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Pickles JC, Fairchild AR, Stone TJ, Brownlee L, Merve A, Yasin SA, Avery A, Ahmed SW, Ogunbiyi O, Gonzalez Zapata J, Peary AF, Edwards M, Wilkhu L, Dryden C, Ladon D, Kristiansen M, Rowe C, Kurian KM, Nicoll JAR, Mitchell C, Bloom T, Hilton DA, Al-Sarraj S, Doey L, Johns PN, Bridges LR, Chakrabarty A, Ismail A, Rathi N, Syed K, Lammie GA, Limback-Stanic C, Smith C, Torgersen A, Rae F, Hill RM, Clifford SC, Grabovska Y, Williamson D, Clarke M, Jones C, Capper D, Sill M, von Deimling A, Pfister SM, Jones DTW, Hargrave D, Chalker J, Jacques TS. DNA methylation-based profiling for paediatric CNS tumour diagnosis and treatment: a population-based study. THE LANCET. CHILD & ADOLESCENT HEALTH 2020; 4:121-130. [PMID: 31786093 DOI: 10.1016/s2352-4642(19)30342-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/11/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Marked variation exists in the use of genomic data in tumour diagnosis, and optimal integration with conventional diagnostic technology remains uncertain despite several studies reporting improved diagnostic accuracy, selection for targeted treatments, and stratification for trials. Our aim was to assess the added value of molecular profiling in routine clinical practice and the impact on conventional and experimental treatments. METHODS This population-based study assessed the diagnostic and clinical use of DNA methylation-based profiling in childhood CNS tumours using two large national cohorts in the UK. In the diagnostic cohort-which included routinely diagnosed CNS tumours between Sept 1, 2016, and Sept 1, 2018-we assessed how the methylation profile altered or refined diagnosis in routine clinical practice and estimated how this would affect standard patient management. For the archival cohort of diagnostically difficult cases, we established how many cases could be solved using modern standard pathology, how many could only be solved using the methylation profile, and how many remained unsolvable. FINDINGS Of 484 patients younger than 20 years with CNS tumours, 306 had DNA methylation arrays requested by the neuropathologist and were included in the diagnostic cohort. Molecular profiling added a unique contribution to clinical diagnosis in 107 (35%; 95% CI 30-40) of 306 cases in routine diagnostic practice-providing additional molecular subtyping data in 99 cases, amended the final diagnosis in five cases, and making potentially significant predictions in three cases. We estimated that it could change conventional management in 11 (4%; 95% CI 2-6) of 306 patients. Among 195 historically difficult-to-diagnose tumours in the archival cohort, 99 (51%) could be diagnosed using standard methods, with the addition of methylation profiling solving a further 34 (17%) cases. The remaining 62 (32%) cases were unresolved despite specialist pathology and methylation profiling. INTERPRETATION Together, these data provide estimates of the impact that could be expected from routine implementation of genomic profiling into clinical practice, and indicate limitations where additional techniques will be required. We conclude that DNA methylation arrays are a useful diagnostic adjunct for childhood CNS tumours. FUNDING The Brain Tumour Charity, Children with Cancer UK, Great Ormond Street Hospital Children's Charity, Olivia Hodson Cancer Fund, Cancer Research UK, and the National Institute of Health Research.
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Affiliation(s)
- Jessica C Pickles
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Amy R Fairchild
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas J Stone
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lorelle Brownlee
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ashirwad Merve
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Shireena A Yasin
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Aimee Avery
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Saira W Ahmed
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Olumide Ogunbiyi
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jamie Gonzalez Zapata
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Abigail F Peary
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Marie Edwards
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lisa Wilkhu
- Specialist Integrated Haematology and Malignancy Diagnostic Service-Acquired Genomics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Carryl Dryden
- Specialist Integrated Haematology and Malignancy Diagnostic Service-Acquired Genomics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Dariusz Ladon
- Specialist Integrated Haematology and Malignancy Diagnostic Service-Acquired Genomics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Mark Kristiansen
- UCL Genomics, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Catherine Rowe
- Department of Neuropathology, North Bristol NHS Trust, Bristol, UK
| | | | - James A R Nicoll
- Cellular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, UK; BRAIN UK, Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - Clare Mitchell
- BRAIN UK, Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - Tabitha Bloom
- BRAIN UK, Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - David A Hilton
- Cellular and Anatomical Pathology, University Hospitals Plymouth NHS Trust, Plymouth, UK
| | - Safa Al-Sarraj
- Department of Clinical Neuropathology, Kings College Hospital NHS Trust, London, UK
| | - Lawrence Doey
- Department of Clinical Neuropathology, Kings College Hospital NHS Trust, London, UK
| | - Paul N Johns
- Department of Cellular Pathology, St George's University Hospital NHS Foundation Trust, London, UK
| | - Leslie R Bridges
- Department of Cellular Pathology, St George's University Hospital NHS Foundation Trust, London, UK
| | - Aruna Chakrabarty
- St James's University Hospital, The Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Azzam Ismail
- St James's University Hospital, The Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Nitika Rathi
- Department of Neuropathology, The Walton Centre NHS Foundation Trust, Liverpool, UK
| | - Khaja Syed
- Department of Neuropathology, The Walton Centre NHS Foundation Trust, Liverpool, UK
| | | | - Clara Limback-Stanic
- Department of Cellular Pathology, Imperial College Healthcare NHS Trust, London, UK
| | - Colin Smith
- Western General Hospital, NHS Lothian, Edinburgh, UK
| | | | - Frances Rae
- Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Rebecca M Hill
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Yura Grabovska
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew Clarke
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Chris Jones
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - David Capper
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany; German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany; Department of Pediatric Oncology, Hematology, Immunology, and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Darren Hargrave
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Jane Chalker
- Specialist Integrated Haematology and Malignancy Diagnostic Service-Acquired Genomics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
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Yang X, Brat D, Li J, Wang X, Tong L. A contemporary molecular view of diffuse gliomas with implications for diagnosis. GLIOMA 2020. [DOI: 10.4103/glioma.glioma_11_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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53
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Brand F, Förster A, Christians A, Bucher M, Thomé CM, Raab MS, Westphal M, Pietsch T, von Deimling A, Reifenberger G, Claus P, Hentschel B, Weller M, Weber RG. FOCAD loss impacts microtubule assembly, G2/M progression and patient survival in astrocytic gliomas. Acta Neuropathol 2020; 139:175-192. [PMID: 31473790 DOI: 10.1007/s00401-019-02067-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/12/2019] [Accepted: 08/19/2019] [Indexed: 12/23/2022]
Abstract
In search of novel genes associated with glioma pathogenesis, we have previously shown frequent deletions of the KIAA1797/FOCAD gene in malignant gliomas, and a tumor suppressor function of the encoded focadhesin impacting proliferation and migration of glioma cells in vitro and in vivo. Here, we examined an association of reduced FOCAD gene copy number with overall survival of patients with astrocytic gliomas, and addressed the molecular mechanisms that govern the suppressive effect of focadhesin on glioma growth. FOCAD loss was associated with inferior outcome in patients with isocitrate dehydrogenase 1 or 2 (IDH)-mutant astrocytic gliomas of WHO grades II-IV. Multivariate analysis considering age at diagnosis as well as IDH mutation, MGMT promoter methylation, and CDKN2A/B homozygous deletion status confirmed reduced FOCAD gene copy number as a prognostic factor for overall survival. Using a yeast two-hybrid screen and pull-down assays, tubulin beta-6 and other tubulin family members were identified as novel focadhesin-interacting partners. Tubulins and focadhesin co-localized to centrosomes where focadhesin was enriched in proximity to centrioles. Focadhesin was recruited to microtubules via its interaction partner SLAIN motif family member 2 and reduced microtubule assembly rates, possibly explaining the focadhesin-dependent decrease in cell migration. During the cell cycle, focadhesin levels peaked in G2/M phase and influenced time-dependent G2/M progression potentially via polo like kinase 1 phosphorylation, providing a possible explanation for focadhesin-dependent cell growth reduction. We conclude that FOCAD loss may promote biological aggressiveness and worsen clinical outcome of diffuse astrocytic gliomas by enhancing microtubule assembly and accelerating G2/M phase progression.
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Affiliation(s)
- Frank Brand
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Alisa Förster
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Anne Christians
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Martin Bucher
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Carina M Thomé
- Neurology Clinic and National Center for Tumor Diseases, Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc S Raab
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn Medical School, Bonn, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Claus
- Department of Neuroanatomy and Cell Biology, Hannover Medical School, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Bettina Hentschel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Ruthild G Weber
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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Okuchi S, Hammam A, Golay X, Kim M, Thust S. Endogenous Chemical Exchange Saturation Transfer MRI for the Diagnosis and Therapy Response Assessment of Brain Tumors: A Systematic Review. Radiol Imaging Cancer 2020; 2:e190036. [PMID: 33778693 PMCID: PMC7983695 DOI: 10.1148/rycan.2020190036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/13/2019] [Accepted: 10/21/2019] [Indexed: 01/09/2023]
Abstract
Purpose To generate a narrative synthesis of published data on the use of endogenous chemical exchange saturation transfer (CEST) MRI in brain tumors. Materials and Methods A systematic database search (PubMed, Ovid Embase, Cochrane Library) was used to collate eligible studies. Two researchers independently screened publications according to predefined exclusion and inclusion criteria, followed by comprehensive data extraction. All included studies were subjected to a bias risk assessment using the Quality Assessment of Diagnostic Accuracy Studies tool. Results The electronic database search identified 430 studies, of which 36 fulfilled the inclusion criteria. The final selection of included studies was categorized into five groups as follows: grading gliomas, 19 studies (area under the receiver operating characteristic curve [AUC], 0.500-1.000); predicting molecular subtypes of gliomas, five studies (AUC, 0.610-0.920); distinction of different brain tumor types, seven studies (AUC, 0.707-0.905); therapy response assessment, three studies (AUC not given); and differentiating recurrence from treatment-related changes, five studies (AUC, 0.880-0.980). A high bias risk was observed in a substantial proportion of studies. Conclusion Endogenous CEST MRI offers valuable, potentially unique information in brain tumors, but its diagnostic accuracy remains incompletely known. Further research is required to assess the method's role in support of molecular genetic diagnosis, to investigate its use in the posttreatment phase, and to compare techniques with a view to standardization.Keywords: Brain/Brain Stem, MR-Imaging, Neuro-OncologySupplemental material is available for this article.© RSNA, 2020.
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Affiliation(s)
- Sachi Okuchi
- From the Department of Brain Repair and Rehabilitation, University College London, Institute of Neurology, London, England (S.O., A.H., X.G., M.K., S.T.); Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan (S.O.); and Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, England (S.T.)
| | - Ahmed Hammam
- From the Department of Brain Repair and Rehabilitation, University College London, Institute of Neurology, London, England (S.O., A.H., X.G., M.K., S.T.); Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan (S.O.); and Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, England (S.T.)
| | - Xavier Golay
- From the Department of Brain Repair and Rehabilitation, University College London, Institute of Neurology, London, England (S.O., A.H., X.G., M.K., S.T.); Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan (S.O.); and Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, England (S.T.)
| | - Mina Kim
- From the Department of Brain Repair and Rehabilitation, University College London, Institute of Neurology, London, England (S.O., A.H., X.G., M.K., S.T.); Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan (S.O.); and Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, England (S.T.)
| | - Stefanie Thust
- From the Department of Brain Repair and Rehabilitation, University College London, Institute of Neurology, London, England (S.O., A.H., X.G., M.K., S.T.); Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan (S.O.); and Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, England (S.T.)
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55
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Liu YQ, Wu F, Li JJ, Li YF, Liu X, Wang Z, Chai RC. Gene Expression Profiling Stratifies IDH-Wildtype Glioblastoma With Distinct Prognoses. Front Oncol 2019; 9:1433. [PMID: 31921684 PMCID: PMC6929203 DOI: 10.3389/fonc.2019.01433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/02/2019] [Indexed: 12/31/2022] Open
Abstract
Objectives: In the present study, we aimed to determine the candidate genes that may function as biomarkers to further distinguish patients with isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM), which are heterogeneous with respect to clinical outcomes. Materials and Methods: We selected 41 candidate genes associated with overall survival (OS) using univariate Cox regression from IDH-wildtype GBM patients based on RNA sequencing (RNAseq) expression data from the Chinese Glioma Genome Atlas (CGGA, n = 105) and The Cancer Genome Atlas (TCGA, n = 139) cohorts. Next, a seven-gene-based risk signature was formulated according to Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm in the CGGA RNAseq database as a training set, while another 525 IDH-wildtype GBM patient TCGA datasets, consisting of RNA sequencing and microarray data, were used for validation. Patient survival in the low- and high-risk groups was calculated using Kaplan-Meier survival curve analysis and the log-rank test. Uni-and multivariate Cox regression analysis was used to assess the prognosis value. Gene oncology (GO) and gene set enrichment analysis (GSEA) were performed for the functional analysis of the seven-gene-based risk signature. Results: We developed a seven-gene-based signature, which allocated each patient to a risk group (low or high). Patients in the high-risk group had dramatically shorter overall survival than their low-risk counterparts in three independent cohorts. Univariate and multivariate analysis showed that the seven-gene signature remained an independent prognostic factor. Moreover, the seven-gene risk signature exhibited a striking prognostic validity, with AUC of 78.4 and 73.9%, which was higher than for traditional “age” (53.7%, 62.4%) and “GBM sub-type” (57.7%, 52.9%) in the CGGA- and TCGA-RNAseq databases, respectively. Subsequent bioinformatics analysis predicted that the seven-gene signature was involved in the inflammatory response, immune response, cell adhesion, and apoptotic process. Conclusions: Our findings indicate that the seven-gene signature could be a potential prognostic biomarker. This study refined the current classification system of IDH-wildtype GBM and may provide a novel perspective for the research and individual therapy of IDH-wildtype GBM.
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Affiliation(s)
- Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Jing-Jun Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Yang-Fang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Xing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Zheng Wang
- Chinese Glioma Genome Atlas Network, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
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Barresi V, Eccher A, Simbolo M, Cappellini R, Ricciardi GK, Calabria F, Cancedda M, Mazzarotto R, Bonetti B, Pinna G, Sala F, Ghimenton C, Scarpa A. Diffuse gliomas in patients aged 55 years or over: A suggestion for IDH mutation testing. Neuropathology 2019; 40:68-74. [PMID: 31758617 DOI: 10.1111/neup.12608] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 01/01/2023]
Abstract
Diffuse gliomas are defined on the isocitrate dehydrogenase (IDH) gene (IDH) mutational mutational status. The most frequent IDH mutation is IDH1 R132H, which is detectable by immunohistochemistry; other IDH mutations are rare (10%). IDH mutant gliomas have better prognosis. Further, IDH wild-type low-grade (II/III) gliomas have clinical behaviors similar to those of glioblastoma (GBM) and it was suggested that they are submitted to similar post-surgical treatment. The incidence of IDH mutant gliomas (2%) and that of GBMs with non-canonical IDH mutations (< 1%) are very low in patients ≥ 55 years. For this reason, it was suggested that immunohistochemistry against IDH1 R132H is sufficient to classify GBM as IDH wild-type in this age group. However, no indication was provided for IDH mutational testing in low-grade diffuse gliomas. To address this issue, 273 diffuse gliomas were tested for IDH1 R132H immunohistochemistry. 2/4 diffuse astrocytomas (DAs), 4/9 anaplastic astrocytomas (AAs), 2/256 GBMs, and 4/4 oligodendrogliomas had positive staining. No other IDH mutations were found in immuno-negative low-grade cases by DNA sequencing. To validate our findings, we considered 311 diffuse gliomas in patients ≥ 55 years in The Cancer Genome Atlas database. Fifty-five out of 311 gliomas had IDH R132H mutations (9/16 DAs; 8/48 AAs; 3/211 GBMs; 35/36 oligodendrogliomas), one DA, and one oligodendroglioma had other IDH mutations. IDH mutant gliomas had significantly higher frequency of O-6-methylguanine-DNA methyltransferase promoter methylation (P = 0.0008) and longer overall survival (P < 0.0001). In conclusion, low-grade gliomas are a minor part of gliomas (117/584) in patients ≥ 55 years, albeit they represent most IDH mutant gliomas in this age group (64/69 cases). IDH non-canonical mutations can be found in immunonegative low-grade gliomas (2/54). In view of its significance for prognosis and therapeutic management, our results suggest that IDH mutational status is assessed in all diffuse gliomas in patients ≥ 55 years by immunohistochemistry, followed by IDH sequencing in low-grade immunonegative cases.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Albino Eccher
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Michele Simbolo
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Rekha Cappellini
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Giuseppe K Ricciardi
- Pathology and Diagnostics, Section of Neuroradiology, Hospital Trust Verona, Verona, Italy
| | | | - Marco Cancedda
- Neurosciences, Unit of Neurosurgery, Hospital Trust of Verona, Verona, Italy
| | - Renzo Mazzarotto
- Department of Surgery and Oncology, Unit of Radiotherapy, Hospital Trust of Verona, Verona, Italy
| | - Bruno Bonetti
- Department of Neurology, University of Verona, Verona, Italy
| | - Giampietro Pinna
- Neurosciences, Unit of Neurosurgery, Hospital Trust of Verona, Verona, Italy
| | - Francesco Sala
- Neurosciences, Unit of Neurosurgery, Hospital Trust of Verona, Verona, Italy
| | - Claudio Ghimenton
- Department of Pathology and Diagnostics, Section of Pathology, Hospital Trust Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy.,ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
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57
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Li KKW, Shi ZF, Malta TM, Chan AKY, Cheng S, Kwan JSH, Yang RR, Poon WS, Mao Y, Noushmehr H, Chen H, Ng HK. Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks. Neurooncol Adv 2019; 1:vdz015. [PMID: 31667475 PMCID: PMC6798792 DOI: 10.1093/noajnl/vdz015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background IDH-mutant glioblastoma is classified by the 2016 CNS WHO as a group with good prognosis. However, the actual number of cases examined in the literature is relatively small. We hypothesize that IDH-mutant glioblastoma is not a uniform group and should be further stratified. Methods We conducted methylation profiles and estimated copy number variations of 57 IDH-mutant glioblastomas. Results Our results showed that 59.6% and 40.4% of tumors belonged to glioma-CpG island methylator phenotype (G-CIMP)-high and G-CIMP-low methylation subgroups, respectively. G-CIMP-low subgroup was associated with significantly worse overall survival (OS) as compared to G-CIMP-high (P = .005). CDKN2A deletion (42.1%) was the most common gene copy number variation, and was significantly associated with G-CIMP-low subgroup (P = .004). Other frequent copy number changes included mesenchymal-epithelial transition (MET) (5.3%), CCND2 (19.3%), PDGFRA (14.0%), CDK4 (12.3%), and EGFR (12.3%) amplification. Both CDKN2A deletion (P = .036) and MET amplification (P < .001) were associated with poor OS in IDH-mutant glioblastomas. Combined epigenetic signature and gene copy number variations separated IDH-mutant glioblastomas into Group 1 (G-CIMP-high), Group 2 (G-CIMP-low without CDKN2A nor MET alteration), and Group 3 (G-CIMP-low with CDKN2A and/or MET alteration). Survival analysis revealed Groups 1 and 2 exhibited a favorable OS (median survival: 619 d [20.6 mo] and 655 d [21.8 mo], respectively). Group 3 exhibited a significant shorter OS (median survival: 252 d [8.4 mo]). Multivariable analysis confirmed the independent prognostic significance of our Groups. Conclusions IDH-mutant glioblastomas should be stratified for risk with combined epigenetic signature and CDKN2A/MET status and some cases have poor outcome.
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Affiliation(s)
- Kay Ka-Wai Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Nanshan District, Shenzhen, China
| | - Zhi-Feng Shi
- Department of Neurosurgery, Hua Shan Hospital, Fudan University, Shanghai, China
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan
| | - Aden Ka-Yin Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
| | - Shaz Cheng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
| | - Johnny Sheung Him Kwan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
| | - Rui Ryan Yang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
| | - Wai Sang Poon
- Department of Neurosurgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
| | - Ying Mao
- Department of Neurosurgery, Hua Shan Hospital, Fudan University, Shanghai, China
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan
| | - Hong Chen
- Department of Pathology, Hua Shan Hospital, Fudan University, Shanghai, China
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Nanshan District, Shenzhen, China
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Molinaro AM, Taylor JW, Wiencke JK, Wrensch MR. Genetic and molecular epidemiology of adult diffuse glioma. Nat Rev Neurol 2019; 15:405-417. [PMID: 31227792 PMCID: PMC7286557 DOI: 10.1038/s41582-019-0220-2] [Citation(s) in RCA: 409] [Impact Index Per Article: 81.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 12/24/2022]
Abstract
The WHO 2007 glioma classification system (based primarily on tumour histology) resulted in considerable interobserver variability and substantial variation in patient survival within grades. Furthermore, few risk factors for glioma were known. Discoveries over the past decade have deepened our understanding of the molecular alterations underlying glioma and have led to the identification of numerous genetic risk factors. The advances in molecular characterization of glioma have reframed our understanding of its biology and led to the development of a new classification system for glioma. The WHO 2016 classification system comprises five glioma subtypes, categorized by both tumour morphology and molecular genetic information, which led to reduced misclassification and improved consistency of outcomes within glioma subtypes. To date, 25 risk loci for glioma have been identified and several rare inherited mutations that might cause glioma in some families have been discovered. This Review focuses on the two dominant trends in glioma science: the characterization of diagnostic and prognostic tumour markers and the identification of genetic and other risk factors. An overview of the many challenges still facing glioma researchers is also included.
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Affiliation(s)
- Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Margaret R Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, USA
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Consequences of IDH1/2 Mutations in Gliomas and an Assessment of Inhibitors Targeting Mutated IDH Proteins. Molecules 2019; 24:molecules24050968. [PMID: 30857299 PMCID: PMC6429355 DOI: 10.3390/molecules24050968] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 11/16/2022] Open
Abstract
Isocitrate dehydrogenases (IDH) 1 and 2 are key metabolic enzymes that generate reduced nicotinamide adenine dinucleotide phosphate (NADPH) to maintain a pool of reduced glutathione and peroxiredoxin, and produce α-ketoglutarate, a co-factor of numerous enzymes. IDH1/2 is mutated in ~70–80% of lower-grade gliomas and the majority of secondary glioblastomas. The mutant IDH1 (R132H), in addition to losing its normal catalytic activity, gains the function of producing the d-(R)-2-hydroxyglutarate (2-HG). Overproduction of 2-HG in cancer cells interferes with cellular metabolism and inhibits histone and DNA demethylases, which results in histone and DNA hypermethylation and the blockade of cellular differentiation. We summarize recent findings characterizing molecular mechanisms underlying oncogenic alterations associated with mutated IDH1/2, and their impact on tumor microenvironment and antitumor immunity. Isoform-selective IDH inhibitors which suppress 2-HG production and induce antitumor responses in cells with IDH1 and IDH2 mutations were developed and validated in preclinical settings. Inhibitors of mutated IDH1/2 enzymes entered clinical trials and represent a novel drug class for targeted therapy of gliomas. We describe the development of small-molecule compounds and peptide vaccines targeting IDH-mutant gliomas and the results of their testing in preclinical and clinical studies. All those results support the translational potential of strategies targeting gliomas carrying IDH1 mutations.
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Jaunmuktane Z, Capper D, Jones DTW, Schrimpf D, Sill M, Dutt M, Suraweera N, Pfister SM, von Deimling A, Brandner S. Methylation array profiling of adult brain tumours: diagnostic outcomes in a large, single centre. Acta Neuropathol Commun 2019; 7:24. [PMID: 30786920 PMCID: PMC6381711 DOI: 10.1186/s40478-019-0668-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 01/28/2019] [Indexed: 01/09/2023] Open
Abstract
The introduction of the classification of brain tumours based on their DNA methylation profile has significantly changed the diagnostic approach for cases with ambiguous histology, non-informative or contradictory molecular profiles or for entities where methylation profiling provides useful information for patient risk stratification, for example in medulloblastoma and ependymoma. We present our experience that combines a conventional molecular diagnostic approach with the complementary use of a DNA methylation-based classification tool, for adult brain tumours originating from local as well as national referrals. We report the frequency of IDH mutations in a large cohort of nearly 1550 patients, EGFR amplifications in almost 1900 IDH-wildtype glioblastomas, and histone mutations in 70 adult gliomas. We demonstrate how additional methylation-based classification has changed and improved our diagnostic approach. Of the 325 cases referred for methylome testing, 179 (56%) had a calibrated score of 0.84 and higher and were included in the evaluation. In these 179 samples, the diagnosis was changed in 45 (25%), refined in 86 (48%) and confirmed in 44 cases (25%). In addition, the methylation arrays contain copy number information that usefully complements the methylation profile. For example, EGFR amplification which is 95% concordant with our Real-Time PCR-based copy number assays. We propose here a diagnostic algorithm that integrates histology, conventional molecular tests and methylation arrays.
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