliomas, harboring 1p19q co-deletion. Recent studies report that IDH-mutant gliomas share a common developmental hierarchy. However, the neural lineages and differentiation stages in IDH-mutant gliomas remain inadequately characterized. METHODS Using bulk transcriptomes and single-cell transcriptomes, we identified genes enriched in IDH-mutant gliomas with or without 1p19q co-deletion, we also assessed the expression pattern of stage-specific signatures and key regulators of oligodendrocyte lineage differentiation. We compared the expression of oligodendrocyte lineage stage-specific markers between quiescent and proliferating malignant single cells. The gene expression profiles were validated using RNAscope analysis and myelin staining and were further substantiated using data of DNA methylation and single-cell ATAC-seq. As a control, we assessed the expression pattern of astrocyte lineage markers. RESULTS Genes concordantly enriched in both subtypes of IDH-mutant gliomas are upregulated in oligodendrocyte progenitor cells (OPC). Signatures of early stages of oligodendrocyte lineage and key regulators of OPC specification and maintenance are enriched in all IDH-mutant gliomas. In contrast, signature of myelin-forming oligodendrocytes, myelination regulators, and myelin components are significantly down-regulated or absent in IDH-mutant gliomas. Further, single-cell transcriptomes of IDH-mutant gliomas are similar to OPC and differentiation-committed oligodendrocyte progenitors, but not to myelinating oligodendrocyte. Most IDH-mutant glioma cells are quiescent; quiescent cells and proliferating cells resemble the same differentiation stage of oligodendrocyte lineage. Mirroring the gene expression profiles along the oligodendrocyte lineage, analyses of DNA methylation and single-cell ATAC-seq data demonstrate that genes of myelination regulators and myelin components are hypermethylated and show inaccessible chromatin status, whereas regulators of OPC specification and maintenance are hypomethylated and show open chromatin status. Markers of astrocyte precursors are not enriched in IDH-mutant gliomas. CONCLUSIONS Our studies show that despite differences in clinical manifestation and genomic alterations, all IDH-mutant gliomas resemble early stages of oligodendrocyte lineage and are stalled in oligodendrocyte differentiation due to blocked myelination program. These findings provide a framework to accommodate biological features and therapy development for IDH-mutant gliomas.
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Affiliation(s)
- Yanfei Wei
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Guanzhang Li
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Jing Feng
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Fan Wu
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zhaoshi Bao
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Wei Zhang
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Xiaodong Su
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jiuyi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Xueling Qi
- Department of Pathology, San Bo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Zejun Duan
- Department of Pathology, San Bo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Yunqiu Zhang
- Center of Growth Metabolism & Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Sandra Ferreyra Vega
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41390, Sweden
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41390, Gothenburg, Sweden
| | - Asgeir Store Jakola
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41390, Sweden
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, 41390, Sweden
| | - Yingyu Sun
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41390, Gothenburg, Sweden.
| | - Tao Jiang
- Beijing Neurosurgical Institute, Beijing, 100070, China.
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, 100070, China.
| | - Xiaolong Fan
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China.
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, 100070, China.
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Yang W, Zhao X, Zheng A, Liu Z, Ma J, Zhang X, Li W, Wang D, Zhu J, Tao H, Zhang Y, Ma T, Liu Q. Identification of MET fusions in solid tumors: A multicenter, large scale study in China. Int J Cancer 2023; 152:1259-1268. [PMID: 36408924 DOI: 10.1002/ijc.34361] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/15/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022]
Abstract
MET amplification and exon 14 skipping are well known as oncogenic drivers in multiple cancer types. However, MET fusions in most cancer types are poorly defined. To explore the profile and analyze the characteristics of MET fusions, a large-cohort study was conducted to screen MET fusions in clinical samples (n = 10 882) using DNA-based NGS. A total of 37 potentially functional MET fusions containing the intact tyrosine kinase domain (TKD) of MET were identified in 36 samples. Further, 15 novel MET fusions were identified in five cancer types, and the incidence of novel MET fusions accounted for 40.5% (15/37). Brain cancer had the highest incidence of MET fusion, with PTPRZ1-MET as the most common fusion (37.0%). All MET breakpoints in brain cancer (n = 27) were also located in intron 1, while those in lung cancer (n = 4) occurred in intron 1, intron 11, intron 14 and exon 14, respectively. The positive consistency of the common fusion group was 100% (11/11), while that of the rare fusion group was 53.8% (7/13). In conclusion, we provided a comprehensive genomic landscape of MET rearrangement and updated the MET fusions database for clinical test. In addition, we revealed that DNA-based NGS might serve as the clinical test for common MET fusions; however, rare MET fusions must be validated by both DNA-based NGS and RNA-based NGS. Prospective trials are necessary to confirm the treatment efficacy of MET inhibitors.
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Affiliation(s)
- Wenhui Yang
- Department of Digestive Oncology, Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ximeng Zhao
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Aiwen Zheng
- Department of Gynecologic Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Zhengchuang Liu
- Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Jie Ma
- Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Xiang Zhang
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Wei Li
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Dan Wang
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Jianhua Zhu
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Houquan Tao
- Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | | | - Tonghui Ma
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Qing Liu
- Department of Neurosurgery, Xiangya Hospital Central South University, Changsha, China
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Wang T, Liu M, Jia M. Integrated Bioinformatic Analysis of the Correlation of HOXA10 Expression with Survival and Immune Cell Infiltration in Lower Grade Glioma. Biochem Genet 2023; 61:238-257. [PMID: 35836029 DOI: 10.1007/s10528-022-10258-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 06/22/2022] [Indexed: 01/24/2023]
Abstract
Homeobox A10 (HOXA10) encodes a transcription factor that regulates developmental processes. Whether HOXA10 mRNA levels in lower grade glioma (LGG) correlate with survival and immune cell infiltration has not been evaluated. The differential expression of HOXA10 in different tumors and their corresponding normal tissues was evaluated by exploring public datasets. The correlations between HOXA10 and survival, tumor immune cell infiltration, diverse gene mutation characteristics, and tumor mutation burden in LGG were also investigated using several independent datasets. Pathway enrichment analysis was conducted to identify HOXA10-associated signaling pathways. We found that HOXA10 expression levels did not significantly differ between LGG tumors and normal tissues. Upon assessing the association between HOXA10 expression and immune cell infiltration in LGG, as expected, HOXA10 gene mRNA levels were positively associated with B-cell and dendritic cell infiltration levels in public online datasets. Different HOXA10 expression groups showed diverse gene mutation characteristics and TMB, and low HOXA10 expression was closely related to improved LGG patient survival. Pathway enrichment analysis of HOXA10-associated genes indicated that the cell cycle signaling pathway may participate in affecting the outcomes of LGG patients. Our findings showed that HOXA10 expression was associated with LGG prognosis and tumor immunity.
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Affiliation(s)
- Ting Wang
- Department of Radiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, Shandong Lung Cancer Institute, Shandong Institute of Neuroimmunology, Jinan, Shandong, China
| | - Mingqian Liu
- Department of Hematology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
| | - Ming Jia
- Department of Cancer Center, The Secondary Hospital, Cheeloo College of Medicine, Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China.
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Wang H, Wang X, Xu L, Zhang J. Co-amplified with PDGFRA, IGFBP7 is a prognostic biomarker correlated with the immune infiltrations of glioma. Cancer Med 2023; 12:4951-4967. [PMID: 36043552 PMCID: PMC9972101 DOI: 10.1002/cam4.5187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/24/2022] [Accepted: 08/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A subgroup of glioma carry genetic 4q12 amplification including platelet derived growth factor receptor α (PDGFRA) and insulin like growth factor binding protein 7 (IGFBP7). However, the prognosis of PDGFRA and IGFBP7 in glioma is unclear. METHODS The prognosis of PDGFRA and IGFBP7 was determined using cox regression and Kaplan-Meier survival analysis. Pathways associated with IGFBP7 were analyzed through gene set enrichment analysis (GSEA). Immune profiling of glioma was determined using "ESTIMATE" and "TIMER" database. RESULTS PDGFRA amplification or expression was not correlated with the outcomes of glioblastoma (GBM). IGFBP7 but not PDGFRA was over-expressed in GBM. IGFBP7 over-expression was correlated with the unfavorable outcomes of GBM. In lower grade glioma (LGG), PDGFRA over-expression was not correlated with the unfavorable prognosis of LGG, while, IGFBP7 was a prognostic biomarker of LGG. LGG patients with IGFBP7 lower expressions had prolonged clinical overall survival. Combination of IDH mutation, LGG grade and IGFBP7 achieved even better prognostic effects in LGG. Moreover, IGFBP7 was over-expressed in glioma patients with wild type IDH or with high grades. IGFBP7 over-expression was correlated with the unfavorable outcomes of glioma. Furthermore, IGFBP7 was hypo-methylated in GBM or LGG patients without IDH mutations. IGFBP7 hyper-methylation was correlated with the lower overall survival of GBM or LGG. LGG patients with wild type IDH and with IGFBP7 hypo-methylation demonstrated even worse prognosis. IGFBP7 was associated with multiple immune-related signaling pathways in GBM or LGG. The stromal score, immune score and the infiltrations of immune cells were also correlated with IGFBP7 and the prognosis of LGG. CONCLUSIONS IGFBP7 but not PDGFRA served an ideal prognostic marker and therapeutic target of glioma.
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Affiliation(s)
- Haiwei Wang
- Fujian Maternity and Child Health Hospital, Fujian Medical University, Fuzhou, China
| | - Xinrui Wang
- Fujian Maternity and Child Health Hospital, Fujian Medical University, Fuzhou, China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Fujian Medical University, Fuzhou, China
| | - Ji Zhang
- Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Yang F, Zhang X, Wang X, Xue Y, Liu X. The new oncogene transmembrane protein 60 is a potential therapeutic target in glioma. Front Genet 2023; 13:1029270. [PMID: 36744183 PMCID: PMC9895843 DOI: 10.3389/fgene.2022.1029270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/19/2022] [Indexed: 01/22/2023] Open
Abstract
Glioma is a malignant tumor with a high fatality rate, originating in the central nervous system. Even after standard treatment, the prognosis remains unsatisfactory, probably due to the lack of effective therapeutic targets. The family of transmembrane proteins (TMEM) is a large family of genes that encode proteins closely related to the malicious behavior of tumors. Thus, it is necessary to explore the molecular and clinical characteristics of newly identified oncogenes, such as transmembrane protein 60 (TMEM60), to develop effective treating options for glioma. We used bioinformatic methods and basic experiments to verify the expression of transmembrane protein 60 in gliomas and its relationship with 1p and 19q (1p19q) status, isocitrate dehydrogenase (IDH) status, patient prognosis, and immune cell infiltration using public databases and clinical samples. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to detect co-expressed genes. Thus, we inhibited the expression of transmembrane protein 60 to observe the proliferation and activity of glioma LN229 cells. We found transmembrane protein 60 was significantly upregulated in glioma compared with that in normal brain tissue at the mRNA. In the subgroups of World Health Organization high grade, isocitrate dehydrogenase wildtype, 1p and 19q non-codeletion, or isocitrate dehydrogenase wild combined with 1p and 19q non-codeletion, the expression of transmembrane protein 60 increased, and the prognosis of glioma patients worsened. In the transmembrane protein 60 high expression group, infiltration of immune cells and stromal cells in the tumor microenvironment increased, tumor purity decreased, and immune cells and pathways were activated. The immune cells mainly included regulatory T-cell, gamma delta T-cell, macrophages M0, neutrophils, and CD8+ T-cells. Overexpression of co-inhibitory receptors (CTLA4, PDL1 and CD96) may promote the increase of depletion of T-cell, thus losing the anti-tumor function in the transmembrane protein 60 high expression group. Finally, we found that transmembrane protein 60 silencing weakened the viability, proliferation, and colony formation of glioma LN229 cells. This is the 0 report on the abnormally high expression of transmembrane protein 60 in glioma and its related clinical features, such as tumor microenvironment, immune response, tumor heterogeneity, and patient prognosis. We also found that transmembrane protein 60 silencing weakened the proliferation and colony formation of glioma LN229 cells. Thus, the new oncogene transmembrane protein 60 might be an effective therapeutic target for the clinical treatment of glioma.
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Fortin Ensign SP, Jenkins RB, Giannini C, Sarkaria JN, Galanis E, Kizilbash SH. Translational significance of CDKN2A/B homozygous deletion in isocitrate dehydrogenase-mutant astrocytoma. Neuro Oncol 2023; 25:28-36. [PMID: 35973817 PMCID: PMC9825307 DOI: 10.1093/neuonc/noac205] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Indexed: 01/26/2023] Open
Abstract
Isocitrate dehydrogenase (IDH) 1 or 2 mutations confer a favorable prognosis compared to IDH-wildtype in astrocytoma, frequently denoting a lower grade malignancy. However, recent molecular profiling has identified specific aggressive tumor subgroups with clear clinical prognostic implications that are independent of histologic grading. The homozygous deletion of CDKN2A/B is the strongest implicated independent indicator of the poor prognosis within IDH-mutant astrocytoma, and the identification of this alteration in these lower histologic grade tumors transforms their biology toward an aggressive grade 4 phenotype clinically. CDKN2A/B homozygous deletion is now sufficient to define a grade 4 tumor in IDH-mutant astrocytomas regardless of histologic appearance, yet there are currently no effective molecularly informed targeted therapies for these tumors. The biological impact of CDKN2A/B homozygous deletion in IDH-mutant tumors and the optimal treatment strategy for this molecular subgroup remains insufficiently explored. Here we review the current understanding of the translational significance of homozygous deletion of CDKN2A/B gene expression in IDH-mutant astrocytoma and associated diagnostic and therapeutic implications.
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Affiliation(s)
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
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Zhang JJ, Zhang Y, Chen Q, Chen QN, Yang X, Zhu XL, Hao CY, Duan HB. A Novel Prognostic Marker and Therapeutic Target Associated with Glioma Progression in a Tumor Immune Microenvironment. J Inflamm Res 2023; 16:895-916. [PMID: 36883185 PMCID: PMC9985882 DOI: 10.2147/jir.s398775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Background Immune microenvironment serves a vital role in glioma progression, and a large number of studies have found that tumor progression can be reduced to some extent by modulating the immune process in tumors. Materials and Methods ImmuneScore of each sample in CGGA datasets were calculated with Estimate R package, and samples were grouped by median ImmuneScore values for differential analysis to obtain immune microenvironment differential genes. We further conducted survival analysis, ROC curve analysis, independent prognostic analysis, and clinical correlation analysis on glioma sample genes in CGGA to obtain glioma prognostic genes, and then identified their intersection with immune microenvironment DEGs by Venn tool. The GEPIA and UALCAN databases were used to verify the differential expression of intersecting genes in the glioma and normal brain and to identify our target gene. After validation of their prognostic value, we constructed a nomogram to calculate the risk score and to estimate the accuracy of prognostic model. We mined co-expression genes, enriched functions and pathways, and correlations to immune cell infiltration of unigene with an online database. Finally, we verified the differential expression of FCGBP in glioma by immunohistochemical staining. Results We finally selected Fc fragment of IgG-binding protein (FCGBP) as our study gene. The prognostic values of FCGBP were validated by a series of analyses. Immunohistochemical staining showed that FCGBP expression increased in gliomas and was up-regulated with the progression of glioma grade. Conclusion As a key unigene in glioma progression, FCGBP contributes to the regulation of immune microenvironment and has the potential to be a prognostic biomarker and immune targets.
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Affiliation(s)
- Jun-Jie Zhang
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Yu Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Qian Chen
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Qi-Ning Chen
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Xin Yang
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Xiao-Lin Zhu
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Chun-Yan Hao
- Department of Geriatrics, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Hu-Bin Duan
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
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Construction of a machine learning-based artificial neural network for discriminating PANoptosis related subgroups to predict prognosis in low-grade gliomas. Sci Rep 2022; 12:22119. [PMID: 36543888 PMCID: PMC9770564 DOI: 10.1038/s41598-022-26389-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
The poor prognosis of gliomas necessitates the search for biomarkers for predicting clinical outcomes. Recent studies have shown that PANoptosis play an important role in tumor progression. However, the role of PANoptosis in in gliomas has not been fully clarified.Low-grade gliomas (LGGs) from TCGA and CGGA database were classified into two PANoptosis patterns based on the expression of PANoptosis related genes (PRGs) using consensus clustering method, followed which the differentially expressed genes (DEGs) between two PANoptosis patterns were defined as PANoptosis related gene signature. Subsequently, LGGs were separated into two PANoptosis related gene clusters with distinct prognosis based on PANoptosis related gene signature. Univariate and multivariate cox regression analysis confirmed the prognostic values of PANoptosis related gene cluster, based on which a nomogram model was constructed to predict the prognosis in LGGs. ESTIMATE algorithm, MCP counter and CIBERSORT algorithm were utilized to explore the distinct characteristics of tumor microenvironment (TME) between two PANoptosis related gene clusters. Furthermore, an artificial neural network (ANN) model based on machine learning methods was developed to discriminate distinct PANoptosis related gene clusters. Two external datasets were used to verify the performance of the ANN model. The Human Protein Atlas website and western blotting were utilized to confirm the expression of the featured genes involved the ANN model. We developed a machine learning based ANN model for discriminating PANoptosis related subgroups with drawing implications in predicting prognosis in gliomas.
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Chai R, Fang S, Pang B, Liu Y, Wang Y, Zhang W, Jiang T. Molecular pathology and clinical implications of diffuse glioma. Chin Med J (Engl) 2022; 135:2914-2925. [PMID: 36728558 PMCID: PMC10106158 DOI: 10.1097/cm9.0000000000002446] [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: 04/03/2022] [Indexed: 02/03/2023] Open
Abstract
ABSTRACT The prognosis for diffusely infiltrating gliomas at World Health Organization (WHO) grade 2-4 remains dismal due to their heterogeneity. The rapid development of genome-wide molecular-profiling-associated studies has greatly promoted the accuracy of glioma classification. Thus, the latest version of the WHO classification of the central nervous system tumors published in 2021 has incorporated more molecular biomarkers together with histological features for the diagnosis of gliomas. Advanced usage of molecular pathology in clinical diagnostic practice provides also new opportunities for the therapy of patients with glioma, including surgery, radiotherapy and chemotherapy, targeted therapy, immunotherapy, and more precision clinical trials. Herein, we highlight the updates in the classification of gliomas according to the latest WHO guidelines and summarize the clinically relevant molecular markers by focusing on their applications in clinical practice. We also review the advances in molecular features of gliomas, which can facilitate the development of glioma therapies, thereby discussing the challenges and future directions of molecular pathology toward precision medicine for patients with glioma.
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Affiliation(s)
- Ruichao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Shengyu Fang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Bo Pang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Yuqing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Yongzhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Wei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Research Unit of Accurate Diagnosis, Treatment, and Translational Medicine of Brain Tumors, Chinese Academy of Medical Sciences, Beijing 100070, China
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38
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Zhu Q, Shen S, Yang C, Li M, Zhang X, Li H, Zhao X, Li M, Cui Y, Ren X, Lin S. A prognostic estimation model based on mRNA-sequence data for patients with oligodendroglioma. Front Neurol 2022; 13:1074593. [PMID: 36588901 PMCID: PMC9795846 DOI: 10.3389/fneur.2022.1074593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Background The diagnosis of oligodendroglioma based on the latest World Health Organization Classification of Tumors of the Central Nervous System (WHO CNS 5) criteria requires the codeletion of chromosome arms 1p and 19q and isocitrate dehydrogenase gene (IDH) mutation (mut). Previously identified prognostic indicators may not be completely suitable for patients with oligodendroglioma based on the new diagnostic criteria. To find potential prognostic indicators for oligodendroglioma, we analyzed the expression of mRNAs of oligodendrogliomas in Chinese Glioma Genome Atlas (CGGA). Methods We collected 165 CGGA oligodendroglioma mRNA-sequence datasets and divided them into two cohorts. Patients in the two cohorts were further classified into long-survival and short-survival subgroups. The most predictive mRNAs were filtered out of differentially expressed mRNAs (DE mRNAs) between long-survival and short-survival patients in the training cohort by least absolute shrinkage and selection operator (LASSO), and risk scores of patients were calculated. Univariate and multivariate analyses were performed to screen factors associated with survival and establish the prognostic model. qRT-PCR was used to validate the expression differences of mRNAs. Results A total of 88 DE mRNAs were identified between the long-survival and the short-survival groups in the training cohort. Seven RNAs were selected to calculate risk scores. Univariate analysis showed that risk level, age, and primary-or-recurrent status (PRS) type were statistically correlated with survival and were used as factors to establish a prognostic model for patients with oligodendroglioma. The model showed an optimal predictive accuracy with a C-index of 0.912 (95% CI, 0.679-0.981) and harbored a good agreement between the predictions and observations in both training and validation cohorts. Conclusion We established a prognostic model based on mRNA-sequence data for patients with oligodendroglioma. The predictive ability of this model was validated in a validation cohort, which demonstrated optimal accuracy. The 7 mRNAs included in the model would help predict the prognosis of patients and guide personalized treatment.
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Affiliation(s)
- Qinghui Zhu
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shaoping Shen
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chuanwei Yang
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Mingxiao Li
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiaokang Zhang
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Haoyi Li
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xuzhe Zhao
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ming Li
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yong Cui
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Xiaohui Ren
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Song Lin
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China,*Correspondence: Song Lin
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Zwaig M, Baguette A, Hu B, Johnston M, Lakkis H, Nakada EM, Faury D, Juretic N, Ellezam B, Weil AG, Karamchandani J, Majewski J, Blanchette M, Taylor MD, Gallo M, Kleinman CL, Jabado N, Ragoussis J. Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data. BMC Cancer 2022; 22:1297. [PMID: 36503484 PMCID: PMC9743522 DOI: 10.1186/s12885-022-10359-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Juvenile Pilocytic Astrocytomas (JPAs) are one of the most common pediatric brain tumors, and they are driven by aberrant activation of the mitogen-activated protein kinase (MAPK) signaling pathway. RAF-fusions are the most common genetic alterations identified in JPAs, with the prototypical KIAA1549-BRAF fusion leading to loss of BRAF's auto-inhibitory domain and subsequent constitutive kinase activation. JPAs are highly vascular and show pervasive immune infiltration, which can lead to low tumor cell purity in clinical samples. This can result in gene fusions that are difficult to detect with conventional omics approaches including RNA-Seq. METHODS To this effect, we applied RNA-Seq as well as linked-read whole-genome sequencing and in situ Hi-C as new approaches to detect and characterize low-frequency gene fusions at the genomic, transcriptomic and spatial level. RESULTS Integration of these datasets allowed the identification and detailed characterization of two novel BRAF fusion partners, PTPRZ1 and TOP2B, in addition to the canonical fusion with partner KIAA1549. Additionally, our Hi-C datasets enabled investigations of 3D genome architecture in JPAs which showed a high level of correlation in 3D compartment annotations between JPAs compared to other pediatric tumors, and high similarity to normal adult astrocytes. We detected interactions between BRAF and its fusion partners exclusively in tumor samples containing BRAF fusions. CONCLUSIONS We demonstrate the power of integrating multi-omic datasets to identify low frequency fusions and characterize the JPA genome at high resolution. We suggest that linked-reads and Hi-C could be used in clinic for the detection and characterization of JPAs.
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Affiliation(s)
- Melissa Zwaig
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
| | - Audrey Baguette
- grid.414980.00000 0000 9401 2774Quantitative Life Sciences and Lady Davis Institute for Medical Research, Montreal, Quebec Canada
| | - Bo Hu
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
| | - Michael Johnston
- grid.22072.350000 0004 1936 7697Alberta Children‘s Hospital Research Institute, Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
| | - Hussein Lakkis
- grid.414980.00000 0000 9401 2774Department of Human Genetics and Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec Canada
| | - Emily M. Nakada
- grid.63984.300000 0000 9064 4811The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Damien Faury
- grid.63984.300000 0000 9064 4811The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Nikoleta Juretic
- grid.63984.300000 0000 9064 4811The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Benjamin Ellezam
- grid.14848.310000 0001 2292 3357Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC, H3T 1C5 Canada
| | - Alexandre G. Weil
- grid.14848.310000 0001 2292 3357Department of Pediatric Neurosurgery, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5 Canada
| | - Jason Karamchandani
- grid.14709.3b0000 0004 1936 8649Department of Pathology, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4 Canada
| | - Jacek Majewski
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
| | - Mathieu Blanchette
- grid.14709.3b0000 0004 1936 8649School of Computer Science and McGill Center for Bioinformatics, McGill University, Montréal, Québec Canada
| | - Michael D. Taylor
- grid.42327.300000 0004 0473 9646Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children Research Institute, Toronto, Canada
| | - Marco Gallo
- grid.22072.350000 0004 1936 7697Alberta Children‘s Hospital Research Institute, Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
| | - Claudia L. Kleinman
- grid.414980.00000 0000 9401 2774Department of Human Genetics and Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec Canada
| | - Nada Jabado
- grid.63984.300000 0000 9064 4811Department of Human Genetics, Department of Pediatrics, and The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Jiannis Ragoussis
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
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Huang B, Pan W, Wang W, Wang Y, Liu P, Geng W. Overexpression of Pleckstrin Homology Domain-Containing Family A Member 4 Is Correlated with Poor Prognostic Outcomes and Immune Infiltration in Lower-Grade Glioma. DISEASE MARKERS 2022; 2022:1292648. [PMID: 36408463 PMCID: PMC9674417 DOI: 10.1155/2022/1292648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/28/2022] [Accepted: 10/22/2022] [Indexed: 10/12/2023]
Abstract
INTRODUCTION The global incidence of brain tumors, the most common of which is lower grade glioma (LGG), remains high. Pleckstrin homology domain-containing family A member 4 (PLEKHA4) has been reported to be related to tumor invasion and growth. However, its role and correlation with immunity in LGG remain elusive. METHODS We evaluated the expression pattern, prognostic value, biological functions, and immune effects of PLEKHA4 in LGG. We also analyzed the association between PLEKHA4 levels in different tumors, patient prognosis, and its role in tumor immunity. Depending on the type of research data, we used statistical methods such as Student's t-tests, Mann-Whitney U tests one-way ANOVA tests Kruskal-Wallis tests Pearson's or Spearman's correlation analysis Chi-square and Fisher's exact tests in this paper. Results and Conclusions. The results revealed that PLEKHA4 levels were markedly elevated in most tumors (such as LGG). High PLEKHA4 levels are associated with poor overall survival (OS), progression-free interval (PFI) rates, and disease-specific survival (DSS) in LGG patients. Cox regression analysis and nomograms showed that PLEKHA4 levels are independent prognostic factors for LGG patients. According to functional enrichment analysis, PLEKHA4 levels in LGG are associated with immune infiltration and immunotherapy. In conclusion, PLEKHA4 is a potential prognostic marker and immunotherapy target for LGG.
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Affiliation(s)
- Baojun Huang
- Department of Anaesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Weijun Pan
- Southern Medical University, Guangzhou, Guangdong, China
| | - Wenchao Wang
- Department of Anaesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yijian Wang
- Department of Anaesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Pan Liu
- Department of Anaesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wujun Geng
- Department of Anaesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Wenzhou Key Laboratory of Perioperative Medicine, Wenzhou, Zhejiang, China
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Mo Z, Xin J, Chai R, Woo PY, Chan DT, Wang J. Epidemiological characteristics and genetic alterations in adult diffuse glioma in East Asian populations. Cancer Biol Med 2022; 19:1440-1459. [PMID: 36350002 PMCID: PMC9630523 DOI: 10.20892/j.issn.2095-3941.2022.0418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/20/2022] [Indexed: 05/06/2024] Open
Abstract
Understanding the racial specificities of diseases-such as adult diffuse glioma, the most common primary malignant tumor of the central nervous system-is a critical step toward precision medicine. Here, we comprehensively review studies of gliomas in East Asian populations and other ancestry groups to clarify the racial differences in terms of epidemiology and genomic characteristics. Overall, we observed a lower glioma incidence in East Asians than in Whites; notably, patients with glioblastoma had significantly younger ages of onset and longer overall survival than the Whites. Multiple genome-wide association studies of various cohorts have revealed single nucleotide polymorphisms associated with overall and subtype-specific glioma susceptibility. Notably, only 3 risk loci-5p15.33, 11q23.3, and 20q13.33-were shared between patients with East Asian and White ancestry, whereas other loci predominated only in particular populations. For instance, risk loci 12p11.23, 15q15-21.1, and 19p13.12 were reported in East Asians, whereas risk loci 8q24.21, 1p31.3, and 1q32.1 were reported in studies in White patients. Although the somatic mutational profiles of gliomas between East Asians and non-East Asians were broadly consistent, a lower incidence of EGFR amplification in glioblastoma and a higher incidence of 1p19q-IDH-TERT triple-negative low-grade glioma were observed in East Asian cohorts. By summarizing large-scale disease surveillance, germline, and somatic genomic studies, this review reveals the unique characteristics of adult diffuse glioma among East Asians, to guide clinical management and policy design focused on patients with East Asian ancestry.
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Affiliation(s)
- Zongchao Mo
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen 518000, China
| | - Junyi Xin
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Ruichao Chai
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Peter Y.M. Woo
- Department of Neurosurgery, Kwong Wah Hospital, Hong Kong SAR, China
- Hong Kong Neuro-Oncology Society, Hong Kong SAR, China
| | - Danny T.M. Chan
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, Hong Kong SAR, China
| | - Jiguang Wang
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen 518000, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong SAR, China
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Tan Z, Zhang Z, Yu K, Yang H, Liang H, Lu T, Ji Y, Chen J, He W, Chen Z, Mei Y, Shen XL. Integrin subunit alpha V is a potent prognostic biomarker associated with immune infiltration in lower-grade glioma. Front Neurol 2022; 13:964590. [PMID: 36388191 PMCID: PMC9642104 DOI: 10.3389/fneur.2022.964590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/15/2022] [Indexed: 09/30/2023] Open
Abstract
As a member of integrin receptor family, ITGAV (integrin subunit α V) is involved in a variety of cell biological processes and overexpressed in various cancers, which may be a potential prognostic factor. However, its prognostic value and potential function in lower-grade glioma (LGG) are still unclear, and in terms of immune infiltration, it has not been fully elucidated. Here, the expression preference, prognostic value, and clinical traits of ITGAV were investigated using The Cancer Genome Atlas database (n = 528) and the Chinese Glioma Genome Atlas dataset (n = 458). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses and gene set enrichment analysis (GSEA) were used to explore the biological function of ITGAV. Using R package "ssGSEA" analysis, it was found thatthe ITGAV mRNA expression level showed intense correlation with tumor immunity, such as tumor-infiltrating immune cells and multiple immune-related genes. In addition, ITGAV is associated with some immune checkpoints and immune checkpoint blockade (ICB) and response to chemotherapy. and the expression of ITGAV protein in LGG patients was verified via immunohistochemistry (IHC). ITGAV expression was higher in LGG tissues than in normal tissues (P < 0.001) and multifactor analysis showed that ITGAV mRNA expression was an independent prognostic factor for LGG overall survival (OS; hazard ratio = 2.113, 95% confidence interval = 1.393-3.204, P < 0.001). GSEA showed that ITGAV expression was correlated with Inflammatory response, complement response, KRAS signal, and interferon response. ssGSEA results showed a positive correlation between ITGAV expression and Th2 cell infiltration level. ITGAV mRNA was overexpressed in LGG, and high ITGAV mRNA levels were found to be associated with poor protein expression and poor OS. ITGAV is therefore a potential biomarker for the diagnosis and prognosis of LGG and may be a potential immunotherapy target.
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Affiliation(s)
- Zilong Tan
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
- The Graduate Department, Jiangxi Medical College of Nanchang University Nanchang, Nanchang, China
| | - Zhe Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
- The Graduate Department, Jiangxi Medical College of Nanchang University Nanchang, Nanchang, China
| | - Kai Yu
- Department of Neurosurgery, People's Hospital of Wuhan University, Wuhan, China
| | - Huan Yang
- Department of Neurosurgery, Changde Hospital of Traditional Chinese Medicine, Changde, China
| | - Huaizhen Liang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tianzhu Lu
- Department of Radiation Oncology, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Yulong Ji
- Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Junjun Chen
- Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Wei He
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhen Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yuran Mei
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiao-Li Shen
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
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Zhang Z, Lai G, Sun L. Basement-Membrane-Related Gene Signature Predicts Prognosis in WHO Grade II/III Gliomas. Genes (Basel) 2022; 13:1810. [PMID: 36292695 PMCID: PMC9602375 DOI: 10.3390/genes13101810] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/29/2022] [Accepted: 10/05/2022] [Indexed: 10/17/2023] Open
Abstract
Gliomas that are classified as grade II or grade III lesions by the World Health Organization (WHO) are highly aggressive, and some may develop into glioblastomas within a short period, thus portending the conferral of a poor prognosis for patients. Previous studies have implicated basement membrane (BM)-related genes in glioma development. In this study, we constructed a prognostic model for WHO grade II/III gliomas in accordance with the risk scores of BM-related genes. Differentially expressed genes (DEGs) in the glioma samples relative to normal samples were screened from the GEO database, and five prognostically relevant BM-related genes, including NELL2, UNC5A, TNC, CSPG4, and SMOC1, were selected using Cox regression analyses for the risk score model. The median risk score was calculated, based on which high- and low-risk groups of patients were generated. The clinical information, pathological information, and risk group were combined to establish a prognostic nomogram. Both the nomogram and risk score model performed well in the independent CGGA cohort. Gene set enrichment analysis (GSEA) and immune profile, drug sensitivity, and tumor mutation burden (TMB) analyses were performed in the two risk groups. A significant enrichment of 'Autophagy-other', 'Collecting duct acid secretion', 'Glycosphingolipid biosynthesis-lacto and neolacto series', 'Valine, leucine, and isoleucine degradation', 'Vibrio cholerae infection', and other pathways were observed for patients with high risk. In addition, higher proportions of monocytes and resting CD4 memory T cells were observed in the low- and high-risk groups, respectively. In conclusion, the BM-related gene risk score model can guide the clinical management of WHO grade II and III gliomas.
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Affiliation(s)
- Zhaogang Zhang
- Department of Radiology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Guichuan Lai
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Lingling Sun
- Department of Radiology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
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Li L, Wu L, Yin X, Li C, Hua Z. Bulk and Single-Cell Transcriptome Analyses Revealed That the Pyroptosis of Glioma-Associated Macrophages Participates in Tumor Progression and Immunosuppression. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1803544. [PMID: 36199426 PMCID: PMC9529448 DOI: 10.1155/2022/1803544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/13/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022]
Abstract
Glioma is the most common of all central nervous system (CNS) malignancies and is associated with a poor prognosis. Pyroptosis has been proven to be associated with the progression of multiple tumors and CNS diseases. However, the relationships between pyroptosis and clinical prognosis and immune cell infiltration are unclear in glioma. In this study, we conducted a comprehensive exploration of pyroptosis in glioma. First, prognosis-related genes were screened at each key regulatory locus in the pyroptosis pathway, and the prognostic ability and coexpression relationships of GSDMD and its upstream pathway genes NLRC4/CASP1/CASP4 were identified and well validated in multiple datasets. Tissue microarray-based immunohistochemistry results showed higher levels of NLRC4 and N-terminal GSDMD in high-grade gliomas, providing conclusive evidence of pyroptosis in gliomas. The robustness of the prognostic model based on these four genes was well validated in TCGA and CGGA cohorts. Bulk RNA-seq-based analysis showed that the group defined as the high-risk group according to the model showed activation of multiple inflammatory response pathways and impaired synaptic gene expression and had a higher infiltration of bone marrow-derived macrophages (BMDMs) and a hypersuppressed immune microenvironment. More importantly, three independent single-cell RNA-seq (scRNA-seq) datasets demonstrated that tumor-infiltrating macrophages, particularly BMDMs but not tissue-resident microglia, showed significant coexpression of the GSDMD and CASP genes, and BMDMs from high-grade gliomas accounted for a higher proportion of immune infiltrating cells and had higher expression of pyroptosis genes. Finally, we revealed the activation of pathways in response to LPS/bacteria and oxidative stress during BMDM development toward the pyroptosis cell fate by pseudotime trajectory analysis, suggesting potential BMDM pyroptosis initiators. The above results provide not only novel insights into the pathological mechanisms of glioma but also novel therapeutic targets for glioma, suggesting the potential application of pyroptosis inhibitors (e.g., disulfiram).
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Affiliation(s)
- Lin Li
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Leyang Wu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Changzhou High-Tech Research Institute of Nanjing University and Jiangsu Target Pharma Laboratories Inc., Changzhou, China
| | - Xingpeng Yin
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chenyang Li
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zichun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Changzhou High-Tech Research Institute of Nanjing University and Jiangsu Target Pharma Laboratories Inc., Changzhou, China
- School of Biopharmacy, China Pharmaceutical University, Nanjing, China
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Li R, Wang YY, Wang SL, Li XP, Chen Y, Li ZA, He JH, Zhou ZH, Li JY, Guo XL, Wang XG, Wu YQ, Ren YQ, Zhang WJ, Wang XM, Guo G. GBP2 as a potential prognostic predictor with immune-related characteristics in glioma. Front Genet 2022; 13:956632. [PMID: 36186425 PMCID: PMC9523311 DOI: 10.3389/fgene.2022.956632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
Guanylate binding protein 2 (GBP2) is a member of the guanine binding protein family, and its relationship with prognostic outcomes and tumor immune microenvironments in glioma remains elusive. We found GBP2 were increased in glioma tissues at both mRNA and protein levels. Kaplan-Meier curves revealed that high GBP2 expression was linked with worse survival of glioma patients, and multivariate Cox regression analysis indicated that high GBP2 expression was an independent prognostic factor for glioma. Combined analysis in immune database revealed that the expression of GBP2 was significantly related to the level of immune infiltration and immunomodulators. Single-cell analysis illustrated the high expression of GBP2 in malignant glioma cells showed the high antigen presentation capability, which were confirmed by real-time polymerase chain reaction (qRT-PCR) data. Additionally, the hsa-mir-26b-5p and hsa-mir-335-5p were predicted as GBP2 regulators and were validated in U87 and U251 cells. Our results first decipher immune-related characteristics and noncoding regulators of GBP2 in glioma, which may provide insights into associated immunotherapies and prognostic predictor.
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Affiliation(s)
- Ren Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yuan-Yuan Wang
- Department of Radiology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shu-Le Wang
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xue-Peng Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yang Chen
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zi-Ao Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jian-Hang He
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zi-Han Zhou
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jia-Yu Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiao-Long Guo
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiao-Gang Wang
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yong-Qiang Wu
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ye-Qing Ren
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Wen-Ju Zhang
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiao-Man Wang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Geng Guo
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- *Correspondence: Geng Guo,
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Zhou Z, Wei J, Kuang L, Zhang K, Liu Y, He Z, Li L, Lu B. Characterization of aging cancer-associated fibroblasts draws implications in prognosis and immunotherapy response in low-grade gliomas. Front Genet 2022; 13:897083. [PMID: 36092895 PMCID: PMC9449154 DOI: 10.3389/fgene.2022.897083] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Due to the highly variable prognosis of low-grade gliomas (LGGs), it is important to find robust biomarkers for predicting clinical outcomes. Aging cancer-associated fibroblasts (CAFs) within the senescent stroma of a tumor microenvironment (TME) have been recently reported to play a key role in tumor development. However, there are few studies focusing on this topic in gliomas. Methods and Results: Based on the transcriptome data from TCGA and CGGA databases, we identified aging CAF-related genes (ACAFRGs) in LGGs by the weighted gene co-expression network analysis (WGCNA) method, followed by which LGG samples were classified into two aging CAF-related gene clusters with distinct prognosis and characteristics of the TME. Machine learning algorithms were used to screen out eight featured ACAFRGs to characterize two aging CAF-related gene clusters, and a nomogram model was constructed to predict the probability of gene cluster A for each LGG sample. Then, a powerful aging CAF scoring system was developed to predict the prognosis and response to immune checkpoint blockage therapy. Finally, the ACAFRGs were verified in two glioma-related external datasets. The performance of the aging CAF score in predicting the immunotherapy response was further validated in two independent cohorts. We also confirmed the expression of ACAFRGs at the protein level in glioma tissues through the Human Protein Atlas website and Western blotting analysis. Conclusion: We developed a robust aging CAF scoring system to predict the prognosis and immunotherapy response in LGGs. Our findings may provide new targets for therapeutics and contribute to the exploration focusing on aging CAFs.
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Affiliation(s)
- Zijian Zhou
- Department of Neurosurgery, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
- *Correspondence: Bin Lu, ; Zijian Zhou,
| | - Jinhong Wei
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Lijun Kuang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Ke Zhang
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Sichuan, China
| | - Yini Liu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Zhongming He
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Luo Li
- Department of Neurosurgery, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Bin Lu
- Department of Neurosurgery, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
- *Correspondence: Bin Lu, ; Zijian Zhou,
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Loddo M, Hardisty KM, Llewelyn A, Haddow T, Thatcher R, Williams G. Utilisation of semiconductor sequencing for detection of actionable fusions in solid tumours. PLoS One 2022; 17:e0246778. [PMID: 35984852 PMCID: PMC9390944 DOI: 10.1371/journal.pone.0246778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 07/22/2022] [Indexed: 11/19/2022] Open
Abstract
Oncogenic fusions represent compelling druggable targets in solid tumours highlighted by the recent site agnostic FDA approval of larotrectinib for NTRK rearrangements. However screening for fusions in routinely processed tissue samples is constrained due to degradation of nucleic acid as a result of formalin fixation., To investigate the clinical utility of semiconductor sequencing optimised for detection of actionable fusion transcripts in formalin fixed samples, we have undertaken an analysis of test trending data generated by a clinically validated next generation sequencing platform designed to capture 867 of the most clinically relevant druggable driver-partner oncogenic fusions. Here we show across a real-life cohort of 1112 patients with solid tumours that actionable fusions occur at high frequency (7.4%) with linkage to a wide range of targeted therapy protocols including seven fusion-drug matches with FDA/EMA approval and/or NCCN/ESMO recommendations and 80 clinical trials. The more prevalent actionable fusions identified were independent of tumour type in keeping with signalling via evolutionary conserved RAS/RAF/MEK/ERK, PI3K/AKT/MTOR, PLCy/PKC and JAK/STAT pathways. Taken together our data indicates that semiconductor sequencing for detection of actionable fusions can be integrated into routine diagnostic pathology workflows enabling the identification of personalised treatment options that have potential to improve clinical cancer management across many tumour types.
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Affiliation(s)
- Marco Loddo
- Oncologica UK Ltd, Cambridge, United Kingdom
- * E-mail: (ML); (GW)
| | | | | | | | | | - Gareth Williams
- Oncologica UK Ltd, Cambridge, United Kingdom
- * E-mail: (ML); (GW)
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Zheng ZQ, Yuan GQ, Kang NL, Nie QQ, Zhang GG, Wang Z. Chromobox 7/8 serve as independent indicators for glioblastoma via promoting proliferation and invasion of glioma cells. Front Neurol 2022; 13:912039. [PMID: 36034290 PMCID: PMC9403790 DOI: 10.3389/fneur.2022.912039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background The chromobox family, a critical component of epigenetic regulators, participates in the tumorigenesis and progression of many malignancies. However, the roles of the CBX family members (CBXs) in glioblastoma (GBM) remain unclear. Methods The mRNA expression of CBXs was analyzed in tissues and cell lines by Oncomine and Cancer Cell Line Encyclopedia (CCLE). The differential expression of CBXs at the mRNA level was explored in The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases with the “beeswarm” R package. The protein expression of CBXs in GBM was further examined on Human Protein Atlas (HPA). The correlations between CBXs and IDH mutation and between CBXs and GBM subtypes were investigated in the TCGA portal and CGGA database with the “survminer” R package. The alteration of CBXs and their prognostic value were further determined via the cBioPortal and CGGA database with the “survival” R package. The univariate and multivariate analyses were performed to screen out the independent prognostic roles of CBXs in the CGGA database. Cytoscape was used to visualize the functions and related pathways of CBXs in GBM. U251 and U87 glioma cells with gene intervention were used to validate the role of CBX7/8 in tumor proliferation and invasion. Proliferation/invasion-related markers were conducted by Western blot and immunostaining. Results CBXs presented significantly differential expressions in pan-cancers. CBX2/3/5/8 were upregulated, whereas CBX6/7 were downregulated at mRNA level in GBM of TCGA and CGGA databases. Similarly, high expression of CBX2/3/5 and low expression of CBX6/8 were further confirmed at the protein level in the HPA. CBX2/6/7 were positively correlated with IDH mutation and CBX1/2/4/5/8 were closely related to GBM subtypes. CBX7 and CBX8 presented the independent prognostic factors for GBM patient survival. GO and KEGG analyses indicated that CBXs were closely related to the histone H3-K36, PcG protein complex, ATPase, and Wnt pathway. The overexpression of CBX7 and underexpression of CBX8 significantly inhibited the proliferation and invasion of glioma cells in vivo and in vitro. Conclusion Our results suggested that CBX7 and CBX8 served as independent prognostic indicators that promoted the proliferation and invasion of glioma cells, providing a promising strategy for diagnosing and treating GBM.
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Affiliation(s)
- Zong-Qing Zheng
- Department of Neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Gui-Qiang Yuan
- Department of Neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Neurosurgery, Changshu Second People's Hospital, Suzhou, China
| | - Na-Ling Kang
- Liver Center, The First Affiliated Hospital, Fujian Medical University, Fujian, China
| | - Qian-Qian Nie
- Department of Neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Guo-Guo Zhang
- Department of Neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhong Wang
- Department of Neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Zhong Wang
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FGFR3-TACCs3 Fusions and Their Clinical Relevance in Human Glioblastoma. Int J Mol Sci 2022; 23:ijms23158675. [PMID: 35955806 PMCID: PMC9369421 DOI: 10.3390/ijms23158675] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/27/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023] Open
Abstract
Oncogenic fusion genes have emerged as successful targets in several malignancies, such as chronic myeloid leukemia and lung cancer. Fusion of the fibroblast growth receptor 3 and the transforming acidic coiled coil containing protein—FGFR3-TACC3 fusion—is prevalent in 3–4% of human glioblastoma. The fusion protein leads to the constitutively activated kinase signaling of FGFR3 and thereby promotes cell proliferation and tumor progression. The subgroup of FGFR3-TACC3 fusion-positive glioblastomas presents with recurrent clinical and histomolecular characteristics, defining a distinctive subtype of IDH-wildtype glioblastoma. This review aims to provide an overview of the available literature on FGFR3-TACC3 fusions in glioblastoma and possible implications for actual clinical practice.
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50
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Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma. Pharmaceutics 2022; 14:pharmaceutics14081573. [PMID: 36015199 PMCID: PMC9413912 DOI: 10.3390/pharmaceutics14081573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 12/01/2022] Open
Abstract
Expanding data suggest that glioblastoma is accountable for the growing prevalence of various forms of stroke formation, such as ischemic stroke and moyamoya disease. However, the underlying deterministic details are still unspecified. Bioinformatics approaches are designed to investigate the relationships between two pathogens as well as fill this study void. Glioblastoma is a form of cancer that typically occurs in the brain or spinal cord and is highly destructive. A stroke occurs when a brain region starts to lose blood circulation and prevents functioning. Moyamoya disorder is a recurrent and recurring arterial disorder of the brain. To begin, adequate gene expression datasets on glioblastoma, ischemic stroke, and moyamoya disease were gathered from various repositories. Then, the association between glioblastoma, ischemic stroke, and moyamoya was established using the existing pipelines. The framework was developed as a generalized workflow to allow for the aggregation of transcriptomic gene expression across specific tissue; Gene Ontology (GO) and biological pathway, as well as the validation of such data, are carried out using enrichment studies such as protein–protein interaction and gold benchmark databases. The results contribute to a more profound knowledge of the disease mechanisms and unveil the projected correlations among the diseases.
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