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Mishchenko TA, Turubanova VD, Gorshkova EN, Krysko O, Vedunova MV, Krysko DV. Glioma: bridging the tumor microenvironment, patient immune profiles and novel personalized immunotherapy. Front Immunol 2024; 14:1299064. [PMID: 38274827 PMCID: PMC10809268 DOI: 10.3389/fimmu.2023.1299064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/11/2023] [Indexed: 01/27/2024] Open
Abstract
Glioma is the most common primary brain tumor, characterized by a consistently high patient mortality rate and a dismal prognosis affecting both survival and quality of life. Substantial evidence underscores the vital role of the immune system in eradicating tumors effectively and preventing metastasis, underscoring the importance of cancer immunotherapy which could potentially address the challenges in glioma therapy. Although glioma immunotherapies have shown promise in preclinical and early-phase clinical trials, they face specific limitations and challenges that have hindered their success in further phase III trials. Resistance to therapy has been a major challenge across many experimental approaches, and as of now, no immunotherapies have been approved. In addition, there are several other limitations facing glioma immunotherapy in clinical trials, such as high intra- and inter-tumoral heterogeneity, an inherently immunosuppressive microenvironment, the unique tissue-specific interactions between the central nervous system and the peripheral immune system, the existence of the blood-brain barrier, which is a physical barrier to drug delivery, and the immunosuppressive effects of standard therapy. Therefore, in this review, we delve into several challenges that need to be addressed to achieve boosted immunotherapy against gliomas. First, we discuss the hurdles posed by the glioma microenvironment, particularly its primary cellular inhabitants, in particular tumor-associated microglia and macrophages (TAMs), and myeloid cells, which represent a significant barrier to effective immunotherapy. Here we emphasize the impact of inducing immunogenic cell death (ICD) on the migration of Th17 cells into the tumor microenvironment, converting it into an immunologically "hot" environment and enhancing the effectiveness of ongoing immunotherapy. Next, we address the challenge associated with the accurate identification and characterization of the primary immune profiles of gliomas, and their implications for patient prognosis, which can facilitate the selection of personalized treatment regimens and predict the patient's response to immunotherapy. Finally, we explore a prospective approach to developing highly personalized vaccination strategies against gliomas, based on the search for patient-specific neoantigens. All the pertinent challenges discussed in this review will serve as a compass for future developments in immunotherapeutic strategies against gliomas, paving the way for upcoming preclinical and clinical research endeavors.
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Affiliation(s)
- Tatiana A. Mishchenko
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Victoria D. Turubanova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- Neuroscience Research Institute, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Ekaterina N. Gorshkova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Olga Krysko
- Cell Death Investigation and Therapy Laboratory, Anatomy and Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Maria V. Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia
| | - Dmitri V. Krysko
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- Cell Death Investigation and Therapy Laboratory, Anatomy and Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Pathophysiology, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- Cancer Research Institute Ghent, Ghent, Belgium
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Lasocki A, Buckland ME, Molinaro T, Xie J, Gaillard F. Radiogenomics Provides Insights into Gliomas Demonstrating Single-Arm 1p or 19q Deletion. AJNR Am J Neuroradiol 2023; 44:1270-1274. [PMID: 37884300 PMCID: PMC10631530 DOI: 10.3174/ajnr.a8034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/15/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND AND PURPOSE IDH-mutant gliomas are further divided on the basis of 1p/19q status: oligodendroglioma, IDH-mutant and 1p/19q-codeleted, and astrocytoma, IDH-mutant (without codeletion). Occasionally, testing may reveal single-arm 1p or 19q deletion (unideletion), which remains within the diagnosis of astrocytoma. Molecular assessment has some limitations, however, raising the possibility that some unideleted tumors could actually be codeleted. This study assessed whether unideleted tumors had MR imaging features and survival more consistent with astrocytomas or oligodendrogliomas. MATERIALS AND METHODS One hundred twenty-one IDH-mutant grade 2-3 gliomas with 1p/19q results were identified. Two neuroradiologists assessed the T2-FLAIR mismatch sign and calcifications, as differentiators of astrocytomas and oligodendrogliomas. MR imaging features and survival were compared among the unideleted tumors, codeleted tumors, and those without 1p or 19q deletion. RESULTS The cohort comprised 65 tumors without 1p or 19q deletion, 12 unideleted tumors, and 44 codeleted. The proportion of unideleted tumors demonstrating the T2-FLAIR mismatch sign (33%) was similar to that in tumors without deletion (49%; P = .39), but significantly higher than codeleted tumors (0%; P = .001). Calcifications were less frequent in unideleted tumors (0%) than in codeleted tumors (25%), but this difference did not reach statistical significance (P = .097). The median survival of patients with unideleted tumors was 7.8 years, which was similar to that in tumors without deletion (8.5 years; P = .72) but significantly shorter than that in codeleted tumors (not reaching median survival after 12 years; P = .013). CONCLUSIONS IDH-mutant gliomas with single-arm 1p or 19q deletion have MR imaging appearance and survival that are similar to those of astrocytomas without 1p or 19q deletion and significantly different from those of 1p/19q-codeleted oligodendrogliomas.
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Affiliation(s)
- Arian Lasocki
- From the Department of Cancer Imaging (A.L.), Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology (A.L.), The University of Melbourne, Parkville, Victoria, Australia
- Department of Radiology (A.L., F.G.), The University of Melbourne, Parkville, Victoria, Australia
| | - Michael E Buckland
- Department of Neuropathology (M.E.B.), Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- School of Medical Sciences (M.E.B.), University of Sydney, Camperdown, New South Wales, Australia
| | - Tahlia Molinaro
- Department of Medical Oncology (T.M.), Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jing Xie
- Centre for Biostatistics and Clinical Trials (J.X.), Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Frank Gaillard
- Department of Radiology (A.L., F.G.), The University of Melbourne, Parkville, Victoria, Australia
- Department of Radiology (F.G.), The Royal Melbourne Hospital, Parkville, Victoria, Australia
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Pandith AA, Zahoor W, Manzoor U, Nisar S, Guru FR, Naikoo NA, Aein QU, Baba SM, Bhat AR, Ganai F, Shah P. Evaluation of chromosome 1p/19q deletion by Fluorescence in Situ Hybridization (FISH) as prognostic factors in malignant glioma patients on treatment with alkylating chemotherapy. Cancer Genet 2023; 278-279:55-61. [PMID: 37625215 DOI: 10.1016/j.cancergen.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/12/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Either deletion or co-deletion of chromosomal arms 1p or 19q is a characteristic and early genetic event in oligodendroglial tumors that is associated with a better prognosis and enhanced response to therapy. Information of 1p/19q status is now regarded as the standard of care when managing oligodendroglial tumors for therapeutic options in anticipation of the increased survival and progression-free survival times associated with it. Keeping this in view, we first time attempted to establish the FISH based detection of 1p/19q deletion in glioma tissue samples to evaluate its role and involvement in the disease. METHOD Overall 39 glioma cases of different histologies were evaluated by fluorescence in situ hybridization (FISH) technique using specific FISH probes with Olympus BX43 fluorescent microscope to detect chromosomes 1p and 19q or co-deletions therein. RESULTS Of the 39 glioma samples, overall 27 (69.2%) were found to have deletion either in 1p, 19q or both. Deletions were observed in 23.0%, 7.6% and 38.4% in 1p, 19q and 1p/19q co-deletions respectively. Overall oligidendrioglioma presented with 53.8% (21 of 39) deletions, astrocytoma group showed 12.8% and GBM accounted for 2.5% deletions. Overall survival and disease free survival was seen significantly better in oligidendrioglioma and astrocytoma with deleted tumors as compared to non-deleted ones (p<0.05). CONCLUSION Allelic losses on 1p and 19q, either discretely or shared, were more frequent in classic oligodendrogliomas than in either astrocytoma or Glioblastoma with better survival and response to therapy.
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Affiliation(s)
- Arshad A Pandith
- Advanced Centre for Human Genetics, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, J & K, India.
| | - Wani Zahoor
- Advanced Centre for Human Genetics, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, J & K, India
| | - Usma Manzoor
- Advanced Centre for Human Genetics, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, J & K, India
| | - Syed Nisar
- Department of Medical Oncology, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, J&K, India
| | - Faisal R Guru
- Department of Medical Oncology, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, J&K, India
| | - Niyaz A Naikoo
- Department of Biotechnology, Higher Education Department, Cluster University, Srinagar, J & K, India
| | - Qurat Ul Aein
- Advanced Centre for Human Genetics, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, J & K, India
| | - Shahid M Baba
- Advanced Centre for Human Genetics, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, J & K, India
| | - Abdul R Bhat
- Department of Neurosurgery, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, J&K, India
| | - Farooq Ganai
- Department of CVTS, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, J&K, India
| | - Parveen Shah
- Department of Pathology, SKIMS, Srinagar, J & K, India
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Masui K, Nitta M, Muragaki Y, Kawamata T, Satomi K, Matsushita Y, Yoshida A, Ichimura K, Tsuda M, Tanaka S, Komori T. A case of "genetically defined" radiation-induced glioma: 29 years after surgery and radiation for pilocytic astrocytoma. Neuropathology 2023; 43:425-428. [PMID: 36949717 DOI: 10.1111/neup.12903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023]
Affiliation(s)
- Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Tokyo, Japan
| | - Masayuki Nitta
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Yoshihiro Muragaki
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Takakazu Kawamata
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Kaishi Satomi
- Division of Brain Tumor Translational Research, National Cancer Center Institute, Tokyo, Japan
- Department of Diagnostic Pathology, National Cancer Center Institute, Tokyo, Japan
| | - Yuko Matsushita
- Division of Brain Tumor Translational Research, National Cancer Center Institute, Tokyo, Japan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Institute, Tokyo, Japan
| | - Koichi Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Institute, Tokyo, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Takashi Komori
- Department of Laboratory Medicine and Pathology, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
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Hua R, Li Q, Gao H, Wang B, He C, Wang Y, Zhang S, Gao L, Shang H, Wang W, Xu J. Association of human telomerase reverse transcriptase promoter mutation with unfavorable prognosis in glioma: A systematic review and meta-analysis. JOURNAL OF RESEARCH IN MEDICAL SCIENCES : THE OFFICIAL JOURNAL OF ISFAHAN UNIVERSITY OF MEDICAL SCIENCES 2023; 28:47. [PMID: 37496645 PMCID: PMC10366975 DOI: 10.4103/jrms.jrms_371_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/28/2022] [Accepted: 01/20/2023] [Indexed: 07/28/2023]
Abstract
Background Glioma is one of the most malignant and aggressive tumors, with an extremely poor prognosis. Human telomerase reverse transcriptase (hTERT) promoter mutation is regarded as a risk factor in tumor growth. Although the prevalence of hTERT promoter (pTERT) mutation in gliomas has been investigated, the results are inconsistent. This meta-analysis aims to investigate the prognostic value of hTERT in glioma patients and its interaction with other biomarkers. Materials and Methods We searched 244 citations from four databases: PubMed (2000-2021), Web of Science (2000-2021), Embase (2010-2021), and Cochrane Library (2000-2021) with 28 articles included. Results We calculated hazard ratios (HRs) using the random effect model and the pooled result suggested that TERT promoter mutation predicted poorer overall survival (HR: 1.53, 95% confidence interval [CI]: 1.34-1.75, P < 0.001, I2: 49.9%, pheterogeneity:0.002) and progression-free survival (HR: 1.55, 95% CI: 1.27-1.88, P < 0.001, I2: 0.0%, pheterogeneity: 0.473). For subgroup analysis, we analyzed multiple factors including iso-citrate dehydrogenase (IDH) genotype, age, diagnosis, pTERT region, so as to locate the sources of heterogeneity. Interestingly, in IDH mutant subgroup, pTERT mutation became a beneficial prognostic factor (HR: 0.73, 95% CI: 0.57-0.93, I2: 22.3%, pheterogeneity: 0.277), which is contrary to the results in pooled analysis. Conclusion In general, pTERT mutation may result in shorter survival time in glioma patients, but longer survival time when glioma patients are combined with IDH mutation.
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Affiliation(s)
- Rongxuan Hua
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Qiuxuan Li
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Han Gao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Boya Wang
- Undergraduate Student of 2018 Eight Program of Clinical Medicine, Peking University People's Hospital, Beijing, China
| | - Chengwei He
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Ying Wang
- Department of Dermatology, Beijing Tong Ren Hospital, Capital Medical University, Beijing, China
| | - Sitian Zhang
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Lei Gao
- Department of Bioinformatics, College of Bioengineering, Capital Medical University, Beijing, China
| | - Hongwei Shang
- Experimental Center for Morphological Research Platform, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Wen Wang
- Department of Experimental Animal Research, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Jingdong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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Ali RH, Alateeqi M, Jama H, Alrumaidhi N, Alqallaf A, Mohammed EM, Almurshed M, Bahzad S. Evaluation of the Oncomine Comprehensive Assay v3 panel for the detection of 1p/19q codeletion in oligodendroglial tumours. J Clin Pathol 2023; 76:103-110. [PMID: 34489310 DOI: 10.1136/jclinpath-2021-207876] [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: 08/09/2021] [Accepted: 08/26/2021] [Indexed: 01/24/2023]
Abstract
AIMS Accurate assessment of 1p/19q codeletion status in diffuse gliomas is of paramount importance for diagnostic, prognostic and predictive purposes. While targeted next generation sequencing (NGS) has been widely implemented for glioma molecular profiling, its role in detecting structural chromosomal variants is less well established, requiring supplementary informatic tools for robust detection. Herein, we evaluated a commercially available amplicon-based targeted NGS panel (Oncomine Comprehensive Assay v3) for the detection of 1p/19q losses in glioma tissues using an Ion Torrent platform and the standard built-in NGS data analysis pipeline solely. METHODS Using as little as 20 ng of DNA from formalin-fixed paraffin-embedded tissues, we analysed 25 previously characterised gliomas for multi-locus copy number losses (CNLs) on 1p and 19q, including 11 oligodendrogliomas (ODG) and 14 non-oligodendroglial (non-ODG) controls. Fluorescence in-situ hybridisation (FISH) was used as a reference standard. RESULTS The software confidently detected combined contiguous 1p/19q CNLs in 11/11 ODGs (100% sensitivity), using a copy number cut-off of ≤1.5 and a minimum of 10 amplicons covering the regions. Only partial non-specific losses were identified in non-ODGs (100% specificity). Copy number averages of ODG and non-ODG groups were significantly different (p<0.001). NGS was concordant with FISH and was superior to it in distinguishing partial from contiguous losses indicative of whole-arm chromosomal deletion. CONCLUSIONS This commercial NGS panel, along with the standard Ion Torrent algorithm, accurately detected 1p/19q losses in ODG samples, obviating the need for specialised custom-made informatic analyses. This can easily be incorporated into routine glioma workflow as an alternative to FISH.
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Affiliation(s)
- Rola H Ali
- Department of Pathology, Kuwait University, Jabriya, Kuwait .,Cytogenetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Mona Alateeqi
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Hiba Jama
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Noor Alrumaidhi
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Ali Alqallaf
- Cytogenetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | | | | | - Shakir Bahzad
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
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Huo X, Guo T, Wang K, Yao B, Li D, Li H, Chen W, Wang L, Wu Z. Methylation-based reclassification and risk stratification of skull-base chordomas. Front Oncol 2022; 12:960005. [PMID: 36439461 PMCID: PMC9691996 DOI: 10.3389/fonc.2022.960005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/11/2022] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Skull-base chordomas are rare malignant bone cancers originating from the remnant of the notochord. Survival is variable, and clinical or molecular factors cannot reliably predict their outcomes. This study therefore identified epigenetic subtypes that defined new chordoma epigenetic profiles and their corresponding characteristics. METHODS Methylation profiles of 46 chordoma-resected neoplasms between 2008 and 2014, along with clinical information, were collected. K-means consensus clustering and principal component analysis were used to identify and validate the clusters. Single-sample gene set enrichment analysis, methylCIBERSORT algorithm, and copy number analysis were used to identify the characteristics of the clusters. RESULTS Unsupervised clustering analysis confirmed two clusters with a progression-free survival difference. Gene set enrichment analysis indicated that the early and late estrogen response pathways and the hypoxia pathway were activated whereas the inflammatory and interferon gamma responses were suppressed. Forty-six potential therapeutic targets corresponding to differentially methylated sites were identified from chordoma patients. Subgroups with a worse outcome were characterized by low immune cell infiltration, higher tumor purity, and higher stemness indices. Moreover, copy number amplifications mostly occurred in cluster 1 tumors and the high-risk group. Additionally, the presence of a CCNE1 deletion was exclusively found in the group of chordoma patients with better outcome, whereas RB1 and CDKN2A/2B deletions were mainly found in the group of chordoma patients with worse outcome. CONCLUSIONS Chordoma prognostic epigenetic subtypes were identified, and their corresponding characteristics were found to be variable.
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Affiliation(s)
- Xulei Huo
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Tengxian Guo
- Department of Neurosurgery, Beijing Fengtai Hospital, Beijing, China
| | - Ke Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Bohan Yao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Da Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Huan Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Wei Chen
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Liang Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhen Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
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Morphogenetic and Imaging Characteristics in Giant Cell Glioblastoma. Curr Oncol 2022; 29:5316-5323. [PMID: 36005160 PMCID: PMC9406765 DOI: 10.3390/curroncol29080422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/14/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
Giant cell glioblastoma is a rare tumor entity of IDH-wildtype glioblastoma. It is usually found in the pediatric population. We describe a particular case of a female patient diagnosed histopathologically with giant cell glioblastoma, who had two recurrences in different lobes of the same cerebral hemisphere, despite positive prognostic factors and appropriate treatment. We performed an immunohistochemical characterization of giant cell glioblastoma as well as an analysis of its aggressiveness using the cytogenetic markers TP53, CDKN2A, and TP73 using the FISH technique. The clinical picture was inconsistant, the suspicion being completely different initially. Paraclinical examination and imaging initially suggested a metastasis to the insular lobe. After surgery, histopathological and immunohistochemical examinations were the basis for the diagnosis. Despite the prognostic factors known so far in the literature, the aggressiveness denoted by multiple relapses and morphogenetic tests particularizes the case and improves the literature by bringing new information about this rare neoplasm of the central nervous system.
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Senhaji N, Squalli Houssaini A, Lamrabet S, Louati S, Bennis S. Molecular and Circulating Biomarkers in Patients with Glioblastoma. Int J Mol Sci 2022; 23:ijms23137474. [PMID: 35806478 PMCID: PMC9267689 DOI: 10.3390/ijms23137474] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 05/16/2022] [Indexed: 02/04/2023] Open
Abstract
Glioblastoma is the most aggressive malignant tumor of the central nervous system with a low survival rate. The difficulty of obtaining this tumor material represents a major limitation, making the real-time monitoring of tumor progression difficult, especially in the events of recurrence or resistance to treatment. The identification of characteristic biomarkers is indispensable for an accurate diagnosis, the rigorous follow-up of patients, and the development of new personalized treatments. Liquid biopsy, as a minimally invasive procedure, holds promise in this regard. The purpose of this paper is to summarize the current literature regarding the identification of molecular and circulating glioblastoma biomarkers and the importance of their integration as a valuable tool to improve patient care.
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Affiliation(s)
- Nadia Senhaji
- Department of Biology, Faculty of Sciences, Moulay Ismail University, Meknes 50000, Morocco
- Laboratory of Biomedical and Translational Research, Faculty of Medicine, Pharmacy and Dental Medicine of Fez, Sidi Mohamed Ben Abdellah University, Fez 30070, Morocco; (A.S.H.); (S.L.); (S.B.)
- Correspondence: ; Tel.: +212-662600394
| | - Asmae Squalli Houssaini
- Laboratory of Biomedical and Translational Research, Faculty of Medicine, Pharmacy and Dental Medicine of Fez, Sidi Mohamed Ben Abdellah University, Fez 30070, Morocco; (A.S.H.); (S.L.); (S.B.)
| | - Salma Lamrabet
- Laboratory of Biomedical and Translational Research, Faculty of Medicine, Pharmacy and Dental Medicine of Fez, Sidi Mohamed Ben Abdellah University, Fez 30070, Morocco; (A.S.H.); (S.L.); (S.B.)
| | - Sara Louati
- Medical Biotechnology Laboratory, Faculty of Medicine and Pharmacy of Rabat, Mohammed Vth University, Rabat 10000, Morocco;
| | - Sanae Bennis
- Laboratory of Biomedical and Translational Research, Faculty of Medicine, Pharmacy and Dental Medicine of Fez, Sidi Mohamed Ben Abdellah University, Fez 30070, Morocco; (A.S.H.); (S.L.); (S.B.)
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Utility of Targeted Next-Generation Sequencing Assay to Detect 1p/19q Co-Deletion in Formalin-fixed Paraffin-embedded Glioma Specimens. Hum Pathol 2022; 126:63-76. [PMID: 35561840 DOI: 10.1016/j.humpath.2022.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Molecular classification of brain neoplasms is important for diagnosis, prognosis, and treatment outcome of histologically similar tumors. Oligodendroglioma is a glioma subtype characterized by 1p/19q co-deletion and IDH1/IDH2 mutations, which predicts a good prognosis, responsiveness to therapy and an improved overall survival compared to other adult gliomas. In a routine clinical setting, 1p/19q co-deletion is detected by interphase-FISH and SNP microarray, and somatic mutations are detected by targeted next generation sequencing (NGS). The aim of this proof-of-principle study was to investigate the feasibility of using targeted NGS to simultaneously detect both 1p/19q co-deletion and somatic mutations. Among two hundred forty-seven consecutive patients with formalin-fixed paraffin-embedded brain tumors with various subtypes, NGS revealed 1p/19q co-deletion in twenty-six oligodendrogliomas and an IDH-wildtype astrocytoma, and partial loss across chromosomes 1p and 19q/whole-arm loss of 1p or 19q/copy neutral loss of heterozygosity in eleven non-oligodendrogliomas. For this 247 brain-tumor cohort, the overall sensitivity, specificity, and accuracy of detecting 1p/19q co-deletion by NGS in oligodendrogliomas were 96.2%, 99.6%, and 99.2%, respectively. The oligodendroglioma cohort had more mutations in IDH1/IDH2, CIC, FUBP1, and TERT, and fewer mutations in ATRX and TP53 than the non-oligodendroglioma cohort. This proof-of-concept study demonstrated that targeted NGS can simultaneously detect both 1p/19q co-deletion and somatic mutations, which can provide a more comprehensive genetic profiling for patients with gliomas using a single assay in a clinical setting.
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Massaad E, Tabbarah A, Barmada M, Rbeiz J, Nasser S, Farra C. FISH analyses for 1p and 19q status on gliomas: Reporting an 8 years' experience from a tertiary care center in the Middle East. Ann Diagn Pathol 2022; 57:151899. [DOI: 10.1016/j.anndiagpath.2022.151899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 07/25/2021] [Accepted: 01/03/2022] [Indexed: 12/15/2022]
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12
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Whitfield BT, Huse JT. Classification of adult-type diffuse gliomas: Impact of the World Health Organization 2021 update. Brain Pathol 2022; 32:e13062. [PMID: 35289001 PMCID: PMC9245936 DOI: 10.1111/bpa.13062] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/16/2022] [Indexed: 12/11/2022] Open
Abstract
Over the last decade, developments in molecular profiling have radically altered the diagnosis, classification, and management of numerous cancer types, with primary brain tumors being no exception. Although historically brain tumors have been classified based on their morphological characteristics, recent advances have allowed refinement of tumor classification based on molecular alterations. This shift toward molecular classification of primary brain tumors is reflected in the 2021 5th edition of the WHO classification of central nervous system tumors (WHO 2021). In this review, we will discuss the most recent updates to the classification of adult‐type diffuse gliomas, a group of highly infiltrative and largely incurable CNS malignancies. It is our hope continued that refinement of molecular criteria will improve diagnosis, prognostication, and eventually treatment of these devastating tumors.
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Affiliation(s)
- Benjamin T Whitfield
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jason T Huse
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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13
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McAleenan A, Jones HE, Kernohan A, Robinson T, Schmidt L, Dawson S, Kelly C, Spencer Leal E, Faulkner CL, Palmer A, Wragg C, Jefferies S, Brandner S, Vale L, Higgins JP, Kurian KM. Diagnostic test accuracy and cost-effectiveness of tests for codeletion of chromosomal arms 1p and 19q in people with glioma. Cochrane Database Syst Rev 2022; 3:CD013387. [PMID: 35233774 PMCID: PMC8889390 DOI: 10.1002/14651858.cd013387.pub2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Complete deletion of both the short arm of chromosome 1 (1p) and the long arm of chromosome 19 (19q), known as 1p/19q codeletion, is a mutation that can occur in gliomas. It occurs in a type of glioma known as oligodendroglioma and its higher grade counterpart known as anaplastic oligodendroglioma. Detection of 1p/19q codeletion in gliomas is important because, together with another mutation in an enzyme known as isocitrate dehydrogenase, it is needed to make the diagnosis of an oligodendroglioma. Presence of 1p/19q codeletion also informs patient prognosis and prediction of the best drug treatment. The main two tests in use are fluorescent in situ hybridisation (FISH) and polymerase chain reaction (PCR)-based loss of heterozygosity (LOH) assays (also known as PCR-based short tandem repeat or microsatellite analysis). Many other tests are available. None of the tests is perfect, although PCR-based LOH is expected to have very high sensitivity. OBJECTIVES To estimate the sensitivity and specificity and cost-effectiveness of different deoxyribonucleic acid (DNA)-based techniques for determining 1p/19q codeletion status in glioma. SEARCH METHODS We searched MEDLINE, Embase and BIOSIS up to July 2019. There were no restrictions based on language or date of publication. We sought economic evaluation studies from the results of this search and using the National Health Service Economic Evaluation Database. SELECTION CRITERIA We included cross-sectional studies in adults with glioma or any subtype of glioma, presenting raw data or cross-tabulations of two or more DNA-based tests for 1p/19q codeletion. We also sought economic evaluations of these tests. DATA COLLECTION AND ANALYSIS We followed procedures outlined in the Cochrane Handbook for Diagnostic Test Accuracy Reviews. Two review authors independently screened titles/abstracts/full texts, performed data extraction, and undertook applicability and risk of bias assessments using QUADAS-2. Meta-analyses used the hierarchical summary ROC model to estimate and compare test accuracy. We used FISH and PCR-based LOH as alternate reference standards to examine how tests compared with those in common use, and conducted a latent class analysis comparing FISH and PCR-based LOH. We constructed an economic model to evaluate cost-effectiveness. MAIN RESULTS We included 53 studies examining: PCR-based LOH, FISH, single nucleotide polymorphism (SNP) array, next-generation sequencing (NGS), comparative genomic hybridisation (CGH), array comparative genomic hybridisation (aCGH), multiplex-ligation-dependent probe amplification (MLPA), real-time PCR, chromogenic in situ hybridisation (CISH), mass spectrometry (MS), restriction fragment length polymorphism (RFLP) analysis, G-banding, methylation array and NanoString. Risk of bias was low for only one study; most gave us concerns about how patients were selected or about missing data. We had applicability concerns about many of the studies because only patients with specific subtypes of glioma were included. 1520 participants contributed to analyses using FISH as the reference, 1304 participants to analyses involving PCR-based LOH as the reference and 262 participants to analyses of comparisons between methods from studies not including FISH or PCR-based LOH. Most evidence was available for comparison of FISH with PCR-based LOH (15 studies, 915 participants): PCR-based LOH detected 94% of FISH-determined codeletions (95% credible interval (CrI) 83% to 98%) and FISH detected 91% of codeletions determined by PCR-based LOH (CrI 78% to 97%). Of tumours determined not to have a deletion by FISH, 94% (CrI 87% to 98%) had a deletion detected by PCR-based LOH, and of those determined not to have a deletion by PCR-based LOH, 96% (CrI 90% to 99%) had a deletion detected by FISH. The latent class analysis suggested that PCR-based LOH may be slightly more accurate than FISH. Most other techniques appeared to have high sensitivity (i.e. produced few false-negative results) for detection of 1p/19q codeletion when either FISH or PCR-based LOH was considered as the reference standard, although there was limited evidence. There was some indication of differences in specificity (false-positive rate) with some techniques. Both NGS and SNP array had high specificity when considered against FISH as the reference standard (NGS: 6 studies, 243 participants; SNP: 6 studies, 111 participants), although we rated certainty in the evidence as low or very low. NGS and SNP array also had high specificity when PCR-based LOH was considered the reference standard, although with much more uncertainty as these results were based on fewer studies (just one study with 49 participants for NGS and two studies with 33 participants for SNP array). G-banding had low sensitivity and specificity when PCR-based LOH was the reference standard. Although MS had very high sensitivity and specificity when both FISH and PCR-based LOH were considered the reference standard, these results were based on only one study with a small number of participants. Real-time PCR also showed high specificity with FISH as a reference standard, although there were only two studies including 40 participants. We found no relevant economic evaluations. Our economic model using FISH as the reference standard suggested that the resource-optimising test depends on which measure of diagnostic accuracy is most important. With FISH as the reference standard, MLPA is likely to be cost-effective if society was willing to pay GBP 1000 or less for a true positive detected. However, as the value placed on a true positive increased, CISH was most cost-effective. Findings differed when the outcome measure changed to either true negative detected or correct diagnosis. When PCR-based LOH was used as the reference standard, MLPA was likely to be cost-effective for all measures of diagnostic accuracy at lower threshold values for willingness to pay. However, as the threshold values increased, none of the tests were clearly more likely to be considered cost-effective. AUTHORS' CONCLUSIONS In our review, most techniques (except G-banding) appeared to have good sensitivity (few false negatives) for detection of 1p/19q codeletions in glioma against both FISH and PCR-based LOH as a reference standard. However, we judged the certainty of the evidence low or very low for all the tests. There are possible differences in specificity, with both NGS and SNP array having high specificity (fewer false positives) for 1p/19q codeletion when considered against FISH as the reference standard. The economic analysis should be interpreted with caution due to the small number of studies.
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Affiliation(s)
- Alexandra McAleenan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hayley E Jones
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ashleigh Kernohan
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tomos Robinson
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne , UK
| | - Lena Schmidt
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire Kelly
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Emmelyn Spencer Leal
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire L Faulkner
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Abigail Palmer
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Christopher Wragg
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Sarah Jefferies
- Department of Oncology, Addenbrooke's Hospital, Cambridge, UK
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Luke Vale
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne, UK
| | - Julian Pt Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kathreena M Kurian
- Bristol Medical School: Brain Tumour Research Centre, Public Health Sciences, University of Bristol, Bristol, UK
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14
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Śledzińska P, Bebyn MG, Furtak J, Kowalewski J, Lewandowska MA. Prognostic and Predictive Biomarkers in Gliomas. Int J Mol Sci 2021; 22:ijms221910373. [PMID: 34638714 PMCID: PMC8508830 DOI: 10.3390/ijms221910373] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Gliomas are the most common central nervous system tumors. New technologies, including genetic research and advanced statistical methods, revolutionize the therapeutic approach to the patient and reveal new points of treatment options. Moreover, the 2021 World Health Organization Classification of Tumors of the Central Nervous System has fundamentally changed the classification of gliomas and incorporated many molecular biomarkers. Given the rapid progress in neuro-oncology, here we compile the latest research on prognostic and predictive biomarkers in gliomas. In adult patients, IDH mutations are positive prognostic markers and have the greatest prognostic significance. However, CDKN2A deletion, in IDH-mutant astrocytomas, is a marker of the highest malignancy grade. Moreover, the presence of TERT promoter mutations, EGFR alterations, or a combination of chromosome 7 gain and 10 loss upgrade IDH-wildtype astrocytoma to glioblastoma. In pediatric patients, H3F3A alterations are the most important markers which predict the worse outcome. MGMT promoter methylation has the greatest clinical significance in predicting responses to temozolomide (TMZ). Conversely, mismatch repair defects cause hypermutation phenotype predicting poor response to TMZ. Finally, we discussed liquid biopsies, which are promising diagnostic, prognostic, and predictive techniques, but further work is needed to implement these novel technologies in clinical practice.
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Affiliation(s)
- Paulina Śledzińska
- Department of Thoracic Surgery and Tumors, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 85-067 Torun, Poland
- The F. Lukaszczyk Oncology Center, Molecular Oncology and Genetics Department, Innovative Medical Forum, 85-796 Bydgoszcz, Poland
| | - Marek G Bebyn
- The F. Lukaszczyk Oncology Center, Molecular Oncology and Genetics Department, Innovative Medical Forum, 85-796 Bydgoszcz, Poland
- Faculty of Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Jacek Furtak
- Department of Neurosurgery, 10th Military Research Hospital and Polyclinic, 85-681 Bydgoszcz, Poland
- Franciszek Lukaszczyk Oncology Center, Department of Neurooncology and Radiosurgery, 85-796 Bydgoszcz, Poland
| | - Janusz Kowalewski
- Department of Thoracic Surgery and Tumors, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 85-067 Torun, Poland
| | - Marzena A Lewandowska
- Department of Thoracic Surgery and Tumors, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 85-067 Torun, Poland
- The F. Lukaszczyk Oncology Center, Molecular Oncology and Genetics Department, Innovative Medical Forum, 85-796 Bydgoszcz, Poland
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15
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FISH analysis of brain smears obtained at intraoperative diagnosis - An accurate and fast method to detect 1p/19q-codeletion in gliomas. J Clin Neurosci 2021; 92:115-119. [PMID: 34509237 DOI: 10.1016/j.jocn.2021.07.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 06/22/2021] [Accepted: 07/25/2021] [Indexed: 11/24/2022]
Abstract
The importance of molecular testing of gliomas is highlighted in the 2016 revised 4th edition of the WHO Classification of Tumours of the Central Nervous System, which applies an integrated diagnosis of histological and molecular features. In this classification system, oligodendrogliomas (ODG) are defined as IDH-mutant and 1p/19q-codeleted. Fluorescence in situ hybridization (FISH) analysis of formalin-fixed paraffin-embedded (FFPE) tissue is a standard method of determining 1p/19q-codeletion. However, it has several disadvantages, including requiring lengthy pretreatment, truncation artefact and lack of on-site access in many centers. In an effort to address these issues, we analysed FISH performed on smears obtained at intraoperative frozen section on 51 gliomas and compared this to FISH performed on subsequent FFPE sections. Four cases were excluded due to uninterpretable FISH results. Of the remaining 47 cases, 17 were concordant for 1p/19q-codeletion, 29 were concordant for lack of 1p/19q-codeletion, and 1 was discordant with 1p/19q-codeletion found on FFPE tissue but not on intraoperative smears. The discordant case was most likely due to sampling error, as the frozen section had not shown definite tumor. The FISH results on intraoperative smears were received within 24-48 h after the sample was collected, compared with 3-4 days for FFPE tissue. FISH on smears obtained at intraoperative frozen section is an accurate and fast method for determining 1p/19q-codeletion.
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16
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de Biase D, Acquaviva G, Visani M, Marucci G, De Leo A, Maloberti T, Sanza V, Di Oto E, Franceschi E, Mura A, Ragazzi M, Serra S, Froio E, Bisagni A, Brandes AA, Pession A, Tallini G. Next-Generation Sequencing Panel for 1p/19q Codeletion and IDH1-IDH2 Mutational Analysis Uncovers Mistaken Overdiagnoses of 1p/19q Codeletion by FISH. J Mol Diagn 2021; 23:1185-1194. [PMID: 34186176 DOI: 10.1016/j.jmoldx.2021.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/15/2021] [Accepted: 06/08/2021] [Indexed: 02/08/2023] Open
Abstract
The 1p/19q codeletion is the result of a translocation between chromosome 1 (Chr1p) and chromosome 19 (Chr19q) with the loss of derivative (1;19)(p10;q10) chromosome. The 1p/19q codeletion has predictive and prognostic significance, and it is essential for the classification of gliomas. In routine practice, the fluorescence in situ hybridization (FISH) diagnosis of 1p/19q codeletion is sometimes unexpected. This study aimed to develop a next-generation sequencing panel for the concurrent definition of the 1p/19q codeletion and IDH1/IDH2 mutation status to resolve these equivocal cases. A total of 65 glioma samples were investigated using a 1p/19q-single-nucleotide polymorphism (SNP)-IDH panel. The panel consists of 192 amplicons, including SNPs mapping to Chr1 and Chr19 and amplicons for IDH1/IDH2 analysis. The 1p/19q SNP-IDH panel consistently identified IDH1/IDH2 mutations. In 49 of 60 cases (81.7%), it provided the same 1p/19q results obtained by FISH. In the remaining 11 cases, the 1p/19q SNP-IDH panel uncovered partial chromosome imbalances as a result of interstitial amplification or deletion of the regions where the FISH probes map, leading to a mistaken overdiagnosis of 1p/19q codeletion by FISH. The 1p/19q SNP-IDH next-generation sequencing panel allows reliable analysis of the 1p/19q codeletion and IDH1/IDH2 mutation at the same time. The panel not only allows resolution of difficult cases but also represents a cost-effective alternative to standard molecular diagnostics procedures.
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Affiliation(s)
- Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy; Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giorgia Acquaviva
- Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Gianluca Marucci
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Antonio De Leo
- Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Thais Maloberti
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Viviana Sanza
- Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Enrico Di Oto
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Enrico Franceschi
- Department of Oncology, Azienda Unitá Sanitaria Locale (AUSL) Bologna, Bologna, Italy
| | - Antonella Mura
- Department of Oncology, Azienda Unitá Sanitaria Locale (AUSL) Bologna, Bologna, Italy
| | - Moira Ragazzi
- Anatomic Pathology Unit, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Silvia Serra
- Anatomic Pathology Unit, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Elisabetta Froio
- Anatomic Pathology Unit, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessandra Bisagni
- Anatomic Pathology Unit, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alba A Brandes
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy; Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanni Tallini
- Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy.
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17
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Sakamoto Y, Zaha S, Suzuki Y, Seki M, Suzuki A. Application of long-read sequencing to the detection of structural variants in human cancer genomes. Comput Struct Biotechnol J 2021; 19:4207-4216. [PMID: 34527193 PMCID: PMC8350331 DOI: 10.1016/j.csbj.2021.07.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/20/2021] [Accepted: 07/25/2021] [Indexed: 01/02/2023] Open
Abstract
In recent years, the so-called long-read sequencing technology has had a substantial impact on various aspects of genome sciences. Here, we introduce recent studies of cancerous structural variants (SVs) using long-read sequencing technologies, namely Pacific Biosciences (PacBio) sequencers, Oxford Nanopore Technologies (ONT) sequencers, and linked-read methods. By taking advantage of long-read lengths, these technologies have enabled the precise detection of SVs, including long insertions by transposable elements, such as LINE-1. In addition to SV detection, the epigenome status (including DNA methylation and haplotype information) surrounding SV loci has also been unveiled by long-read sequencing technologies, to identify the effects of SVs. Among the various research fields in which long-read sequencing has been applied, cancer genomics has shown the most remarkable advances. In fact, many studies are beginning to shed light on the detection of SVs and the elucidation of their complex structures in various types of cancer. In the particular case of cancers, we summarize the technical limitations of the application of this technology to the analysis of clinical samples. We will introduce recent achievements from this viewpoint. However, a similar approach will be started for other applications in the near future. Therefore, by complementing the current short-read sequencing analysis, long-read sequencing should reveal the complex nature of human genomes in their healthy and disease states, which will open a new opportunity for a better understanding of disease development and for a novel strategy for drug development.
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Affiliation(s)
- Yoshitaka Sakamoto
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Suzuko Zaha
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
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18
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Miyake Y, Fujii K, Nakamaura T, Ikegaya N, Matsushita Y, Gobayashi Y, Iwashita H, Udaka N, Kumagai J, Murata H, Takemoto Y, Yamanaka S, Ichimura K, Tateishi K, Yamamoto T. IDH-Mutant Astrocytoma With Chromosome 19q13 Deletion Manifesting as an Oligodendroglioma-Like Morphology. J Neuropathol Exp Neurol 2021; 80:247-253. [PMID: 33432322 DOI: 10.1093/jnen/nlaa161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Partial deletions in chromosomes 1p and 19q are found in a subset of astrocytic tumors; however, it remains unclear how these alterations affect their histological features and prognosis. Herein, we present 3 cases of isocitrate dehydrogenase (IDH)-mutant astrocytoma with chromosome 19q13 deletion. In the first case, the primary tumor harbored an IDH1 mutation with chromosome 1p/19q partial deletions, which covered 19q13 and exhibited a durable initial response to radiotherapy and temozolomide (TMZ) treatment. However, the tumor lost the chromosome 1p/19q partial deletions at recurrence and became resistant to TMZ. Histologically, an oligodendroglioma-like feature was found in the primary tumor but not in the recurrent tumor. Capicua transcriptional repressor (CIC), located on 19q13, was less expressed in the primary tumor but was highly expressed in the recurrent tumor. Similar histological findings were observed in 2 other astrocytic tumors with IDH1 or IDH2 mutations. These tumors also had chromosome 19q13 deletion, including the CIC gene, weakly expressed CIC, and oligodendroglioma-like morphology. These tumors recurred at 6 and 32 months, respectively. These findings suggest that IDH-mutant astrocytoma with chromosome 19q13 partial deletion, including the CIC gene, may induce an oligodendroglioma-like phenotype, but the clinical prognosis may not be similar to that of genetically defined oligodendroglioma.
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Affiliation(s)
- Yohei Miyake
- From the Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Keita Fujii
- From the Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Neurosurgery, Yokohama City Minato Red Cross Hospital, Yokohama, Japan
| | - Taishi Nakamaura
- From the Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naoki Ikegaya
- From the Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Yuko Matsushita
- From the Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | | | - Hiromichi Iwashita
- Department of Pathology, Yokohama City University Hospital, Yokohama, Japan
| | - Naoko Udaka
- Department of Pathology, Yokohama City University Hospital, Yokohama, Japan
| | - Jiro Kumagai
- Department of Pathology, Yokohama City Minato Red Cross Hospital, Yokohama, Japan
| | - Hidetoshi Murata
- From the Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Yasunori Takemoto
- Department of Neurosurgery, Yokohama City Minato Red Cross Hospital, Yokohama, Japan
| | - Shoji Yamanaka
- Department of Pathology, Yokohama City University Hospital, Yokohama, Japan
| | - Koichi Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Kensuke Tateishi
- From the Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Tetsuya Yamamoto
- From the Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
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19
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Sharaf R, Pavlick DC, Frampton GM, Cooper M, Jenkins J, Danziger N, Haberberger J, Alexander BM, Cloughesy T, Yong WH, Liau LM, Nghiemphu PL, Ji M, Lai A, Ramkissoon SH, Albacker LA. FoundationOne CDx testing accurately determines whole arm 1p19q codeletion status in gliomas. Neurooncol Adv 2021; 3:vdab017. [PMID: 33778493 PMCID: PMC7986056 DOI: 10.1093/noajnl/vdab017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Molecular profiling of gliomas is vital to ensure diagnostic accuracy, inform prognosis, and identify clinical trial options for primary and recurrent tumors. This study aimed to determine the accuracy of reporting the whole arm 1p19q codeletion status from the FoundationOne platform. METHODS Testing was performed on glioma samples as part of clinical care and analyzed up to 395 cancer-associated genes (including IDH1/2). The whole arm 1p19q codeletion status was predicted from the same assay using a custom research-use only algorithm, which was validated using 463 glioma samples with available fluorescence in-situ hybridization (FISH) data. For 519 patients with available outcomes data, progression-free and overall survival were assessed based on whole arm 1p19q codeletion status derived from sequencing data. RESULTS Concordance between 1p19q status based on FISH and our algorithm was 96.7% (449/463) with a positive predictive value (PPV) of 100% and a positive percent agreement (PPA) of 91.0%. All discordant samples were positive for codeletion by FISH and harbored genomic alterations inconsistent with oligodendrogliomas. Median overall survival was 168 months for the IDH1/2 mutant, codeleted group, and 122 months for IDH1/2 mutant-only (hazard ratio (HR): 0.42; P < .05). CONCLUSIONS 1p19q codeletion status derived from FoundationOne testing is highly concordant with FISH results. Genomic profiling may be a reliable substitute for traditional FISH testing while also providing IDH1/2 status.
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Affiliation(s)
- Radwa Sharaf
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Dean C Pavlick
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Garrett M Frampton
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Maureen Cooper
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Jacqueline Jenkins
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Natalie Danziger
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - James Haberberger
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Brian M Alexander
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Timothy Cloughesy
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - William H Yong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Phioanh L Nghiemphu
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Matthew Ji
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Albert Lai
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Shakti H Ramkissoon
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Lee A Albacker
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
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Three-Dimensional Nuclear Telomere Profiling as a Biomarker for Recurrence in Oligodendrogliomas: A Pilot Study. Int J Mol Sci 2020; 21:ijms21228539. [PMID: 33198352 PMCID: PMC7696868 DOI: 10.3390/ijms21228539] [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: 08/11/2020] [Revised: 10/27/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022] Open
Abstract
Mechanisms of recurrence in oligodendrogliomas are poorly understood. Recurrence might be driven by telomere dysfunction-mediated genomic instability. In a pilot study, we investigated ten patients with oligodendrogliomas at the time of diagnosis (first surgery) and after recurrence (second surgery) using three-dimensional nuclear telomere analysis performed with quantitative software TeloView® (Telo Genomics Corp, Toronto, Ontario, Canada). 1p/19q deletion status of each patient was determined by fluorescent in situ hybridization on touch preparation slides. We found that a very specific 3D telomeric profile was associated with two pathways of recurrence in oligodendrogliomas independent of their 1p/19q status: a first group of 8 patients displayed significantly different 3D telomere profiles between both surgeries (p < 0.0001). Their recurrence happened at a mean of 231.375 ± 117.42 days and a median time to progression (TTP) of 239 days, a period defined as short-term recurrence; and a second group of three patients displayed identical 3D telomere profiles between both surgery samples (p > 0.05). Their recurrence happened at a mean of 960.666 ± 86.19 days and a median TTP of 930 days, a period defined as long-term recurrence. Our results suggest a potential link between nuclear telomere architecture and telomere dysfunction with time to recurrence in oligodendrogliomas, independently of the 1p/19q status.
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21
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Kong Z, Jiang C, Zhang Y, Liu S, Liu D, Liu Z, Chen W, Liu P, Yang T, Lyu Y, Zhao D, You H, Wang Y, Ma W, Feng F. Thin-Slice Magnetic Resonance Imaging-Based Radiomics Signature Predicts Chromosomal 1p/19q Co-deletion Status in Grade II and III Gliomas. Front Neurol 2020; 11:551771. [PMID: 33192984 PMCID: PMC7642873 DOI: 10.3389/fneur.2020.551771] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Objective: Chromosomal 1p/19q co-deletion is recognized as a diagnostic, prognostic, and predictive biomarker in lower grade glioma (LGG). This study aims to construct a radiomics signature to non-invasively predict the 1p/19q co-deletion status in LGG. Methods: Ninety-six patients with pathology-confirmed LGG were retrospectively included and randomly assigned into training (n = 78) and validation (n = 18) dataset. Three-dimensional contrast-enhanced T1 (3D-CE-T1)-weighted magnetic resonance (MR) images and T2-weighted MR images were acquired, and simulated-conventional contrast-enhanced T1 (SC-CE-T1)-weighted images were generated. One hundred and seven shape, first-order, and texture radiomics features were extracted from each imaging modality and selected using the least absolute shrinkage and selection operator on the training dataset. A 3D-radiomics signature based on 3D-CE-T1 and T2-weighted features and a simulated-conventional (SC) radiomics signature based on SC-CE-T1 and T2-weighted features were established using random forest. The radiomics signatures were validated independently and evaluated using receiver operating characteristic (ROC) curves. Tumors with IDH mutations were also separately assessed. Results: Four radiomics features were selected to construct the 3D-radiomics signature and displayed accuracies of 0.897 and 0.833, areas under the ROC curves (AUCs) of 0.940 and 0.889 in the training and validation datasets, respectively. The SC-radiomics signature was constructed with 4 features, but the AUC values were lower than that of the 3D signature. In the IDH-mutated subgroup, the 3D-radiomics signature presented AUCs of 0.950–1.000. Conclusions: The MRI-based radiomics signature can differentiate 1p/19q co-deletion status in LGG with or without predetermined IDH status. 3D-CE-T1-weighted radiomics features are more favorable than SC-CE-T1-weighted features in the establishment of radiomics signatures.
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Affiliation(s)
- Ziren Kong
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chendan Jiang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yiwei Zhang
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sirui Liu
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Delin Liu
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zeyu Liu
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenlin Chen
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Penghao Liu
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianrui Yang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuelei Lyu
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Radiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Dachun Zhao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui You
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenbin Ma
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Feng Feng
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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22
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Ball MK, Kollmeyer TM, Praska CE, McKenna ML, Giannini C, Raghunathan A, Jentoft ME, Lachance DH, Kipp BR, Jenkins RB, Ida CM. Frequency of false-positive FISH 1p/19q codeletion in adult diffuse astrocytic gliomas. Neurooncol Adv 2020; 2:vdaa109. [PMID: 33205043 PMCID: PMC7654379 DOI: 10.1093/noajnl/vdaa109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Background Oligodendroglioma is genetically defined by concomitant IDH (IDH1/IDH2) mutation and whole-arm 1p/19q codeletion. Codeletion of 1p/19q traditionally evaluated by fluorescence in situ hybridization (FISH) cannot distinguish partial from whole-arm 1p/19q codeletion. Partial 1p/19q codeletion called positive by FISH is diagnostically a "false-positive" result. Chromosomal microarray (CMA) discriminates partial from whole-arm 1p/19q codeletion. Herein, we aimed to estimate the frequency of partial 1p/19q codeletion that would lead to a false-positive FISH result. Methods FISH 1p/19q codeletion test probe coordinates were mapped onto Oncoscan CMA data to determine the rate of partial 1p/19q codeletion predicted to be positive by FISH. Diffuse astrocytic gliomas with available CMA data (2015-2018) were evaluated and classified based on IDH1-R132H/ATRX/p53 immunohistochemistry, IDH/TERT promoter targeted sequencing, and/or CMA according to classification updates. Predicted false-positive cases were verified by FISH whenever possible. Results The overall estimated false-positive FISH 1p/19q codeletion rate was 3.6% (8/223). Predicted false positives were verified by FISH in 6 (of 8) cases. False-positive rates did not differ significantly (P = .49) between IDH-mutant (4.6%; 4/86) and IDH-wildtype (2.9%; 4/137) tumors. IDH-wildtype false positives were all WHO grade IV, whereas IDH-mutant false positives spanned WHO grades II-IV. Testing for 1p/19q codeletion would not have been indicated for most false positives based on current classification recommendations. Conclusion Selective 1p/19q codeletion testing and cautious interpretation for conflicting FISH and histopathological findings are recommended to avoid potential misdiagnosis.
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Affiliation(s)
- Matthew K Ball
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas M Kollmeyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Corinne E Praska
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Michelle L McKenna
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Aditya Raghunathan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark E Jentoft
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Cristiane M Ida
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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23
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Molecular Classification of Diffuse Gliomas. Can J Neurol Sci 2020; 47:464-473. [DOI: 10.1017/cjn.2020.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
ABSTRACT:Technological advances in the field of molecular genetics have improved the ability to classify brain tumors into subgroups with distinct clinical features and important therapeutic implications. The World Health Organization’s newest update on classification of gliomas (2016) incorporated isocitrate dehydrogenase 1 and 2 mutations, ATRX loss, 1p/19q codeletion status, and TP53 mutations to allow for improved classification of glioblastomas, low-grade and anaplastic gliomas. This paper reviews current advances in the understanding of diffuse glioma classification and the impact of molecular markers and DNA methylation studies on survival of patients with these tumors. We also discuss whether the classification and grading of diffuse gliomas should be based on histological findings, molecular markers, or DNA methylation subgroups in future iterations of the classification system.
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24
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Gatzert S, Durgam A, Raghuram K, Agarwal A. Primary diffuse leptomeningeal oligodendrogliomatosis with an isolated 1p deletion. Br J Neurosurg 2019:1-6. [PMID: 31752539 DOI: 10.1080/02688697.2019.1688253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We report a case of primary diffuse leptomeningeal oligodendrogliomatosis with an isolated 1p deletion confirmed by fluorescent in situ hybridization (FISH) analysis in 52 year-old man. The MRI scan in a patient presenting with progressive headache, nausea and diplopia revealed diffuse leptomeningeal thickening and enhancement without definitive evidence of an intraparenchymal lesion. Biopsy of thickened, enhancing meninges within the left sylvian fissure revealed subarachnoid proliferation of oligodendroglial cells with varying degrees of de-differentiation and sparing of the underlying cortex. An isolated 1p deletion was confirmed by FISH analysis. This is the first reported adult case of a 1p deletion in primary diffuse leptomeningeal oligodendrogliomatosis.
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Affiliation(s)
- Samuel Gatzert
- Department of Radiology, UT Southwestern Medical School, Dallas, TX, USA
| | - Aditya Durgam
- Department of Radiology, UT Southwestern Medical School, Dallas, TX, USA
| | | | - Amit Agarwal
- Department of Radiology, UT Southwestern Medical School, Dallas, TX, USA
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25
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Rau A, Flister M, Rui H, Auer PL. Exploring drivers of gene expression in the Cancer Genome Atlas. Bioinformatics 2019; 35:62-68. [PMID: 30561551 DOI: 10.1093/bioinformatics/bty551] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
Motivation The Cancer Genome Atlas (TCGA) has greatly advanced cancer research by generating, curating and publicly releasing deeply measured molecular data from thousands of tumor samples. In particular, gene expression measures, both within and across cancer types, have been used to determine the genes and proteins that are active in tumor cells. Results To more thoroughly investigate the behavior of gene expression in TCGA tumor samples, we introduce a statistical framework for partitioning the variation in gene expression due to a variety of molecular variables including somatic mutations, transcription factors (TFs), microRNAs, copy number alternations, methylation and germ-line genetic variation. As proof-of-principle, we identify and validate specific TFs that influence the expression of PTPN14 in breast cancer cells. Availability and implementation We provide a freely available, user-friendly, browseable interactive web-based application for exploring the results of our transcriptome-wide analyses across 17 different cancers in TCGA at http://ls-shiny-prod.uwm.edu/edge_in_tcga. All TCGA Open Access tier data are available at the Broad Institute GDAC Firehose and were downloaded using the TCGA2STAT R package. TCGA Controlled Access tier data are available via controlled access through the Genomic Data Commons (GDC). R scripts used to download, format and analyze the data and produce the interactive R/Shiny web app have been made available on GitHub at https://github.com/andreamrau/EDGE-in-TCGA.
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Affiliation(s)
- Andrea Rau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Michael Flister
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.,Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA.,Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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26
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D'Haene N, Meléndez B, Blanchard O, De Nève N, Lebrun L, Van Campenhout C, Salmon I. Design and Validation of a Gene-Targeted, Next-Generation Sequencing Panel for Routine Diagnosis in Gliomas. Cancers (Basel) 2019; 11:cancers11060773. [PMID: 31167453 PMCID: PMC6627812 DOI: 10.3390/cancers11060773] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/17/2019] [Accepted: 05/31/2019] [Indexed: 01/06/2023] Open
Abstract
The updated 2016 World Health Organization (WHO) classification system for gliomas integrates molecular alterations and histology to provide a greater diagnostic and prognostic utility than the previous, histology-based classification. The increasing number of markers that are tested in a correct diagnostic procedure makes gene-targeted, next-generation sequencing (NGS) a powerful tool in routine pathology practice. We designed a 14-gene NGS panel specifically aimed at the diagnosis of glioma, which allows simultaneous detection of mutations and copy number variations, including the 1p/19q-codeletion and Epidermal Growth Factor Receptor (EGFR) amplification. To validate this panel, we used reference mutated DNAs, nontumor and non-glioma samples, and 52 glioma samples that were previously characterized. The panel was then prospectively applied to 91 brain lesions. A specificity of 100% and sensitivity of 99.4% was achieved for mutation detection. Orthogonal methods, such as in situ hybridization and immunohistochemical techniques, were used for validation, which showed high concordance. The molecular alterations that were identified allowed diagnosis according to the updated WHO criteria, and helped in the differential diagnosis of difficult cases. This NGS panel is an accurate and sensitive method, which could replace multiple tests for the same sample. Moreover, it is a rapid and cost-effective approach that can be easily implemented in the routine diagnosis of gliomas.
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Affiliation(s)
- Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Bárbara Meléndez
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Oriane Blanchard
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Nancy De Nève
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Laetitia Lebrun
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Claude Van Campenhout
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Isabelle Salmon
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
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27
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Evangelou P, Groll M, Oppermann H, Gaunitz F, Eisenlöffel C, Müller W, Eschrich K, Schänzer A, Nestler U. Assessment of ApoC1, LuzP6, C12orf75 and OCC-1 in cystic glioblastoma using MALDI-TOF mass spectrometry, immunohistochemistry and qRT-PCR. Med Mol Morphol 2019; 52:217-225. [PMID: 31006040 PMCID: PMC6885021 DOI: 10.1007/s00795-019-00223-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/08/2019] [Indexed: 12/24/2022]
Abstract
Mass spectrometric analysis of glioblastoma cyst fluids has disclosed a protein peak with m/z 6424–6433. Among the proteins, potentially generating this peak are ApoC1 and LuzP6. To further elucidate protein expression of glioblastoma cells, we analyzed MALDI–TOF results of cyst fluid, performed immunohistochemistry and mRNA analysis. MALDI–TOF protein extraction from 24 glioblastoma cyst fluids was performed with a weak cation exchange. 50 glioblastoma samples were stained with two custom-made antibodies against LuzP6 and commercial antibodies against ApoC1, C12orf75 and OCC-1 and analyzed. For mRNA detection, 16 tissue samples were stored in RNAlater, extracted using the miRNeasy kit and reversely transcribed. For 12 patients, synopsis of results from all three examinations was possible. MALDI–TOF confirmed the peak at 6433 Da in 75% of samples. Immunohistochemically, LuzP6 was detected in 92% (LuzP61–29) and 96% (LuzP630–58) of samples and ApoC1 in 66%. Mean mRNA levels were highest for ApoC1, followed by LuzP6. No correlation between mRNA expression, immunohistochemical staining and intensity of the MALDI–TOF peaks was found. An unequivocal identification of one protein as the source for the 6433 peak is not possible, but our results point to ApoC1 and LuzP6 as the underlying proteins.
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Affiliation(s)
- Petros Evangelou
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Mathias Groll
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Henry Oppermann
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Frank Gaunitz
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Christian Eisenlöffel
- Institute of Neuropathology, University Hospital Leipzig, Liebigstrasse 26, 04103, Leipzig, Germany
| | - Wolf Müller
- Institute of Neuropathology, University Hospital Leipzig, Liebigstrasse 26, 04103, Leipzig, Germany
| | - Klaus Eschrich
- Rudolf Schoenheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103, Leipzig, Germany
| | - Anne Schänzer
- Institute of Neuropathology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Ulf Nestler
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany.
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28
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Wood MD, Halfpenny AM, Moore SR. Applications of molecular neuro-oncology - a review of diffuse glioma integrated diagnosis and emerging molecular entities. Diagn Pathol 2019; 14:29. [PMID: 30967140 PMCID: PMC6457044 DOI: 10.1186/s13000-019-0802-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/12/2019] [Indexed: 11/10/2022] Open
Abstract
Insights into the molecular underpinnings of primary central nervous system tumors have radically changed the approach to tumor diagnosis and classification. Diagnostic emphasis has shifted from the morphology of a tumor under the microscope to an integrated approach based on morphologic and molecular features, including gene mutations, chromosomal copy number alterations, and gene rearrangements. In 2016, the World Health Organization provided guidelines for making an integrated diagnosis that incorporates both morphologic and molecular features in a subset of brain tumors. The integrated diagnosis now applies to infiltrating gliomas, a category that includes diffusely infiltrating astrocytoma grades II, III, and IV, and oligodendroglioma, grades II and III, thereby encompassing the most common primary intra-axial central nervous system tumors. Other neoplasms such as medulloblastoma, embryonal tumor with multilayered rosettes, certain supratentorial ependymomas, and atypical teratoid/rhabdoid tumor are also eligible for integrated diagnosis, which can sometimes be aided by characteristic immunohistochemical markers. Since 2016, advances in molecular neuro-oncology have resulted in periodic updates and clarifications to the integrated diagnostic approach. These advances reflect expanding knowledge on the molecular pathology of brain tumors, but raise a challenge in rapidly incorporating new molecular findings into diagnostic practice. This review provides a background on the molecular characteristics of primary brain tumors, emphasizing the molecular basis for classification of infiltrating gliomas, the most common entities that are eligible for an integrated diagnosis. We then discuss entities within the diffuse gliomas that do not receive an integrated diagnosis by WHO 2016 criteria, but have distinctive molecular features that are important to recognize because their clinical behavior can influence clinical management and prognosis. Particular attention is given to the histone H3 G34R/G34V mutant astrocytomas, an entity to consider when faced with an infiltrating glioma in the cerebral hemisphere of children and young adults, and to the group of histologically lower grade diffuse astrocytic gliomas with molecular features of glioblastoma, an important category of tumors to recognize due to their aggressive clinical behavior.
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Affiliation(s)
- Matthew D Wood
- OHSU Department of Pathology, Division of Anatomic Pathology, Section of Neuropathology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97213, USA.
| | - Aaron M Halfpenny
- OHSU Department of Pathology, Division of Anatomic Pathology, Section of Neuropathology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97213, USA
| | - Stephen R Moore
- Knight Diagnostic Laboratories and Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, USA
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29
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Romo CG, Palsgrove DN, Sivakumar A, Elledge CR, Kleinberg LR, Chaichana KL, Gocke CD, Rodriguez FJ, Holdhoff M. Widely metastatic IDH1-mutant glioblastoma with oligodendroglial features and atypical molecular findings: a case report and review of current challenges in molecular diagnostics. Diagn Pathol 2019; 14:16. [PMID: 30738431 PMCID: PMC6368694 DOI: 10.1186/s13000-019-0793-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/01/2019] [Indexed: 01/06/2023] Open
Abstract
Background Gliomas with 1p/19q-codeletion as well as mutation of isocitrate dehydrogenase (IDH) 1 are typically characterized as oligodendrogliomas with comparatively good response to treatment with radiation and chemotherapy. Case presentation We present the case of a 28-year-old man with an IDH1 and TP53 mutant high grade glioma with abnormalities in chromosomes 1 and 19 suggestive of anaplastic oligodendroglioma that rapidly progressed to widespread metastatic disease. Biopsy of a liver lesion confirmed metastasis of the patient’s known brain primary and chemotherapy with temozolomide was initiated. The patient’s rapidly growing tumor burden with fulminant liver failure and tumor lysis led to multisystem failure of which the patient died. Further molecular testing illustrated features more consistent with glioblastoma: multiple large chromosomal aberrations including loss of whole chromosome 1 and 2q; gain/amplification of MYCN, MET, and CDK4; loss of CDKN2A/B; and an ATRX mutation. Conclusion This case illustrates the importance of higher level molecular diagnostic testing for patients with particularly aggressive disease progression that is not concordant with standard prognoses. Additional data on cases with atypical alterations of 1p and 19q are needed to better understand the distinct biology of these cancers so that appropriate therapies can be developed. Electronic supplementary material The online version of this article (10.1186/s13000-019-0793-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carlos G Romo
- Brain Cancer Program, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1550 Orleans Street, 1M16, Baltimore, MD, 21287, USA
| | - Doreen N Palsgrove
- Department of Pathology, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Ananyaa Sivakumar
- Brain Cancer Program, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1550 Orleans Street, 1M16, Baltimore, MD, 21287, USA
| | - Christen R Elledge
- Department of Radiation Oncology, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Lawrence R Kleinberg
- Department of Radiation Oncology, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Kaisorn L Chaichana
- Department of Neurosurgery, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Fausto J Rodriguez
- Department of Pathology, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Matthias Holdhoff
- Brain Cancer Program, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1550 Orleans Street, 1M16, Baltimore, MD, 21287, USA.
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30
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Villa C, Miquel C, Mosses D, Bernier M, Di Stefano AL. The 2016 World Health Organization classification of tumours of the central nervous system. Presse Med 2018; 47:e187-e200. [PMID: 30449638 DOI: 10.1016/j.lpm.2018.04.015] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/30/2018] [Accepted: 04/04/2018] [Indexed: 11/16/2022] Open
Abstract
The 2016 WHO classification of tumours of the central nervous system represents the new paradigm among the specialists in the brain tumours and proposes a new approach combining histopathological and molecular features into diagnosis named 'integrated diagnosis'. The aim of this challenge is to overstep the interobserver variability of diagnosis based on previous classifications in order to ensure homogenous biological entities with a more accurate clinical significance. Over the last two decades, several molecular aberrations into gliomagenesis were highlighted and then confirmed as emerging biomarkers through prognostic stratification. In particular, IDH1/IDH2 genes mutations, 1p/19q codeletion and mutations in genes encoding histone H3 variants drastically changed the knowledge about diffuse gliomas inducing the WHO working group to consider the phenotype-genotype approach. In the present review, the historical development of the diagnosis of brain tumours from the 3D spatial configuration to the integration of multidisciplinary data up to recent molecular alterations is discussed. At the national level, the RENOCLIP network (supported by the National Cancer Institute) contributes to improve the standardization of histological diagnosis and the facilitation of access to molecular biology platforms for the detection of genetic aberrations necessary for integrated diagnosis. Importantly, the French POLA cohort allowed to test the clinical impact of the new criteria introduced by 2016 WHO classification of CNS tumours confirming the high accuracy in predicting clinical behaviour for diffuse gliomas.
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Affiliation(s)
- Chiara Villa
- Foch Hospital, Department of Pathological Cytology and Anatomy, 40, rue Worth, 92151 Suresnes, France; Inserm U1016, CNRS UMR 8104, Paris Descartes University, Cochin Institute, 24, rue du faubourg Saint-Jacques, 75014 Paris, France; University of Liège, CHU de Liège, Department of Endocrinology, Sart Tilman B35, 4000 Liège, Belgium.
| | - Catherine Miquel
- Saint-Louis Hospital, Department of Pathological Anatomy, 75010 Paris, France
| | - Dominic Mosses
- University of Manchester, Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, M13 9PL Manchester M13 9PT, Manchester, United Kingdom
| | - Michèle Bernier
- Foch Hospital, Department of Pathological Cytology and Anatomy, 40, rue Worth, 92151 Suresnes, France
| | - Anna Luisa Di Stefano
- Foch Hospital, Department of Neurology, 75013 Suresnes, France; Inserm U1127, CNRS UMR 7225, Sorbonne University UPMC Université Paris 06, Brain and Spine Institute, 92151 Paris, France
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A new method of identifying glioblastoma subtypes and creation of corresponding animal models. Oncogene 2018; 37:4781-4791. [PMID: 29769617 DOI: 10.1038/s41388-018-0305-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 12/17/2022]
Abstract
Glioblastoma (GBM) accounts for up to 50% of brain parenchymal tumors. It is the most malignant type of brain cancer with very poor survival and limited remedies. Cancer subtyping is important for cancer research and therapy. Here, we report a new subtyping method for GBM based on the genetic alterations of CDKN2A and TP53 genes. CDKN2A and TP53 are the most frequently mutated genes with mutation rates of 60 and 30%, respectively. We found that patients with deletion of CDKN2A possess worse survival than those with TP53 mutation. Interestingly, survival of patients with both TP53 mutation and CDKN2A deletion is no worse than for those with only one of these genetic alterations, but similar to those with TP53 mutation alone. Next, we investigated differences in the gene expression profile between TP53 and CDKN2A samples. Consistent with the survival data, the samples with both TP53 mutation and CDKN2A deletion showed a gene expression profile similar to those samples with TP53 mutation alone. Finally, we found that activation of RAS pathway plus Cdkn2a/b silencing can induce GBM, in a similar way to tumor induction by RAS activation plus TP53 silencing. In conclusion, we show that the genetic alterations of CDKN2A and TP53 may be used to stratify GBM, and the new animal models matching this stratification method were generated.
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Abstract
The most aggressive brain malignancy, glioblastoma, accounts for 60-70% of all gliomas and is uniformly fatal. According to the molecular signature, glioblastoma is divided into four subtypes (proneural, neural, classical, and mesenchymal), each with its own genetic background. The Cancer Genome Atlas project provides information about the most common genetic changes in glioblastoma. They involve mutations in TP53, TERT, and PTEN, and amplifications in EFGR, PDGFRA, CDK4, CDK6, MDM2, and MDM4. Recently, epigenetics was used to demonstrate the oncogenic roles of miR-124, miR-137, and miR-128. The most important findings so far are mutations in IDH1/2 and MGMT promoter methylation, which are routinely used as predictive biomarkers in patient care. Current clinical treatment leaves patients with only a 10% chance for 5-year survival. Attempts to define the mutational profile of glioblastoma to identify clinically relevant changes have not yet yielded significant results. This can be attributed to inter- and intra-tumor heterogeneity that is present in most glioblastomas, as well as hypermutation that appears as a consequence of chemotherapy. The evolving field of radiogenomics aims to classify glioblastoma using a combination of magnetic resonance imaging and genomic information. In the era of genomic medicine, next-generation sequencing is extensively used in glioblastoma research because it can detect multiple changes in a single biological sample; its potential in detecting circulating cell-free DNA has been tested in cerebrospinal fluid and plasma, and it shows promise in the examination of the cellular content of extracellular vesicles as a potential source of biomarkers. Next-generation sequencing is making its way into glioblastoma diagnostics. Gene panels like GlioSeq, which includes the most commonly mutated genes, are currently being tested on snap frozen and formalin fixed paraffin embedded tissues. This new methodology is helping to define the "next generation of glioblastomas" - clinically defined and better understood, with greater potential to improve patient care. However, limitations of the necessary infrastructure, space for data storage, technical expertise, and data ownership need to be considered carefully.
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Affiliation(s)
- Ivana Jovčevska
- a Medical Center for Molecular Biology, Institute of Biochemistry, Faculty of Medicine , University of Ljubljana , Ljubljana , Slovenia
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Akagi Y, Yoshimoto K, Hata N, Kuga D, Hatae R, Amemiya T, Sangatsuda Y, Suzuki SO, Iwaki T, Mizoguchi M, Iihara K. Reclassification of 400 consecutive glioma cases based on the revised 2016WHO classification. Brain Tumor Pathol 2018; 35:81-89. [PMID: 29569163 DOI: 10.1007/s10014-018-0313-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 03/19/2018] [Indexed: 12/11/2022]
Abstract
In this study, we reclassified 400 consecutive glioma cases including pediatric cases, using the revised 2016 WHO classification with samples collected from the Kyushu University Brain Tumor Bank. The IDH1/2, H3F3A, key genetic markers in the 2016 classification, were analyzed using high-resolution melting, with DNA extracted from frozen tissues. The 1p/19q codeletions were evaluated using a microsatellite-based loss of heterozygosity analysis, with 18 markers, to detect loss of the entire chromosome arm. In the integrated diagnosis, 29 oligodendroglioma cases and 28 anaplastic oligodendroglioma cases were diagnosed as "IDH-mutant and 1p/19q-codeleted," while 2 oligodendroglioma cases and 5 anaplastic oligodendroglioma cases were diagnosed as not otherwise specified (NOS). These "NOS" cases were either IDH-mutants or 1p/19q-codeleted, although characteristic oligodendroglial features were evident histologically. Better overall survival of patients with oligodendroglioma correlated with the molecular characteristic of "IDH-mutant and 1p/19q-codeleted," rather than the WHO grade. Eleven "glioblastoma, IDH-wild-type" cases were classified as "1p/19q-codeleted", however, chromosome 10 loss was also detected in 10 out of 11 cases. The 2016 WHO criteria for glioma classification leads to better diagnosis of patients. However, there are technical pitfalls and problems to be solved in the molecular analysis of routine diagnostics.
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Affiliation(s)
- Yojiro Akagi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan.
| | - Nobuhiro Hata
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan
| | - Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan
| | - Takeo Amemiya
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan
| | - Satoshi O Suzuki
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Toru Iwaki
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Kitakyushu Municipal Medical Center, Kitakyushu, Japan
| | - Koji Iihara
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan
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34
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Dolezal JM, Dash AP, Prochownik EV. Diagnostic and prognostic implications of ribosomal protein transcript expression patterns in human cancers. BMC Cancer 2018. [PMID: 29530001 PMCID: PMC5848553 DOI: 10.1186/s12885-018-4178-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background Ribosomes, the organelles responsible for the translation of mRNA, are comprised of four rRNAs and ~ 80 ribosomal proteins (RPs). Although canonically assumed to be maintained in equivalent proportions, some RPs have been shown to possess differential expression across tissue types. Dysregulation of RP expression occurs in a variety of human diseases, notably in many cancers, and altered expression of some RPs correlates with different tumor phenotypes and patient survival. Little work has been done, however, to characterize overall patterns of RP transcript (RPT) expression in human cancers. Methods To investigate the impact of global RPT expression patterns on tumor phenotypes, we analyzed RPT expression of ~ 10,000 human tumors and over 700 normal tissues from The Cancer Genome Atlas (TCGA) using t-distributed stochastic neighbor embedding (t-SNE). Clusters of tumors identified by t-SNE were then analyzed with chi-squared and t-tests to compare phenotypic data, ANOVA to compare individual RPT expression, and Kaplan-Meier curves to assess survival differences. Results Normal tissues and cancers possess distinct and readily discernible RPT expression patterns that are independent of their absolute levels of expression. In tumors, RPT patterning is distinct from that of normal tissues, identifies heretofore unrecognized tumor subtypes, and in many cases correlates with molecular, pathological, and clinical features, including survival. Conclusions RPT expression patterns are both tissue-specific and tumor-specific. These could be used as a powerful and novel method of tumor classification, offering a potential clinical tool for prognosis and therapeutic stratification. Electronic supplementary material The online version of this article (10.1186/s12885-018-4178-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James M Dolezal
- Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.
| | - Arie P Dash
- Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Edward V Prochownik
- Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.,Department of Microbiology and Molecular Genetics, The University of Pittsburgh Medical Center; The University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, USA
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35
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Nguyen T, Tagett R, Diaz D, Draghici S. A novel approach for data integration and disease subtyping. Genome Res 2017; 27:2025-2039. [PMID: 29066617 PMCID: PMC5741060 DOI: 10.1101/gr.215129.116] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 09/13/2017] [Indexed: 11/24/2022]
Abstract
Advances in high-throughput technologies allow for measurements of many types of omics data, yet the meaningful integration of several different data types remains a significant challenge. Another important and difficult problem is the discovery of molecular disease subtypes characterized by relevant clinical differences, such as survival. Here we present a novel approach, called perturbation clustering for data integration and disease subtyping (PINS), which is able to address both challenges. The framework has been validated on thousands of cancer samples, using gene expression, DNA methylation, noncoding microRNA, and copy number variation data available from the Gene Expression Omnibus, the Broad Institute, The Cancer Genome Atlas (TCGA), and the European Genome-Phenome Archive. This simultaneous subtyping approach accurately identifies known cancer subtypes and novel subgroups of patients with significantly different survival profiles. The results were obtained from genome-scale molecular data without any other type of prior knowledge. The approach is sufficiently general to replace existing unsupervised clustering approaches outside the scope of bio-medical research, with the additional ability to integrate multiple types of data.
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Affiliation(s)
- Tin Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, Nevada 89557, USA
| | - Rebecca Tagett
- Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
| | - Diana Diaz
- Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
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36
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Pesenti C, Paganini L, Fontana L, Veniani E, Runza L, Ferrero S, Bosari S, Menghi M, Marfia G, Caroli M, Silipigni R, Guerneri S, Tabano S, Miozzo M. Mass spectrometry-based assay for the molecular diagnosis of glioma: concomitant detection of chromosome 1p/19q codeletion, and IDH1, IDH2, and TERT mutation status. Oncotarget 2017; 8:57134-57148. [PMID: 28915660 PMCID: PMC5593631 DOI: 10.18632/oncotarget.19103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/19/2017] [Indexed: 02/06/2023] Open
Abstract
The World Health Organization recently revised the diagnosis of glioma, to integrate molecular parameters, including IDH mutations and codeletion (loss of heterozygosity; LOH) of chromosome arms 1p/19q, into the definitions of adult glioma histological subtypes. Mutations in the TERT promoter may also be useful for glioma diagnosis and prognosis. The integration of molecular markers into routine diagnosis requires their rapid and reliable assessment. We propose a MassARRAY (MS)-based test that can identify 1p/19q codeletion using quantitative SNP genotyping and, simultaneously, characterize hotspot mutations in the IDH1, IDH2, and TERT genes in tumor DNA. We determined the reliability of the MS approach testing 50 gliomas and comparing the MS results with those obtained by standard methods, such as short tandem repeat genotyping, array comparative genomic hybridization (array-CGH) and Fluorescence In Situ Hybridization (FISH) for 1p/19q codeletion and Sanger sequencing for hotspots mutations. The results indicate that MS is suitable for the accurate, rapid, and cost-effective evaluation of chromosome deletions combined with hotspot mutation detection. This MS approach could be similarly exploited in evaluation of LOH in other situations of clinical and/or research importance.
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Affiliation(s)
- Chiara Pesenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Leda Paganini
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laura Fontana
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Emanuela Veniani
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Letterio Runza
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Ferrero
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Silvano Bosari
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Giovanni Marfia
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
- Neurosurgery Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Manuela Caroli
- Neurosurgery Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Rosamaria Silipigni
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvana Guerneri
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvia Tabano
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Monica Miozzo
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
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Chen R, Smith-Cohn M, Cohen AL, Colman H. Glioma Subclassifications and Their Clinical Significance. Neurotherapeutics 2017; 14:284-297. [PMID: 28281173 PMCID: PMC5398991 DOI: 10.1007/s13311-017-0519-x] [Citation(s) in RCA: 426] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The impact of targeted therapies in glioma has been modest. All the therapies that have demonstrated a significant survival benefit for gliomas in Phase III trials, including radiation, chemotherapy (temozolomide and PCV [procarbazine, lomustine, vincristine]), and tumor-treating fields, are based on nonspecific targeting of proliferating cells. Recent advances in the molecular understanding of gliomas suggest some potential reasons for the failure of more targeted therapies in gliomas. Specifically, the histologic-based glioma classification is composed of multiple different molecular subtypes with distinct biology, natural history, and prognosis. As a result of these insights, the diagnosis and classification of gliomas have recently been updated by the World Health Organization. However, these changes and other novel observations regarding glioma biomarkers and subtypes highlight several clinical challenges. First, the field is faced with the difficulty of reinterpreting the results of prior studies and retrospective data using the new classifications to clarify prognostic assessments and treatment recommendations for patients. Second, the new classifications and insights require rethinking the design and stratification of future clinical trials. Last, these observations provide the essential framework for the development and testing of new specific targeted therapies for particular glioma subtypes. This review aims to summarize the current literature regarding glioma subclassifications and their clinical relevance in this evolving field.
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Affiliation(s)
- Ricky Chen
- Department of Neurology, Clinical Neurosciences Center, University of Utah, Salt Lake City, UT, USA
| | - Matthew Smith-Cohn
- Department of Neurology, Clinical Neurosciences Center, University of Utah, Salt Lake City, UT, USA
| | - Adam L Cohen
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Howard Colman
- Department of Neurosurgery, Huntsman Cancer Institute and Clinical Neuroscience Center, University of Utah, Salt Lake City, UT, USA.
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Reifenberger G, Wirsching HG, Knobbe-Thomsen CB, Weller M. Advances in the molecular genetics of gliomas - implications for classification and therapy. Nat Rev Clin Oncol 2016; 14:434-452. [PMID: 28031556 DOI: 10.1038/nrclinonc.2016.204] [Citation(s) in RCA: 409] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genome-wide molecular-profiling studies have revealed the characteristic genetic alterations and epigenetic profiles associated with different types of gliomas. These molecular characteristics can be used to refine glioma classification, to improve prediction of patient outcomes, and to guide individualized treatment. Thus, the WHO Classification of Tumours of the Central Nervous System was revised in 2016 to incorporate molecular biomarkers - together with classic histological features - in an integrated diagnosis, in order to define distinct glioma entities as precisely as possible. This paradigm shift is markedly changing how glioma is diagnosed, and has important implications for future clinical trials and patient management in daily practice. Herein, we highlight the developments in our understanding of the molecular genetics of gliomas, and review the current landscape of clinically relevant molecular biomarkers for use in classification of the disease subtypes. Novel approaches to the genetic characterization of gliomas based on large-scale DNA-methylation profiling and next-generation sequencing are also discussed. In addition, we illustrate how advances in the molecular genetics of gliomas can promote the development and clinical translation of novel pathogenesis-based therapeutic approaches, thereby paving the way towards precision medicine in neuro-oncology.
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Affiliation(s)
- Guido Reifenberger
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Moorenstrasse. 5, D-40225 Düsseldorf, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Heidelberg, partner site Essen/Düsseldorf, Moorenstrasse 5, D-40225 Düsseldorf, Germany
| | - Hans-Georg Wirsching
- Department of Neurology and Brain Tumour Centre, Cancer Centre Zürich, University Hospital and University of Zürich, Frauenklinikstrasse 26, CH-8091 Zürich, Switzerland.,Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, C3-111, PO Box 19024, Seattle, Washington 98109-1024, USA
| | - Christiane B Knobbe-Thomsen
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Moorenstrasse. 5, D-40225 Düsseldorf, Germany
| | - Michael Weller
- Department of Neurology and Brain Tumour Centre, Cancer Centre Zürich, University Hospital and University of Zürich, Frauenklinikstrasse 26, CH-8091 Zürich, Switzerland
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Dubbink HJ, Atmodimedjo PN, van Marion R, Krol NMG, Riegman PHJ, Kros JM, van den Bent MJ, Dinjens WNM. Diagnostic Detection of Allelic Losses and Imbalances by Next-Generation Sequencing: 1p/19q Co-Deletion Analysis of Gliomas. J Mol Diagn 2016; 18:775-786. [PMID: 27461031 DOI: 10.1016/j.jmoldx.2016.06.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 05/06/2016] [Accepted: 06/01/2016] [Indexed: 02/05/2023] Open
Abstract
Cancer cells are genomically unstable and accumulate tumor type-specific molecular aberrations, which may represent hallmarks for predicting prognosis and targets for therapy. Co-deletion of chromosomes 1p and 19q marks gliomas with an oligodendroglioma component and predicts a better prognosis and response to chemotherapy. In the current study, we present a novel method to detect chromosome 1p/19q co-deletion or loss of heterozygosity (LOH) in a diagnostic setting, based on single-nucleotide polymorphism (SNP) analysis and next-generation sequencing (NGS). We selected highly polymorphic SNPs distributed evenly over both chromosome arms. To experimentally determine the sensitivity and specificity of targeted SNP analysis, we used DNAs extracted from 49 routine formalin-fixed, paraffin-embedded glioma tissues and compared the outcome with diagnostic microsatellite-based LOH analysis and calculated estimates. We show that targeted SNP analysis by NGS allows reliable detection of 1p and/or 19q deletion in a background of 70% of normal cells according to calculated outcomes, is more sensitive than microsatellite-based LOH analysis, and requires much less DNA. This specific and sensitive SNP assay is broadly applicable for simultaneous allelic imbalance analysis of multiple genomic regions and can be incorporated easily into NGS mutation analyses. The combined mutation and chromosomal imbalance analysis in a single NGS assay is suited perfectly for routine glioma diagnostics and other diagnostic molecular pathology applications.
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Affiliation(s)
- Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Niels M G Krol
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter H J Riegman
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martin J van den Bent
- Department of Neuro-Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
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40
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Basaran R, Uslu S, Gucluer B, Onoz M, Isik N, Tiryaki M, Yakicier C, Sav A, Elmaci I. Impact of 1p/19q codeletion on the diagnosis and prognosis of different grades of meningioma. Br J Neurosurg 2016; 30:571-6. [PMID: 27173440 DOI: 10.1080/02688697.2016.1181155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Meningiomas are one of the most common tumours to affect the central nervous system. Genetic mutations are important in meningeal tumourigenesis, progression and prognosis. In this study, we aimed to examine the effect of 1p/19q deletion on the diagnosis and prognosis of meningioma subtypes using the fluorescence in situ hybridization (FISH) method. METHODS Twenty-four patients with meningioma were retrospectively studied. Tumour samples were obtained from 10 typical, 11 atypical and three anaplastic malignant meningiomas. The most representative tumour sections were screened for 1p/19q deletion using the FISH method. RESULTS Of the 24 patients, eight were women (33.3%) and 16 (66.7%) were men. The mean age was 56.6 years. The higher-grade meningioma was usually seen in males and had a higher rate of deletion on 1p (p = 0.001). There was a statistically significant difference between the grades and the rate of deletion on 19q (p = 0.042) and between the grades and the rates of polysomy, monosomy and amplification on 19q (p = 0.002; p = 0.001; p = 0.002, respectively). There was no statistical difference between 1p/19q codeletion and the grades of meningioma (p > 0.05). We detected higher level of Ki-67 in the condition of codeletion but did not find a statistical difference (p = 0.0553). CONCLUSION Deletion on 1p, as well as deletion, polysomy, monosomy and amplification on 19q, are detected more frequently in high grade meningiomas. This amplification is most likely due to the amplification of oncogenes.
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Affiliation(s)
- Recep Basaran
- a Department of Neurosurgery , Istanbul Medeniyet University, Goztepe Education and Research Hospital , Istanbul , Turkey
| | - Serap Uslu
- b Department of Histology and Embryology , Istanbul Medeniyet University School of Medicine , Istanbul , Turkey
| | - Berrin Gucluer
- c Department of Pathology , Istanbul Medeniyet University, Goztepe Education and Research Hospital , Istanbul , Turkey
| | - Mustafa Onoz
- d Department of Neurosurgery , Memorial Hospital , Istanbul , Turkey
| | - Nejat Isik
- a Department of Neurosurgery , Istanbul Medeniyet University, Goztepe Education and Research Hospital , Istanbul , Turkey
| | - Mehmet Tiryaki
- e Department of Neurosurgery , Dr. Lutfi Kirdar Kartal Education and Research Hospital , Istanbul , Turkey
| | - Cengiz Yakicier
- f Department of Molecular Genetics, Acibadem University School of Medicine , Istanbul , Turkey
| | - Aydin Sav
- g Department of Pathology, Acibadem University School of Medicine , Istanbul , Turkey
| | - Ilhan Elmaci
- d Department of Neurosurgery , Memorial Hospital , Istanbul , Turkey
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Ikemura M, Shibahara J, Mukasa A, Takayanagi S, Aihara K, Saito N, Aburatani H, Fukayama M. Utility of ATRX immunohistochemistry in diagnosis of adult diffuse gliomas. Histopathology 2016; 69:260-7. [PMID: 26741321 DOI: 10.1111/his.12927] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/04/2016] [Indexed: 12/31/2022]
Abstract
AIMS We performed an immunohistochemical analysis of alpha-thalassaemia/mental retardation syndrome X-linked (ATRX) expression in adult diffuse gliomas, with reference to clinicopathological and genetic features, to determine the utility of this analysis in diagnostic practice. METHODS AND RESULTS A total of 193 adult diffuse gliomas underwent immunohistochemical analysis. In areas in which internal controls, neurones, glia and blood vessels were properly stained, the ATRX immunoreactivity of tumour cells was either almost totally absent or completely retained in all cases. There was perfect concordance between the immunohistochemical results and ATRX mutation status, which was known in 19 cases. ATRX loss was observed in 54.5, 30.8 and 0.0% of grades II/III astrocytomas, oligoastrocytomas and oligodendrogliomas, respectively, and 12.7% of glioblastomas. In grades II/III gliomas, most ATRX-loss cases (92.3%) had IDH1/2 mutations. ATRX loss was associated significantly with TP53 mutation and p53 overexpression (P < 0.001), but was never accompanied by 1p/19q co-deletion. IDH1/2 mutation in ATRX-loss tumours was less frequent in glioblastomas than in grades II/III gliomas (P < 0.001). Further, there was no significant association between ATRX loss and p53 overexpression in glioblastomas. ATRX-loss glioblastomas affected younger patients (P < 0.001) and occurred more frequently in locations other than the cerebral hemispheres (P = 0.006). Most grades II/III gliomas (93.3%) were categorized into three molecular subtypes based on the status of IDH1/2 mutation, ATRX immunohistochemistry and 1p/19q co-deletion. CONCLUSIONS Distinct histological and molecular characteristics of adult diffuse gliomas with and without ATRX immunoreactivity indicate the utility of ATRX immunohistochemistry in diagnostic practice.
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Affiliation(s)
- Masako Ikemura
- Department of Pathology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Junji Shibahara
- Department of Pathology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Akitake Mukasa
- Department of Neurosurgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Shunsaku Takayanagi
- Department of Neurosurgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Koki Aihara
- Department of Neurosurgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.,Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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Masui K, Mischel PS, Reifenberger G. Molecular classification of gliomas. HANDBOOK OF CLINICAL NEUROLOGY 2016; 134:97-120. [PMID: 26948350 DOI: 10.1016/b978-0-12-802997-8.00006-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The identification of distinct genetic and epigenetic profiles in different types of gliomas has revealed novel diagnostic, prognostic, and predictive molecular biomarkers for refinement of glioma classification and improved prediction of therapy response and outcome. Therefore, the new (2016) World Health Organization (WHO) classification of tumors of the central nervous system breaks with the traditional principle of diagnosis based on histologic criteria only and incorporates molecular markers. This will involve a multilayered approach combining histologic features and molecular information in an "integrated diagnosis". We review the current state of diagnostic molecular markers for gliomas, focusing on isocitrate dehydrogenase 1 or 2 (IDH1/IDH2) gene mutation, α-thalassemia/mental retardation syndrome X-linked (ATRX) gene mutation, 1p/19q co-deletion and telomerase reverse transcriptase (TERT) promoter mutation in adult tumors, as well as v-raf murine sarcoma viral oncogene homolog B1 (BRAF) and H3 histone family 3A (H3F3A) aberrations in pediatric gliomas. We also outline prognostic and predictive molecular markers, including O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation, and discuss the potential clinical relevance of biologic glioblastoma subtypes defined by integration of multiomics data. Commonly used methods for individual marker detection as well as novel large-scale DNA methylation profiling and next-generation sequencing approaches are discussed. Finally, we illustrate how advances in molecular diagnostics affect novel strategies of targeted therapy, thereby raising new challenges and identifying new leads for personalized treatment of glioma patients.
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Affiliation(s)
- Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Shinjku-ku, Tokyo, Japan; Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA, USA
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany.
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43
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Cahill DP, Sloan AE, Nahed BV, Aldape KD, Louis DN, Ryken TC, Kalkanis SN, Olson JJ. The role of neuropathology in the management of patients with diffuse low grade glioma: A systematic review and evidence-based clinical practice guideline. J Neurooncol 2015; 125:531-49. [PMID: 26530263 DOI: 10.1007/s11060-015-1909-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/29/2015] [Indexed: 10/22/2022]
Abstract
TARGET POPULATION Adult patients (age ≥18 years) who have suspected low-grade diffuse glioma. QUESTION What are the optimal neuropathological techniques to diagnose low-grade diffuse glioma in the adult? RECOMMENDATION LEVEL I: Histopathological analysis of a representative surgical sample of the lesion should be used to provide the diagnosis of low-grade diffuse glioma. LEVEL III Both frozen section and cytopathologic/smear evaluation should be used to aid the intra-operative assessment of low-grade diffuse glioma diagnosis. A resection specimen is preferred over a biopsy specimen, to minimize the potential for sampling error issues. TARGET POPULATION Patients with histologically-proven WHO grade II diffuse glioma. QUESTION In adult patients (age ≥18 years) with histologically-proven WHO grade II diffuse glioma, is testing for IDH1 mutation (R132H and/or others) warranted? If so, is there a preferred method? RECOMMENDATION LEVEL II IDH gene mutation assessment, via IDH1 R132H antibody and/or IDH1/2 mutation hotspot sequencing, is highly-specific for low-grade diffuse glioma, and is recommended as an additional test for classification and prognosis. TARGET POPULATION Patients with histologically-proven WHO grade II diffuse glioma. QUESTION In adult patients (age ≥18 years) with histologically-proven WHO grade II diffuse glioma, is testing for 1p/19q loss warranted? If so, is there a preferred method? RECOMMENDATION LEVEL III 1p/19q loss-of-heterozygosity testing, by FISH, array-CGH or PCR, is recommended as an additional test in oligodendroglial cases for prognosis and potential treatment planning. TARGET POPULATION Patients with histologically-proven WHO grade II diffuse glioma. QUESTION In adult patients (age ≥18 years) with histologically-proven WHO grade II diffuse glioma, is MGMT promoter methylation testing warranted? If so, is there a preferred method? RECOMMENDATION There is insufficient evidence to recommend methyl-guanine methyl-transferase (MGMT) promoter methylation testing as a routine for low-grade diffuse gliomas. It is recommended that patients be enrolled in properly designed clinical trials to assess the value of this and related markers for this target population. TARGET POPULATION Patients with histologically-proven WHO grade II diffuse glioma. QUESTION In adult patients (age ≥18 years) with histologically-proven WHO grade II diffuse glioma, is Ki-67/MIB1 immunohistochemistry warranted? If so, is there a preferred method to quantitate results? RECOMMENDATION LEVEL III Ki67/MIB1 immunohistochemistry is recommended as an option for prognostic assessment.
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Affiliation(s)
- Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, 32 Fruit Street, Yankey 9E, Boston, MA, 02114, USA.
| | | | | | - Kenneth D Aldape
- University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - David N Louis
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Timothy C Ryken
- Department of Neurosurgery, Kansas University Medical Center, Kansas City, KS, USA
| | - Steven N Kalkanis
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, USA
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Pinkham M, Telford N, Whitfield G, Colaco R, O'Neill F, McBain C. FISHing Tips: What Every Clinician Should Know About 1p19q Analysis in Gliomas Using Fluorescence in situ Hybridisation. Clin Oncol (R Coll Radiol) 2015; 27:445-53. [DOI: 10.1016/j.clon.2015.04.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/01/2015] [Accepted: 04/07/2015] [Indexed: 11/25/2022]
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Hayashi S, Sasaki H, Kimura T, Abe T, Nakamura T, Kitamura Y, Miwa T, Kameyama K, Hirose Y, Yoshida K. Molecular-genetic and clinical characteristics of gliomas with astrocytic appearance and total 1p19q loss in a single institutional consecutive cohort. Oncotarget 2015; 6:15871-81. [PMID: 25991674 PMCID: PMC4599243 DOI: 10.18632/oncotarget.3869] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 04/02/2015] [Indexed: 12/18/2022] Open
Abstract
The prognostic significance of 1p19q loss in astrocytic gliomas has been inconclusive.We collected 57 gliomas with total 1p19q loss from among 218 cases of WHO grade-II/III gliomas operated at Keio University Hospital between 1990 and 2010. These tumors were classified as oligodendroglial or "astrocytic" by a WHO-criteria-based institutional diagnosis. Chromosomal copy number aberrations (CNAs), IDH 1/2 mutations, MGMT promoter methylation, and expression of p53 and ATRX were assessed. Survival outcome was compared between the two histological groups.Of the 57 codeleted gliomas, 37, 16, and four were classified as oligodendroglial, "astrocytic", and unclassified, respectively. Comparative genomic hybridization revealed that although chromosome 7q/7 gain was more frequent in "astrocytic" gliomas, other CNAs occurred at a similar frequency in both groups. None of the "astrocytic" gliomas showed p53 accumulation, and ATRX loss was found in three of the 15 "astrocytic" gliomas. The estimated overall survival (OS) curves in the patients with codeleted oligodendroglial and "astrocytic" gliomas overlapped, and the median OS was 187 and 184 months, respectively. Histopathological re-assessment by a single pathologist showed consistent results.Gliomas with total 1p19q loss with "astrocytic" features have molecular and biological characteristics comparable to those of oligodendroglial tumors.
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Affiliation(s)
- Saeko Hayashi
- Department of Neurosurgery, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Hikaru Sasaki
- Department of Neurosurgery, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Tokuhiro Kimura
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
- Present address: Department of Pathology, Yamaguchi University Graduate, School of Medicine, Minami-kogushi, Ube, Yamaguchi, Japan
| | - Takayuki Abe
- Center for Clinical Research, Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Takumi Nakamura
- Department of Neurosurgery, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Yohei Kitamura
- Department of Neurosurgery, Saiseikai Utsunomiya Hospital, Takebayashi, Utsunomiya, Tochigi, Japan
| | - Tomoru Miwa
- Department of Neurosurgery, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Kaori Kameyama
- Division of Diagnostic Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Yuichi Hirose
- Department of Neurosurgery, Fujita Health University School of Medicine, Kutsukake-cho, Toyoake, Aichi, Japan
| | - Kazunari Yoshida
- Department of Neurosurgery, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
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46
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Suzuki H, Aoki K, Chiba K, Sato Y, Shiozawa Y, Shiraishi Y, Shimamura T, Niida A, Motomura K, Ohka F, Yamamoto T, Tanahashi K, Ranjit M, Wakabayashi T, Yoshizato T, Kataoka K, Yoshida K, Nagata Y, Sato-Otsubo A, Tanaka H, Sanada M, Kondo Y, Nakamura H, Mizoguchi M, Abe T, Muragaki Y, Watanabe R, Ito I, Miyano S, Natsume A, Ogawa S. Mutational landscape and clonal architecture in grade II and III gliomas. Nat Genet 2015; 47:458-68. [PMID: 25848751 DOI: 10.1038/ng.3273] [Citation(s) in RCA: 601] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/13/2015] [Indexed: 12/16/2022]
Abstract
Grade II and III gliomas are generally slowly progressing brain cancers, many of which eventually transform into more aggressive tumors. Despite recent findings of frequent mutations in IDH1 and other genes, knowledge about their pathogenesis is still incomplete. Here, combining two large sets of high-throughput sequencing data, we delineate the entire picture of genetic alterations and affected pathways in these glioma types, with sensitive detection of driver genes. Grade II and III gliomas comprise three distinct subtypes characterized by discrete sets of mutations and distinct clinical behaviors. Mutations showed significant positive and negative correlations and a chronological hierarchy, as inferred from different allelic burdens among coexisting mutations, suggesting that there is functional interplay between the mutations that drive clonal selection. Extensive serial and multi-regional sampling analyses further supported this finding and also identified a high degree of temporal and spatial heterogeneity generated during tumor expansion and relapse, which is likely shaped by the complex but ordered processes of multiple clonal selection and evolutionary events.
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Affiliation(s)
- Hiromichi Suzuki
- 1] Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan. [2] Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Kosuke Aoki
- 1] Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan. [2] Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Kenichi Chiba
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University School of Medicine, Nagoya, Japan
| | - Atsushi Niida
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuya Motomura
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Fumiharu Ohka
- 1] Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan. [2] Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Takashi Yamamoto
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Kuniaki Tanahashi
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Melissa Ranjit
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | | | | | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yasunobu Nagata
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Aiko Sato-Otsubo
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Hiroko Tanaka
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masashi Sanada
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yutaka Kondo
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Hideo Nakamura
- Department of Neurosurgery, Kumamoto University, Kumamoto, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuya Abe
- Department of Neurosurgery, Oita University, Oita, Japan
| | - Yoshihiro Muragaki
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Reiko Watanabe
- Division of Clinical Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Ichiro Ito
- Division of Clinical Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Satoru Miyano
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Atsushi Natsume
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
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Abstract
The WHO grading scheme for glial neoplasms assigns Grade II to 5 distinct tumors of astrocytic or oligodendroglial lineage: diffuse astrocytoma, oligodendroglioma, oligoastrocytoma, pleomorphic xanthoastrocytoma, and pilomyxoid astrocytoma. Although commonly referred to collectively as among the "low-grade gliomas," these 5 tumors represent molecularly and clinically unique entities. Each is the subject of active basic research aimed at developing a more complete understanding of its molecular biology, and the pace of such research continues to accelerate. Additionally, because managing and predicting the course of these tumors has historically proven challenging, translational research regarding Grade II gliomas continues in the hopes of identifying novel molecular features that can better inform diagnostic, prognostic, and therapeutic strategies. Unfortunately, the basic and translational literature regarding the molecular biology of WHO Grade II gliomas remains nebulous. The authors' goal for this review was to present a comprehensive discussion of current knowledge regarding the molecular characteristics of these 5 WHO Grade II tumors on the chromosomal, genomic, and epigenomic levels. Additionally, they discuss the emerging evidence suggesting molecular differences between adult and pediatric Grade II gliomas. Finally, they present an overview of current strategies for using molecular data to classify low-grade gliomas into clinically relevant categories based on tumor biology.
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Affiliation(s)
- Nicholas F Marko
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.
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Ducray F, Dehais C, Delattre JY. An overview of current and future treatment options for adults anaplastic oligodendroglial tumors. Expert Opin Orphan Drugs 2014. [DOI: 10.1517/21678707.2014.928617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Collins VP, Ichimura K, Di Y, Pearson D, Chan R, Thompson LC, Gabe R, Brada M, Stenning SP. Prognostic and predictive markers in recurrent high grade glioma; results from the BR12 randomised trial. Acta Neuropathol Commun 2014; 2:68. [PMID: 24952577 PMCID: PMC4229733 DOI: 10.1186/2051-5960-2-68] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 06/04/2014] [Indexed: 02/07/2023] Open
Abstract
We evaluated the prognostic and predictive value of a range of molecular changes in the setting of a randomised trial comparing standard PCV (procarbazine, CCNU (1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea) and vincristine) chemotherapy with the standard temozolomide (TMZ) 5-day (200 mg/m2/day) schedule and a 21-day (100 mg/m2/day) schedule in chemo-naïve, high-grade glioma (non-oligodendroglial tumours; WHO (World Health Organisation) grades III and IV) patients at first progression following radiotherapy. 354 samples (79.2%) from the first operation of the 447 randomised patients provided enough tumour DNA for some or all parts of the study. Genome-wide array comparative genomic hybridisation (aCGH), mutation analysis of IDH1/2 and TP53 and methylation analyses of the MGMT CpG-island was done. 84% of grade III tumours and 17% of grade IV had IDH1 or IDH2 mutations that conferred a better prognosis in both; MGMT methylation (defined as average value across 16 CpGs ≥ 10%) occurred in 75% of tumours and was also associated with improved survival. Both were of independent prognostic value after accounting for clinical factors and tumour grade. None of the molecular changes investigated gave clear evidence of a predictive benefit of TMZ over PCV or 21-day TMZ over 5-day TMZ although power was limited and a role for MGMT methylation could not be ruled out. Loss of 1p and 19q was seen in only 4 patients although hemizygous loss of 1p36 occurred in 20%. The findings support reports that IDH1/2 mutations and MGMT methylation can be used in addition to tumour grade and clinical factors to predict survival in patients with recurrent high grade gliomas when treated with any of the therapy regimes used.
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Abstract
PURPOSE OF REVIEW This review summarizes recent studies on the predictive value of molecular markers in adult gliomas, including 1p/19q codeletion, MGMT methylation, IDH mutation and markers identified using omics and next-generation sequencing studies. RECENT FINDINGS The long-term results of the Radiation Therapy Oncology Group and European Organization for Research and Treatment of Cancer trials in anaplastic oligodendroglial glioma have shown that the 1p/19q codeletion predicts an overall survival benefit from early PCV (procarbazine CCNU vincristine) chemotherapy. This benefit can also be predicted using gene expression-based molecular subtypes of gliomas while the predictive value of the IDH mutation in this context requires further study. In elderly patients with glioblastoma, the analysis of MGMT methylation status in two phase III trials suggests that this alteration may guide treatment decisions; however, this finding still needs confirmation in prospective studies. Omics and next-generation sequencing studies have identified additional potential predictive markers. In particular, IDH mutations, BRAF V600E mutations and FGFR gene fusions might predict efficacy of therapies targeted against these alterations. SUMMARY Currently, the 1p/19q codeletion is the only well established predictive marker with clinical utility. However, it is likely that other molecular markers such as MGMT methylation, IDH mutation and those identified using omics and next-generation sequencing studies will further guide treatment decisions in adult gliomas.
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