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van den Bent MJ, Franceschi E, Touat M, French PJ, Idbaih A, Lombardi G, Rudà R, Schweizer L, Capper D, Sanson M, Wesseling P, Weller M, Eoli M, Anghileri E, Bielle F, Euskirchen P, Geurts M, Wen PY, Preusser M. Updated EANO guideline on rational molecular testing of gliomas, glioneuronal, and neuronal tumors in adults for targeted therapy selection-Update 1. Neuro Oncol 2025; 27:331-337. [PMID: 39387386 PMCID: PMC11812046 DOI: 10.1093/neuonc/noae213] [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: 06/03/2024] [Indexed: 10/15/2024] Open
Abstract
The standard of care for adult patients with gliomas, glioneuronal, and neuronal tumors consists of combinations of surgery, radiotherapy, and chemotherapy. For many systemic cancers, targeted treatments are a major part of the standard treatment; however, the predictive significance of most of the targets for treatment in systemic cancer is less well-established in central nervous system tumors. In 2023 the European Association for NeuroOncology (EANO) Guideline Committee presented evidence-based recommendations for rational testing of molecular targets for targeted treatments. From all targets reviewed, only testing for BRAF V600E mutations was of proven clinical benefit; despite regulatory approvals for tumor agnostic treatment of NTRK gene fusions and high tumor mutational burden (TMB) for patients with adult brain tumors, the evidence of clinical benefit for adult patients was still limited. This guideline has a modular structure, allowing regular updating of individual sections and adding new ones. The present version (Update 1) presents a review of the rationale of testing for PTEN, H3F3A, MTAP, RET and IDH, and presents an update of the text on TMB high and mismatch repair deficiency. It also presents an overview of the therapeutic yield of routine next-generation sequencing for mutations and fusion detection. The Supplemental File II accompanying this version contains an in-depth review of all targets, whereas, in the main manuscript, the final recommendations of the revised and new targets are presented. Updates will be made on a regular basis.
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Affiliation(s)
- Martin J van den Bent
- Brain Tumor Center at Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Enrico Franceschi
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, AUSL di Bologna, Via Altura 3, Bologna, Italy
| | - Mehdi Touat
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neuro-oncologie, Paris, France
| | - Pim J French
- Brain Tumor Center at Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ahmed Idbaih
- Sorbonne Université, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpitaux Universitaires La Pitié Salpêtière - Charles Foix, DMU Neurosciences, Service de Neuro-Oncologie, Paris, France
| | | | - Roberta Rudà
- Division of Neuro-Oncology, Department of Neuroscience, University of Turin, Turin, Italy
| | - Leonille Schweizer
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - David Capper
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marc Sanson
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neuro-oncologie, Paris, France
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Marica Eoli
- Sperimental Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo BestaMilan, Italy
| | - Elena Anghileri
- Neuro-oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo BestaMilan, Italy
| | - Franck Bielle
- Sorbonne Université, AP-HP, Institut–du Cerveau - Paris Brai– Institute - ICM, Inserm, CNRS, Hôpitaux Universitaires La Pitié –Salpêtrière - Charles Foix, DMU Neurosciences, Département de Neuropathologie, Paris, France
| | - Phillipp Euskirchen
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marjolein Geurts
- Brain Tumor Center at Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Patrick Y Wen
- Center For Neuro-Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Matthias Preusser
- Division of Oncology, Department of Medicine 1, Medical University, Vienna, Austria
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Barateiro LGRP, de Oliveira Cavagna R, dos Reis MB, de Paula FE, Teixeira GR, Moreno DA, Bonatelli M, Santana I, Saggioro FP, Neder L, Stavale JN, Malheiros SMF, Garcia‐Rivello H, Christiansen S, Nunes S, da Costa MJG, Pinheiro J, Júnior CA, Mançano BM, Reis RM. Somatic mutational profiling and clinical impact of driver genes in Latin-Iberian medulloblastomas: Towards precision medicine. Neuropathology 2025; 45:30-37. [PMID: 38736183 PMCID: PMC11788001 DOI: 10.1111/neup.12979] [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: 01/29/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/14/2024]
Abstract
Medulloblastoma (MB) is the most prevalent malignant brain tumor in children, known for its heterogeneity and treatment-associated toxicity, and there is a critical need for new therapeutic targets. We analyzed the somatic mutation profile of 15 driver genes in 69 Latin-Iberian molecularly characterized medulloblastomas using the Illumina TruSight Tumor 15 panel. We classified the variants based on their clinical impact and oncogenicity. Among the patients, 66.7% were MBSHH, 13.0% MBWNT, 7.3% MBGrp3, and 13.0% MBGrp4. Among the 63 variants found, 54% were classified as Tier I/II and 31.7% as oncogenic/likely oncogenic. We observed 33.3% of cases harboring at least one mutation. TP53 (23.2%, 16/69) was the most mutated gene, followed by PIK3CA (5.8%, 4/69), KIT (4.3%, 3/69), PDGFRA (2.9%, 2/69), EGFR (1.4%, 1/69), ERBB2 (1.4%, 1/69), and NRAS (1.4%, 1/69). Approximately 41% of MBSHH tumors exhibited mutations, TP53 (32.6%) being the most frequently mutated gene. Tier I/II and oncogenic/likely oncogenic TP53 variants were associated with relapse, progression, and lower survival rates. Potentially actionable variants in the PIK3CA and KIT genes were identified. Latin-Iberian medulloblastomas, particularly the MBSHH, exhibit higher mutation frequencies than other populations. We corroborate the TP53 mutation status as an important prognostic factor, while PIK3CA and KIT are potential therapeutic targets.
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Affiliation(s)
| | | | | | | | - Gustavo Ramos Teixeira
- Molecular Diagnostic LaboratoryBarretos Cancer HospitalBarretosBrazil
- Department of PathologyBarretos Cancer HospitalBarretosBrazil
| | | | - Murilo Bonatelli
- Molecular Diagnostic LaboratoryBarretos Cancer HospitalBarretosBrazil
| | - Iara Santana
- Department of PathologyBarretos Cancer HospitalBarretosBrazil
| | | | - Luciano Neder
- Ribeirão Preto Medical SchoolUniversity of São PauloSão PauloBrazil
| | | | | | | | | | | | | | | | | | | | - Rui Manuel Reis
- Molecular Oncology Research CenterBarretos Cancer HospitalBarretosBrazil
- Molecular Diagnostic LaboratoryBarretos Cancer HospitalBarretosBrazil
- Life and Health Sciences Research Institute (ICVS), Medical SchoolUniversity of MinhoBragaPortugal
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3
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Weller J, Potthoff A, Zeyen T, Schaub C, Duffy C, Schneider M, Herrlinger U. Current status of precision oncology in adult glioblastoma. Mol Oncol 2024; 18:2927-2950. [PMID: 38899374 PMCID: PMC11619805 DOI: 10.1002/1878-0261.13678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/05/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The concept of precision oncology, the application of targeted drugs based on comprehensive molecular profiling, has revolutionized treatment strategies in oncology. This review summarizes the current status of precision oncology in glioblastoma (GBM), the most common and aggressive primary brain tumor in adults with a median survival below 2 years. Targeted treatments without prior target verification have consistently failed. Patients with BRAF V600E-mutated GBM benefit from BRAF/MEK-inhibition, whereas targeting EGFR alterations was unsuccessful due to poor tumor penetration, tumor cell heterogeneity, and pathway redundancies. Systematic screening for actionable molecular alterations resulted in low rates (< 10%) of targeted treatments. Efficacy was observed in one-third and currently appears to be limited to BRAF-, VEGFR-, and mTOR-directed treatments. Advancing precision oncology for GBM requires consideration of pathways instead of single alterations, new trial concepts enabling rapid and adaptive drug evaluation, a focus on drugs with sufficient bioavailability in the CNS, and the extension of target discovery and validation to the tumor microenvironment, tumor cell networks, and their interaction with immune cells and neurons.
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Affiliation(s)
- Johannes Weller
- Department of Neurooncology, Center for NeurologyUniversity Hospital BonnGermany
| | | | - Thomas Zeyen
- Department of Neurooncology, Center for NeurologyUniversity Hospital BonnGermany
| | - Christina Schaub
- Department of Neurooncology, Center for NeurologyUniversity Hospital BonnGermany
| | - Cathrina Duffy
- Department of Neurooncology, Center for NeurologyUniversity Hospital BonnGermany
| | | | - Ulrich Herrlinger
- Department of Neurooncology, Center for NeurologyUniversity Hospital BonnGermany
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Choate KA, Pratt EPS, Jennings MJ, Winn RJ, Mann PB. IDH Mutations in Glioma: Molecular, Cellular, Diagnostic, and Clinical Implications. BIOLOGY 2024; 13:885. [PMID: 39596840 PMCID: PMC11592129 DOI: 10.3390/biology13110885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 10/21/2024] [Accepted: 10/28/2024] [Indexed: 11/29/2024]
Abstract
In 2021, the World Health Organization classified isocitrate dehydrogenase (IDH) mutant gliomas as a distinct subgroup of tumors with genetic changes sufficient to enable a complete diagnosis. Patients with an IDH mutant glioma have improved survival which has been further enhanced by the advent of targeted therapies. IDH enzymes contribute to cellular metabolism, and mutations to specific catalytic residues result in the neomorphic production of D-2-hydroxyglutarate (D-2-HG). The accumulation of D-2-HG results in epigenetic alterations, oncogenesis and impacts the tumor microenvironment via immunological modulations. Here, we summarize the molecular, cellular, and clinical implications of IDH mutations in gliomas as well as current diagnostic techniques.
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Affiliation(s)
- Kristian A. Choate
- Upper Michigan Brain Tumor Center, Northern Michigan University, Marquette, MI 49855, USA; (K.A.C.); (E.P.S.P.); (M.J.J.); (R.J.W.)
| | - Evan P. S. Pratt
- Upper Michigan Brain Tumor Center, Northern Michigan University, Marquette, MI 49855, USA; (K.A.C.); (E.P.S.P.); (M.J.J.); (R.J.W.)
- Department of Chemistry, Northern Michigan University, Marquette, MI 49855, USA
| | - Matthew J. Jennings
- Upper Michigan Brain Tumor Center, Northern Michigan University, Marquette, MI 49855, USA; (K.A.C.); (E.P.S.P.); (M.J.J.); (R.J.W.)
- School of Clinical Sciences, Northern Michigan University, Marquette, MI 49855, USA
| | - Robert J. Winn
- Upper Michigan Brain Tumor Center, Northern Michigan University, Marquette, MI 49855, USA; (K.A.C.); (E.P.S.P.); (M.J.J.); (R.J.W.)
- Department of Biology, Northern Michigan University, Marquette, MI 49855, USA
| | - Paul B. Mann
- Upper Michigan Brain Tumor Center, Northern Michigan University, Marquette, MI 49855, USA; (K.A.C.); (E.P.S.P.); (M.J.J.); (R.J.W.)
- School of Clinical Sciences, Northern Michigan University, Marquette, MI 49855, USA
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5
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Nakashima T, Yamamoto R, Ohno M, Sugino H, Takahashi M, Funakoshi Y, Nambu S, Uneda A, Yanagisawa S, Uzuka T, Arakawa Y, Hanaya R, Ishida J, Yoshimoto K, Saito R, Narita Y, Suzuki H. Development of a rapid and comprehensive genomic profiling test supporting diagnosis and research for gliomas. Brain Tumor Pathol 2024; 41:50-60. [PMID: 38332448 DOI: 10.1007/s10014-023-00476-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/25/2023] [Indexed: 02/10/2024]
Abstract
A prompt and reliable molecular diagnosis for brain tumors has become crucial in precision medicine. While Comprehensive Genomic Profiling (CGP) has become feasible, there remains room for enhancement in brain tumor diagnosis due to the partial lack of essential genes and limitations in broad copy number analysis. In addition, the long turnaround time of commercially available CGPs poses an additional obstacle to the timely implementation of results in clinics. To address these challenges, we developed a CGP encompassing 113 genes, genome-wide copy number changes, and MGMT promoter methylation. Our CGP incorporates not only diagnostic genes but also supplementary genes valuable for research. Our CGP enables us to simultaneous identification of mutations, gene fusions, focal and broad copy number alterations, and MGMT promoter methylation status, with results delivered within a minimum of 4 days. Validation of our CGP, through comparisons with whole-genome sequencing, RNA sequencing, and pyrosequencing, has certified its accuracy and reliability. We applied our CGP for 23 consecutive cases of intracranial mass lesions, which demonstrated its efficacy in aiding diagnosis and prognostication. Our CGP offers a comprehensive and rapid molecular profiling for gliomas, which could potentially apply to clinical practices and research primarily in the field of brain tumors.
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Affiliation(s)
- Takuma Nakashima
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
- Department of Neurosurgery, Nagoya University School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Ryo Yamamoto
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
- Department of Neurosurgery, Nagoya University School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Makoto Ohno
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Hirokazu Sugino
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Masamichi Takahashi
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Yusuke Funakoshi
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Shohei Nambu
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Atsuhito Uneda
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Shunsuke Yanagisawa
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Takeo Uzuka
- Department of Neurosurgery, Dokkyo Medical University, 880 Kitakobaya-Shi, Mibu, Shimotsuga-Gun, Tochigi, 321-0293, Japan
| | - Yoshiki Arakawa
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, 54 Kawahara-Cho Shogoin Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Ryosuke Hanaya
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1, Sakuragaoka, Kagoshima, 890-8544, Japan
| | - Joji Ishida
- Department of Neurosurgery, Okayama University Graduate School of Medicine, 2-5-1 Shikata-Cho, Kita-Ku, Okayama, 700-8558, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Science, Kyushu University, 3-1-1, Maidashi, Higashi-Ku, Fukuoka City, 812-8582, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan.
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Bertero L, Mangherini L, Ricci AA, Cassoni P, Sahm F. Molecular neuropathology: an essential and evolving toolbox for the diagnosis and clinical management of central nervous system tumors. Virchows Arch 2024; 484:181-194. [PMID: 37658995 PMCID: PMC10948579 DOI: 10.1007/s00428-023-03632-4] [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: 06/15/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023]
Abstract
Molecular profiling has transformed the diagnostic workflow of CNS tumors during the last years. The latest WHO classification of CNS tumors (5th edition), published in 2021, pushed forward the integration between histopathological features and molecular hallmarks to achieve reproducible and clinically relevant diagnoses. To address these demands, pathologists have to appropriately deal with multiple molecular assays mainly including DNA methylation profiling and DNA/RNA next generation sequencing. Tumor classification by DNA methylation profiling is now a critical tool for many diagnostic tasks in neuropathology including the assessment of complex cases, to evaluate novel tumor types and to perform tumor subgrouping in hetereogenous entities like medulloblastoma or ependymoma. DNA/RNA NGS allow the detection of multiple molecular alterations including single nucleotide variations, small insertions/deletions (InDel), and gene fusions. These molecular markers can provide key insights for diagnosis, for example, if a tumor-specific mutation is detected, but also for treatment since targeted therapies are progressively entering the clinical practice. In the present review, a brief, but comprehensive overview of these tools will be provided, discussing their technical specifications, diagnostic value, and potential limitations. Moreover, the importance of molecular profiling will be shown in a representative series of CNS neoplasms including both the most frequent tumor types and other selected entities for which molecular characterization plays a critical role.
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Affiliation(s)
- Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin and Città Della Salute E Della Scienza University Hospital, Via Santena 7, 10126, Turin, Italy
| | - Luca Mangherini
- Pathology Unit, Department of Medical Sciences, University of Turin and Città Della Salute E Della Scienza University Hospital, Via Santena 7, 10126, Turin, Italy
| | - Alessia Andrea Ricci
- Pathology Unit, Department of Medical Sciences, University of Turin and Città Della Salute E Della Scienza University Hospital, Via Santena 7, 10126, Turin, Italy
| | - Paola Cassoni
- Pathology Unit, Department of Medical Sciences, University of Turin and Città Della Salute E Della Scienza University Hospital, Via Santena 7, 10126, Turin, Italy
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, Im Neuenheimer Feld 672, 69120, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
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7
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van Opijnen MP, Broekman MLD, Cuppen E, Dubbink HJ, Ter Elst A, van Eijk R, Mühlebner A, Jansen C, van der Geize R, Speel EJM, Groenen PJTA, de Vos FYF, Wesseling P, de Leng WWJ, Maas SLN. Next generation sequencing of high-grade adult-type diffuse glioma in the Netherlands: interlaboratory variation in the primary diagnostic and recurrent setting. J Neurooncol 2024; 166:485-492. [PMID: 38285243 PMCID: PMC10876806 DOI: 10.1007/s11060-024-04568-8] [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: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024]
Abstract
PURPOSE Next generation sequencing (NGS) is an important tool used in clinical practice to obtain the required molecular information for accurate diagnostics of high-grade adult-type diffuse glioma (HGG). Since individual centers use either in-house produced or standardized panels, interlaboratory variation could play a role in the practice of HGG diagnosis and treatment. This study aimed to investigate the current practice in NGS application for both primary and recurrent HGG. METHODS This nationwide Dutch survey used the expertise of (neuro)pathologists and clinical scientists in molecular pathology (CSMPs) by sending online questionnaires on clinical and technical aspects. Primary outcome was an overview of panel composition in the different centers for diagnostic practice of HGG. Secondary outcomes included practice for recurrent HGG and future perspectives. RESULTS Out of twelve neuro-oncology centers, the survey was filled out by eleven (neuro)pathologists and seven CSMPs. The composition of the diagnostic NGS panels differed in each center with numbers of genes ranging from 12 to 523. Differences are more pronounced when tests are performed to find therapeutic targets in the case of recurrent disease: about half of the centers test for gene fusions (60%) and tumor mutational burden (40%). CONCLUSION Current notable interlaboratory variations as illustrated in this study should be reduced in order to refine diagnostics and improve precision oncology. In-house developed tests, standardized panels and routine application of broad gene panels all have their own advantages and disadvantages. Future research would be of interest to study the clinical impact of variation in diagnostic approaches.
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Affiliation(s)
- Mark P van Opijnen
- Department of Neurosurgery, Haaglanden Medical Center, The Hague, The Netherlands.
- Department of Neurosurgery, Leiden University Medical Center, Leiden, The Netherlands.
| | - Marike L D Broekman
- Department of Neurosurgery, Haaglanden Medical Center, The Hague, The Netherlands
- Department of Neurosurgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Arja Ter Elst
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Angelika Mühlebner
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Casper Jansen
- Laboratorium Pathologie Oost-Nederland, Hengelo, The Netherlands
| | | | - Ernst-Jan M Speel
- Department of Pathology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | - Filip Y F de Vos
- Department of Medical Oncology, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Pieter Wesseling
- Department of Pathology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sybren L N Maas
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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8
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Kim T, Lee A, Ahn S, Park JS, Jeun SS, Lee YS. Comprehensive Molecular Genetic Analysis in Glioma Patients by Next Generation Sequencing. Brain Tumor Res Treat 2024; 12:23-39. [PMID: 38317486 PMCID: PMC10864139 DOI: 10.14791/btrt.2023.0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/16/2023] [Accepted: 11/10/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Glioma is caused by multiple genomic alterations. The evolving classification of gliomas emphasizes the significance of molecular testing. Next generation sequencing (NGS) offers the assessment of parallel combinations of multiple genetic alterations and identifying actionable mutations that guide treatment. This study comprehensively analyzed glioma patients using multi-gene NGS panels, providing powerful insights to inform diagnostic classification and targeted therapies. METHODS We conducted a targeted panel-based NGS analysis on formalin-fixed and paraffin-embedded nucleic acids extracted from a total of 147 glioma patients. These samples underwent amplicon capture-based library preparation and sequenced using the Oncomine Comprehensive Assay platform. The resulting sequencing data were then analyzed using the bioinformatics tools. RESULTS A total of 301 mutations, were found in 132 out of 147 tumors (89.8%). These mutations were in 68 different genes. In 62 tumor samples (42.2%), copy number variations (CNVs) with gene amplifications occurred in 25 genes. Moreover, 25 tumor samples (17.0%) showed gene fusions in 6 genes and intragenic deletion in a gene. Our analysis identified actionable targets in several genes, including 11 with mutations, 8 with CNVs, and 3 with gene fusions and intragenic deletion. These findings could impact FDA-approved therapies, NCCN guideline-based treatments, and clinical trials. CONCLUSION We analyzed precisely diagnosing the classification of gliomas, detailing the frequency and co-occurrence of genetic alterations and identifying genetic alterations with potential therapeutic targets by NGS-based molecular analysis. The high-throughput NGS analysis is an efficient and powerful tool to comprehensively support molecular testing in neurooncology.
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Affiliation(s)
- Taeeun Kim
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahwon Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Stephan Ahn
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae Sung Park
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sin Soo Jeun
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Youn Soo Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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Penkova A, Kuziakova O, Gulaia V, Tiasto V, Goncharov NV, Lanskikh D, Zhmenia V, Baklanov I, Farniev V, Kumeiko V. Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects. Front Mol Biosci 2023; 10:1216102. [PMID: 37908227 PMCID: PMC10613994 DOI: 10.3389/fmolb.2023.1216102] [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: 06/08/2023] [Accepted: 09/04/2023] [Indexed: 11/02/2023] Open
Abstract
Glioma is one of the most intractable types of cancer, due to delayed diagnosis at advanced stages. The clinical symptoms of glioma are unclear and due to a variety of glioma subtypes, available low-invasive testing is not effective enough to be introduced into routine medical laboratory practice. Therefore, recent advances in the clinical diagnosis of glioma have focused on liquid biopsy approaches that utilize a wide range of techniques such as next-generation sequencing (NGS), droplet-digital polymerase chain reaction (ddPCR), and quantitative PCR (qPCR). Among all techniques, NGS is the most advantageous diagnostic method. Despite the rapid cheapening of NGS experiments, the cost of such diagnostics remains high. Moreover, high-throughput diagnostics are not appropriate for molecular profiling of gliomas since patients with gliomas exhibit only a few diagnostic markers. In this review, we highlighted all available assays for glioma diagnosing for main pathogenic glioma DNA sequence alterations. In the present study, we reviewed the possibility of integrating routine molecular methods into the diagnosis of gliomas. We state that the development of an affordable assay covering all glioma genetic aberrations could enable early detection and improve patient outcomes. Moreover, the development of such molecular diagnostic kits could potentially be a good alternative to expensive NGS-based approaches.
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Affiliation(s)
- Alina Penkova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Olga Kuziakova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Gulaia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vladlena Tiasto
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Nikolay V. Goncharov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Daria Lanskikh
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Zhmenia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Ivan Baklanov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Vladislav Farniev
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vadim Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
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10
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Braun FK, Rothhammer-Hampl T, Lorenz J, Pohl S, Menevse AN, Vollmann-Zwerenz A, Bumes E, Büttner M, Zoubaa S, Proescholdt M, Schmidt NO, Hau P, Beckhove P, Winner B, Riemenschneider MJ. Scaffold-Based (Matrigel™) 3D Culture Technique of Glioblastoma Recovers a Patient-like Immunosuppressive Phenotype. Cells 2023; 12:1856. [PMID: 37508520 PMCID: PMC10378658 DOI: 10.3390/cells12141856] [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: 06/02/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Conventional 2D cultures are commonly used in cancer research though they come with limitations such as the lack of microenvironment or reduced cell heterogeneity. In this study, we investigated in what respect a scaffold-based (Matrigel™) 3D culture technique can ameliorate the limitations of 2D cultures. NGS-based bulk and single-cell sequencing of matched pairs of 2D and 3D models showed an altered transcription of key immune regulatory genes in around 36% of 3D models, indicating the reoccurrence of an immune suppressive phenotype. Changes included the presentation of different HLA surface molecules as well as cellular stressors. We also investigated the 3D tumor organoids in a co-culture setting with tumor-infiltrating lymphocytes (TILs). Of note, lymphocyte-mediated cell killing appeared less effective in clearing 3D models than their 2D counterparts. IFN-γ release, as well as live cell staining and proliferation analysis, pointed toward an elevated resistance of 3D models. In conclusion, we found that the scaffold-based (Matrigel™) 3D culture technique affects the transcriptional profile in a subset of GBM models. Thus, these models allow for depicting clinically relevant aspects of tumor-immune interaction, with the potential to explore immunotherapeutic approaches in an easily accessible in vitro system.
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Affiliation(s)
- Frank K Braun
- Department of Neuropathology, Regensburg University Hospital, 93053 Regensburg, Germany
| | | | - Julia Lorenz
- Department of Neuropathology, Regensburg University Hospital, 93053 Regensburg, Germany
| | - Sandra Pohl
- Department of Neuropathology, Regensburg University Hospital, 93053 Regensburg, Germany
| | - Ayse-Nur Menevse
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany
| | - Arabel Vollmann-Zwerenz
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, Regensburg University Hospital, 93053 Regensburg, Germany
| | - Elisabeth Bumes
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, Regensburg University Hospital, 93053 Regensburg, Germany
| | - Maren Büttner
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Munich, Germany
| | - Saida Zoubaa
- Department of Neuropathology, Regensburg University Hospital, 93053 Regensburg, Germany
| | - Martin Proescholdt
- Department of Neurosurgery, Regensburg University Hospital, 93053 Regensburg, Germany
| | - Nils O Schmidt
- Department of Neurosurgery, Regensburg University Hospital, 93053 Regensburg, Germany
| | - Peter Hau
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, Regensburg University Hospital, 93053 Regensburg, Germany
| | - Philipp Beckhove
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Beate Winner
- Department of Stem Cell Biology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
- IZKF Junior Research Group 3 and BMBF Research Group Neuroscience, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
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11
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Guarnaccia M, Guarnaccia L, La Cognata V, Navone SE, Campanella R, Ampollini A, Locatelli M, Miozzo M, Marfia G, Cavallaro S. A Targeted Next-Generation Sequencing Panel to Genotype Gliomas. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070956. [PMID: 35888045 PMCID: PMC9320073 DOI: 10.3390/life12070956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/12/2022]
Abstract
Gliomas account for the majority of primary brain tumors. Glioblastoma is the most common and malignant type. Based on their extreme molecular heterogeneity, molecular markers can be used to classify gliomas and stratify patients into diagnostic, prognostic, and therapeutic clusters. In this work, we developed and validated a targeted next-generation sequencing (NGS) approach to analyze variants or chromosomal aberrations correlated with tumorigenesis and response to treatment in gliomas. Our targeted NGS analysis covered 13 glioma-related genes (ACVR1, ATRX, BRAF, CDKN2A, EGFR, H3F3A, HIST1H3B, HIST1H3C, IDH1, IDH2, P53, PDGFRA, PTEN), a 125 bp region of the TERT promoter, and 54 single nucleotide polymorphisms (SNPs) along chromosomes 1 and 19 for reliable assessment of their copy number alterations (CNAs). Our targeted NGS approach provided a portrait of gliomas’ molecular heterogeneity with high accuracy, specificity, and sensitivity in a single workflow, enabling the detection of variants associated with unfavorable outcomes, disease progression, and drug resistance. These preliminary results support its use in routine diagnostic neuropathology.
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Affiliation(s)
- Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, Italy; (M.G.); (V.L.C.)
| | - Laura Guarnaccia
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
- Department of Clinical Sciences and Community Health, University of Milan, Via Festa del Perdono 7, 20122 Milan, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, Italy; (M.G.); (V.L.C.)
| | - Stefania Elena Navone
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
| | - Rolando Campanella
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
| | - Antonella Ampollini
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
| | - Marco Locatelli
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
- “Aldo Ravelli” Research Center, Via Antonio di Rudinì 8, 20142 Milan, Italy
- Department of Medical-Surgical Physiopathology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Monica Miozzo
- Department of Health Sciences, University of Milan, 20122 Milan, Italy;
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milan, Italy
| | - Giovanni Marfia
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
- Clinical Pathology Unit, Aerospace Medicine Institute “A. Mosso”, Italian Air Force, Viale dell’Aviazione 1, 20138 Milan, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, Italy; (M.G.); (V.L.C.)
- Correspondence: ; Tel.: +39-09-57338128
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12
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Chan AKY, Shi ZF, Li KKW, Wang WW, Chen H, Chung NYF, Chan DTM, Poon WS, Loong HHF, Liu XZ, Zhang ZY, Mao Y, Ng HK. Combinations of Single-Gene Biomarkers Can Precisely Stratify 1,028 Adult Gliomas for Prognostication. Front Oncol 2022; 12:839302. [PMID: 35558510 PMCID: PMC9090434 DOI: 10.3389/fonc.2022.839302] [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: 12/19/2021] [Accepted: 03/04/2022] [Indexed: 11/23/2022] Open
Abstract
Advanced genomic techniques have now been incorporated into diagnostic practice in neuro-oncology in the literature. However, these assays are expensive and time-consuming and demand bioinformatics expertise for data interpretation. In contrast, single-gene tests can be run much more cheaply, with a short turnaround time, and are available in general pathology laboratories. The objective of this study was to establish a molecular grading scheme for adult gliomas using combinations of commonly available single-gene tests. We retrospectively evaluated molecular diagnostic data of 1,275 cases of adult diffuse gliomas from three institutions where we were testing for IDH1/2 mutation, TERTp mutation, 1p19q codeletion, EGFR amplification, 10q deletion, BRAF V600E, and H3 mutations liberally in our regular diagnostic workup. We found that a molecular grading scheme of Group 1 (1p19q codeleted, IDH mutant), Group 2 (IDH mutant, 1p19q non-deleted, TERT mutant), Group 3 (IDH mutant, 1p19q non-deleted, TERT wild type), Group 4 (IDH wild type, BRAF mutant), Group 5 (IDH wild type, BRAF wild type and not possessing the criteria of Group 6), and Group 6 (IDH wild type, and any one of TERT mutant, EGFR amplification, 10q deletion, or H3 mutant) could significantly stratify this large cohort of gliomas for risk. A total of 1,028 (80.6%) cases were thus classifiable with sufficient molecular data. There were 270 cases of molecular Group 1, 59 cases of molecular Group 2, 248 cases of molecular Group 3, 27 cases of molecular Group 4, 117 cases of molecular Group 5, and 307 cases of molecular Group 6. The molecular groups were independent prognosticators by multivariate analyses and in specific instances, superseded conventional histological grades. We were also able to validate the usefulness of the Groups with a cohort retrieved from The Cancer Genome Atlas (TCGA) where similar molecular tests were liberally available. We conclude that a single-gene molecular stratification system, useful for fine prognostication, is feasible and can be adopted by a general pathology laboratory.
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Affiliation(s)
- Aden Ka-Yin Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, Hong Kong SAR, China
| | - Zhi-Feng Shi
- Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, Hong Kong SAR, China.,Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Kay Ka-Wai Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, Hong Kong SAR, China
| | - Wei-Wei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Nellie Yuk-Fei Chung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Danny Tat-Ming Chan
- Division of Neurosurgery, Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wai-Sang Poon
- Division of Neurosurgery, Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Herbert Ho-Fung Loong
- Department of Clinical Oncology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xian-Zhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhen-Yu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Mao
- Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, Hong Kong SAR, China.,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.,Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, Hong Kong SAR, China
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13
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Next generation sequencing in adult patients with glioblastoma in Switzerland: a multi-centre decision analysis. J Neurooncol 2022; 158:359-367. [PMID: 35486306 DOI: 10.1007/s11060-022-04022-7] [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: 03/07/2022] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Glioblastoma is the most common malignant primary brain tumour in adults and driven by various genomic alterations. Next generation sequencing (NGS) provides timely information about the genetic landscape of tumours and might detect targetable mutations. To date, differences exist in the application and NGS assays used as it remains unclear to what extent these variants may affect clinical decision making. In this survey-based study, we investigated the use of NGS in adult patients with glioblastoma in Switzerland. METHODS All eight primary care centres for Neuro-Oncology in Switzerland participated in this survey. The NGS assays used as well as the criteria for the application of NGS in newly diagnosed glioblastoma were investigated. Decision trees were analysed for consensus and discrepancies using the objective consensus methodology. RESULTS Seven out of eight centres perform NGS in patients with newly diagnosed glioblastoma using custom made or commercially available assays. The criteria most relevant to decision making were age, suitability of standard treatment and fitness. NGS is most often used in fitter patients under the age of 60 years who are not suitable for standard therapy, while it is rarely performed in patients in poor general health. CONCLUSION NGS is frequently applied in glioblastomas in adults in Neuro-Oncology centres in Switzerland despite seldom changing the course of treatment to date.
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14
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Alammar H, Nassani R, Alshehri MM, Aljohani AA, Alrfaei BM. Deficiency in the Treatment Description of mTOR Inhibitor Resistance in Medulloblastoma, a Systematic Review. Int J Mol Sci 2021; 23:ijms23010464. [PMID: 35008889 PMCID: PMC8745694 DOI: 10.3390/ijms23010464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/19/2021] [Accepted: 12/30/2021] [Indexed: 01/01/2023] Open
Abstract
Medulloblastoma is a common fatal pediatric brain tumor. More treatment options are required to prolong survival and decrease disability. mTOR proteins play an essential role in the disease pathogenesis, and are an essential target for therapy. Three generations of mTOR inhibitors have been developed and are clinically used for immunosuppression and chemotherapy for multiple cancers. Only a few mTOR inhibitors have been investigated for the treatment of medulloblastoma and other pediatric tumors. The first-generation mTOR, sirolimus, temsirolimus, and everolimus, went through phase I clinical trials. The second-generation mTOR, AZD8055 and sapanisertib, suppressed medulloblastoma cell growth; however, limited studies have investigated possible resistance pathways. No clinical trials have been found to treat medulloblastoma using third-generation mTOR inhibitors. This systematic review highlights the mechanisms of resistance of mTOR inhibitors in medulloblastoma and includes IDO1, T cells, Mnk2, and eIF4E, as they prolong malignant cell survival. The findings promote the importance of combination therapy in medulloblastoma due to its highly resistant nature.
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Affiliation(s)
- Hajar Alammar
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh 11426, Saudi Arabia; (H.A.); (A.A.A.)
| | - Rayan Nassani
- King Abdullah International Medical Research Center, Department of Cellular Therapy and Cancer Research, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard-Health Affairs, Riyadh 11426, Saudi Arabia; (R.N.); (M.M.A.)
| | - Mana M. Alshehri
- King Abdullah International Medical Research Center, Department of Cellular Therapy and Cancer Research, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard-Health Affairs, Riyadh 11426, Saudi Arabia; (R.N.); (M.M.A.)
| | - Alaa A. Aljohani
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh 11426, Saudi Arabia; (H.A.); (A.A.A.)
| | - Bahauddeen M. Alrfaei
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh 11426, Saudi Arabia; (H.A.); (A.A.A.)
- King Abdullah International Medical Research Center, Department of Cellular Therapy and Cancer Research, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard-Health Affairs, Riyadh 11426, Saudi Arabia; (R.N.); (M.M.A.)
- Correspondence:
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15
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González-Tablas M, Prieto C, Arandia D, Jara-Acevedo M, Otero Á, Pascual D, Ruíz L, Álvarez-Twose I, García-Montero AC, Orfao A, Tabernero MD. Whole-Exome Sequencing Reveals Recurrent but Heterogeneous Mutational Profiles in Sporadic WHO Grade 1 Meningiomas. Front Oncol 2021; 11:740782. [PMID: 34868937 PMCID: PMC8635692 DOI: 10.3389/fonc.2021.740782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/27/2021] [Indexed: 01/08/2023] Open
Abstract
Human WHO grade 1 meningiomas are generally considered benign tumors; despite this, they account for ≈50% of all recurrent meningiomas. Currently, limited data exist about the mutational profiles of grade 1 meningiomas and patient outcome. We investigated the genetic variants present in 32 WHO grade 1 meningiomas using whole exome sequencing, and correlated gene mutational profiles with tumor cytogenetics and patient outcome. Overall, WHO grade 1 meningiomas harbored numerous and heterogeneous genetic variants, which most frequently affected the NF2 (47%) gene and to a less extent the PNMA6A (22%), TIGD1 (16%), SMO (13%), PTEN (13%), CREG2 (9%), EEF1A1 (6%), POLR2A (6%), ARID1B (3%), and FAIM3 (3%) genes. Notably, non-synonymous genetic variants of SMO and POLR2A were restricted to diploid meningiomas, whereas NF2 mutations were only found among tumors that showed -22/22q─ (with or without a complex karyotype). Based on NF2 mutations and tumor cytogenetics, four genetic profiles were defined with an impact on patient recurrence-free survival (RFS). These included (1) two good-prognosis tumor subgroups-diploid meningiomas (n=9) and isolated -22/22q─ associated with NF2 mutation (n=7)-with RFS rates at 10 y of 100%; and (2) two subgroups of poor-prognosis meningiomas-isolated -22/22q─ without NF2 mutation (n=3) and tumors with complex karyotypes (n=11)-with a RFS rate at 10 y of 48% (p=0.003). Our results point out the existence of recurrent but heterogeneous mutational profiles in WHO grade 1 meningiomas which have an impact on patient outcome.
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Affiliation(s)
- María González-Tablas
- Instituto de Investigación Biomédica de Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Centre for Cancer Research (Centro de Investigación del Cáncer de Salamanca (CIC)-Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Centro Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca (USAL), IBSAL) and Department of Medicine, University of Salamanca, Salamanca, Spain.,Biomedical Research Networking Centre on Cancer- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) (CB16/12/00400), Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Prieto
- Instituto de Investigación Biomédica de Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Bioinformatics Service Servicio de Apoyo a la Investigación de la Universidad de Salamanca (NUNCLEUS), University of Salamanca, Salamanca, Spain
| | - Daniel Arandia
- Instituto de Investigación Biomédica de Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Neurosurgery Service, University Hospital of Salamanca, Salamanca, Spain
| | - María Jara-Acevedo
- Instituto de Investigación Biomédica de Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Sequencing Service Servicio de Apoyo a la Investigación de la Universidad de Salamanca (NUNCLEUS), University of Salamanca, Salamanca, Spain
| | - Álvaro Otero
- Instituto de Investigación Biomédica de Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Neurosurgery Service, University Hospital of Salamanca, Salamanca, Spain
| | - Daniel Pascual
- Instituto de Investigación Biomédica de Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Neurosurgery Service, University Hospital of Salamanca, Salamanca, Spain
| | - Laura Ruíz
- Instituto de Investigación Biomédica de Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Neurosurgery Service, University Hospital of Salamanca, Salamanca, Spain
| | - Iván Álvarez-Twose
- Instituto de Estudios de Mastocitosis de Castilla La Mancha, Virgen del Valle Hospital, Toledo, Spain.,Spanish Network on Mastocytosis Red Española de Mastocitosis (REMA), Salamanca, Spain
| | - Andrés Celestino García-Montero
- Instituto de Investigación Biomédica de Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Centre for Cancer Research (Centro de Investigación del Cáncer de Salamanca (CIC)-Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Centro Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca (USAL), IBSAL) and Department of Medicine, University of Salamanca, Salamanca, Spain.,Spanish Network on Mastocytosis Red Española de Mastocitosis (REMA), Salamanca, Spain.,Spanish National DNA Bank Carlos III, University of Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Instituto de Investigación Biomédica de Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Centre for Cancer Research (Centro de Investigación del Cáncer de Salamanca (CIC)-Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Centro Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca (USAL), IBSAL) and Department of Medicine, University of Salamanca, Salamanca, Spain.,Biomedical Research Networking Centre on Cancer- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) (CB16/12/00400), Instituto de Salud Carlos III, Madrid, Spain.,Spanish National DNA Bank Carlos III, University of Salamanca, Salamanca, Spain
| | - María Dolores Tabernero
- Instituto de Investigación Biomédica de Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Centre for Cancer Research (Centro de Investigación del Cáncer de Salamanca (CIC)-Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Centro Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca (USAL), IBSAL) and Department of Medicine, University of Salamanca, Salamanca, Spain.,Biomedical Research Networking Centre on Cancer- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) (CB16/12/00400), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Estudios de Ciencias de la Salud de Castilla y León (IECSCYL-IBSAL), Salamanca, Spain
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