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Yin J, Liu G, Zhang Y, Zhou Y, Pan Y, Zhang Q, Yu R, Gao S. Gender differences in gliomas: From epidemiological trends to changes at the hormonal and molecular levels. Cancer Lett 2024; 598:217114. [PMID: 38992488 DOI: 10.1016/j.canlet.2024.217114] [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: 05/29/2024] [Revised: 06/28/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Gender plays a crucial role in the occurrence and development of cancer, as well as in the metabolism of nutrients and energy. Men and women display significant differences in the incidence, prognosis, and treatment response across various types of cancer, including certain sex-specific tumors. It has been observed that male glioma patients have a higher incidence and worse prognosis than female patients, but there is currently a limited systematic evaluation of sex differences in gliomas. The purpose of this study is to provide an overview of the association between fluctuations in sex hormone levels and changes in their receptor expression with the incidence, progression, treatment, and prognosis of gliomas. Estrogen may have a protective effect on glioma patients, while exposure to androgens increases the risk of glioma. We also discussed the specific genetic and molecular differences between genders in terms of the malignant nature and prognosis of gliomas. Factors such as TP53, MGMT methylation status may play a crucial role. Therefore, it is essential to consider the gender of patients while treating glioma, particularly the differences at the hormonal and molecular levels. This approach can help in the adoption of an individualized treatment strategy.
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Affiliation(s)
- Jiale Yin
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, China; Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Gai Liu
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, China; Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Yue Zhang
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, China; Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Yu Zhou
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, China; Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Yuchun Pan
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, China; Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Qiaoshan Zhang
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, China; Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Rutong Yu
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, China; Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Shangfeng Gao
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, China; Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
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2
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Lucchini S, Constantinou M, Marino S. Unravelling the mosaic: Epigenetic diversity in glioblastoma. Mol Oncol 2024. [PMID: 39148319 DOI: 10.1002/1878-0261.13706] [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: 11/28/2023] [Revised: 06/21/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024] Open
Abstract
Glioblastoma is the most common primary malignant brain tumour. Despite decades of intensive research in the disease, its prognosis remains poor, with an average survival of only 14 months after diagnosis. The remarkable level of intra- and interpatient heterogeneity is certainly contributing to the lack of progress in tackling this tumour. Epigenetic dysregulation plays an important role in glioblastoma biology and significantly contributes to intratumour heterogeneity. However, it is becoming increasingly clear that it also contributes to intertumour heterogeneity, which historically had mainly been linked to diverse genetic events occurring in different patients. In this review, we explore how DNA methylation, chromatin remodelling, microRNA (miRNA) dysregulation, and long noncoding RNA (lncRNA) alterations contribute to intertumour heterogeneity in glioblastoma, including its implications for advanced tumour stratification, which is the essential first step for developing more effective patient-specific therapeutic approaches.
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Affiliation(s)
- Sara Lucchini
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Myrianni Constantinou
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Silvia Marino
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Brain Tumour Centre, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Health NHS Trust, London, UK
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3
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Chen S, Jiang Y, Wang C, Tong S, He Y, Lu W, Zhang Z. Epigenetic clocks and gliomas: unveiling the molecular interactions between aging and tumor development. Front Mol Biosci 2024; 11:1446428. [PMID: 39130373 PMCID: PMC11310061 DOI: 10.3389/fmolb.2024.1446428] [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: 06/09/2024] [Accepted: 07/08/2024] [Indexed: 08/13/2024] Open
Abstract
Gliomas, the most prevalent and aggressive primary brain tumors, represent a diverse group of malignancies originating from glial cells. These tumors account for significant brain tumor-related morbidity and mortality, with higher incidence rates in North America and Europe compared to Asia and Africa. Genetic predispositions and environmental factors, particularly ionizing radiation, critically impact glioma risk. Epigenetics, particularly DNA methylation, plays a pivotal role in glioma research, with IDH-mutant gliomas showing aberrant methylation patterns contributing to tumorigenesis. Epigenetic clocks, biomarkers based on DNA methylation patterns predicting biological age, have revealed significant insights into aging and tumor development. Recent studies demonstrate accelerated epigenetic aging in gliomas, correlating with increased cancer risk and poorer outcomes. This review explores the mechanisms of epigenetic clocks, their biological significance, and their application in glioma research. Furthermore, the clinical implications of epigenetic clocks in diagnosing, prognosticating, and treating gliomas are discussed. The integration of epigenetic clock data into personalized medicine approaches holds promise for enhancing therapeutic strategies and patient outcomes in glioma treatment.
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Affiliation(s)
- Shiliang Chen
- Department of Clinical Lab, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Yi Jiang
- Department of Intensive Care Unit, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, Jiangsu, China
| | - Cong Wang
- Department of Clinical Lab, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Shiyuan Tong
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Yibo He
- Department of Clinical Lab, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Wenqiang Lu
- Department of Thoracic Surgery, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, Jiangsu, China
| | - Zhezhong Zhang
- Department of Clinical Lab, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
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4
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Richardson TE, Walker JM, Hambardzumyan D, Brem S, Hatanpaa KJ, Viapiano MS, Pai B, Umphlett M, Becher OJ, Snuderl M, McBrayer SK, Abdullah KG, Tsankova NM. Genetic and epigenetic instability as an underlying driver of progression and aggressive behavior in IDH-mutant astrocytoma. Acta Neuropathol 2024; 148:5. [PMID: 39012509 PMCID: PMC11252228 DOI: 10.1007/s00401-024-02761-7] [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: 05/23/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/17/2024]
Abstract
In recent years, the classification of adult-type diffuse gliomas has undergone a revolution, wherein specific molecular features now represent defining diagnostic criteria of IDH-wild-type glioblastomas, IDH-mutant astrocytomas, and IDH-mutant 1p/19q-codeleted oligodendrogliomas. With the introduction of the 2021 WHO CNS classification, additional molecular alterations are now integrated into the grading of these tumors, given equal weight to traditional histologic features. However, there remains a great deal of heterogeneity in patient outcome even within these established tumor subclassifications that is unexplained by currently codified molecular alterations, particularly in the IDH-mutant astrocytoma category. There is also significant intercellular genetic and epigenetic heterogeneity and plasticity with resulting phenotypic heterogeneity, making these tumors remarkably adaptable and robust, and presenting a significant barrier to the design of effective therapeutics. Herein, we review the mechanisms and consequences of genetic and epigenetic instability, including chromosomal instability (CIN), microsatellite instability (MSI)/mismatch repair (MMR) deficits, and epigenetic instability, in the underlying biology, tumorigenesis, and progression of IDH-mutant astrocytomas. We also discuss the contribution of recent high-resolution transcriptomics studies toward defining tumor heterogeneity with single-cell resolution. While intratumoral heterogeneity is a well-known feature of diffuse gliomas, the contribution of these various processes has only recently been considered as a potential driver of tumor aggressiveness. CIN has an independent, adverse effect on patient survival, similar to the effect of histologic grade and homozygous CDKN2A deletion, while MMR mutation is only associated with poor overall survival in univariate analysis but is highly correlated with higher histologic/molecular grade and other aggressive features. These forms of genomic instability, which may significantly affect the natural progression of these tumors, response to therapy, and ultimately clinical outcome for patients, are potentially measurable features which could aid in diagnosis, grading, prognosis, and development of personalized therapeutics.
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Affiliation(s)
- Timothy E Richardson
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA.
| | - Jamie M Walker
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Neurosurgery, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mariano S Viapiano
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Neurosurgery, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Balagopal Pai
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa Umphlett
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
| | - Oren J Becher
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Samuel K McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Nadejda M Tsankova
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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5
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Lin H, Liu C, Hu A, Zhang D, Yang H, Mao Y. Understanding the immunosuppressive microenvironment of glioma: mechanistic insights and clinical perspectives. J Hematol Oncol 2024; 17:31. [PMID: 38720342 PMCID: PMC11077829 DOI: 10.1186/s13045-024-01544-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 04/10/2024] [Indexed: 05/12/2024] Open
Abstract
Glioblastoma (GBM), the predominant and primary malignant intracranial tumor, poses a formidable challenge due to its immunosuppressive microenvironment, thereby confounding conventional therapeutic interventions. Despite the established treatment regimen comprising surgical intervention, radiotherapy, temozolomide administration, and the exploration of emerging modalities such as immunotherapy and integration of medicine and engineering technology therapy, the efficacy of these approaches remains constrained, resulting in suboptimal prognostic outcomes. In recent years, intensive scrutiny of the inhibitory and immunosuppressive milieu within GBM has underscored the significance of cellular constituents of the GBM microenvironment and their interactions with malignant cells and neurons. Novel immune and targeted therapy strategies have emerged, offering promising avenues for advancing GBM treatment. One pivotal mechanism orchestrating immunosuppression in GBM involves the aggregation of myeloid-derived suppressor cells (MDSCs), glioma-associated macrophage/microglia (GAM), and regulatory T cells (Tregs). Among these, MDSCs, though constituting a minority (4-8%) of CD45+ cells in GBM, play a central component in fostering immune evasion and propelling tumor progression, angiogenesis, invasion, and metastasis. MDSCs deploy intricate immunosuppressive mechanisms that adapt to the dynamic tumor microenvironment (TME). Understanding the interplay between GBM and MDSCs provides a compelling basis for therapeutic interventions. This review seeks to elucidate the immune regulatory mechanisms inherent in the GBM microenvironment, explore existing therapeutic targets, and consolidate recent insights into MDSC induction and their contribution to GBM immunosuppression. Additionally, the review comprehensively surveys ongoing clinical trials and potential treatment strategies, envisioning a future where targeting MDSCs could reshape the immune landscape of GBM. Through the synergistic integration of immunotherapy with other therapeutic modalities, this approach can establish a multidisciplinary, multi-target paradigm, ultimately improving the prognosis and quality of life in patients with GBM.
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Affiliation(s)
- Hao Lin
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai Clinical Medical Center of Neurosurgery, Neurosurgical Institute of Fudan University, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Chaxian Liu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai Clinical Medical Center of Neurosurgery, Neurosurgical Institute of Fudan University, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Ankang Hu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai Clinical Medical Center of Neurosurgery, Neurosurgical Institute of Fudan University, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Duanwu Zhang
- Children's Hospital of Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, People's Republic of China.
| | - Hui Yang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.
- Institute for Translational Brain Research, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai Clinical Medical Center of Neurosurgery, Neurosurgical Institute of Fudan University, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai Clinical Medical Center of Neurosurgery, Neurosurgical Institute of Fudan University, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.
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6
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Hana T, Mukasa A, Nomura M, Nagae G, Yamamoto S, Tatsuno K, Ueda H, Fukuda S, Umeda T, Tanaka S, Nejo T, Kitagawa Y, Yamazawa E, Takahashi S, Koike T, Kushihara Y, Takami H, Takayanagi S, Aburatani H, Saito N. Region-specific DNA hydroxymethylation along the malignant progression of IDH-mutant gliomas. Cancer Sci 2024; 115:1706-1717. [PMID: 38433527 PMCID: PMC11093199 DOI: 10.1111/cas.16127] [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: 08/30/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
The majority of low-grade isocitrate dehydrogenase-mutant (IDHmt) gliomas undergo malignant progression (MP), but their underlying mechanism remains unclear. IDHmt gliomas exhibit global DNA methylation, and our previous report suggested that MP could be partly attributed to passive demethylation caused by accelerated cell cycles. However, during MP, there is also active demethylation mediated by ten-eleven translocation, such as DNA hydroxymethylation. Hydroxymethylation is reported to potentially contribute to gene expression regulation, but its role in MP remains under investigation. Therefore, we conducted a comprehensive analysis of hydroxymethylation during MP of IDHmt astrocytoma. Five primary/malignantly progressed IDHmt astrocytoma pairs were analyzed with oxidative bisulfite and the Infinium EPIC methylation array, detecting 5-hydroxymethyl cytosine at over 850,000 locations for region-specific hydroxymethylation assessment. Notably, we observed significant sharing of hydroxymethylated genomic regions during MP across the samples. Hydroxymethylated CpGs were enriched in open sea and intergenic regions (p < 0.001), and genes undergoing hydroxymethylation were significantly associated with cancer-related signaling pathways. RNA sequencing data integration identified 91 genes with significant positive/negative hydroxymethylation-expression correlations. Functional analysis suggested that positively correlated genes are involved in cell-cycle promotion, while negatively correlated ones are associated with antineoplastic functions. Analyses of The Cancer Genome Atlas clinical data on glioma were in line with these findings. Motif-enrichment analysis suggested the potential involvement of the transcription factor KLF4 in hydroxymethylation-based gene regulation. Our findings shed light on the significance of region-specific DNA hydroxymethylation in glioma MP and suggest its potential role in cancer-related gene expression and IDHmt glioma malignancy.
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Affiliation(s)
- Taijun Hana
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Akitake Mukasa
- Department of Neurosurgery, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Masashi Nomura
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Genta Nagae
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Shogo Yamamoto
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Kenji Tatsuno
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Hiroki Ueda
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
- Advanced Data Science Division, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Shiro Fukuda
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Takayoshi Umeda
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Takahide Nejo
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
- Department of Neurological SurgeryUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Yosuke Kitagawa
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Erika Yamazawa
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Satoshi Takahashi
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Tsukasa Koike
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Yoshihiro Kushihara
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hirokazu Takami
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shunsaku Takayanagi
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroyuki Aburatani
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
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7
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Nassiri F, Ajisebutu A, Patil V, Mamatjan Y, Liu J, Wang JZ, Voisin MR, Nejad R, Mansouri S, Karimi S, Chakravarthy A, Chen E, De Carvalho DD, Aldape K, Zadeh G. Metabologenomic characterization uncovers a clinically aggressive IDH mutant glioma subtype. Acta Neuropathol 2024; 147:68. [PMID: 38583102 DOI: 10.1007/s00401-024-02713-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 04/08/2024]
Abstract
Mutations in the pivotal metabolic isocitrate dehydrogenase (IDH) enzymes are recognized to drive the molecular footprint of diffuse gliomas, and patients with IDH mutant gliomas have overall favorable outcomes compared to patients with IDH wild-type tumors. However, survival still varies widely among patients with IDH mutated tumors. Here, we aimed to characterize molecular signatures that explain the range of IDH mutant gliomas. By integrating matched epigenome-wide methylome, transcriptome, and global metabolome data in 154 patients with gliomas, we identified a group of IDH mutant gliomas with globally altered metabolism that resembled IDH wild-type tumors. IDH-mutant gliomas with altered metabolism have significantly shorter overall survival from their IDH mutant counterparts that is not fully accounted for by recognized molecular prognostic markers of CDKN2A/B loss and glioma CpG Island Methylator Phenotype (GCIMP) status. IDH-mutant tumors with dysregulated metabolism harbored distinct epigenetic alterations that converged to drive proliferative and stem-like transcriptional profiles, providing a window to target novel dependencies in gliomas.
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Affiliation(s)
- Farshad Nassiri
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada.
| | - Andrew Ajisebutu
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Vikas Patil
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Yasin Mamatjan
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Jeff Liu
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Justin Z Wang
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Mathew R Voisin
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Romina Nejad
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Sheila Mansouri
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Shirin Karimi
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Eric Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Kenneth Aldape
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre, MacFeeters Hamilton Neuro-Oncology Program, University Health Network and University of Toronto, Toronto, ON, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada.
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8
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Alhalabi OT, Dao Trong P, Kaes M, Jakobs M, Kessler T, Oehler H, König L, Eichkorn T, Sahm F, Debus J, von Deimling A, Wick W, Wick A, Krieg SM, Unterberg AW, Jungk C. Repeat surgery of recurrent glioma for molecularly informed treatment in the age of precision oncology: A risk-benefit analysis. J Neurooncol 2024; 167:245-255. [PMID: 38334907 PMCID: PMC11023957 DOI: 10.1007/s11060-024-04595-5] [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: 01/01/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
PURPOSE Surgery for recurrent glioma provides cytoreduction and tissue for molecularly informed treatment. With mostly heavily pretreated patients involved, it is unclear whether the benefits of repeat surgery outweigh its potential risks. METHODS Patients receiving surgery for recurrent glioma WHO grade 2-4 with the goal of tissue sampling for targeted therapies were analyzed retrospectively. Complication rates (surgical, neurological) were compared to our institutional glioma surgery cohort. Tissue molecular diagnostic yield, targeted therapies and post-surgical survival rates were analyzed. RESULTS Between 2017 and 2022, tumor board recommendation for targeted therapy through molecular diagnostics was made for 180 patients. Of these, 70 patients (38%) underwent repeat surgery. IDH-wildtype glioblastoma was diagnosed in 48 patients (69%), followed by IDH-mutant astrocytoma (n = 13; 19%) and oligodendroglioma (n = 9; 13%). Gross total resection (GTR) was achieved in 50 patients (71%). Tissue was processed for next-generation sequencing in 64 cases (91%), and for DNA methylation analysis in 58 cases (83%), while immunohistochemistry for mTOR phosphorylation was performed in 24 cases (34%). Targeted therapy was recommended in 35 (50%) and commenced in 21 (30%) cases. Postoperatively, 7 patients (11%) required revision surgery, compared to 7% (p = 0.519) and 6% (p = 0.359) of our reference cohorts of patients undergoing first and second craniotomy, respectively. Non-resolving neurological deterioration was documented in 6 cases (10% vs. 8%, p = 0.612, after first and 4%, p = 0.519, after second craniotomy). Median survival after repeat surgery was 399 days in all patients and 348 days in GBM patients after repeat GTR. CONCLUSION Surgery for recurrent glioma provides relevant molecular diagnostic information with a direct consequence for targeted therapy under a reasonable risk of postoperative complications. With satisfactory postoperative survival it can therefore complement a multi-modal glioma therapy approach.
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Affiliation(s)
- Obada T Alhalabi
- Department of Neurosurgery, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Department of Neurosurgery, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Philip Dao Trong
- Department of Neurosurgery, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Department of Neurosurgery, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Manuel Kaes
- Department of Neurosurgery, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Department of Neurosurgery, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Martin Jakobs
- Department of Neurosurgery, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Department of Neurosurgery, Medical Faculty, Heidelberg University, Heidelberg, Germany
- Department of Neurosurgery, Division for Stereotactic Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Tobias Kessler
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Hannah Oehler
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Laila König
- Department of Radiation Oncology, Heidelberg Ion Beam Therapy Centre (HIT), National Center for Radiation Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg University Hospital, Heidelberg, Germany
| | - Tanja Eichkorn
- Department of Radiation Oncology, Heidelberg Ion Beam Therapy Centre (HIT), National Center for Radiation Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen Debus
- Department of Radiation Oncology, Heidelberg Ion Beam Therapy Centre (HIT), National Center for Radiation Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Radiation Oncology, Heidelberg Ion Beam Therapy Centre (HIT), National Center for Radiation Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Antje Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sandro M Krieg
- Department of Neurosurgery, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Department of Neurosurgery, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Andreas W Unterberg
- Department of Neurosurgery, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Department of Neurosurgery, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Christine Jungk
- Department of Neurosurgery, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany.
- Department of Neurosurgery, Medical Faculty, Heidelberg University, Heidelberg, Germany.
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9
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Malta TM, Sabedot TS, Morosini NS, Datta I, Garofano L, Vallentgoed W, Varn FS, Aldape K, D'Angelo F, Bakas S, Barnholtz-Sloan JS, Gan HK, Hasanain M, Hau AC, Johnson KC, Cazacu S, deCarvalho AC, Khasraw M, Kocakavuk E, Kouwenhoven MC, Migliozzi S, Niclou SP, Niers JM, Ormond DR, Paek SH, Reifenberger G, Sillevis Smitt PA, Smits M, Stead LF, van den Bent MJ, Van Meir EG, Walenkamp A, Weiss T, Weller M, Westerman BA, Ylstra B, Wesseling P, Lasorella A, French PJ, Poisson LM, Verhaak RG, Iavarone A, Noushmehr H. The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen. Cancer Res 2024; 84:741-756. [PMID: 38117484 PMCID: PMC10911804 DOI: 10.1158/0008-5472.can-23-2093] [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: 07/14/2023] [Revised: 09/15/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
Tumor adaptation or selection is thought to underlie therapy resistance in glioma. To investigate longitudinal epigenetic evolution of gliomas in response to therapeutic pressure, we performed an epigenomic analysis of 132 matched initial and recurrent tumors from patients with IDH-wildtype (IDHwt) and IDH-mutant (IDHmut) glioma. IDHwt gliomas showed a stable epigenome over time with relatively low levels of global methylation. The epigenome of IDHmut gliomas showed initial high levels of genome-wide DNA methylation that was progressively reduced to levels similar to those of IDHwt tumors. Integration of epigenomics, gene expression, and functional genomics identified HOXD13 as a master regulator of IDHmut astrocytoma evolution. Furthermore, relapse of IDHmut tumors was accompanied by histologic progression that was associated with survival, as validated in an independent cohort. Finally, the initial cell composition of the tumor microenvironment varied between IDHwt and IDHmut tumors and changed differentially following treatment, suggesting increased neoangiogenesis and T-cell infiltration upon treatment of IDHmut gliomas. This study provides one of the largest cohorts of paired longitudinal glioma samples with epigenomic, transcriptomic, and genomic profiling and suggests that treatment of IDHmut glioma is associated with epigenomic evolution toward an IDHwt-like phenotype. SIGNIFICANCE Standard treatments are related to loss of DNA methylation in IDHmut glioma, resulting in epigenetic activation of genes associated with tumor progression and alterations in the microenvironment that resemble treatment-naïve IDHwt glioma.
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Affiliation(s)
- Tathiane M. Malta
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thais S. Sabedot
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | | | - Indrani Datta
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Luciano Garofano
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Wies Vallentgoed
- Neurology Department, The Brain Tumour Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Frederick S. Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | | | - Fulvio D'Angelo
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Spyridon Bakas
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Hui K. Gan
- Olivia Newton-John Cancer Research Institute, Austin Health, Heidelberg, Melbourne, Australia
| | - Mohammad Hasanain
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Kevin C. Johnson
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
| | - Simona Cazacu
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Ana C. deCarvalho
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | | | - Emre Kocakavuk
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center (WTZ), National Center for Tumor Diseases (NCT) West, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Mathilde C.M. Kouwenhoven
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Simona Migliozzi
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Johanna M. Niers
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - D. Ryan Ormond
- University of Colorado School of Medicine, Department of Neurosurgery, Aurora, Colorado
| | - Sun Ha Paek
- Department of Neurosurgery, Cancer Research Institute, Hypoxia Ischemia Disease Institute, Seoul National University, Seoul, Republic of Korea (South)
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Dusseldorf, Germany
| | - Peter A. Sillevis Smitt
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- The Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Marion Smits
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Lucy F. Stead
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Martin J. van den Bent
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- The Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Erwin G. Van Meir
- Department of Neurosurgery and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Tobias Weiss
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Bart A. Westerman
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Pieter Wesseling
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
- Laboratory for Childhood Cancer Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Anna Lasorella
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida
| | - Pim J. French
- Neurology Department, The Brain Tumour Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Laila M. Poisson
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Roel G.W. Verhaak
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Neurosurgery, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Antonio Iavarone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Houtan Noushmehr
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
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10
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Jacob JR, Singh R, Okamoto M, Chakravarti A, Palanichamy K. miRNA-194-3p represses NF-κB in gliomas to attenuate iPSC genes and proneural to mesenchymal transition. iScience 2024; 27:108650. [PMID: 38226170 PMCID: PMC10788216 DOI: 10.1016/j.isci.2023.108650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/01/2023] [Accepted: 12/04/2023] [Indexed: 01/17/2024] Open
Abstract
Severe tumor heterogeneity drives the aggressive and treatment refractory nature of glioblastomas (GBMs). While limiting GBM heterogeneity offers promising therapeutic potential, the underlying mechanisms that regulate GBM plasticity remain poorly understood. We utilized 14 patient-derived and four commercially available cell lines to uncover miR-194-3p as a key epigenetic determinant of stemness and transcriptional subtype in GBM. We demonstrate that miR-194-3p degrades TAB2, an important mediator of NF-κB activity, decreasing NF-κB transcriptional activity. The loss in NF-κB activity following miR-194-3p overexpression or TAB2 silencing decreased expression of induced pluripotent stem cell (iPSC) genes, inhibited the oncogenic IL-6/STAT3 signaling axis, suppressed the mesenchymal transcriptional subtype in relation to the proneural subtype, and induced differentiation from the glioma stem cell (GSC) to monolayer (ML) phenotype. miR-194-3p/TAB2/NF-κB signaling axis acts as an epigenetic switch that regulates GBM plasticity and targeting this signaling axis represents a potential strategy to limit transcriptional heterogeneity in GBMs.
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Affiliation(s)
- John Ryan Jacob
- Department of Radiation Oncology, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Rajbir Singh
- Department of Radiation Oncology, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Masa Okamoto
- Department of Radiation Oncology, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH 43210, USA
- Department of Radiation Oncology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Kamalakannan Palanichamy
- Department of Radiation Oncology, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH 43210, USA
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11
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Nafe R, Hattingen E. The Spectrum of Molecular Pathways in Gliomas-An Up-to-Date Review. Biomedicines 2023; 11:2281. [PMID: 37626776 PMCID: PMC10452344 DOI: 10.3390/biomedicines11082281] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
During the last 20 years, molecular alterations have gained increasing significance in the diagnosis and biological assessment of tumors. Gliomas represent the largest group of tumors of the central nervous system, and the main aim of this review is to present the current knowledge on molecular pathways and their alterations in gliomas. A wide range of new insights has been gained, including evidence for the involvement of the WNT pathway or the hippo pathway in the pathobiology of gliomas, indicating a broad involvement of different pathways formerly not considered to play a central role in gliomas. Even new aspects of angiogenic, apoptotic, and metabolic pathways are presented, as well as the rapidly growing field of epigenetic processes, including non-coding RNAs. The two major conclusions drawn from the present review are the distinct interconnectivity of the whole spectrum of molecular pathways and the prominent role of non-coding RNAs, especially circular RNAs, in the regulation of specific targets. All these new insights are discussed, even considering the topic of the resistance to therapy of gliomas, along with aspects that are still incompletely understood, like the role of hydroxymethylation, or even ferroptosis, in the pathobiology of gliomas.
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Affiliation(s)
- Reinhold Nafe
- Department of Neuroradiology, Clinics of Johann Wolfgang Goethe-University, Schleusenweg 2-16, D-60528 Frankfurt am Main, Germany;
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12
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Bredel M, Espinosa L, Kim H, Scholtens DM, McElroy JP, Rajbhandari R, Meng W, Kollmeyer TM, Malta TM, Quezada MA, Harsh GR, Lobo-Jarne T, Solé L, Merati A, Nagaraja S, Nair S, White JJ, Thudi NK, Fleming JL, Webb A, Natsume A, Ogawa S, Weber RG, Bertran J, Haque SJ, Hentschel B, Miller CR, Furnari FB, Chan TA, Grosu AL, Weller M, Barnholtz-Sloan JS, Monje M, Noushmehr H, Jenkins RB, Rogers CL, MacDonald DR, Pugh SL, Chakravarti A. Haploinsufficiency of NFKBIA reshapes the epigenome antipodal to the IDH mutation and imparts disease fate in diffuse gliomas. Cell Rep Med 2023; 4:101082. [PMID: 37343523 PMCID: PMC10314122 DOI: 10.1016/j.xcrm.2023.101082] [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: 04/22/2022] [Revised: 11/18/2022] [Accepted: 05/18/2023] [Indexed: 06/23/2023]
Abstract
Genetic alterations help predict the clinical behavior of diffuse gliomas, but some variability remains uncorrelated. Here, we demonstrate that haploinsufficient deletions of chromatin-bound tumor suppressor NFKB inhibitor alpha (NFKBIA) display distinct patterns of occurrence in relation to other genetic markers and are disproportionately present at recurrence. NFKBIA haploinsufficiency is associated with unfavorable patient outcomes, independent of genetic and clinicopathologic predictors. NFKBIA deletions reshape the DNA and histone methylome antipodal to the IDH mutation and induce a transcriptome landscape partly reminiscent of H3K27M mutant pediatric gliomas. In IDH mutant gliomas, NFKBIA deletions are common in tumors with a clinical course similar to that of IDH wild-type tumors. An externally validated nomogram model for estimating individual patient survival in IDH mutant gliomas confirms that NFKBIA deletions predict comparatively brief survival. Thus, NFKBIA haploinsufficiency aligns with distinct epigenome changes, portends a poor prognosis, and should be incorporated into models predicting the disease fate of diffuse gliomas.
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Affiliation(s)
- Markus Bredel
- Department of Radiation Oncology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA.
| | - Lluís Espinosa
- Cancer Research Program, Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Institut Mar d'Investigacions Mèdiques, Hospital del Mar, 08003 Barcelona, Spain
| | - Hyunsoo Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Denise M Scholtens
- Division of Biostatistics-Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joseph P McElroy
- Center for Biostatistics-Department of Biomedical Informatics, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Rajani Rajbhandari
- Department of Radiation Oncology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Wei Meng
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Thomas M Kollmeyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI 48202, USA
| | - Michael A Quezada
- Department of Neurology & Neurological Sciences and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Griffith R Harsh
- Department of Neurological Surgery, University of California at Davis School of Medicine, Sacramento, CA 95817, USA
| | - Teresa Lobo-Jarne
- Cancer Research Program, Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Institut Mar d'Investigacions Mèdiques, Hospital del Mar, 08003 Barcelona, Spain
| | - Laura Solé
- Cancer Research Program, Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Institut Mar d'Investigacions Mèdiques, Hospital del Mar, 08003 Barcelona, Spain
| | - Aran Merati
- Department of Radiation Oncology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Surya Nagaraja
- Department of Neurology & Neurological Sciences and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sindhu Nair
- Department of Radiation Oncology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Jaclyn J White
- Department of Neurosurgery, Wake Forest University School of Medicine, Winston-Salem, NC 27103, USA
| | - Nanda K Thudi
- Department of Radiation Oncology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Jessica L Fleming
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Amy Webb
- Center for Biostatistics-Department of Biomedical Informatics, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Atsushi Natsume
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 464-8601, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Ruthild G Weber
- Institute for Human Genetics, Hannover Medical School, 30625 Hannover, Germany
| | - Joan Bertran
- Biosciences Department, Faculty of Sciences, Technology, and Engineering. University of Vic-Central University of Catalonia, 08500 Vic, Spain
| | - S Jaharul Haque
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Bettina Hentschel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany
| | - C Ryan Miller
- Division of Neuropathology-Department of Pathology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Frank B Furnari
- Laboratory of Tumor Biology, Division of Regenerative Medicine-Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anca-Ligia Grosu
- Department of Radiation Oncology, Comprehensive Cancer Center, University of Freiburg, 79106 Freiburg, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, 8091 Zurich, Switzerland
| | - Jill S Barnholtz-Sloan
- Division of Cancer Epidemiology and Genetics-National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michelle Monje
- Department of Neurology & Neurological Sciences and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI 48202, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - David R MacDonald
- London Regional Cancer Program, Western University, London, ON N6A 5W9, Canada
| | - Stephanie L Pugh
- NRG Oncology Statistics and Data Management Center, Philadelphia, PA 19103, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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Rončević A, Koruga N, Soldo Koruga A, Rončević R, Rotim T, Šimundić T, Kretić D, Perić M, Turk T, Štimac D. Personalized Treatment of Glioblastoma: Current State and Future Perspective. Biomedicines 2023; 11:1579. [PMID: 37371674 DOI: 10.3390/biomedicines11061579] [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: 03/14/2023] [Revised: 05/24/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
Glioblastoma (GBM) is the most aggressive glial tumor of the central nervous system. Despite intense scientific efforts, patients diagnosed with GBM and treated with the current standard of care have a median survival of only 15 months. Patients are initially treated by a neurosurgeon with the goal of maximal safe resection of the tumor. Obtaining tissue samples during surgery is indispensable for the diagnosis of GBM. Technological improvements, such as navigation systems and intraoperative monitoring, significantly advanced the possibility of safe gross tumor resection. Usually within six weeks after the surgery, concomitant radiotherapy and chemotherapy with temozolomide are initiated. However, current radiotherapy regimens are based on population-level studies and could also be improved. Implementing artificial intelligence in radiotherapy planning might be used to individualize treatment plans. Furthermore, detailed genetic and molecular markers of the tumor could provide patient-tailored immunochemotherapy. In this article, we review current standard of care and possibilities of personalizing these treatments. Additionally, we discuss novel individualized therapeutic options with encouraging results. Due to inherent heterogeneity of GBM, applying patient-tailored treatment could significantly prolong survival of these patients.
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Affiliation(s)
- Alen Rončević
- Department of Neurosurgery, University Hospital Center Osijek, 31000 Osijek, Croatia
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Nenad Koruga
- Department of Neurosurgery, University Hospital Center Osijek, 31000 Osijek, Croatia
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Anamarija Soldo Koruga
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Neurology, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Robert Rončević
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Diagnostic and Interventional Radiology, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Tatjana Rotim
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Diagnostic and Interventional Radiology, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Tihana Šimundić
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Nephrology, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Domagoj Kretić
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Diagnostic and Interventional Radiology, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Marija Perić
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Cytology, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Tajana Turk
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Diagnostic and Interventional Radiology, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Damir Štimac
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Radiology, National Memorial Hospital Vukovar, 32000 Vukovar, Croatia
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14
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Kurimoto M, Rockenbach Y, Kato A, Natsume A. Prediction of Tumor Development and Urine-Based Liquid Biopsy for Molecule-Targeted Therapy of Gliomas. Genes (Basel) 2023; 14:1201. [PMID: 37372381 DOI: 10.3390/genes14061201] [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: 12/30/2022] [Revised: 05/21/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The timing of the acquisition of tumor-specific gene mutations and the systems by which these gene mutations are acquired during tumorigenesis were clarified. Advances in our understanding of tumorigenesis are being made every day, and therapies targeting fundamental genetic alterations have great potential for cancer treatment. Moreover, our research team successfully estimated tumor progression using mathematical modeling and attempted early diagnosis of brain tumors. We developed a nanodevice that enables urinary genetic diagnosis in a simple and noninvasive manner. Mainly on the basis of our research and experience, this review article presents novel therapies being developed for central nervous system cancers and six molecules, which upon mutation cause tumorigenesis and tumor progression. Further understanding of the genetic characteristics of brain tumors will lead to the development of precise drugs and improve individual treatment outcomes.
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Affiliation(s)
- Michihiro Kurimoto
- Department of Neurosurgery, Aichi Children's Health and Medical Center, Obu 464-8710, Japan
| | - Yumi Rockenbach
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
| | - Akira Kato
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
| | - Atsushi Natsume
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
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15
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Shin HJ, Hua JT, Li H. Recent advances in understanding DNA methylation of prostate cancer. Front Oncol 2023; 13:1182727. [PMID: 37234978 PMCID: PMC10206257 DOI: 10.3389/fonc.2023.1182727] [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: 03/09/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Epigenetic modifications, such as DNA methylation, is widely studied in cancer. DNA methylation patterns have been shown to distinguish between benign and malignant tumors in various cancers, including prostate cancer. It may also contribute to oncogenesis, as it is frequently associated with downregulation of tumor suppressor genes. Aberrant patterns of DNA methylation, in particular the CpG island hypermethylator phenotype (CIMP), have shown associative evidence with distinct clinical features and outcomes, such as aggressive subtypes, higher Gleason score, prostate-specific antigen (PSA), and overall tumor stage, overall worse prognosis, as well as reduced survival. In prostate cancer, hypermethylation of specific genes is significantly different between tumor and normal tissues. Methylation patterns could distinguish between aggressive subtypes of prostate cancer, including neuroendocrine prostate cancer (NEPC) and castration resistant prostate adenocarcinoma. Further, DNA methylation is detectable in cell-free DNA (cfDNA) and is reflective of clinical outcome, making it a potential biomarker for prostate cancer. This review summarizes recent advances in understanding DNA methylation alterations in cancers with the focus on prostate cancer. We discuss the advanced methodology used for evaluating DNA methylation changes and the molecular regulators behind these changes. We also explore the clinical potential of DNA methylation as prostate cancer biomarkers and its potential for developing targeted treatment of CIMP subtype of prostate cancer.
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Affiliation(s)
- Hyun Jin Shin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
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16
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Neuronal and tumourigenic boundaries of glioblastoma plasticity. Trends Cancer 2023; 9:223-236. [PMID: 36460606 DOI: 10.1016/j.trecan.2022.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 12/03/2022]
Abstract
Glioblastoma (GBM) remains the most lethal primary brain cancer largely due to recurrence of treatment-resistant disease. Current therapies are ultimately ineffective as GBM tumour cells adapt their identity to escape treatment. Recent advances in single-cell epigenetics and transcriptomics highlight heterogeneous cell populations in GBM tumours originating from unique cancerous genetic aberrations. However, they also suggest that tumour cells conserve molecular properties of parent neuronal cells, with their permissive epigenetic profiles enabling them to morph along a finite number of reprogramming routes to evade treatment. Here, we review the known tumourigenic, neurodevelopmental and brain-injury boundaries of GBM plasticity, and propose that effective treatment of GBM requires the addition of therapeutics that restrain GBM plasticity.
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17
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Roura AJ, Szadkowska P, Poleszak K, Dabrowski MJ, Ellert-Miklaszewska A, Wojnicki K, Ciechomska IA, Stepniak K, Kaminska B, Wojtas B. Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications. Clin Epigenetics 2023; 15:29. [PMID: 36850002 PMCID: PMC9972689 DOI: 10.1186/s13148-023-01446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM, WHO grade IV) is an aggressive, primary brain tumor. Despite extensive tumor resection followed by radio- and chemotherapy, life expectancy of GBM patients did not improve over decades. Several studies reported transcription deregulation in GBMs, but regulatory mechanisms driving overexpression of GBM-specific genes remain largely unknown. Transcription in open chromatin regions is directed by transcription factors (TFs) that bind to specific motifs, recruit co-activators/repressors and the transcriptional machinery. Identification of GBM-related TFs-gene regulatory networks may reveal new and targetable mechanisms of gliomagenesis. RESULTS We predicted TFs-regulated networks in GBMs in silico and intersected them with putative TF binding sites identified in the accessible chromatin in human glioma cells and GBM patient samples. The Cancer Genome Atlas and Glioma Atlas datasets (DNA methylation, H3K27 acetylation, transcriptomic profiles) were explored to elucidate TFs-gene regulatory networks and effects of the epigenetic background. In contrast to the majority of tumors, c-Jun expression was higher in GBMs than in normal brain and c-Jun binding sites were found in multiple genes overexpressed in GBMs, including VIM, FOSL2 or UPP1. Binding of c-Jun to the VIM gene promoter was stronger in GBM-derived cells than in cells derived from benign glioma as evidenced by gel shift and supershift assays. Regulatory regions of the majority of c-Jun targets have distinct DNA methylation patterns in GBMs as compared to benign gliomas, suggesting the contribution of DNA methylation to the c-Jun-dependent gene expression. CONCLUSIONS GBM-specific TFs-gene networks identified in GBMs differ from regulatory pathways attributed to benign brain tumors and imply a decisive role of c-Jun in controlling genes that drive glioma growth and invasion as well as a modulatory role of DNA methylation.
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Affiliation(s)
- Adria-Jaume Roura
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Paulina Szadkowska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
- grid.13339.3b0000000113287408Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Katarzyna Poleszak
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Michal J. Dabrowski
- grid.425308.80000 0001 2158 4832Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Ellert-Miklaszewska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Kamil Wojnicki
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Iwona A. Ciechomska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Karolina Stepniak
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bozena Kaminska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bartosz Wojtas
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
- grid.419305.a0000 0001 1943 2944Laboratory of Sequencing, Nencki Institute of Experimental Biology, ul. Ludwika Pasteura 3, 02-093 Warsaw, Poland
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18
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Ferreyra Vega S, Olsson Bontell T, Kling T, Jakola AS, Carén H. Longitudinal DNA methylation analysis of adult-type IDH-mutant gliomas. Acta Neuropathol Commun 2023; 11:23. [PMID: 36739454 PMCID: PMC9899392 DOI: 10.1186/s40478-023-01520-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/24/2023] [Indexed: 02/06/2023] Open
Abstract
Diffuse gliomas are the most prevalent malignant primary brain tumors in adults and remain incurable despite standard therapy. Tumor recurrence is currently inevitable, which contributes to a persistent high morbidity and mortality in these patients. In this study, we examined the genome-wide DNA methylation profiles of primary and recurrent adult-type IDH-mutant gliomas to elucidate DNA methylation changes associated with tumor progression (with or without malignant transformation). We analyzed DNA methylation profiles of 37 primary IDH-mutant gliomas and 42 paired recurrences using the DNA methylation EPIC beadChip array. DNA methylation-based classification reflected the tumor progression over time. We observed a methylation subtype switch in a proportion of IDH-mutant astrocytomas; the primary tumors were subclassified as low-grade astrocytomas, which progressed to high-grade astrocytomas in the recurrent tumors. The CNS WHO grade 4 IDH-mutant astrocytomas did not always resemble methylation subclasses of higher grades. The number of differentially methylated CpG sites increased over time, and astrocytomas accumulated more differentially methylated CpG sites than oligodendrogliomas during tumor progression. Few differentially methylated CpG sites were shared between patients. We demonstrated that DNA methylation profiles are mostly maintained during IDH-mutant glioma progression, but CpG site-specific methylation alterations can occur.
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Affiliation(s)
- Sandra Ferreyra Vega
- grid.8761.80000 0000 9919 9582Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Blå Stråket 7, 413 45 Gothenburg, Sweden ,grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- grid.8761.80000 0000 9919 9582Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden ,grid.1649.a000000009445082XDepartment of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Teresia Kling
- grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Asgeir Store Jakola
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Blå Stråket 7, 413 45, Gothenburg, Sweden. .,Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden. .,Department of Neurosurgery, St. Olavs University Hospital, Trondheim, Norway.
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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19
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Miller JJ, Gonzalez Castro LN, McBrayer S, Weller M, Cloughesy T, Portnow J, Andronesi O, Barnholtz-Sloan JS, Baumert BG, Berger MS, Bi WL, Bindra R, Cahill DP, Chang SM, Costello JF, Horbinski C, Huang RY, Jenkins RB, Ligon KL, Mellinghoff IK, Nabors LB, Platten M, Reardon DA, Shi DD, Schiff D, Wick W, Yan H, von Deimling A, van den Bent M, Kaelin WG, Wen PY. Isocitrate dehydrogenase (IDH) mutant gliomas: A Society for Neuro-Oncology (SNO) consensus review on diagnosis, management, and future directions. Neuro Oncol 2023; 25:4-25. [PMID: 36239925 PMCID: PMC9825337 DOI: 10.1093/neuonc/noac207] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Isocitrate dehydrogenase (IDH) mutant gliomas are the most common adult, malignant primary brain tumors diagnosed in patients younger than 50, constituting an important cause of morbidity and mortality. In recent years, there has been significant progress in understanding the molecular pathogenesis and biology of these tumors, sparking multiple efforts to improve their diagnosis and treatment. In this consensus review from the Society for Neuro-Oncology (SNO), the current diagnosis and management of IDH-mutant gliomas will be discussed. In addition, novel therapies, such as targeted molecular therapies and immunotherapies, will be reviewed. Current challenges and future directions for research will be discussed.
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Affiliation(s)
- Julie J Miller
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - L Nicolas Gonzalez Castro
- Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Samuel McBrayer
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, Texas, 75235, USA
| | - Michael Weller
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091 Zurich, Switzerland
| | | | - Jana Portnow
- Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Ovidiu Andronesi
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Jill S Barnholtz-Sloan
- Informatics and Data Science (IDS), Center for Biomedical Informatics and Information Technology (CBIIT), Trans-Divisional Research Program (TDRP), Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Bethesda, MD, USA
| | - Brigitta G Baumert
- Cantonal Hospital Graubunden, Institute of Radiation-Oncology, Chur, Switzerland
| | - Mitchell S Berger
- Department of Neurosurgery, University of California-San Francisco, San Francisco, California, USA
| | - Wenya Linda Bi
- Harvard Medical School, Boston, MA, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ranjit Bindra
- Department of Therapeutic Radiology, Brain Tumor Center, Yale School of Medicine, New Haven, CT, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Susan M Chang
- Department of Neurosurgery, University of California-San Francisco, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurosurgery, University of California-San Francisco, San Francisco, California, USA
| | - Craig Horbinski
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Raymond Y Huang
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Robert B Jenkins
- Individualized Medicine Research, Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, Minnesota 55901, USA
| | - Keith L Ligon
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Ingo K Mellinghoff
- Department of Neurology, Evnin Family Chair in Neuro-Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - L Burt Nabors
- Department of Neurology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael Platten
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - David A Reardon
- Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Diana D Shi
- Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - David Schiff
- Division of Neuro-Oncology, Department of Neurology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Wolfgang Wick
- Neuro-Oncology at the German Cancer Research Center (DKFZ), Program Chair of Neuro-Oncology at the National Center for Tumor Diseases (NCT), and Neurology and Chairman at the Neurology Clinic in Heidelberg, Heidelberg, Germany
| | - Hai Yan
- Genetron Health Inc, Gaithersburg, Maryland 20879, USA
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, and, Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), and, DKTK, INF 224, 69120 Heidelberg, Germany
| | - Martin van den Bent
- Brain Tumour Centre, Erasmus MC Cancer Institute, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - William G Kaelin
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Patrick Y Wen
- Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
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20
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Di Stefano AL, Nichelli L, Berzero G, Valabregue R, Touat M, Capelle L, Pontoizeau C, Bielle F, Lerond J, Giry M, Villa C, Baussart B, Dehais C, Galanaud D, Baldini C, Savatovsky J, Dhermain F, Deelchand DK, Ottolenghi C, Lehéricy S, Marjańska M, Branzoli F, Sanson M. In Vivo 2-Hydroxyglutarate Monitoring With Edited MR Spectroscopy for the Follow-up of IDH-Mutant Diffuse Gliomas: The IDASPE Prospective Study. Neurology 2023; 100:e94-e106. [PMID: 36180241 PMCID: PMC9827125 DOI: 10.1212/wnl.0000000000201137] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 07/05/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND AND OBJECTIVES D-2-hydroxyglutarate (2HG) characterizes IDH-mutant gliomas and can be detected and quantified with edited MRS (MEGA-PRESS). In this study, we investigated the clinical, radiologic, and molecular parameters affecting 2HG levels. METHODS MEGA-PRESS data were acquired in 71 patients with glioma (24 untreated, 47 treated) on a 3 T system. Eighteen patients were followed during cytotoxic (n = 12) or targeted (n = 6) therapy. 2HG was measured in tumor samples using gas chromatography coupled to mass spectrometry (GCMS). RESULTS MEGA-PRESS detected 2HG with a sensitivity of 95% in untreated patients and 62% in treated patients. Sensitivity depended on tumor volume (>27 cm3; p = 0.02), voxel coverage (>75%; p = 0.002), and expansive presentation (defined by equal size of T1 and FLAIR abnormalities, p = 0.04). 2HG levels were positively correlated with IDH-mutant allelic fraction (p = 0.03) and total choline levels (p < 0.001) and were higher in IDH2-mutant compared with IDH1 R132H-mutant and non-R132H IDH1-mutant patients (p = 0.002). In patients receiving IDH inhibitors, 2HG levels decreased within a few days, demonstrating the on-target effect of the drug, but 2HG level decrease did not predict tumor response. Patients receiving cytotoxic treatments showed a slower decrease in 2HG levels, consistent with tumor response and occurring before any tumor volume change on conventional MRI. At progression, 1p/19q codeleted gliomas, but not the non-codeleted, showed detectable in vivo 2HG levels, pointing out to different modes of progression characterizing these 2 entities. DISCUSSION MEGA-PRESS edited MRS allows in vivo monitoring of 2-hydroxyglutarate, confirming efficacy of IDH inhibition and suggests different patterns of tumor progression in astrocytomas compared with oligodendrogliomas.
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Affiliation(s)
- Anna Luisa Di Stefano
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Lucia Nichelli
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Giulia Berzero
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Romain Valabregue
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Mehdi Touat
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Laurent Capelle
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Clément Pontoizeau
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Franck Bielle
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Julie Lerond
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Marine Giry
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Chiara Villa
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Bertrand Baussart
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Caroline Dehais
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Damien Galanaud
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Capucine Baldini
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Julien Savatovsky
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Frédéric Dhermain
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Dinesh K Deelchand
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Chris Ottolenghi
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Stéphane Lehéricy
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Małgorzata Marjańska
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Francesca Branzoli
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France
| | - Marc Sanson
- From the Sorbonne Université (A.L.D.S.,M.D.P.D., L.N., M.D.P.D., J.L., M.G., S.L., Francesca Branzoli), Inserm, CNRS, Paris Brain Institute-Institut du Cerveau (ICM), Paris, France. Equipe labellisée LNCC; Service de Neurologie 2-Mazarin (A.L.D.S.,M.D.P.D., M.D.P.D., C.D.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Neuroradiologie Diagnostique et Interventionnelle (L.N., D.G., S.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Neurology Unit (G.B.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Centre de NeuroImagerie de Recherche (CENIR) (R.V., S.L., Francesca Branzoli), Institut du Cerveau (ICM), Paris, France; Service de Neurochirurgie (L.C., B.B.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Service de Biochimie Métabolique (C.P.), AP-HP, Hôpital Necker, Paris, France; Laboratoire R Escourolle (J.L.), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Drug Development Department (DITEP) (C.B.), Gustave Roussy, Villejuif, France; Service de Radiologie (J.S.), Fondation Ophtalmologique Adolphe de Rothschild, Paris, France; Radiotherapy Department (F.D.), Gustave Roussy University Hospital, Villejuif, Cedex, France; Center for Magnetic Resonance Research (D.K.D., M.M.), Department of Radiology, Minneapolis, MN; and OncoNeuroTek Tumor Bank (M.D.P.D.), Institut du Cerveau et de la Moelle épinière (ICM), Paris, France.
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21
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Zi M, Xingyu C, Yang C, Xiaodong S, Shixian L, Shicheng W. Improved antitumor immunity of chemotherapy in OSCC treatment by Gasdermin-E mediated pyroptosis. Apoptosis 2022; 28:348-361. [PMID: 36370260 DOI: 10.1007/s10495-022-01792-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2022] [Indexed: 11/13/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is a malignant tumor with high mortality and poor prognosis. Many OSCC patients have low response rate to current treatments including immunotherapies largely due to the immune-suppressive tumor microenvironment (TME). Chemotherapy could induce immunogenic cell death (ICD), a type of cell death such as pyroptosis and necroptosis, which has proved to be capable to alter the immune-suppressive TME and beneficial for better anti-tumor effect. GSDME, a key protein of pyroptosis, is however often silenced in tumors due to abnormal methylation. To overcome these limitations, we utilizied methyltransferase inhibitor (decitabine, DAC) to trigger pyroptosis of tumor cells, combined with chemodrug cisplatin (DDP) and immune checkpoints inhibitors to amplify the immunotherapies outcomes. To the best of our knowledge, this is the first study of tumor suppressive effect of GSDME in OSCC. Our investigation demonstrated that stimulation of GSDME expression could improve the sensitivity of chemotherapeutics, activate inflammatory tumor cell pyroptosis and alter the tumor immune-suppressive microenvironment, providing an important perspective for clinical OSCC treatment.
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Affiliation(s)
- Mei Zi
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology; School of Materials Science and Engineering, Peking University, No.22, Zhongguancun South Avenue, Haidian District, Beijing, 100871, People's Republic of China
| | - Chen Xingyu
- Biomedical Pioneering Innovation Center (BIOPIC)State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Chen Yang
- Laboratory of Biomaterials and Regenerative Medicine, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, People's Republic of China
| | - Su Xiaodong
- Biomedical Pioneering Innovation Center (BIOPIC)State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Lv Shixian
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology; School of Materials Science and Engineering, Peking University, No.22, Zhongguancun South Avenue, Haidian District, Beijing, 100871, People's Republic of China.
| | - Wei Shicheng
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology; School of Materials Science and Engineering, Peking University, No.22, Zhongguancun South Avenue, Haidian District, Beijing, 100871, People's Republic of China.
- Laboratory of Biomaterials and Regenerative Medicine, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, People's Republic of China.
- , No.22, Zhongguancun South Avenue, Haidian District, Beijing, 100081, People's Republic of China.
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22
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Noushmehr H, Herrgott G, Morosini NS, Castro AV. Noninvasive approaches to detect methylation-based markers to monitor gliomas. Neurooncol Adv 2022; 4:ii22-ii32. [PMID: 36380867 PMCID: PMC9650474 DOI: 10.1093/noajnl/vdac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023] Open
Abstract
In this review, we summarize the current approaches used to detect glioma tissue-derived DNA methylation markers in liquid biopsy specimens with the aim to diagnose, prognosticate and potentially track treatment response and evolution of patients with gliomas.
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Affiliation(s)
- Houtan Noushmehr
- Department of Neurosurgery, Omics Laboratory, Henry Ford Health System, Detroit, Michigan, USA
| | - Grayson Herrgott
- Department of Neurosurgery, Omics Laboratory, Henry Ford Health System, Detroit, Michigan, USA
| | - Natalia S Morosini
- Department of Neurosurgery, Omics Laboratory, Henry Ford Health System, Detroit, Michigan, USA
| | - Ana Valeria Castro
- Department of Neurosurgery, Omics Laboratory, Henry Ford Health System, Detroit, Michigan, USA
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23
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von Knebel Doeberitz N, Paech D, Sturm D, Pusch S, Turcan S, Saunthararajah Y. Changing paradigms in oncology: Toward noncytotoxic treatments for advanced gliomas. Int J Cancer 2022; 151:1431-1446. [PMID: 35603902 PMCID: PMC9474618 DOI: 10.1002/ijc.34131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022]
Abstract
Glial-lineage malignancies (gliomas) recurrently mutate and/or delete the master regulators of apoptosis p53 and/or p16/CDKN2A, undermining apoptosis-intending (cytotoxic) treatments. By contrast to disrupted p53/p16, glioma cells are live-wired with the master transcription factor circuits that specify and drive glial lineage fates: these transcription factors activate early-glial and replication programs as expected, but fail in their other usual function of forcing onward glial lineage-maturation-late-glial genes have constitutively "closed" chromatin requiring chromatin-remodeling for activation-glioma-genesis disrupts several epigenetic components needed to perform this work, and simultaneously amplifies repressing epigenetic machinery instead. Pharmacologic inhibition of repressing epigenetic enzymes thus allows activation of late-glial genes and terminates glioma self-replication (self-replication = replication without lineage-maturation), independent of p53/p16/apoptosis. Lineage-specifying master transcription factors therefore contrast with p53/p16 in being enriched in self-replicating glioma cells, reveal a cause-effect relationship between aberrant epigenetic repression of late-lineage programs and malignant self-replication, and point to specific epigenetic targets for noncytotoxic glioma-therapy.
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Affiliation(s)
| | - Daniel Paech
- Division of RadiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of NeuroradiologyBonn University HospitalBonnGermany
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ) HeidelbergHeidelbergGermany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)HeidelbergGermany
- Department of Pediatric Oncology, Hematology & ImmunologyHeidelberg University HospitalHeidelbergGermany
| | - Stefan Pusch
- Department of NeuropathologyInstitute of Pathology, Ruprecht‐Karls‐University HeidelbergHeidelbergGermany
- German Cancer Consortium (DKTK), Clinical Cooperation Unit (CCU) Neuropathology, German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Sevin Turcan
- Department of NeurologyHeidelberg University HospitalHeidelbergGermany
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology ResearchTaussig Cancer Institute, Cleveland ClinicClevelandOhioUSA
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24
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Noorani I, Mischel PS, Swanton C. Leveraging extrachromosomal DNA to fine-tune trials of targeted therapy for glioblastoma: opportunities and challenges. Nat Rev Clin Oncol 2022; 19:733-743. [PMID: 36131011 DOI: 10.1038/s41571-022-00679-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2022] [Indexed: 11/09/2022]
Abstract
Glioblastoma evolution is facilitated by intratumour heterogeneity, which poses a major hurdle to effective treatment. Evidence indicates a key role for oncogene amplification on extrachromosomal DNA (ecDNA) in accelerating tumour evolution and thus resistance to treatment, particularly in glioblastomas. Oncogenes contained within ecDNA can reach high copy numbers and expression levels, and their unequal segregation can result in more rapid copy number changes in response to therapy than is possible through natural selection of intrachromosomal genomic loci. Notably, targeted therapies inhibiting oncogenic pathways have failed to improve glioblastoma outcomes. In this Perspective, we outline reasons for this disappointing lack of clinical translation and present the emerging evidence implicating ecDNA as an important driver of tumour evolution. Furthermore, we suggest that through detection of ecDNA, patient selection for clinical trials of novel agents can be optimized to include those most likely to benefit based on current understanding of resistance mechanisms. We discuss the challenges to successful translation of this approach, including accurate detection of ecDNA in tumour tissue with novel technologies, development of faithful preclinical models for predicting the efficacy of novel agents in the presence of ecDNA oncogenes, and understanding the mechanisms of ecDNA formation during cancer evolution and how they could be attenuated therapeutically. Finally, we evaluate the feasibility of routine ecDNA characterization in the clinic and how this process could be integrated with other methods of molecular stratification to maximize the potential for clinical translation of precision medicines.
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Affiliation(s)
- Imran Noorani
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UK.
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine and Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
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25
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Chen D, Liu Z, Wang J, Yang C, Pan C, Tang Y, Zhang P, Liu N, Li G, Li Y, Wu Z, Xia F, Zhang C, Nie H, Tang Z. Integrative genomic analysis facilitates precision strategies for glioblastoma treatment. iScience 2022; 25:105276. [PMID: 36300002 PMCID: PMC9589211 DOI: 10.1016/j.isci.2022.105276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/29/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma (GBM) is the most common form of malignant primary brain tumor with a dismal prognosis. Currently, the standard treatments for GBM rarely achieve satisfactory results, which means that current treatments are not individualized and precise enough. In this study, a multiomics-based GBM classification was established and three subclasses (GPA, GPB, and GPC) were identified, which have different molecular features both in bulk samples and at single-cell resolution. A robust GBM poor prognostic signature (GPS) score model was then developed using machine learning method, manifesting an excellent ability to predict the survival of GBM. NVP−BEZ235, GDC−0980, dasatinib and XL765 were ultimately identified to have subclass-specific efficacy targeting patients with a high risk of poor prognosis. Furthermore, the GBM classification and GPS score model could be considered as potential biomarkers for immunotherapy response. In summary, an integrative genomic analysis was conducted to advance individual-based therapies in GBM. A multiomics-based classification of GBM was established Single-cell transcriptomic profiling of GBM subclasses was revealed using Scissor A robust prognostic risk model was developed for GBM by machine learning method Prediction of potential agents based on molecular and prognostic risk stratification
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Affiliation(s)
- Danyang Chen
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhicheng Liu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jingxuan Wang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chen Yang
- State Key Laboratory of Oncogenes and Related Genes, Department of Liver Surgery and Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Chao Pan
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yingxin Tang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ping Zhang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Na Liu
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Gaigai Li
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yan Li
- State Key Laboratory of Oncogenes and Related Genes, Department of Liver Surgery and Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China,Department of Immunology, Sun Yat-Sen University, Zhongshan School of Medicine, Guangzhou, Guangdong 510080, China
| | - Zhuojin Wu
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Feng Xia
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Cuntai Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hao Nie
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Corresponding author
| | - Zhouping Tang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Corresponding author
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Molecular markers related to patient outcome in patients with IDH-mutant astrocytomas grade 2 to 4: A systematic review. Eur J Cancer 2022; 175:214-223. [PMID: 36152406 DOI: 10.1016/j.ejca.2022.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND Grading and classification of IDH-mutant astrocytomas has shifted from solely histology towards histology combined with molecular diagnostics. In this systematic review, we give an overview of all currently known clinically relevant molecular markers within IDH-mutant astrocytomas grade 2 to 4. METHODS A literature search was performed in five electronic databases for English original papers on patient outcome with respect to a molecular marker as determined by DNA/RNA sequencing, micro-arrays, or DNA methylation profiling in IDH-mutant astrocytomas grade 2 to 4. Papers were included if molecular diagnostics were performed on tumour tissue of at least 15 IDH-mutant astrocytoma patients, and if the investigated molecular markers were not limited to the diagnostic markers MGMT, ATRX, TERT, and/or TP53. RESULTS The literature search identified 4508 unique articles, published between August 2012 and December 2021, of which ultimately 44 articles were included. Numerous molecular markers from these papers were significantly correlated to patient outcome. The associations between patient outcome and non-canonical IDH mutations, PI3K mutations, high expression of MSH2, high expression of RAD18, homozygous deletion of CDKN2A/B, amplification of PDGFRA, copy number neutral loss of chromosomal arm 17p, loss of chromosomal arm 19q, the G-CIMP-low DNA methylation cluster, high total CNV, and high tumour mutation burden were confirmed in multiple studies. CONCLUSIONS Multiple genetic and epigenetic markers are associated with survival in IDH-mutant astrocytoma patients. Commonly affected are the RB signalling pathway, the RTK-PI3K-mTOR signalling pathway, genomic stability markers, and (epigenetic) gene regulation.
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ADAR2 Protein Is Associated with Overall Survival in GBM Patients and Its Decrease Triggers the Anchorage-Independent Cell Growth Signature. Biomolecules 2022; 12:biom12081142. [PMID: 36009036 PMCID: PMC9405742 DOI: 10.3390/biom12081142] [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: 09/22/2021] [Revised: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Epitranscriptomic mechanisms, such as A-to-I RNA editing mediated by ADAR deaminases, contribute to cancer heterogeneity and patients’ stratification. ADAR enzymes can change the sequence, structure, and expression of several RNAs, affecting cancer cell behavior. In glioblastoma, an overall decrease in ADAR2 RNA level/activity has been reported. However, no data on ADAR2 protein levels in GBM patient tissues are available; and most data are based on ADARs overexpression experiments. Methods: We performed IHC analysis on GBM tissues and correlated ADAR2 levels and patients’ overall survival. We silenced ADAR2 in GBM cells, studied cell behavior, and performed a gene expression/editing analysis. Results: GBM tissues do not all show a low/no ADAR2 level, as expected by previous studies. Although, different amounts of ADAR2 protein were observed in different patients, with a low level correlating with a poor patient outcome. Indeed, reducing the endogenous ADAR2 protein in GBM cells promotes cell proliferation and migration and changes the cell’s program to an anchorage-independent growth mode. In addition, deep-seq data and bioinformatics analysis indicated multiple RNAs are differently expressed/edited upon siADAR2. Conclusion: ADAR2 protein is an important deaminase in GBM and its amount correlates with patient prognosis.
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Wenger A, Ferreyra Vega S, Schepke E, Löfgren M, Olsson Bontell T, Tisell M, Nilsson D, Kling T, Carén H. DNA methylation alterations across time and space in paediatric brain tumours. Acta Neuropathol Commun 2022; 10:105. [PMID: 35842717 PMCID: PMC9287974 DOI: 10.1186/s40478-022-01406-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
DNA methylation is increasingly used for tumour classification and has expanded upon the > 100 currently known brain tumour entities. A correct diagnosis is the basis for suitable treatment for patients with brain tumours, which is the leading cause of cancer-related death in children. DNA methylation profiling is required for diagnosis of certain tumours, and used clinically for paediatric brain tumours in several countries. We therefore evaluated if the methylation-based classification is robust in different locations of the same tumour, and determined how the methylation pattern changed over time to relapse. We sampled 3-7 spatially separated biopsies per patient, and collected samples from paired primary and relapse brain tumours from children. Altogether, 121 samples from 46 paediatric patients with brain tumours were profiled with EPIC methylation arrays. The methylation-based classification was mainly homogeneous for all included tumour types that were successfully classified, which is promising for clinical diagnostics. There were indications of multiple subclasses within tumours and switches in the relapse setting, but not confirmed as the classification scores were below the threshold. Site-specific methylation alterations did occur within the tumours and varied significantly between tumour types for the temporal samples, and as a trend in spatial samples. More alterations were present in high-grade tumours compared to low-grade, and significantly more alterations with longer relapse times. The alterations in the spatial and temporal samples were significantly depleted in CpG islands, exons and transcription start sites, while enriched in OpenSea and regions not affiliated with a gene, suggesting a random location of the alterations in less conserved regions. In conclusion, more DNA methylation changes accumulated over time and more alterations occurred in high-grade tumours. The alterations mainly occurred in regions without gene affiliation, and did not affect the methylation-based classification, which largely remained homogeneous in paediatric brain tumours.
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Affiliation(s)
- Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Sandra Ferreyra Vega
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden.,Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Elizabeth Schepke
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden.,Childhood Cancer Centre, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maja Löfgren
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Magnus Tisell
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Daniel Nilsson
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden.
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Qin J, Yu Z, Yao Y, Liang Y, Tang Y, Wang B. Susceptibility-weighted imaging cannot distinguish radionecrosis from recurrence in brain metastases after radiotherapy: a comparison with high-grade gliomas. Clin Radiol 2022; 77:e585-e591. [PMID: 35676103 DOI: 10.1016/j.crad.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/06/2022] [Indexed: 11/16/2022]
Abstract
AIM To explore the efficiency of susceptibility-weighted imaging (SWI) in the differential diagnosis of recurrence from radionecrosis in brain metastases (BM) and in high-grade gliomas (HGG). MATERIALS AND METHODS From September 2016 to November 2018, 56 patients with BM and 42 patients with HGG were included in this retrospective study. BM and HGG were assigned to the recurrence and radionecrosis groups according to their histopathology or follow-up results. The proportion of dark signal intensity (proDSI), which was defined as the area of dark signal on SWI or the enhancing area on contrast-enhanced T1-weighted imaging (T1WI), was calculated for each patient. Analysis of variance (ANOVA) with Tukey's honestly significant difference test was used for the repeat multiple comparisons. Receiver operating characteristic curve analysis was performed to validate the diagnostic performance. RESULTS For HGG, the proDSI in the recurrence group was significantly lower than that in the radionecrosis group (0.13 ± 0.05 versus 0.43 ± 0.11, p<0.001); however, for BM, no statistical difference was found between groups (0.49 ± 0.09 versus 0.46 ± 0.08, p=0.26). proDSI had the best diagnostic performance (AUC = 0.87, 95% CI: 0.76-0.98; sensitivity = 0.87; specificity = 0.88) for HGG, when a cut-off value of 0.21 was selected. CONCLUSIONS Semi-quantitative analysis using SWI is feasible for the differential diagnosis between recurrence and radionecrosis in HGG, but is not feasible in BM. Semi-quantitative assessment based on SWI should interpreted with caution in BM after radiotherapy in clinical practice.
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Affiliation(s)
- J Qin
- School of Medicine, Qingdao University, Qingdao, 266021, PR China; Department of Radiology, Rizhao Central Hospital, Rizhao, 276800, PR China
| | - Z Yu
- Department of Health Management Center, Qilu Hospital of Shandong University, Jinan, 250012, PR China; Nursing Theory & Practice Innovation Research Center of Shandong University, Jinan, 250012, PR China
| | - Y Yao
- Department of Radiology, Qilu Hospital of Shandong University, Jinan, 250012, PR China
| | - Y Liang
- Department of Radiology, Qilu Hospital of Shandong University, Jinan, 250012, PR China
| | - Y Tang
- Department of Radiology, Rizhao Central Hospital, Rizhao, 276800, PR China
| | - B Wang
- Department of Radiology, Qilu Hospital of Shandong University, Jinan, 250012, PR China.
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Wu W, Wang Y, Xiang J, Li X, Wahafu A, Yu X, Bai X, Yan G, Wang C, Wang N, Du C, Xie W, Wang M, Wang J. A Novel Multi-Omics Analysis Model for Diagnosis and Survival Prediction of Lower-Grade Glioma Patients. Front Oncol 2022; 12:729002. [PMID: 35646656 PMCID: PMC9133344 DOI: 10.3389/fonc.2022.729002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 03/24/2022] [Indexed: 01/13/2023] Open
Abstract
Background Lower-grade gliomas (LGGs) are characterized by remarkable genetic heterogeneity and different clinical outcomes. Classification of LGGs is improved by the development of molecular stratification markers including IDH mutation and 1p/19q chromosomal integrity, which are used as a hallmark of survival and therapy sensitivity of LGG patients. However, the reproducibility and sensitivity of the current classification remain ambiguous. This study aimed to construct more accurate risk-stratification approaches. Methods According to bioinformatics, the sequencing profiles of methylation and transcription and imaging data derived from LGG patients were analyzed and developed predictable risk score and radiomics score. Moreover, the performance of predictable models was further validated. Results In this study, we determined a cluster of 6 genes that were correlated with IDH mutation/1p19q co-deletion status. Risk score model was calculated based on 6 genes and showed gratifying sensitivity and specificity for survival prediction and therapy response of LGG patients. Furthermore, a radiomics risk score model was established to noninvasively assist judgment of risk score in pre-surgery. Taken together, a predictable nomogram that combined transcriptional signatures and clinical characteristics was established and validated to be preferable to the histopathological classification. Our novel multi-omics nomograms showed a satisfying performance. To establish a user-friendly application, the nomogram was further developed into a web-based platform: https://drw576223193.shinyapps.io/Nomo/, which could be used as a supporting method in addition to the current histopathological-based classification of gliomas. Conclusions Our novel multi-omics nomograms showed the satisfying performance of LGG patients and assisted clinicians to draw up individualized clinical management.
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Affiliation(s)
- Wei Wu
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Center of Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yichang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Center of Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jianyang Xiang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Center of Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaodong Li
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Center of Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Alafate Wahafu
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Center of Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiao Yu
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaobin Bai
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ge Yan
- Department of Medical Imaging, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chunbao Wang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ning Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Changwang Du
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wanfu Xie
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Maode Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Center of Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jia Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Center of Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Ma L, Gong J, Zhao M, Kong X, Gao P, Jiang Y, Liu Y, Feng X, Si S, Cao Y. A Novel Stool Methylation Test for the Non-Invasive Screening of Gastric and Colorectal Cancer. Front Oncol 2022; 12:860701. [PMID: 35419280 PMCID: PMC8995552 DOI: 10.3389/fonc.2022.860701] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Abstract
Background Because of poor compliance or low sensitivity, existing diagnostic approaches are unable to provide an efficient diagnosis of patients with gastric and colorectal cancer. Here, we developed the ColoCaller test, which simultaneously detects the methylation status of the SDC2, TFPI2, WIF1, and NDRG4 genes in stool DNA, to optimize the screening of gastric and colorectal cancer in high-risk populations. Methods A total of 217 stool samples from patients with gastrointestinal cancer and from patients with negative endoscopy were prospectively collected, complete with preoperative and postoperative clinical data from patients. The methylation of these samples was detected using ColoCaller, which was designed by selecting CpGs with a two-step screening strategy, and was interpreted using a prediction model built using libSVM to evaluate its clinical value for gastric and colorectal cancer screening. Results Compared to pathological diagnosis, the sensitivity and specificity of the ColoCaller test in 217 stool DNA samples were 95.56% and 91.86%, respectively, for colorectal cancer, and 67.5% and 97.81%, respectively, for gastric cancer. The detection limit was as low as 1% in 8 ng of DNA. Conclusion In this study, we developed and established a new test, ColoCaller, which can be used as a screening tool or as an auxiliary diagnostic approach in high-risk populations with gastric and colorectal cancer to promote timely diagnosis and treatment.
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Affiliation(s)
- Liang Ma
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Jian Gong
- Department of Research and Development, Apexbio Biotechnology (Suzhou) Co., Ltd., Suzhou, China
| | - Meimei Zhao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Xiaomu Kong
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Peng Gao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yongwei Jiang
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yi Liu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Xiaoyan Feng
- Department of Research and Development, Apexbio Biotechnology (Suzhou) Co., Ltd., Suzhou, China
| | - Shuang Si
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Yongtong Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
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32
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Courant F, Maravat M, Chen W, Gosset D, Blot L, Hervouet-Coste N, Sarou-Kanian V, Morisset-Lopez S, Decoville M. Expression of the Human Serotonin 5-HT 7 Receptor Rescues Phenotype Profile and Restores Dysregulated Biomarkers in a Drosophila melanogaster Glioma Model. Cells 2022; 11:1281. [PMID: 35455961 PMCID: PMC9028361 DOI: 10.3390/cells11081281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 02/01/2023] Open
Abstract
Gliomas are the most common primary brain tumors in adults. Significant progress has been made in recent years in identifying the molecular alterations involved in gliomas. Among them, an amplification/overexpression of the EGFR (Epidermal Growth Factor Receptor) proto-oncogene and its associated signaling pathways have been widely described. However, current treatments remain ineffective for glioblastomas, the most severe forms. Thus, the identification of other pharmacological targets could open new therapeutic avenues. We used a glioma model in Drosophila melanogaster that results from the overexpression of constitutively active forms of EGFR and PI3K specifically in glial cells. We observed hyperproliferation of glial cells that leads to an increase in brain size and lethality at the third instar larval stage. After expression of the human serotonin 5-HT7 receptor in this glioma model, we observed a decrease in larval lethality associated with the presence of surviving adults and a return to a normal morphology of brain for some Drosophila. Those phenotypic changes are accompanied by the normalization of certain metabolic biomarkers measured by High-Resolution Magic Angle Spinning NMR (HR-MAS NMR). The 5-HT7R expression in glioma also restores some epigenetic modifications and characteristic markers of the signaling pathways associated with tumor growth. This study demonstrates the role of the serotonin 5-HT7 receptor as a tumor suppressor gene which is in agreement with transcriptomic analysis obtained on human glioblastomas.
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Affiliation(s)
- Florestan Courant
- Centre de Biophysique Moléculaire—CBM, UPR 4301, CNRS, Rue Charles Sadron, CEDEX 02, F-45071 Orléans, France; (F.C.); (W.C.); (D.G.); (L.B.); (N.H.-C.); (M.D.)
| | - Marion Maravat
- Conditions Extrêmes et Matériaux: Haute Température et Irradiation—CEMHTI-CNRS UPR 3079, CEDEX 02, F-45071 Orléans, France; (M.M.); (V.S.-K.)
| | - Wanyin Chen
- Centre de Biophysique Moléculaire—CBM, UPR 4301, CNRS, Rue Charles Sadron, CEDEX 02, F-45071 Orléans, France; (F.C.); (W.C.); (D.G.); (L.B.); (N.H.-C.); (M.D.)
| | - David Gosset
- Centre de Biophysique Moléculaire—CBM, UPR 4301, CNRS, Rue Charles Sadron, CEDEX 02, F-45071 Orléans, France; (F.C.); (W.C.); (D.G.); (L.B.); (N.H.-C.); (M.D.)
| | - Lauren Blot
- Centre de Biophysique Moléculaire—CBM, UPR 4301, CNRS, Rue Charles Sadron, CEDEX 02, F-45071 Orléans, France; (F.C.); (W.C.); (D.G.); (L.B.); (N.H.-C.); (M.D.)
| | - Nadège Hervouet-Coste
- Centre de Biophysique Moléculaire—CBM, UPR 4301, CNRS, Rue Charles Sadron, CEDEX 02, F-45071 Orléans, France; (F.C.); (W.C.); (D.G.); (L.B.); (N.H.-C.); (M.D.)
| | - Vincent Sarou-Kanian
- Conditions Extrêmes et Matériaux: Haute Température et Irradiation—CEMHTI-CNRS UPR 3079, CEDEX 02, F-45071 Orléans, France; (M.M.); (V.S.-K.)
| | - Séverine Morisset-Lopez
- Centre de Biophysique Moléculaire—CBM, UPR 4301, CNRS, Rue Charles Sadron, CEDEX 02, F-45071 Orléans, France; (F.C.); (W.C.); (D.G.); (L.B.); (N.H.-C.); (M.D.)
| | - Martine Decoville
- Centre de Biophysique Moléculaire—CBM, UPR 4301, CNRS, Rue Charles Sadron, CEDEX 02, F-45071 Orléans, France; (F.C.); (W.C.); (D.G.); (L.B.); (N.H.-C.); (M.D.)
- UFR Sciences et Techniques, Université d’Orléans, 6 Avenue du Parc Floral, F-45100 Orléans, France
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Draaisma K, Tesileanu CMS, de Heer I, Klein M, Smits M, Reijneveld JC, Clement PM, De Vos F, Wick A, Mulholland P, Taphoorn M, Weller M, Chinot OL, Kros JM, Verschuere T, Coens C, Golfinopoulos V, Gorlia T, Idbaih A, Robe PA, van den Bent MJ, French PJ. Prognostic significance of DNA methylation profiles at MRI enhancing tumor recurrence: a report from the EORTC 26091 TAVAREC trial. Clin Cancer Res 2022; 28:2440-2448. [PMID: 35294545 DOI: 10.1158/1078-0432.ccr-21-3725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/19/2021] [Accepted: 03/14/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Despite recent advances in the molecular characterization of gliomas, it remains unclear which patients benefit most from which second line treatments. The TAVAREC trial was a randomized, open-label phase 2 trial assessing the benefit of the addition of the angiogenesis inhibitor bevacizumab to treatment with temozolomide in patients with a first enhancing recurrence of WHO grade 2 or 3 glioma without 1p/19q codeletion. We evaluated the prognostic significance of genome wide DNA methylation profiles and copy number variations on the TAVAREC trial samples. EXPERIMENTAL DESIGN IDH-mutation status was determined via Sanger sequencing and immunohistochemistry. DNA methylation analysis was performed using the MethylationEPIC BeadChip (Illumina) from which 1p/19q codeletion, MGMT promoter methylation (MGMT-STP27) and homozygous deletion of CDKN2A/B were determined. DNA-methylation classes were determined according to classifiers developed in Heidelberg and TCGA ("Heidelberg" and "TCGA" classifier respectively). RESULTS DNA methylation profiles of 122 samples were successfully determined. As expected, most samples were IDH-mutant (89/122) and MGMT promotor methylated (89/122). Methylation classes were prognostic for time to progression. However, Heidelberg methylation classes determined at time of diagnosis were no longer prognostic following enhancing recurrence of the tumor. In contrast, TCGA methylation classes of primary samples remained prognostic also following enhancing recurrence. Homozygous deletions in CDKN2A/B were found in 10/87 IDH-mutated samples and were prognostically unfavorable at recurrence. CONCLUSIONS DNA methylome Heidelberg classification at time of diagnosis is no longer of prognostic value at the time of enhancing recurrence. CDKN2A/B deletion status was predictive of survival from progression of IDH-mutated tumors.
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Affiliation(s)
- Kaspar Draaisma
- Erasmus MC Cancer Institute, Rotterdam, Rotterdam, Netherlands
| | | | | | - Martin Klein
- Amsterdam UMC Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | | | | | - Filip De Vos
- University Medical Center Utrecht, Utrecht, Netherlands
| | - Antje Wick
- University Hospital Heidelberg, Heidelberg, Germany
| | | | | | - Michael Weller
- University Hospital and University of Zurich, Zurich, Switzerland
| | | | | | | | | | | | - Thierry Gorlia
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
| | | | - Pierre A Robe
- University Medical Center Utrecht, Utrecht, Utrecht, Netherlands
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Sienkiewicz K, Chen J, Chatrath A, Lawson JT, Sheffield NC, Zhang L, Ratan A. Detecting molecular subtypes from multi-omics datasets using SUMO. CELL REPORTS METHODS 2022; 2:100152. [PMID: 35211690 PMCID: PMC8865426 DOI: 10.1016/j.crmeth.2021.100152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 08/27/2021] [Accepted: 12/21/2021] [Indexed: 12/31/2022]
Abstract
We present a data integration framework that uses non-negative matrix factorization of patient-similarity networks to integrate continuous multi-omics datasets for molecular subtyping. It is demonstrated to have the capability to handle missing data without using imputation and to be consistently among the best in detecting subtypes with differential prognosis and enrichment of clinical associations in a large number of cancers. When applying the approach to data from individuals with lower-grade gliomas, we identify a subtype with a significantly worse prognosis. Tumors assigned to this subtype are hypomethylated genome wide with a gain of AP-1 occupancy in demethylated distal enhancers. The tumors are also enriched for somatic chromosome 7 (chr7) gain, chr10 loss, and other molecular events that have been suggested as diagnostic markers for "IDH wild type, with molecular features of glioblastoma" by the cIMPACT-NOW consortium but have yet to be included in the World Health Organization (WHO) guidelines.
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Affiliation(s)
- Karolina Sienkiewicz
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jinyu Chen
- Department of Mathematics and Computational Biology Program, National University of Singapore, Singapore 119076, Singapore
| | - Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - John T. Lawson
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Nathan C. Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
- University of Virginia Cancer Center, Charlottesville, VA 22908, USA
| | - Louxin Zhang
- Department of Mathematics and Computational Biology Program, National University of Singapore, Singapore 119076, Singapore
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
- University of Virginia Cancer Center, Charlottesville, VA 22908, USA
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35
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Lv SQ, Fu Z, Yang L, Li QR, Zhu J, Gai QJ, Mao M, He J, Qin Y, Yao XX, Lan X, Wang YX, Lu HM, Xiang Y, Zhang ZX, Huang GH, Yang W, Kang P, Sun Z, Shi Y, Yao XH, Bian XW, Wang Y. Comprehensive omics analyses profile genesets related with tumor heterogeneity of multifocal glioblastomas and reveal LIF/CCL2 as biomarkers for mesenchymal subtype. Theranostics 2022; 12:459-473. [PMID: 34987659 PMCID: PMC8690928 DOI: 10.7150/thno.65739] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/27/2021] [Indexed: 01/22/2023] Open
Abstract
Rationale: Around 10%-20% patients with glioblastoma (GBM) are diagnosed with more than one tumor lesions or multifocal GBM (mGBM). However, the understanding on genetic, DNA methylomic, and transcriptomic characteristics of mGBM is still limited. Methods: In this study, we collected nine tumor foci from three mGBM patients followed by whole genome sequencing, whole genome bisulfite sequencing, RNA sequencing, and immunohistochemistry. The data were further examined using public GBM databases and GBM cell line. Results: Analysis on genetic data confirmed common features of GBM, including gain of chr.7 and loss of chr.10, loss of critical tumor suppressors, high frequency of PDGFA and EGFR amplification. Through profiling DNA methylome of individual tumor foci, we found that promoter methylation status of genes involved in detection of chemical stimulus, immune response, and Hippo/YAP1 pathway was significantly changed in mGBM. Although both CNV and promoter methylation alteration were involved in heterogeneity of different tumor foci from same patients, more CNV events than promoter hypomethylation events were shared by different tumor foci, implying CNV were relatively earlier than promoter methylation alteration during evolution of different tumor foci from same mGBM. Moreover, different tumor foci from same mGBM assumed different molecular subtypes and mesenchymal subtype was prevalent in mGBM, which might explain the worse prognosis of mGBM than single GBM. Interestingly, we noticed that LIF and CCL2 was tightly correlated with mesenchymal subtype tumor focus in mGBM and predicted poor survival of GBM patients. Treatment with LIF and CCL2 produced mesenchymal-like transcriptome in GBM cells. Conclusions: Together, our work herein comprehensively profiled multi-omics features of mGBM and emphasized that components of extracellular microenvironment, such as LIF and CCL2, contributed to the evolution and prognosis of tumor foci in mGBM patients.
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36
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Salas LA, Stewart TG, Mobley BC, Peng C, Liu J, Loganathan SN, Wang J, Ma Y, Berger MS, Absher D, Hu Y, Moots PL, Christensen BC, Clark SW. Phase I Study of High-Dose L-methylfolate in Combination with Temozolomide and Bevacizumab in Recurrent IDH wild-type High-Grade Glioma. CANCER RESEARCH COMMUNICATIONS 2022; 2:1-9. [PMID: 35392283 PMCID: PMC8983000 DOI: 10.1158/2767-9764.crc-21-0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Purpose IDH mutations in low-grade gliomas (LGGs) results in improved survival and DNA hypermethylation compared to IDH wild-type LGGs. IDH-mutant LGGs become hypomethylated during progression. It's uncertain if methylation changes occur during IDH wild-type GBM progression and if the methylome can be reprogrammed. This phase I study evaluated the safety, tolerability, efficacy and methylome changes after L-methylfolate (LMF) treatment, in combination with temozolomide and bevacizumab in patients with recurrent high-grade glioma. Patients and Methods Fourteen patients total, 13 with GBM, one with anaplastic astrocytoma, all IDH wild-type were enrolled in the study. All patients received LMF at either 15, 30, 60, or 90 mg daily plus temozolomide (75mg/m2 5 days per month) and bevacizumab (10mg/kg every two weeks). Results No MTD was identified. LMF treated had mOS of 9.5 months (95% CI, 9.1-35.4) comparable to bevacizumab historical control 8.6 months (95% CI, 6.8-10.8). Six patients treated with LMF survived more than 650 days. Across all treatment doses the most adverse events were diarrhea (7%, 1 patient, grade 2), reflux (7%, 1 patient, grade 2), and dysgeusia (7%, 1 patient, grade 2). In the six brains donated at death, there was a 25% increase in DNA methylated CpGs compared to the paired initial tumor. Conclusions LMF in combination with temozolomide and bevacizumab was well tolerated in patients with recurrent IDH wild-type high-grade glioma. This small study did not establish a superior efficacy with addition of LMF compared to standard bevacizumab therapy, however, this study did show methylome reprogramming in high-grade glioma.
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Affiliation(s)
- Lucas A. Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Thomas G. Stewart
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Bret C. Mobley
- Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Chengwei Peng
- Department of Medicine, Yale Medical School, New Haven, Connecticut
| | - Jing Liu
- Department of Neurosurgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sudan N. Loganathan
- Department of Neurosurgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jialiang Wang
- Department of Neurosurgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yanjun Ma
- Tennessee Oncology PLLC, Nashville, Tennessee
| | | | | | - Yang Hu
- CD Genomics, Shirley, New York
| | - Paul L. Moots
- Department of Neurology, Vanderbilt University Medical Center
| | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Stephen W. Clark
- Department of Neurology, Vanderbilt University Medical Center.,Division of Neuro-Oncology, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee.,Epiphany Biosciences, San Francisco, California.,Sir Galahad Labs, Nashville, Tennessee.,Corresponding Author: Stephen W. Clark, Department of Neurology, Division of Neuro-Oncology, Vanderbilt University Medical Center, 1161 21 Avenue South, Nashville, TN 37232. Phone: 615-936-0060; E-mail:
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37
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Ferreyra Vega S, Wenger A, Kling T, Olsson Bontell T, Jakola AS, Carén H. Spatial heterogeneity in DNA methylation and chromosomal alterations in diffuse gliomas and meningiomas. Mod Pathol 2022; 35:1551-1561. [PMID: 35701666 PMCID: PMC9596370 DOI: 10.1038/s41379-022-01113-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 02/07/2023]
Abstract
Adult-type diffuse gliomas and meningiomas are the most common primary intracranial tumors of the central nervous system. DNA methylation profiling is a novel diagnostic technique increasingly used also in the clinic. Although molecular heterogeneity is well described in these tumors, DNA methylation heterogeneity is less studied. We therefore investigated the intratumor genetic and epigenetic heterogeneity in diffuse gliomas and meningiomas, with focus on potential clinical implications. We further investigated tumor purity as a source for heterogeneity in the tumors. We analyzed genome-wide DNA methylation profiles generated from 126 spatially separated tumor biopsies from 39 diffuse gliomas and meningiomas. Moreover, we evaluated five methods for measurement of tumor purity and investigated intratumor heterogeneity by assessing DNA methylation-based classification, chromosomal copy number alterations and molecular markers. Our results demonstrated homogeneous methylation-based classification of IDH-mutant gliomas and further corroborates subtype heterogeneity in glioblastoma IDH-wildtype and high-grade meningioma patients after excluding samples with low tumor purity. We detected a large number of differentially methylated CpG sites within diffuse gliomas and meningiomas, particularly in tumors of higher grades. The presence of CDKN2A/B homozygous deletion differed in one out of two patients with IDH-mutant astrocytomas, CNS WHO grade 4. We conclude that diffuse gliomas and high-grade meningiomas are characterized by intratumor heterogeneity, which should be considered in clinical diagnostics and in the assessment of methylation-based and molecular markers.
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Affiliation(s)
- Sandra Ferreyra Vega
- grid.8761.80000 0000 9919 9582Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden ,grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Wenger
- grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresia Kling
- grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- grid.8761.80000 0000 9919 9582Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden ,grid.1649.a000000009445082XDepartment of Clinical Pathology and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Asgeir Store Jakola
- grid.8761.80000 0000 9919 9582Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden ,grid.1649.a000000009445082XDepartment of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden ,grid.52522.320000 0004 0627 3560Department of Neurosurgery, St.Olavs University Hospital, Trondheim, Norway
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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Yabo YA, Niclou SP, Golebiewska A. Cancer cell heterogeneity and plasticity: A paradigm shift in glioblastoma. Neuro Oncol 2021; 24:669-682. [PMID: 34932099 PMCID: PMC9071273 DOI: 10.1093/neuonc/noab269] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Phenotypic plasticity has emerged as a major contributor to intra-tumoral heterogeneity and treatment resistance in cancer. Increasing evidence shows that glioblastoma (GBM) cells display prominent intrinsic plasticity and reversibly adapt to dynamic microenvironmental conditions. Limited genetic evolution at recurrence further suggests that resistance mechanisms also largely operate at the phenotypic level. Here we review recent literature underpinning the role of GBM plasticity in creating gradients of heterogeneous cells including those that carry cancer stem cell (CSC) properties. A historical perspective from the hierarchical to the nonhierarchical concept of CSCs towards the recent appreciation of GBM plasticity is provided. Cellular states interact dynamically with each other and with the surrounding brain to shape a flexible tumor ecosystem, which enables swift adaptation to external pressure including treatment. We present the key components regulating intra-tumoral phenotypic heterogeneity and the equilibrium of phenotypic states, including genetic, epigenetic, and microenvironmental factors. We further discuss plasticity in the context of intrinsic tumor resistance, where a variable balance between preexisting resistant cells and adaptive persisters leads to reversible adaptation upon treatment. Innovative efforts targeting regulators of plasticity and mechanisms of state transitions towards treatment-resistant states are needed to restrict the adaptive capacities of GBM.
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Affiliation(s)
- Yahaya A Yabo
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Anna Golebiewska
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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39
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Liu H, Zhang Y, Chen W, Zhang Y, Zhang W. TMEM130 regulates cell migration through DNA methylation in nasopharyngeal carcinoma. Cancer Biomark 2021; 34:265-273. [PMID: 34958002 DOI: 10.3233/cbm-210338] [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] [Indexed: 12/24/2022]
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC), the common malignant head and neck cancer, is highly prevalent in southern China. The molecular mechanism underlying NPC tumorigenesis is unclear. We used 5-Aza-CdR, a DNA methyltransferase inhibitor, to treat NPC cell lines and discovered that the expression of TMEM130 changed significantly compared with the untreatment cells. This study aimed to identify the relationship between the DNA methylation status of TMEM130 and NPC, and to explore the function of TMEM130 in NPC cell migration. METHODS qRT-PCR was performed to investigate the transcriptional expression of TMEM130 in NPC. Bisulfite sequencing PCR and 5-Aza-CdR treatment were used to detect the methylation level of the TMEM130 promoter. Gene Expression Omnibus (GEO) datasets were obtained to identifiy the methylation status and mRNA expression of TMEM130 in NPC and normal control tissues. Transwell and western blot analyses were used to detect cell migration ability after transfection of TMEM130/NC plasmids in NPC cells. RESULTS The transcriptional expression of TMEM130 was decreased in NPC cell lines compared with in the NP69 cell line. TMEM130 promoter was significantly hyper methylated in three NPC cell lines (C666, CNE, and HONE) but hypo methylated in NP69 cells. The methylation level was higher in NPC than normal control tissues. Additionally, treatment of NPC cells with 5-Aza-CdR increased the TMEM130 mRNA expression level. Overexpression of TMEM130 in NPC cell lines suppressed cell migration ability and affected some epithelial-mesenchymal transition-associated gene expression. CONCLUSIONS This study is the first to investigate the expression and function of TMEM130 in NPC. It was found that TMEM130 hyper methylation might contribute to NPC migration and this gene might act as a tumor suppressor gene. TMEM130 is a promising biomarker for NPC diagnosis.
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Noor H, Zaman A, Teo C, Sughrue ME. PODNL1 Methylation Serves as a Prognostic Biomarker and Associates with Immune Cell Infiltration and Immune Checkpoint Blockade Response in Lower-Grade Glioma. Int J Mol Sci 2021; 22:ijms222212572. [PMID: 34830454 PMCID: PMC8625785 DOI: 10.3390/ijms222212572] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/27/2022] Open
Abstract
Lower-grade glioma (LGG) is a diffuse infiltrative tumor of the central nervous system, which lacks targeted therapy. We investigated the role of Podocan-like 1 (PODNL1) methylation in LGG clinical outcomes using the TCGA-LGG transcriptomics dataset. We identified four PODNL1 CpG sites, cg07425555, cg26969888, cg18547299, and cg24354933, which were associated with unfavorable overall survival (OS) and disease-free survival (DFS) in univariate and multivariate analysis after adjusting for age, gender, tumor-grade, and IDH1-mutation. In multivariate analysis, the OS and DFS hazard ratios ranged from 0.44 to 0.58 (p < 0.001) and 0.62 to 0.72 (p < 0.001), respectively, for the four PODNL1 CpGs. Enrichment analysis of differential gene and protein expression and analysis of 24 infiltrating immune cell types showed significantly increased infiltration in LGGs and its histological subtypes with low-methylation levels of the PODNL1 CpGs. High PODNL1 expression and low-methylation subgroups of the PODNL1 CpG sites were associated with significantly increased PD-L1, PD-1, and CTLA4 expressions. PODNL1 methylation may thus be a potential indicator of immune checkpoint blockade response, and serve as a biomarker for determining prognosis and immune subtypes in LGG.
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Affiliation(s)
- Humaira Noor
- Cure Brain Cancer Biomarkers and Translational Research Group, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2031, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Randwick, NSW 2031, Australia
- Faculty of Medicine, University of New South Wales, Randwick, NSW 2031, Australia;
- Correspondence:
| | - Ashraf Zaman
- Faculty of Medicine, University of New South Wales, Randwick, NSW 2031, Australia;
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
| | - Charles Teo
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
| | - Michael E. Sughrue
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
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41
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Johnson KC, Anderson KJ, Courtois ET, Gujar AD, Barthel FP, Varn FS, Luo D, Seignon M, Yi E, Kim H, Estecio MRH, Zhao D, Tang M, Navin NE, Maurya R, Ngan CY, Verburg N, de Witt Hamer PC, Bulsara K, Samuels ML, Das S, Robson P, Verhaak RGW. Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response. Nat Genet 2021; 53:1456-1468. [PMID: 34594038 PMCID: PMC8570135 DOI: 10.1038/s41588-021-00926-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 07/27/2021] [Indexed: 02/08/2023]
Abstract
Glioma intratumoral heterogeneity enables adaptation to challenging microenvironments and contributes to therapeutic resistance. We integrated 914 single-cell DNA methylomes, 55,284 single-cell transcriptomes and bulk multi-omic profiles across 11 adult IDH mutant or IDH wild-type gliomas to delineate sources of intratumoral heterogeneity. We showed that local DNA methylation disorder is associated with cell-cell DNA methylation differences, is elevated in more aggressive tumors, links with transcriptional disruption and is altered during the environmental stress response. Glioma cells under in vitro hypoxic and irradiation stress increased local DNA methylation disorder and shifted cell states. We identified a positive association between genetic and epigenetic instability that was supported in bulk longitudinally collected DNA methylation data. Increased DNA methylation disorder associated with accelerated disease progression and recurrently selected DNA methylation changes were enriched for environmental stress response pathways. Our work identified an epigenetically facilitated adaptive stress response process and highlights the importance of epigenetic heterogeneity in shaping therapeutic outcomes.
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Affiliation(s)
- Kevin C. Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,These authors contributed equally,Co-corresponding authors: and
| | - Kevin J. Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,These authors contributed equally
| | - Elise T. Courtois
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Amit D. Gujar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Floris P. Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Brain Tumor Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Frederick S. Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Diane Luo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Martine Seignon
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Marcos RH Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, US
| | - Dacheng Zhao
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, US
| | - Nicholas E. Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, US
| | - Rahul Maurya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Niels Verburg
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurosurgery, Brain Tumor Center Amsterdam, de Boelelaan 1117, Amsterdam, The Netherlands
| | - Philip C de Witt Hamer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurosurgery, Brain Tumor Center Amsterdam, de Boelelaan 1117, Amsterdam, The Netherlands
| | - Ketan Bulsara
- Division of Neurosurgery, The University of Connecticut Health Center, Farmington, CT, US
| | | | - Sunit Das
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for SickKids, University of Toronto.,Institute of Medical Science, University of Toronto.,Division of Neurosurgery, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, University of Toronto
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,Genetics and Genome Sciences, University of Connecticut School of Medicine
| | - Roel GW Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,Co-corresponding authors: and
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SPOP mutation induces DNA methylation via stabilizing GLP/G9a. Nat Commun 2021; 12:5716. [PMID: 34588438 PMCID: PMC8481544 DOI: 10.1038/s41467-021-25951-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/06/2021] [Indexed: 12/31/2022] Open
Abstract
Mutations in SPOP E3 ligase gene are reportedly associated with genome-wide DNA hypermethylation in prostate cancer (PCa) although the underlying mechanisms remain elusive. Here, we demonstrate that SPOP binds and promotes polyubiquitination and degradation of histone methyltransferase and DNMT interactor GLP. SPOP mutation induces stabilization of GLP and its partner protein G9a and aberrant upregulation of global DNA hypermethylation in cultured PCa cells and primary PCa specimens. Genome-wide DNA methylome analysis shows that a subset of tumor suppressor genes (TSGs) including FOXO3, GATA5, and NDRG1, are hypermethylated and downregulated in SPOP-mutated PCa cells. DNA methylation inhibitor 5-azacytidine effectively reverses expression of the TSGs examined, inhibits SPOP-mutated PCa cell growth in vitro and in mice, and enhances docetaxel anti-cancer efficacy. Our findings reveal the GLP/G9a-DNMT module as a mediator of DNA hypermethylation in SPOP-mutated PCa. They suggest that SPOP mutation could be a biomarker for effective treatment of PCa with DNA methylation inhibitor alone or in combination with taxane chemotherapeutics. The molecular mechanism underlying the DNA hypermethylation phenotype observed in the SPOP-mutant prostate cancers is unclear. Here, the authors show that mutant SPOP induces global aberrant DNA methylation patterns through GLP/G9a and renders prostate cancer cells susceptible to DNA demethylating agents.
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Yu W, Wu P, Wang F, Miao L, Han B, Jiang Z. Construction of Novel Methylation-Driven Gene Model and Investigation of PARVB Function in Glioblastoma. Front Oncol 2021; 11:705547. [PMID: 34568031 PMCID: PMC8461318 DOI: 10.3389/fonc.2021.705547] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/23/2021] [Indexed: 12/17/2022] Open
Abstract
Background Glioblastoma multiforme (GBM) is characterized by widespread genetic and transcriptional heterogeneity. Aberrant DNA methylation plays a vital role in GBM progression by regulating gene expression. However, little is known about the role of methylation and its association with prognosis in GBM. Our aim was to explore DNA methylation-driven genes (DMDGs) and provide evidence for survival prediction and individualized treatment of GBM patients. Methods Use of the MethylMix R package identified DMDGs in GBM. The prognostic signature of DMDGs based on the risk score was constructed by multivariate Cox regression analysis. Receiver operating characteristics (ROC) curve and C-index were applied to assess the predictive performance of the DMDG prognostic signature. The predictive ability of the multigene signature model was validated in TCGA and CGGA cohorts. Finally, the role of DMDG β-Parvin (PARVB) was explored in vitro. Results The prognostic signature of DMDGs was constructed based on six genes (MDK, NMNAT3, PDPN, PARVB, SERPINB1, and UPP1). The low-risk cohort had significantly better survival than the high-risk cohort (p < 0.001). The area under the curve of the ROC of the six-gene signature was 0.832, 0.927, and 0.980 within 1, 2, and 3 years, respectively. The C-index of 0.704 indicated superior specificity and sensitivity. The six-gene model has been demonstrated to be an independent prognostic factor for GBM. In addition, joint survival analysis indicated that the MDK, NMNAT3, PARVB, SERPINB1, and UPP1 genes were significantly associated with prognosis and therapeutic targets for GBM. Importantly, our DMDG prognostic model was more suitable and accurate for low-grade gliomas. Finally, we verified that PARVB induced epithelial-mesenchymal transition partially through the JAK2/STAT3 pathway, which in turn promoted GBM cell proliferation, migration, and invasion. Conclusion This study demonstrated the potential value of the prognostic signature of DMDGs and provided important bioinformatic and potential therapeutic target data to facilitate individualized treatment for GBM, and to elucidate the specific mechanism by which PARVB promotes GBM progression.
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Affiliation(s)
- Wanli Yu
- Department of Neurosurgery, Gaoxin Hospital of the First Affiliated Hospital of Nanchang University, Nanchang, China.,Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Pengfei Wu
- Department of Neurosurgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China.,Anhui Key Laboratory of Brain Function and Diseases, Hefei, China
| | - Fang Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Li Miao
- Central Laboratory, Gaoxin Hospital of the First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Bo Han
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhiqun Jiang
- Department of Neurosurgery, Gaoxin Hospital of the First Affiliated Hospital of Nanchang University, Nanchang, China.,Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Aoki K, Suzuki H, Yamamoto T, Yamamoto KN, Maeda S, Okuno Y, Ranjit M, Motomura K, Ohka F, Tanahashi K, Hirano M, Nishikawa T, Shimizu H, Kitano Y, Yamaguchi J, Yamazaki S, Nakamura H, Takahashi M, Narita Y, Nakada M, Deguchi S, Mizoguchi M, Momii Y, Muragaki Y, Abe T, Akimoto J, Wakabayashi T, Saito R, Ogawa S, Haeno H, Natsume A. Mathematical Modeling and Mutational Analysis Reveal Optimal Therapy to Prevent Malignant Transformation in Grade II IDH-Mutant Gliomas. Cancer Res 2021; 81:4861-4873. [PMID: 34333454 PMCID: PMC9635454 DOI: 10.1158/0008-5472.can-21-0985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/10/2021] [Accepted: 07/23/2021] [Indexed: 01/07/2023]
Abstract
Isocitrate dehydrogenase-mutant low-grade gliomas (IDHmut-LGG) grow slowly but frequently undergo malignant transformation, which eventually leads to premature death. Chemotherapy and radiotherapy treatments prolong survival, but can also induce genetic (or epigenetic) alterations involved in transformation. Here, we developed a mathematical model of tumor progression based on serial tumor volume data and treatment history of 276 IDHmut-LGGs classified by chromosome 1p/19q codeletion (IDHmut/1p19qcodel and IDHmut/1p19qnoncodel) and performed genome-wide mutational analyses, including targeted sequencing and longitudinal whole-exome sequencing data. These analyses showed that tumor mutational burden correlated positively with malignant transformation rate, and chemotherapy and radiotherapy significantly suppressed tumor growth but increased malignant transformation rate per cell by 1.8 to 2.8 times compared with before treatment. This model revealed that prompt adjuvant chemoradiotherapy prolonged malignant transformation-free survival in small IDHmut-LGGs (≤ 50 cm3). Furthermore, optimal treatment differed according to genetic alterations for large IDHmut-LGGs (> 50 cm3); adjuvant therapies delayed malignant transformation in IDHmut/1p19qnoncodel but often accelerated it in IDHmut/1p19qcodel. Notably, PI3K mutation was not associated with malignant transformation but increased net postoperative proliferation rate and decreased malignant transformation-free survival, prompting the need for adjuvant therapy in IDHmut/1p19qcodel. Overall, this model uncovered therapeutic strategies that could prevent malignant transformation and, consequently, improve overall survival in patients with IDHmut-LGGs. SIGNIFICANCE: A mathematical model successfully estimates malignant transformation-free survival and reveals a link between genetic alterations and progression, identifying precision medicine approaches for optimal treatment of IDH-mutant low-grade gliomas.
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Affiliation(s)
- Kosuke Aoki
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Aichi, Japan.,Corresponding Authors: Kosuke Aoki, Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya 4668550, Japan. Phone: 815-2744-2353; E-mail: ; Hiroshi Haeno, ; and Atsushi Natsume,
| | - Hiromichi Suzuki
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Takashi Yamamoto
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Kimiyo N. Yamamoto
- Departments of General and Gastroenterological Surgery, Osaka Medical College Hospital, Takatsuki-shi, Osaka, Japan
| | - Sachi Maeda
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Aichi, Japan.,Department of Virology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Melissa Ranjit
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Kazuya Motomura
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Kuniaki Tanahashi
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Masaki Hirano
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Tomohide Nishikawa
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Hiroyuki Shimizu
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Yotaro Kitano
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Junya Yamaguchi
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Shintaro Yamazaki
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Hideo Nakamura
- Department of Neurosurgery, Kumamoto University, Kumamoto, Japan.,Department of Neurosurgery, Kurume University, Kurume, Fukuoka, Japan
| | - Masamichi Takahashi
- Department of Neurosurgery and Neuro-oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro-oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Mitsutoshi Nakada
- Department of Neurosurgery, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shoichi Deguchi
- Division of Neurosurgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences Kyushu University, Fukuoka, Japan
| | - Yasutomo Momii
- Department of Neurosurgery, Oita University, Yufu, Oita, Japan
| | - Yoshihiro Muragaki
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Tatsuya Abe
- Department of Neurosurgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Jiro Akimoto
- Department of Neurosurgery, Tokyo Medical University, Tokyo, Japan
| | - Toshihiko Wakabayashi
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Haeno
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.,Corresponding Authors: Kosuke Aoki, Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya 4668550, Japan. Phone: 815-2744-2353; E-mail: ; Hiroshi Haeno, ; and Atsushi Natsume,
| | - Atsushi Natsume
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Aichi, Japan.,Corresponding Authors: Kosuke Aoki, Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya 4668550, Japan. Phone: 815-2744-2353; E-mail: ; Hiroshi Haeno, ; and Atsushi Natsume,
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Jenkins EPW, Finch A, Gerigk M, Triantis IF, Watts C, Malliaras GG. Electrotherapies for Glioblastoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100978. [PMID: 34292672 PMCID: PMC8456216 DOI: 10.1002/advs.202100978] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/20/2021] [Indexed: 05/08/2023]
Abstract
Non-thermal, intermediate frequency (100-500 kHz) electrotherapies present a unique therapeutic strategy to treat malignant neoplasms. Here, pulsed electric fields (PEFs) which induce reversible or irreversible electroporation (IRE) and tumour-treating fields (TTFs) are reviewed highlighting the foundations, advances, and considerations of each method when applied to glioblastoma (GBM). Several biological aspects of GBM that contribute to treatment complexity (heterogeneity, recurrence, resistance, and blood-brain barrier(BBB)) and electrophysiological traits which are suggested to promote glioma progression are described. Particularly, the biological responses at the cellular and molecular level to specific parameters of the electrical stimuli are discussed offering ways to compare these parameters despite the lack of a universally adopted physical description. Reviewing the literature, a disconnect is found between electrotherapy techniques and how they target the biological complexities of GBM that make treatment difficult in the first place. An attempt is made to bridge the interdisciplinary gap by mapping biological characteristics to different methods of electrotherapy, suggesting important future research topics and directions in both understanding and treating GBM. To the authors' knowledge, this is the first paper that attempts an in-tandem assessment of the biological effects of different aspects of intermediate frequency electrotherapy methods, thus offering possible strategies toward GBM treatment.
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Affiliation(s)
- Elise P. W. Jenkins
- Division of Electrical EngineeringDepartment of EngineeringUniversity of CambridgeCambridgeCB3 0FAUK
| | - Alina Finch
- Institute of Cancer and Genomic ScienceUniversity of BirminghamBirminghamB15 2TTUK
| | - Magda Gerigk
- Division of Electrical EngineeringDepartment of EngineeringUniversity of CambridgeCambridgeCB3 0FAUK
| | - Iasonas F. Triantis
- Department of Electrical and Electronic EngineeringCity, University of LondonLondonEC1V 0HBUK
| | - Colin Watts
- Institute of Cancer and Genomic ScienceUniversity of BirminghamBirminghamB15 2TTUK
| | - George G. Malliaras
- Division of Electrical EngineeringDepartment of EngineeringUniversity of CambridgeCambridgeCB3 0FAUK
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Khalil A, Nemer G. The potential oncogenic role of the RAS-like GTP-binding gene RIT1 in glioblastoma. Cancer Biomark 2021; 29:509-519. [PMID: 32831193 DOI: 10.3233/cbm-191264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Glioblastoma is the most common type of malignant brain tumors and the most feared cancer among adults. The poor prognosis among patients affected with this type of cancer is associated with its high-invasiveness and the lack of successful therapies. A comprehensive understanding for the early molecular mechanisms in glioblastoma would definitely enhance the diagnosis and the treatment strategies. Deregulated expression of key genes that are known to be involved in early neurogenesis could be the instigator of brain tumorigenesis. Ras Like Without CAAX 1 (RIT1) gene that encodes an unusual "orphan" GTPase protein belongs to this category of critical genes that are known to be involved in controlling sequential proliferation and differentiation of adult hippocampal neural progenitor cells. In this study, we surveyed RIT1 gene expression by in-silico approaches to determine its spatio-temporal pattern in glioblastoma. Our results revealed a significant and progressive upregulation of RIT1 mRNA levels in various publicly available datasets. RIT1 expression ranked among the top upregulated genes in glioblastoma cohorts and it correlated with poor overall survival. Genetic and epigenetic analysis of RIT1 didn't reveal any significant aberration that could underlie its deregulated expression. Yet, our results highlighted the possibility of its activity to be transcriptionally controlled by STAT3, one of the main players in the onset of glioblastoma. In conclusion, our study presented for the first time a potential oncogenic role for RIT1 in glioblastoma. Knowing that the RAS superfamily of proteins has created an evolution in the cancer field, RIT1 should be added to this list through further investigations on its possible usage as a biomarker and therapeutic target in glioblastoma.
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Affiliation(s)
- Athar Khalil
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Georges Nemer
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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47
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Xia Q, Liu L, Li Y, Zhang P, Han D, Dong L. Therapeutic Perspective of Temozolomide Resistance in Glioblastoma Treatment. Cancer Invest 2021; 39:627-644. [PMID: 34254870 DOI: 10.1080/07357907.2021.1952595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Glioblastoma (GB) is the most lethal form of primary brain neoplasm. TMZ is the first-line standard treatment, but the strong resistance constrains the efficacy in clinical use. GB contains glioma stem cells (GSCs), which contribute to TMZ resistance, promote cell survival evolvement, and repopulate the tumor mass. This review summarizes the TMZ-resistance mechanisms and discusses several potential therapies from the conservative opinion of GSC-targeted therapy orientation to the current view of TMZ resistance-aimed efficacy, which will provide an understanding of the role of heterogeneity in drug resistance and improve therapeutic efficacy in general.
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Affiliation(s)
- Qin Xia
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Liqun Liu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yang Li
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Pei Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Da Han
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Lei Dong
- School of Life Science, Beijing Institute of Technology, Beijing, China
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48
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Zhang H, Xu L, Zhong Z, Liu Y, Long Y, Zhou S. Lower-Grade Gliomas: Predicting DNA Methylation Subtyping and its Consequences on Survival with MR Features. Acad Radiol 2021; 28:e199-e208. [PMID: 32241714 DOI: 10.1016/j.acra.2020.02.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 11/26/2022]
Abstract
RATIONALE AND OBJECTIVES To explore associations between MR imaging features, DNA methylation subtyping, and survival in lower-grade gliomas (LGG). MATERIALS AND METHODS The MR data from 170 patients generated with the Cancer Imaging Archive were reviewed. The correlation was evaluated by Fisher's Exact Test, Pearson Chi-Square and binary regression analysis. Survival analysis was conducted by using time-dependent ROC analysis and the Kaplan-Meier method (the worst prognosis subgroup). RESULTS Identified were 9 (5.3%) M1-subtype, 18 (10.6%) M2-subtype, 48 (28.2%) M3-subtype, 31 (18.2%) M4-subtype and 64 (37.6%) M5-subtype. Patients with M4-subtype had the shortest median OS (49.3 vs. 28.4) months(p < 0.05). The time-dependent ROC for the M4-subtype was 0.83 (95% confidence interval 0.72-0.95) for survival at 12 months, 0.82 (95% confidence interval 0.70-0.94) for survival at 24 months, and 0.74 (95% confidence interval 0.62-0.86) for survival at 36 months. After uni- and multivariate analysis, a nomogram was built based on proportion contrast-enhanced (CE) tumor, extranodular growth, volume_cutoff_median, and location. For the prediction of M4-subtype, the nomogram showed good discrimination, with an area under the curve (AUC) of 0.886 (95% CI: 0.820-952) and was well calibrated. On multivariate logistic regression analysis, volume ≥60cm3 (OR: 0.200; p < 0.001; 95%CI: 0.048-0.834) was associated with M1-subtype (AUC: 0.690). Hemorrhage (OR: 5.443; p = 0.002; 95%CI: 1.844-16.069) and volume > median (OR: 3.256; p = 0.05; 95%CI: 0.992-10.686) were associated with M2-subtype (AUC: 0.733). Proportion CE tumor<=5% (OR: 3.968; P=0.002; 95%CI: 1.634-9.635) was associated with M3-subtype (AUC: 0.632). Poorly-defined (OR: 2.258; p = 0.05; 95%CI: 1.000-5.101) and volume > median (OR: 2.447; p = 0.01; 95%CI: 1.244-4.813) were associated with M5-subtype (AUC: 0.645). Decision curve analysis indicated predictions for all models were clinically useful. CONCLUSION This preliminary radiogenomics analysis of lower-grade gliomas demonstrated associations between MR features and DNA methylation subtyping. The shortest survival was observed in patients with M4-subtype. And we have constructed nomogram that enables more accurate predictions of M4-subtype.
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49
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Wong QHW, Li KKW, Wang WW, Malta TM, Noushmehr H, Grabovska Y, Jones C, Chan AKY, Kwan JSH, Huang QJQ, Wong GCH, Li WC, Liu XZ, Chen H, Chan DTM, Mao Y, Zhang ZY, Shi ZF, Ng HK. Molecular landscape of IDH-mutant primary astrocytoma Grade IV/glioblastomas. Mod Pathol 2021; 34:1245-1260. [PMID: 33692446 DOI: 10.1038/s41379-021-00778-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/13/2022]
Abstract
WHO 2016 classified glioblastomas into IDH-mutant and IDH-wildtype with the former having a better prognosis but there was no study on IDH-mutant primary glioblastomas only, as previous series included secondary glioblastomas. We recruited a series of 67 IDH-mutant primary glioblastomas/astrocytoma IV without a prior low-grade astrocytoma and examined them using DNA-methylation profiling, targeted sequencing, RNA sequencing and TERT promoter sequencing, and correlated the molecular findings with clinical parameters. The median OS of 39.4 months of 64 cases and PFS of 25.9 months of 57 cases were better than the survival data of IDH-wildtype glioblastomas and IDH-mutant secondary glioblastomas retrieved from datasets. The molecular features often seen in glioblastomas, such as EGFR amplification, combined +7/-10, and TERT promoter mutations were only observed in 6/53 (11.3%), 4/53 (7.5%), and 2/67 (3.0%) cases, respectively, and gene fusions were found only in two cases. The main mechanism for telomere maintenance appeared to be alternative lengthening of telomeres as ATRX mutation was found in 34/53 (64.2%) cases. In t-SNE analyses of DNA-methylation profiles, with an exceptional of one case, a majority of our cases clustered to IDH-mutant high-grade astrocytoma subclass (40/53; 75.5%) and the rest to IDH-mutant astrocytoma subclass (12/53; 22.6%). The latter was also enriched with G-CIMP high cases (12/12; 100%). G-CIMP-high status and MGMT promoter methylation were independent good prognosticators for OS (p = 0.022 and p = 0.002, respectively) and TP53 mutation was an independent poor prognosticator (p = 0.013) when correlated with other clinical parameters. Homozygous deletion of CDKN2A/B was not correlated with OS (p = 0.197) and PFS (p = 0.278). PDGFRA amplification or mutation was found in 16/59 (27.1%) of cases and was correlated with G-CIMP-low status (p = 0.010). Aside from the three well-known pathways of pathogenesis in glioblastomas, chromatin modifying and mismatch repair pathways were common aberrations (88.7% and 20.8%, respectively), the former due to high frequency of ATRX involvement. We conclude that IDH-mutant primary glioblastomas have better prognosis than secondary glioblastomas and have major molecular differences from other commoner glioblastomas. G-CIMP subgroups, MGMT promoter methylation, and TP53 mutation are useful prognostic adjuncts.
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Affiliation(s)
- Queenie Hoi-Wing Wong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Kay Ka-Wai Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wei-Wei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, USA
| | - Yura Grabovska
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Chris Jones
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Aden Ka-Yin Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Johnny Sheung-Him Kwan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Queenie Jun-Qi Huang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Gabriel Chun-Hei Wong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wen-Cai Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xian-Zhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Danny Tat-Ming Chan
- Division of Neurosurgery, Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.
| | - Zhen-Yu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Zhi-Feng Shi
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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50
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Brognaro E. The inverse paradigm and the ancestral cell of IDH-wildtype glioblastoma. Clin Transl Oncol 2021; 24:13-23. [PMID: 34152549 DOI: 10.1007/s12094-021-02663-0] [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: 03/30/2021] [Accepted: 06/04/2021] [Indexed: 11/30/2022]
Abstract
Rethinking IDH-wildtype glioblastoma through its unique features can help researchers find innovative and effective treatments. It is currently emerging that, after decades of therapeutic impasse, some traditional concepts regarding IDH-wildtype glioblastoma need to be supplemented and updated to overcome therapeutic resistance. Indeed, multiple clinical aspects and recent indirect and direct experimental data are providing evidence that the supratentorial brain parenchyma becomes entirely and quiescently micro-infiltrated long before primary tumor bulk growth. Furthermore, they are indicating that the known micro-infiltration that occurs during the IDH-wildtype glioblastoma growth and evolution is not at the origin of distant relapses. It follows that the ubiquitous supratentorial brain parenchyma micro-infiltration as a source for the development of widespread distant recurrences is actually due to the silent stage that precedes tumor growth rather than to the latter. All this implies that, in addition to the heterogeneity of the primary bulk, there is a second crucial cause of therapeutic resistance that has never hitherto been identified and challenged. In this regard, the ancestral founder cancer stem cell (CSC) appears as the key cell that can link the two causes of resistance.
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Affiliation(s)
- Enrico Brognaro
- Department of Neurosurgery, S. Maria della Misericordia Hospital, Viale Tre Martiri, 45100, Rovigo, Italy.
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