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Jeising S, Nickel AC, Trübel J, Felsberg J, Picard D, Leprivier G, Wolter M, Huynh MK, Olivera MB, Kaulich K, Häberle L, Esposito I, Klau GW, Steinmann J, Beez T, Rapp M, Sabel M, Dietrich S, Remke M, Cornelius JF, Reifenberger G, Qin N. A clinically compatible in vitro drug-screening platform identifies therapeutic vulnerabilities in primary cultures of brain metastases. J Neurooncol 2024; 169:613-623. [PMID: 38985431 PMCID: PMC11341655 DOI: 10.1007/s11060-024-04763-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024]
Abstract
PURPOSE Brain metastases represent the most common intracranial tumors in adults and are associated with a poor prognosis. We used a personalized in vitro drug screening approach to characterize individual therapeutic vulnerabilities in brain metastases. METHODS Short-term cultures of cancer cells isolated from brain metastasis patients were molecularly characterized using next-generation sequencing and functionally evaluated using high-throughput in vitro drug screening to characterize pharmacological treatment sensitivities. RESULTS Next-generation sequencing identified matched genetic alterations in brain metastasis tissue samples and corresponding short-term cultures, suggesting that short-term cultures of brain metastases are suitable models for recapitulating the genetic profile of brain metastases that may determine their sensitivity to anti-cancer drugs. Employing a high-throughput in vitro drug screening platform, we successfully screened the cultures of five brain metastases for response to 267 anticancer compounds and related drug response to genetic data. Among others, we found that targeted treatment with JAK3, HER2, or FGFR3 inhibitors showed anti-cancer effects in individual brain metastasis cultures. CONCLUSION Our preclinical study provides a proof-of-concept for combining molecular profiling with in vitro drug screening for predictive evaluation of therapeutic vulnerabilities in brain metastasis patients. This approach could advance the use of patient-derived cancer cells in clinical practice and might eventually facilitate decision-making for personalized drug treatment.
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Affiliation(s)
- Sebastian Jeising
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Ann-Christin Nickel
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Johanna Trübel
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, University Hospital Düsseldorf, Düsseldorf, Germany
- Spatial & Functional Screening Core Facility, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Jörg Felsberg
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Daniel Picard
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, University Hospital Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Gabriel Leprivier
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Marietta Wolter
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - My Ky Huynh
- Department of Computer Science, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marlene B Olivera
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, University Hospital Düsseldorf, Düsseldorf, Germany
- Spatial & Functional Screening Core Facility, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Kerstin Kaulich
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Lena Häberle
- Institute of Pathology, Medical Faculty, Heinrich Heine University, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Irene Esposito
- Institute of Pathology, Medical Faculty, Heinrich Heine University, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Gunnar W Klau
- Department of Computer Science, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Julia Steinmann
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Thomas Beez
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Marion Rapp
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Michael Sabel
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Marc Remke
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, University Hospital Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center of Saarland, Homburg/Saar, Germany
| | - Jan F Cornelius
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Nan Qin
- Department of Hematology, Oncology, and Clinical Immunology, Medical Faculty, Heinrich Heine University, University Hospital Düsseldorf, Düsseldorf, Germany.
- Spatial & Functional Screening Core Facility, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University, and University Hospital Düsseldorf, Düsseldorf, Germany.
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf (MSSO ABCD), Düsseldorf, Germany.
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Hansen STE, Jacobsen KS, Kofoed MS, Petersen JK, Boldt HB, Dahlrot RH, Schulz MK, Poulsen FR. Prognostic factors to predict postoperative survival in patients with recurrent glioblastoma. World Neurosurg X 2024; 23:100308. [PMID: 38584878 PMCID: PMC10997900 DOI: 10.1016/j.wnsx.2024.100308] [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: 06/04/2023] [Revised: 11/27/2023] [Accepted: 02/21/2024] [Indexed: 04/09/2024] Open
Abstract
Background There are no generally accepted criteria for selecting patients with recurrent glioblastoma for surgery. This retrospective study in a Danish population-based cohort aimed to identify prognostic factors affecting postoperative survival after repeated surgery for recurrent glioblastoma and to test if the preoperative New Scale for Recurrent Glioblastoma Surgery (NSGS) developed by Park CK et al could assist in the selection of patients for repeat glioblastoma surgery. Methods Clinical data from 66 patients with recurrent glioblastoma and repeated surgery were analyzed. Kaplan-Meier plots were produced to illustrate survival in each of the three NSGS prognostic groups, and Cox proportional hazard regression was used to identify prognostic variables. Multivariable analysis was used to identify differences in survival in the three prognostic groups. Results Six variables significantly affected postoperative survival: preoperative Karnofsky Performance Status (KPS) < 70 (p = 0.002), decreased KPS after second surgery (p = 0.012), ependymal involvement (p = 0.002), tumor volume ≧ 50 cm3 (p = 0.021), age (p = 0.033) and Ki-67 (p = 0.005). Retrospective application of the criteria previously published by Park CK et al showed that median postoperative survival for the three prognostic groups was 390 days (0 points), 279 days (1 point), and 80 days (2 points), respectively. Conclusion Several prognostic variables to predict postoperative survival in patients with recurrent glioblastoma were identified and should be considered when selecting patient for repeat surgery. The NSGS scoring system was useful as there were significant differences in postoperative survival between its three prognostic groups.
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Affiliation(s)
- Stella TE. Hansen
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- BRIDGE (Brain Research Interdisciplinary Guided Excellence), University of Southern Denmark, Odense, Denmark
| | - Kasper S. Jacobsen
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- BRIDGE (Brain Research Interdisciplinary Guided Excellence), University of Southern Denmark, Odense, Denmark
| | - Mikkel S. Kofoed
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark
| | | | - Henning B. Boldt
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Rikke H. Dahlrot
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Mette K. Schulz
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- BRIDGE (Brain Research Interdisciplinary Guided Excellence), University of Southern Denmark, Odense, Denmark
| | - Frantz R. Poulsen
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- BRIDGE (Brain Research Interdisciplinary Guided Excellence), University of Southern Denmark, Odense, Denmark
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Yang J, Pu Z, Tao X, Liu J, Li K, Shi J, Qiao H, Fan X. Expression of KCNN4 in adult-type diffuse gliomas and its correlations with clinicopathological features and patient prognosis. Transl Oncol 2024; 44:101947. [PMID: 38555740 PMCID: PMC10998241 DOI: 10.1016/j.tranon.2024.101947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/19/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND The KCa3.1 channel (KCNN4) is extensively investigated as an oncogene in human cancers. The current study aimed to explore the clinicopathological significance of KCNN4 expression in patients with primary adult-type diffuse gliomas. METHODS Demographic, RNA-seq, and follow-up data of 477 patients were retrospectively reviewed. Patients were divided into the experimental and validation groups (278 and 199). KCNN4-related genes were determined by Pearson correlation analysis, and enrichment analyses and tumor-infiltrating immune cell assessments were applied to explore the potential mechanisms of KCNN4 involving glioma progression. The Kaplan-Meier method and the Cox regression analysis were used to evaluate the prognostic value of KCNN4 expression. RESULTS KCNN4 showed significantly higher expression level in glioblastoma, IDH-wildtype, followed by astrocytoma, IDH-mutant and oligodendroglioma, IDH-mutant and 1p/19q-codeleted (p < 0.001). Enrichment analyses and tumor-infiltrating immune cell assessments suggested that KCNN4 could involve glioma progression through extracellular regulation, affecting immune response, and modulating subcellular trafficking. At last, the Kaplan-Meier analysis showed that high KCNN4 expression was significantly correlated with poor progression-free and overall survival (p < 0.001 for both). While multivariate Cox regression analysis obtained an insignificant result. CONCLUSIONS KCNN4 was identified to be overexpressed in glioma cells and its expression level is positively related to tumor malignancy. It potentially participates in glioma biology by affecting extracellular regulation, subcellular trafficking, and immune escape. Additionally, high KCNN4 expression was correlated with poor survival outcomes of patients. The results can shed new light on the mechanisms of glioma progression, and provide a potential therapeutic target for treating gliomas.
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Affiliation(s)
- Jun Yang
- Beijing Neurosurgical Institute, Capital Medical University, 119 South 4th Ring Road West, Beijing 100070, China
| | - Zhuonan Pu
- Beijing Neurosurgical Institute, Capital Medical University, 119 South 4th Ring Road West, Beijing 100070, China
| | - Xiaorong Tao
- Beijing Neurosurgical Institute, Capital Medical University, 119 South 4th Ring Road West, Beijing 100070, China
| | - Jiajia Liu
- Beijing Neurosurgical Institute, Capital Medical University, 119 South 4th Ring Road West, Beijing 100070, China
| | - Ke Li
- Beijing Neurosurgical Institute, Capital Medical University, 119 South 4th Ring Road West, Beijing 100070, China
| | - Jiawei Shi
- Beijing Neurosurgical Institute, Capital Medical University, 119 South 4th Ring Road West, Beijing 100070, China
| | - Hui Qiao
- Beijing Neurosurgical Institute, Capital Medical University, 119 South 4th Ring Road West, Beijing 100070, China.
| | - Xing Fan
- Beijing Neurosurgical Institute, Capital Medical University, 119 South 4th Ring Road West, Beijing 100070, China.
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Tomoszková S, Škarda J, Lipina R. Potential Diagnostic and Clinical Significance of Selected Genetic Alterations in Glioblastoma. Int J Mol Sci 2024; 25:4438. [PMID: 38674026 PMCID: PMC11050250 DOI: 10.3390/ijms25084438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Glioblastoma is currently considered the most common and, unfortunately, also the most aggressive primary brain tumor, with the highest morbidity and mortality rates. The average survival of patients diagnosed with glioblastoma is 14 months, and only 2% of patients survive 3 years after surgery. Based on our clinical experience and knowledge from extensive clinical studies, survival is mainly related to the molecular biological properties of glioblastoma, which are of interest to the general medical community. Our study examined a total of 71 retrospective studies published from 2016 through 2022 and available on PubMed that deal with mutations of selected genes in the pathophysiology of GBM. In conclusion, we can find other mutations within a given gene group that have different effects on the prognosis and quality of survival of a patient with glioblastoma. These mutations, together with the associated mutations of other genes, as well as intratumoral heterogeneity itself, offer enormous potential for further clinical research and possible application in therapeutic practice.
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Affiliation(s)
- Silvia Tomoszková
- Neurosurgery Clinic, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic;
- Medical Faculty, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic;
| | - Jozef Škarda
- Medical Faculty, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic;
- Institute of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic
| | - Radim Lipina
- Neurosurgery Clinic, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic;
- Medical Faculty, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic;
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5
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Einarsson HB, Frederiksen AL, Pedersen IS, Ettrup MS, Wirenfeldt M, Boldt H, Nguyen N, Andersen MS, Bjarkam CR, Poulsen FR. PDP type brain tumor in association with multiple endocrine neoplasia type 1. Heliyon 2024; 10:e27418. [PMID: 38510015 PMCID: PMC10951523 DOI: 10.1016/j.heliyon.2024.e27418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/15/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Multiple endocrine neoplasia type 1 (MEN1) is a rare autosomal dominant syndrome caused by inactivating pathogenic variants in the tumor suppressor gene menin 1 on chromosome 11q13 (Falchetti et al., 2009). The syndrome is characterized by neoplasia in two or more endocrine glands and has a high degree of penetrance. Pathogenic germline multiple neoplasia type 1 variants primarily result in neoplasia affecting the parathyroid glands, the pancreatic islet cells, and the anterior pituitary in combination. Primary hyperparathyroidism is the most common pathological manifestation of the syndrome, followed by pancreatic neuroendocrine tumors. Important genetic confirmation has been provided showing that ependymoma should be considered as a neoplasm that can occur in patients with MEN1 (Kato et al., 1996; Cuevas-Ocampo et al., 2017). The biphasic histopathological tumor entity shown in the present case we name Pleomorphic Xanthoastocytoma grade 3 differential pathology (PDP) in association with Multiple Endocrine Neoplasia type 1. This MEN1 associated tumor subtype is an extension of the findings on MEN1 associated ependymoma, where we show that the clinical phenotype itself may potentially be triggered by a frameshift germline pathogenic variant for the MEN1 gene, in combination with cyclin-dependent kinase inhibitor 1B gene germline variant and cyclin dependent kinase inhibitor 2A somatic deletion downstream of menin.
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Affiliation(s)
| | - Anja Lisbeth Frederiksen
- Molecular Diagnostics, Aalborg University Hospital and Clinical Cancer Research Center, Aalborg University Hospital, Denmark
- Department of Clinical Medicine, Aalborg University, Denmark
| | - Inge Soekilde Pedersen
- Molecular Diagnostics, Aalborg University Hospital and Clinical Cancer Research Center, Aalborg University Hospital, Denmark
- Department of Clinical Medicine, Aalborg University, Denmark
| | | | - Martin Wirenfeldt
- Department of Pathology, Hospital South West Jutland, Denmark
- Department of Regional Health Research, University of Southern, Denmark
- Department of Clinical Research and BRIDGE, Brain Research – Inter-Disciplinary Guided Excellence, University of Southern, Denmark
| | - Henning Boldt
- Department of Pathology, Odense University Hospital, Denmark
| | - Nina Nguyen
- Department of Neuroradiology, Odense University Hospital, Denmark
| | | | | | - Frantz Rom Poulsen
- Department of Neurosurgery, Odense University Hospital, Denmark
- Department of Clinical Research and BRIDGE, Brain Research – Inter-Disciplinary Guided Excellence, University of Southern, Denmark
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6
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Shirai Y, Ueno T, Kojima S, Ikeuchi H, Kitada R, Koyama T, Takahashi F, Takahashi K, Ichimura K, Yoshida A, Sugino H, Mano H, Narita Y, Takahashi M, Kohsaka S. The development of a custom RNA-sequencing panel for the identification of predictive and diagnostic biomarkers in glioma. J Neurooncol 2024; 167:75-88. [PMID: 38363490 PMCID: PMC10978676 DOI: 10.1007/s11060-024-04563-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/02/2024] [Indexed: 02/17/2024]
Abstract
PURPOSE Various molecular profiles are needed to classify malignant brain tumors, including gliomas, based on the latest classification criteria of the World Health Organization, and their poor prognosis necessitates new therapeutic targets. The Todai OncoPanel 2 RNA Panel (TOP2-RNA) is a custom-target RNA-sequencing (RNA-seq) using the junction capture method to maximize the sensitivity of detecting 455 fusion gene transcripts and analyze the expression profiles of 1,390 genes. This study aimed to classify gliomas and identify their molecular targets using TOP2-RNA. METHODS A total of 124 frozen samples of malignant gliomas were subjected to TOP2-RNA for classification based on their molecular profiles and the identification of molecular targets. RESULTS Among 55 glioblastoma cases, gene fusions were detected in 11 cases (20%), including novel MET fusions. Seven tyrosine kinase genes were found to be overexpressed in 15 cases (27.3%). In contrast to isocitrate dehydrogenase (IDH) wild-type glioblastoma, IDH-mutant tumors, including astrocytomas and oligodendrogliomas, barely harbor fusion genes or gene overexpression. Of the 34 overexpressed tyrosine kinase genes, MDM2 and CDK4 in glioblastoma, 22 copy number amplifications (64.7%) were observed. When comparing astrocytomas and oligodendrogliomas in gene set enrichment analysis, the gene sets related to 1p36 and 19q were highly enriched in astrocytomas, suggesting that regional genomic DNA copy number alterations can be evaluated by gene expression analysis. CONCLUSIONS TOP2-RNA is a highly sensitive assay for detecting fusion genes, exon skipping, and aberrant gene expression. Alterations in targetable driver genes were identified in more than 50% of glioblastoma. Molecular profiling by TOP2-RNA provides ample predictive, prognostic, and diagnostic biomarkers that may not be identified by conventional assays and, therefore, is expected to increase treatment options for individual patients with glioma.
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Affiliation(s)
- Yukina Shirai
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
- Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8431, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Shinya Kojima
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Hiroshi Ikeuchi
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
- Department of General Thoracic Surgery, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8431, Japan
| | - Rina Kitada
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Takafumi Koyama
- Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Fumiyuki Takahashi
- Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8431, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8431, Japan
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8431, Japan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Hirokazu Sugino
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Masamichi Takahashi
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan.
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan.
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7
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Weller M, Felsberg J, Hentschel B, Gramatzki D, Kubon N, Wolter M, Reusche M, Roth P, Krex D, Herrlinger U, Westphal M, Tonn JC, Regli L, Maurage CA, von Deimling A, Pietsch T, Le Rhun E, Reifenberger G. Improved prognostic stratification of patients with isocitrate dehydrogenase-mutant astrocytoma. Acta Neuropathol 2024; 147:11. [PMID: 38183430 PMCID: PMC10771615 DOI: 10.1007/s00401-023-02662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 01/08/2024]
Abstract
Prognostic factors and standards of care for astrocytoma, isocitrate dehydrogenase (IDH)-mutant, CNS WHO grade 4, remain poorly defined. Here we sought to explore disease characteristics, prognostic markers, and outcome in patients with this newly defined tumor type. We determined molecular biomarkers and assembled clinical and outcome data in patients with IDH-mutant astrocytomas confirmed by central pathology review. Patients were identified in the German Glioma Network cohort study; additional cohorts of patients with CNS WHO grade 4 tumors were identified retrospectively at two sites. In total, 258 patients with IDH-mutant astrocytomas (114 CNS WHO grade 2, 73 CNS WHO grade 3, 71 CNS WHO grade 4) were studied. The median age at diagnosis was similar for all grades. Karnofsky performance status at diagnosis inversely correlated with CNS WHO grade (p < 0.001). Despite more intensive treatment upfront with higher grade, CNS WHO grade was strongly prognostic: median overall survival was not reached for grade 2 (median follow-up 10.4 years), 8.1 years (95% CI 5.4-10.8) for grade 3, and 4.7 years (95% CI 3.4-6.0) for grade 4. Among patients with CNS WHO grade 4 astrocytoma, median overall survival was 5.5 years (95% CI 4.3-6.7) without (n = 58) versus 1.8 years (95% CI 0-4.1) with (n = 12) homozygous CDKN2A deletion. Lower levels of global DNA methylation as detected by LINE-1 methylation analysis were strongly associated with CNS WHO grade 4 (p < 0.001) and poor outcome. MGMT promoter methylation status was not prognostic for overall survival. Histomolecular stratification based on CNS WHO grade, LINE-1 methylation level, and CDKN2A status revealed four subgroups of patients with significantly different outcomes. In conclusion, CNS WHO grade, global DNA methylation status, and CDKN2A homozygous deletion are prognostic in patients with IDH-mutant astrocytoma. Combination of these parameters allows for improved prediction of outcome. These data aid in designing upcoming trials using IDH inhibitors.
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Affiliation(s)
- Michael Weller
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland.
- Department of Neurology, University of Zurich, Zurich, Switzerland.
| | - Jörg Felsberg
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Bettina Hentschel
- Institute for Medical Informatics, Statistics and Epidemiology, University Leipzig, Leipzig, Germany
| | - Dorothee Gramatzki
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Nadezhda Kubon
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Marietta Wolter
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Matthias Reusche
- Institute for Medical Informatics, Statistics and Epidemiology, University Leipzig, Leipzig, Germany
| | - Patrick Roth
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurology, University of Zurich, Zurich, Switzerland
| | - Dietmar Krex
- Faculty of Medicine, Department of Neurosurgery, Technische Universität Dresden, University Hospital Carl Gustav Carus, Dresden, Germany
| | | | - Manfred Westphal
- Department of Neurosurgery, University of Hamburg, Hamburg, Germany
| | - Joerg C Tonn
- Department of Neurosurgery, Ludwig-Maximilians-University Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Luca Regli
- Department of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Neurosurgery, University of Zurich, Zurich, Switzerland
| | - Claude-Alain Maurage
- Department of Pathology, Centre Biologie Pathologie, Lille University Hospital, Hopital Nord, Lille, France
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Center (DKFZ), and German Cancer Consortium (DKTK), Partner Site Heidelberg, Heidelberg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn Medical Center, DGNN Brain Tumor Reference Center, Bonn, Germany
| | - Emilie Le Rhun
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurology, University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Neurosurgery, University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, Lille University Hospital, Lille, France
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Düsseldorf, Germany
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8
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Penkova A, Kuziakova O, Gulaia V, Tiasto V, Goncharov NV, Lanskikh D, Zhmenia V, Baklanov I, Farniev V, Kumeiko V. Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects. Front Mol Biosci 2023; 10:1216102. [PMID: 37908227 PMCID: PMC10613994 DOI: 10.3389/fmolb.2023.1216102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/04/2023] [Indexed: 11/02/2023] Open
Abstract
Glioma is one of the most intractable types of cancer, due to delayed diagnosis at advanced stages. The clinical symptoms of glioma are unclear and due to a variety of glioma subtypes, available low-invasive testing is not effective enough to be introduced into routine medical laboratory practice. Therefore, recent advances in the clinical diagnosis of glioma have focused on liquid biopsy approaches that utilize a wide range of techniques such as next-generation sequencing (NGS), droplet-digital polymerase chain reaction (ddPCR), and quantitative PCR (qPCR). Among all techniques, NGS is the most advantageous diagnostic method. Despite the rapid cheapening of NGS experiments, the cost of such diagnostics remains high. Moreover, high-throughput diagnostics are not appropriate for molecular profiling of gliomas since patients with gliomas exhibit only a few diagnostic markers. In this review, we highlighted all available assays for glioma diagnosing for main pathogenic glioma DNA sequence alterations. In the present study, we reviewed the possibility of integrating routine molecular methods into the diagnosis of gliomas. We state that the development of an affordable assay covering all glioma genetic aberrations could enable early detection and improve patient outcomes. Moreover, the development of such molecular diagnostic kits could potentially be a good alternative to expensive NGS-based approaches.
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Affiliation(s)
- Alina Penkova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Olga Kuziakova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Gulaia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vladlena Tiasto
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Nikolay V. Goncharov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Daria Lanskikh
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Zhmenia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Ivan Baklanov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Vladislav Farniev
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vadim Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
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9
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Sahm F, Brandner S, Bertero L, Capper D, French PJ, Figarella-Branger D, Giangaspero F, Haberler C, Hegi ME, Kristensen BW, Kurian KM, Preusser M, Tops BBJ, van den Bent M, Wick W, Reifenberger G, Wesseling P. Molecular diagnostic tools for the World Health Organization (WHO) 2021 classification of gliomas, glioneuronal and neuronal tumors; an EANO guideline. Neuro Oncol 2023; 25:1731-1749. [PMID: 37279174 PMCID: PMC10547522 DOI: 10.1093/neuonc/noad100] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Indexed: 06/08/2023] Open
Abstract
In the 5th edition of the WHO CNS tumor classification (CNS5, 2021), multiple molecular characteristics became essential diagnostic criteria for many additional CNS tumor types. For those tumors, an integrated, "histomolecular" diagnosis is required. A variety of approaches exists for determining the status of the underlying molecular markers. The present guideline focuses on the methods that can be used for assessment of the currently most informative diagnostic and prognostic molecular markers for the diagnosis of gliomas, glioneuronal and neuronal tumors. The main characteristics of the molecular methods are systematically discussed, followed by recommendations and information on available evidence levels for diagnostic measures. The recommendations cover DNA and RNA next-generation-sequencing, methylome profiling, and select assays for single/limited target analyses, including immunohistochemistry. Additionally, because of its importance as a predictive marker in IDH-wildtype glioblastomas, tools for the analysis of MGMT promoter methylation status are covered. A structured overview of the different assays with their characteristics, especially their advantages and limitations, is provided, and requirements for input material and reporting of results are clarified. General aspects of molecular diagnostic testing regarding clinical relevance, accessibility, cost, implementation, regulatory, and ethical aspects are discussed as well. Finally, we provide an outlook on new developments in the landscape of molecular testing technologies in neuro-oncology.
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Affiliation(s)
- Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- CCU Neuropathology, German Concortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology and Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - David Capper
- Department of Neuropathology, Charité, Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pim J French
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Center, 3015 GD Rotterdam, The Netherlands
| | - Dominique Figarella-Branger
- Aix-Marseille University, APHM, CNRS, INP, Institute Neurophysiopathol, CHU Timone, Service d’Anatomie Pathologique et de Neuropathologie, Marseille, France
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, University Sapienza of Rome, Rome, Italy
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Austria
| | - Monika E Hegi
- Neuroscience Research Center and Neurosurgery, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Bjarne W Kristensen
- Department of Clinical Medicine and Biotech Research and Innovation Center (BRIC), University of Copenhagen, Denmark
- Department of Pathology, The Bartholin Institute, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Matthias Preusser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Austria
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Martin van den Bent
- The Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Wolfgang Wick
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, and German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Düsseldorf, Germany
| | - Pieter Wesseling
- Department of Pathology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands (P.W.)
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10
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Haghighi SS, Ghaderian SMH, Rakhshan A, Motamed N. Evaluation of the Expression of miRNAs, LncRNAs, and their Target Gene, Caspase 3 in Glioblastoma Multiform: A Case-Control Study. Mol Biotechnol 2023; 65:1444-1452. [PMID: 36637626 DOI: 10.1007/s12033-022-00632-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/01/2022] [Indexed: 01/14/2023]
Abstract
Glioblastoma multiform (GBM) is an invasive cancer that causes high mortality in patients. Disruption of the apoptosis process is one of the main pathogenesis of the disease. Recently, LncRNAs and miRNAs have been shown to play an important role in the process of apoptosis. To follow the aim of study, 100 patients participated in the two groups of 50 individuals, including 50 GBM patients and 50 healthy individuals as the control group. Mononuclear cells were isolated from peripheral blood samples and RNA extraction was done. The expression changes of miR-17-5p, miR-20-5p, LINC01605, FAS-AS1, and Caspase 3 were examined using RT-PCR in both groups. Expression of LINC01605, miR-20-5p, and miR-17-5p increased in patients, while Caspase 3 and FAS-AS1 decreased; the difference was statistically significant between the two groups. In addition, it was found that these factors have the appropriate sensitivity and specificity as diagnostic markers. Finally, It is suggested to use the LINC01605, FAS-AS1, miR-20-5p, miR-17-5p, and Caspase 3 as apoptosis predictors in the GM patients.
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Affiliation(s)
- Shirin Setoodeh Haghighi
- Department of Cellular and Molecular Biology, Kish International Campus, University of Tehran, Kish, Iran
| | | | - Azadeh Rakhshan
- Department of Pathology, School of Medicine, Shohada-E-Tajrish Educational Hospital, ShahidBeheshti University of Medical Sciences, Tehran, Iran
| | - Nasrin Motamed
- Department of Cellular and Molecular Biology, Kish International Campus, University of Tehran, Kish, Iran.
- Department of Cell & Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, 14155-6455, Iran.
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11
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Qin Z, Liang W, Zhang Z, Li P, Wang T, Chen Q, Guo B, Zhong Y, Kang H, Wang L. Activated KRAS reprograms neural progenitor cells to glioma stem cell‑like phenotype. Int J Oncol 2023; 63:88. [PMID: 37326110 PMCID: PMC10552691 DOI: 10.3892/ijo.2023.5536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Glioma is the most common primary brain tumor. Glioma stem cells (GSCs) are the origin of gliomagenesis and may develop from normal neural progenitor cells (NPCs). However, how neoplastic transformation occurs in normal NPCs and the role of the Ras/Raf/MAPK pathway in NPC transformation is unclear. The present study generated NPCs from human embryonic stem cells (ESCs) carrying gene alterations in the Ras/Raf/MAPK pathway. The CCK‑8 proliferation, single‑cell clonal expansion, cell migration, RT‑qPCR, immunofluorescence staining, western blotting, transcriptome and Seahorse analyses, and intracranial implantation assay were performed to identify the characterization of transformed NPCs in vitro and in vivo. Brain organoids were used to verify the phenotypes transforming in NPCs. KRAS‑activated NPCs exhibited increased proliferation and migration in vitro. KRAS‑activated NPCs showed atypical morphology and formed aggressive tumors in immunodeficient mice. At the molecular level, KRAS‑activated NPCs displayed neoplasm‑associated metabolic and gene expression profiles. Moreover, activation of KRAS led to substantial cell proliferation and abnormal structure in ESC‑derived brain organoids. The present study showed that activated KRAS transformed normal NPCs to GSC‑like cells and established a simple cellular model to investigate gliomagenesis.
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Affiliation(s)
- Zixi Qin
- Department of Pathology, Medical College, Jinan University, Guangzhou, Guangdong 510632
| | - Weiye Liang
- Department of Pathology, Medical College, Jinan University, Guangzhou, Guangdong 510632
| | - Zixuan Zhang
- Department of Pathology, Medical College, Jinan University, Guangzhou, Guangdong 510632
| | - Peiwen Li
- Department of Pathology, Medical College, Jinan University, Guangzhou, Guangdong 510632
| | - Tianyu Wang
- Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, P.R. China
| | - Qianyu Chen
- Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, P.R. China
| | - Baoyin Guo
- Department of Pathology, Medical College, Jinan University, Guangzhou, Guangdong 510632
| | - Ying Zhong
- Department of Pathology, Medical College, Jinan University, Guangzhou, Guangdong 510632
| | - Hui Kang
- Department of Pathology, Medical College, Jinan University, Guangzhou, Guangdong 510632
| | - Lihui Wang
- Department of Pathology, Medical College, Jinan University, Guangzhou, Guangdong 510632
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12
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Villani V, Casini B, Tanzilli A, Lecce M, Rasile F, Telera S, Pace A, Piludu F, Terrenato I, Rollo F, De Nicola F, Fanciulli M, Pallocca M, Ciliberto G, Carosi M. The Glioma-IRE project − Molecular profiling in patients with glioma: steps toward an individualized diagnostic and therapeutic approach. J Transl Med 2023; 21:215. [PMID: 36959606 PMCID: PMC10035236 DOI: 10.1186/s12967-023-04057-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/12/2023] [Indexed: 03/25/2023] Open
Abstract
Background This study aimed to characterize the genetic profile of patients with glioma and discuss the impact of next-generation sequencing in glioma diagnosis and treatment. Methods Between 2019 and 2022, we analyzed the genetic profile of 99 patients with glioma through the Oncomine Focus Assay. The assay enables the detection of mutations in 52 driver genes, including single nucleotide variants (SNVs), copy number variants (CNVs), and gene fusions. We also collected and analyzed patients’ clinic characteristics and treatment outcomes. Results Over a period of 35 months, 700 patients with glioma followed by our neuro-oncology unit were screened, and 99 were enrolled in the study; most of the patients were excluded for inadequate non-morphological MRI or lack/inadequacy of the tissue samples. Based on our findings, most patients with glioma present mutations, such as SNVs, CNVs or gene fusions. Our data were similar to those reported by The Cancer Genome Atlas Program in terms of frequency of SNVs and CNVs, while we observed more cases of gene fusions. Median overall survival, progression-free survival, and time to progression were significantly lower for patients with grade VI glioblastoma than those with other gliomas. Only four patients were offered a targeted treatment based on the mutation detected; however, only one received treatment, the others could not receive the selected treatment because of worsening clinical status. Conclusion Routine timely molecular profiling in patients with glioma should be implemented to offer patients an individualized diagnostic approach and provide them with advanced targeted therapy options if available.
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Affiliation(s)
- Veronica Villani
- grid.417520.50000 0004 1760 5276Neuro-Oncology Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Beatrice Casini
- grid.417520.50000 0004 1760 5276Pathology Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Antonio Tanzilli
- grid.417520.50000 0004 1760 5276Neuro-Oncology Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Mario Lecce
- grid.417520.50000 0004 1760 5276Division of Neurosurgery, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Fabrizio Rasile
- grid.417520.50000 0004 1760 5276Division of Neurosurgery, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Stefano Telera
- grid.417520.50000 0004 1760 5276Division of Neurosurgery, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Andrea Pace
- grid.417520.50000 0004 1760 5276Neuro-Oncology Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Francesca Piludu
- grid.417520.50000 0004 1760 5276Radiology and Diagnostic Imaging Department, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Irene Terrenato
- grid.417520.50000 0004 1760 5276UOSD Clinical Trial Center Biostatistics and Bioinformatics, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Francesca Rollo
- grid.417520.50000 0004 1760 5276Pathology Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Francesca De Nicola
- grid.417520.50000 0004 1760 5276Department of Research, Diagnosis and Innovative Technologies, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Maurizio Fanciulli
- grid.417520.50000 0004 1760 5276Department of Research, Diagnosis and Innovative Technologies, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Matteo Pallocca
- grid.417520.50000 0004 1760 5276UOSD Clinical Trial Center Biostatistics and Bioinformatics, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Gennaro Ciliberto
- grid.417520.50000 0004 1760 5276Scientific Direction, IRCCS National Cancer Institute Regina Elena, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Mariantonia Carosi
- grid.417520.50000 0004 1760 5276Pathology Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
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13
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Leu S, Hutter G, Boulay JL. Proteome-based insights for IDH-mutant glioma classification. Cell Rep Med 2023; 4:100909. [PMID: 36652918 PMCID: PMC9873937 DOI: 10.1016/j.xcrm.2022.100909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In this issue, Bader et al.1 characterize the proteomes of diffuse glioma brain tumors by liquid chromatography mass spectrometry and classify isocitrate dehydrogenase (IDH)-mutant gliomas into two subtypes, which differ in oncogenic pathways and aerobic/anaerobic energy metabolism.
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Affiliation(s)
- Severina Leu
- Department of Neurosurgery and Laboratory of Brain Tumor Immunotherapy and Biology, Department of BioMedicine, University Hospital Basel and University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland
| | - Gregor Hutter
- Department of Neurosurgery and Laboratory of Brain Tumor Immunotherapy and Biology, Department of BioMedicine, University Hospital Basel and University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland
| | - Jean-Louis Boulay
- Department of Neurosurgery and Laboratory of Brain Tumor Immunotherapy and Biology, Department of BioMedicine, University Hospital Basel and University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland.
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14
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Romanidou O, Apostolou P, Kouvelakis K, Tsangaras K, Eliades A, Achilleos A, Loizides C, Lemesios C, Ioannides M, Kypri E, Koumbaris G, Papadopoulou K, Papathanasiou A, Rigakos G, Xanthakis I, Fostira F, Kotoula V, Fountzilas G, Patsalis PC. Molecular profile and clinical features of patients with gliomas using a broad targeted next generation-sequencing panel. Oncol Lett 2022; 25:38. [PMID: 36589665 PMCID: PMC9773316 DOI: 10.3892/ol.2022.13624] [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: 09/13/2022] [Accepted: 11/02/2022] [Indexed: 12/13/2022] Open
Abstract
Gliomas are the most common malignant primary brain tumors characterized by poor prognosis. The genotyping of tumors using next generation sequencing (NGS) platforms enables the identification of genetic alterations that constitute diagnostic, prognostic and predictive biomarkers. The present study investigated the molecular profile of 32 tumor samples from 32 patients with high-grade gliomas by implementing a broad 80-gene targeted NGS panel while reporting their clinicopathological characteristics and outcomes. Subsequently, 14 of 32 tumor specimens were also genotyped using a 55-gene NGS panel to validate the diagnostic accuracy and clinical utility of the extended panel. The median follow-up was 19.2 months. In total, 129 genetic alterations including 33 structural variants were identified in 38 distinct genes. Among 96 variants (single nucleotide variants and insertions and deletions), 38 were pathogenic and 58 variants of unknown clinical significance. TP53 was the most frequently mutated gene, followed by PTEN and IDH1 genes. Glioma patients with IDH1 mutant tumors were younger and had significantly longer overall survival compared to patients with wild-type IDH1 tumors. Similarly, tumors with TP53 mutations were more likely observed in younger patients with glioma. Subsequently, a comparison of mutational profiles of samples analyzed by both panels was also performed. Implementation of the comprehensive pan-cancer and the MOL panels resulted in the identification of 37 and 15 variants, respectively. Of those, 13 were common. Comprehensive pan-cancer panel identified 24 additional variants, 22 of which were located in regions that were not targeted by the MOL panel. By contrast, the MOL panel identified two additional variants. Overall, the present study demonstrated that using an extended tumor profile assay instead of a glioma-specific tumor profile panel identified additional genetic changes that may be taken into consideration as potential therapeutic targets for glioma diagnosis and molecular classification.
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Affiliation(s)
- Ourania Romanidou
- Department of Medicine, Medical Oncology Unit, Giannitsa General Hospital, 58100 Giannitsa, Greece
| | - Paraskevi Apostolou
- Molecular Diagnostics Laboratory, InRASTES, National Centre for Scientific Research Demokritos, 15341 Athens, Greece
| | - Kyriakos Kouvelakis
- Section of Biostatistics, Hellenic Cooperative Oncology Group, Data Office, 11526 Athens, Greece
| | | | | | | | | | | | | | - Elena Kypri
- NIPD Genetics Ltd., 2409 Nicosia, Republic of Cyprus
| | | | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, 54006 Thessaloniki, Greece
| | - Athanasios Papathanasiou
- Molecular Diagnostics Laboratory, InRASTES, National Centre for Scientific Research Demokritos, 15341 Athens, Greece
| | - Georgios Rigakos
- Third Department of Medical Oncology, Hygeia Hospital, 15123 Athens, Greece
| | - Ioannis Xanthakis
- Oncology Department, European Interbalkan Medical Center, 55535 Thessaloniki, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, InRASTES, National Centre for Scientific Research Demokritos, 15341 Athens, Greece
| | - Vassiliki Kotoula
- Department of Pathology, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, 54006 Thessaloniki, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, 54006 Thessaloniki, Greece,Aristotle University of Thessaloniki, 54006 Thessaloniki, Greece,Department of Medical Oncology, German Oncology Center, 4108 Limassol, Republic of Cyprus
| | - Philippos C. Patsalis
- NIPD Genetics Ltd., 2409 Nicosia, Republic of Cyprus,School of Medicine, University of Nicosia Medical School, 2417 Nicosia, Republic of Cyprus,Correspondence to: Professor Philippos C. Patsalis, NIPD Genetics Ltd., 31 Neas Engomis, Engomi, 2409 Nicosia, Republic of Cyprus, E-mail:
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15
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Mortensen D, Ulhøi BP, Lukacova S, Alsner J, Stougaard M, Nyengaard JR. Impact of new molecular criteria on diagnosis and survival of adult glioma patients. IBRO Neurosci Rep 2022; 13:299-305. [PMID: 36204252 PMCID: PMC9529576 DOI: 10.1016/j.ibneur.2022.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
The fifth edition WHO classification of Tumors of the Central nervous system (WHO-CNS5) integrated new molecular parameters to refine CNS tumor classification. This study aimed to reclassify a retrospective cohort of adult glioma patients according to WHO-CNS5, and assess if overall survival (OS) correlated with the revised diagnosis. Further, the diagnostic impact of methylation profiling (MP) was evaluated. Adult gliomas diagnosed according to 2016 WHO-CNS (n = 226) were evaluated according to WHO-CNS5 criteria. All patients had diagnostic NGS performed. 29 patients had 850k MP performed due to challenging tumor cases. OS was analyzed using Kaplan-Meier plots and log-rank test. 19 patients were reclassified. Specifically, diffuse astrocytic glioma, IDH-wildtype, with molecular features of glioblastoma (DAG-G) were reclassified as glioblastoma (n = 15). Shifts to glioblastoma were because of TERT promoter (TERTp) mutation (n = 9), EGFR amplification (n = 2), EGFR amplification and TERTp mutation (n = 1), and TERTp mutation with gain of chromosome 7, but uncertain chromosome 10 status due to lack of NGS coverage (n = 3). Lower grade IDH-mutant astrocytomas were reclassified as astrocytoma IDH-mutant, WHO grade 4 due to CDKN2A/B homozygous deletion (n = 4). No significant difference in OS was found for reclassified DAG-G in whole group (p = 0.59) and for TERTp mutation only (p = 0.44), compared to glioblastoma. MP resulted in revised diagnosis (n = 2), confirmed diagnosis (n = 15) and no match (n = 12). Our study showed similar overall survival for glioblastoma and DAG patients, supporting that isolated TERTp mutation may have a prognostic role in IDH-wildtype gliomas. Further, our study suggests MP is useful for confirming the diagnoses in challenging tumors. Retrospective cohort of adult glioma reclassified using WHO-CNS5 molecular criteria. 8.4% of the cohort received a new diagnosis and often a higher WHO grade. TERT promoter mutation suggested as a prognostic factor in IDH wildtype gliomas. DNA methylation profiling useful for diagnostically difficult cases.
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Affiliation(s)
- Danny Mortensen
- Core Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, Denmark
- Department of Pathology, Aarhus University Hospital, Denmark
- Correspondence to: Department of Clinical Medicine, Core Center for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Palle Juul Jensens Boulevard 99, C112, Level 1, DK-8200 Aarhus N, Denmark.
| | | | | | - Jan Alsner
- Department of Oncology, Aarhus University Hospital, Denmark
| | | | - Jens Randel Nyengaard
- Core Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, Denmark
- Department of Pathology, Aarhus University Hospital, Denmark
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16
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Tsuriel S, Hannes V, Hasona A, Raz M, Hershkovitz D. Digital PCR-Based Method for Detecting CDKN2A Loss in Brain Tumours. Mol Diagn Ther 2022; 26:689-698. [PMID: 36129665 DOI: 10.1007/s40291-022-00610-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 12/30/2022]
Abstract
INTRODUCTION CDKN2A is a key tumour suppressor gene and loss of CDKN2A can be found in many tumours. In astrocytoma grade IV, CDKN2A is deleted in more than 50% of tumours. In many instances, low-grade gliomas with homozygous loss of CDKN2A behave like high grade tumours. The available techniques for CDKN2A loss are laborious, expensive, unreliable, or unavailable in most pathology institutes. Therefore, although it is essential for accurate brain tumour diagnosis, the routine diagnosis does not include testing for CDKN2A deletion. METHODS We developed a digital polymerase chain reaction (dPCR) assay for CDKN2A loss detection. The assay is based on counting the copy number of CDKN2A gene and of a reference gene on the same chromosome. It was tested for the detection limit with regard to tumour content and minimal DNA quantity. It was then tested on 24 clinical samples with known CDKN2A status. Additionally, we tested 44 gliomas with unknown CDKN2A status. RESULTS We found that the newly developed assay is reliable in tissue with more than 50% tumour content and more than 0.4 ng of DNA. The validation cohort showed complete concordance, and we were able to detect homozygous loss in 16 gliomas with unknown CDKN2A status. DISCUSSION The method presented can give a fast, cost-effective, clinically reliable evaluation of CDKN2A loss in tissue with more than 50% tumour content. Its ability to work with old samples and with low amounts of DNA makes it the favoured assay in cases where other techniques fail.
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Affiliation(s)
- Shlomo Tsuriel
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel.
| | - Victoria Hannes
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
| | - Asala Hasona
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | - Michal Raz
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
| | - Dov Hershkovitz
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel.
- Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel.
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17
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IDH-mutant astrocytoma with an evolutional progression to CDKN2A/B homozygous deletion and NTRK fusion during recurrence: A case report. Pathol Res Pract 2022; 239:154163. [DOI: 10.1016/j.prp.2022.154163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/22/2022]
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18
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Wang P, He J, Ma X, Weng L, Wu Q, Zhao P, Ban C, Hao X, Hao Z, Yuan P, Hao F, Wang S, Zhang H, Xie S, Gao Y. Applying MAP-MRI to Identify the WHO Grade and Main Genetic Features of Adult-type Diffuse Gliomas: A Comparison of Three Diffusion-weighted MRI Models. Acad Radiol 2022:S1076-6332(22)00546-3. [DOI: 10.1016/j.acra.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/27/2022] [Accepted: 10/07/2022] [Indexed: 11/08/2022]
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19
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The evolution of pleomorphic xanthoastrocytoma: from genesis to molecular alterations and mimics. J Transl Med 2022; 102:670-681. [PMID: 35031693 DOI: 10.1038/s41374-021-00708-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 11/08/2022] Open
Abstract
Pleomorphic xanthoastrocytomas (PXAs) are rare tumors accounting for less than 1% of astrocytomas. They commonly occur in young patients and have relatively favorable prognosis. However, they are well known to have heterogenous morphology and biological behavior with the potential to recur and disseminate throughout the central nervous system, especially their anaplastic counterparts. Recent advances in the molecular characterization have discovered BRAFp.V600E mutations in conjunction with CDKN2A/B deletions and TERTp mutations to be the most frequent alterations in PXAs. These tumors can present a diagnostic challenge as they share overlapping histopathological, genomic as well as methylation profile with various other tumor types, particularly epithelioid glioblastomas (eGBs). This review provides the spectrum of evolution of PXAs from their genesis to recent molecular insights and attempts to review pathogenesis and relationship to other tumors that they mimic especially eGB. It is postulated based on evidence from literature that PXA and eGB are possibly related and not distinct entities, being two ends of a continuous spectrum of malignant progression (grade 2-grade 4) with anaplastic PXA (grade 3) lying in between. Future WHO classifications will have to possibly redefine these tumors using more confirmatory data from larger studies.
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20
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LINC01426 aggravates the malignant progression of glioma through miR-661/Mdm2 axis. Brain Res Bull 2022; 188:110-121. [PMID: 35772605 DOI: 10.1016/j.brainresbull.2022.06.012] [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: 03/10/2021] [Revised: 04/20/2022] [Accepted: 06/26/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Long intergenic non-protein coding RNA 1426 (LINC01426) is up-regulated in glioma and functions as a tumor promoter. However, the role of LINC01426 in glioma required further exploration. Therefore, this article mainly studied the role and possible mechanism of LINC01426 in glioma. METHODS The area under the receiver operating characteristic curve was used to determine the diagnostic value of LINC01426. The effect of LINC01426 on tumor growth was analyzed by tumorigenesis assay and immunohistochemical analysis. Bioinformatics analysis, dual-luciferase assay, RNA pull-down, Pearson test, and real-time quantitative PCR (RT-qPCR) were applied to verify the relationship between target genes. The expressions and effects of LINC01426, miR-661 and MDM2 proto-oncogene (Mdm2) in glioma were examined by bioinformatics analysis combined with molecular and functional experiments (RT-qRCR, 3-(4,5)-dimethylthiahiazo (-z-y1)-3,5-di-phenytetrazoliumromide, clone formation, BrdU, flow cytometry). The expressions of proliferation and apoptosis-related proteins were determined by Western blot. RESULTS LINC01426, which was high-expressed in glioma and was related to poor prognosis, could be used as a diagnostic marker for glioma. SiLINC01426 inhibited the malignant phenotype of glioma cells in vitro and attenuated tumor growth and PCNA expression in vivo, while the effects of LINC01426 were the opposite. LINC01426 targeted and inversely correlated with miR-661, which was low-expressed in glioma. MiR-661 inhibitor evidently overturned the effect of siLINC01426 on biological functions, proliferation, and apoptosis-related proteins of glioma cells. Mdm2 bound to miR-661. Moreover, siMdm2 reversed the effects of miR-661 inhibitor on the biological characteristics and Mdm2/p53/p21 expression of glioma cells. CONCLUSION LINC01426 aggravated the malignant progression of glioma through miR-661/Mdm2 axis.
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21
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The Value of FET PET/CT in Recurrent Glioma with a Different IDH Mutation Status: The Relationship between Imaging and Molecular Biomarkers. Int J Mol Sci 2022; 23:ijms23126787. [PMID: 35743228 PMCID: PMC9224265 DOI: 10.3390/ijms23126787] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/04/2022] Open
Abstract
The evaluation of treatment response remains a challenge in glioma cases because the neuro oncological therapy can lead to the development of treatment-related changes (TRC) that mimic true progression (TP). Positron emission tomography (PET) using O-(2-[18F] fluoroethyl-)-L-tyrosine (18F-FET) has been shown to be a useful tool for detecting TRC and TP. We assessed the diagnostic performance of different 18F-FET PET segmentation approaches and different imaging biomarkers for differentiation between late TRC and TP in glioma patients. Isocitrate dehydrogenase (IDH) status was evaluated as a predictor of disease outcome. In our study, the proportion of TRC in IDH wild type (IDHwt) and IDH mutant (IDHm) subgroups was without significant difference. We found that the diagnostic value of static and dynamic biomarkers of 18F-FET PET for discrimination between TRC and TP depends on the IDH mutation status of the tumor. Dynamic 18F-FET PET acquisition proved helpful in the IDH wild type (IDHwt) subgroup, as opposed to the IDH mutant (IDHm) subgroup, providing an early indication to discontinue dynamic imaging in the IDHm subgroup.
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22
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Higa N, Akahane T, Hamada T, Yonezawa H, Uchida H, Makino R, Watanabe S, Takajo T, Yokoyama S, Kirishima M, Matsuo K, Fujio S, Hanaya R, Tanimoto A, Yoshimoto K. Distribution and favorable prognostic implication of genomic EGFR alterations in IDH-wildtype glioblastoma. Cancer Med 2022; 12:49-60. [PMID: 35695190 PMCID: PMC9844636 DOI: 10.1002/cam4.4939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/08/2022] [Accepted: 06/03/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND We aimed to evaluate the mutation profile, transcriptional variants, and prognostic impact of the epidermal growth factor receptor (EGFR) gene in isocitrate dehydrogenase (IDH)-wildtype glioblastomas (GBMs). METHODS We sequenced EGFR, evaluated the EGFR splicing profile using a next-generation sequencing oncopanel, and analyzed the outcomes in 138 grade IV IDH-wildtype GBM cases. RESULTS EGFR mutations were observed in 10% of GBMs. A total of 23.9% of the GBMs showed EGFR amplification. Moreover, 25% of the EGFR mutations occurred in the kinase domain. Notably, EGFR alterations were a predictor of good prognosis (p = 0.035). GBM with EGFR alterations was associated with higher Karnofsky Performance Scale scores (p = 0.014) and lower Ki-67 scores (p = 0.005) than GBM without EGFR alterations. EGFRvIII positivity was detected in 21% of EGFR-amplified GBMs. We identified two other EGFR variants in GBM cases with deletions of exons 6-7 (Δe 6-7) and exons 2-14 (Δe 2-14). In one case, the initial EGFRvIII mutation transformed into an EGFR Δe 2-14 mutation during recurrence. CONCLUSIONS We found that the EGFR gene profiles of GBM differ among cohorts and that EGFR alterations are good prognostic markers of overall survival in patients with IDH-wildtype GBM. Additionally, we identified rare EGFR variants with longitudinal and temporal transformations of EGFRvIII.
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Affiliation(s)
- Nayuta Higa
- Department of Neurosurgery, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Toshiaki Akahane
- Department of Pathology, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan,Center for Human Genome and Gene AnalysisKagoshima University HospitalKagoshimaJapan
| | - Taiji Hamada
- Department of Pathology, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Hajime Yonezawa
- Department of Neurosurgery, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Hiroyuki Uchida
- Department of Neurosurgery, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Ryutaro Makino
- Department of Neurosurgery, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Shoji Watanabe
- Department of Neurosurgery, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Tomoko Takajo
- Department of Neurosurgery, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Seiya Yokoyama
- Department of Pathology, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Mari Kirishima
- Department of Pathology, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Kei Matsuo
- Department of Pathology, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Shingo Fujio
- Department of Neurosurgery, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Ryosuke Hanaya
- Department of Neurosurgery, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Akihide Tanimoto
- Department of Pathology, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan,Center for Human Genome and Gene AnalysisKagoshima University HospitalKagoshimaJapan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan,Department of Neurosurgery, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
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23
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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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24
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Brat DJ, Aldape K, Bridge JA, Canoll P, Colman H, Hameed MR, Harris BT, Hattab EM, Huse JT, Jenkins RB, Lopez-Terrada DH, McDonald WC, Rodriguez FJ, Souter LH, Colasacco C, Thomas NE, Yount MH, van den Bent MJ, Perry A. Molecular Biomarker Testing for the Diagnosis of Diffuse Gliomas. Arch Pathol Lab Med 2022; 146:547-574. [PMID: 35175291 PMCID: PMC9311267 DOI: 10.5858/arpa.2021-0295-cp] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The diagnosis and clinical management of patients with diffuse gliomas (DGs) have evolved rapidly over the past decade with the emergence of molecular biomarkers that are used to classify, stratify risk, and predict treatment response for optimal clinical care. OBJECTIVE.— To develop evidence-based recommendations for informing molecular biomarker testing for pediatric and adult patients with DGs and provide guidance for appropriate laboratory test and biomarker selection for optimal diagnosis, risk stratification, and prediction. DESIGN.— The College of American Pathologists convened an expert panel to perform a systematic review of the literature and develop recommendations. A systematic review of literature was conducted to address the overarching question, "What ancillary tests are needed to classify DGs and sufficiently inform the clinical management of patients?" Recommendations were derived from quality of evidence, open comment feedback, and expert panel consensus. RESULTS.— Thirteen recommendations and 3 good practice statements were established to guide pathologists and treating physicians on the most appropriate methods and molecular biomarkers to include in laboratory testing to inform clinical management of patients with DGs. CONCLUSIONS.— Evidence-based incorporation of laboratory results from molecular biomarker testing into integrated diagnoses of DGs provides reproducible and clinically meaningful information for patient management.
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Affiliation(s)
- Daniel J Brat
- From the Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois (Brat)
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland (Aldape)
| | - Julia A Bridge
- The Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska (Bridge)
- Cytogenetics, ProPath, Dallas, Texas (Bridge)
| | - Peter Canoll
- The Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Canoll)
| | - Howard Colman
- The Department of Neurosurgery and Huntsman Cancer Institute, University of Utah, Salt Lake City (Colman)
| | - Meera R Hameed
- The Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York (Hameed)
| | - Brent T Harris
- The Department of Neurology and Pathology, MedStar Georgetown University Hospital, Washington, DC (Harris)
| | - Eyas M Hattab
- The Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, Kentucky (Hattab)
| | - Jason T Huse
- The Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston (Huse)
| | - Robert B Jenkins
- The Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (Jenkins)
| | - Dolores H Lopez-Terrada
- The Departments of Pathology and Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas (Lopez-Terrada)
| | - William C McDonald
- The Department of Pathology, Abbott Northwestern Hospital, Minneapolis, Minnesota (McDonald)
| | - Fausto J Rodriguez
- The Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland (Rodriguez)
| | | | - Carol Colasacco
- Surveys, College of American Pathologists, Northfield, Illinois (Colasacco, Thomas)
| | - Nicole E Thomas
- Surveys, College of American Pathologists, Northfield, Illinois (Colasacco, Thomas)
| | | | - Martin J van den Bent
- The Brain Tumor Center at Erasmus MC Cancer Institute University Medical Center Rotterdam, Rotterdam, the Netherlands (van den Bent)
| | - Arie Perry
- The Departments of Pathology and Neurological Surgery, University of California San Francisco School of Medicine, San Francisco (Perry)
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25
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Evaluation of Temozolomide Treatment for Glioblastoma Using Amide Proton Transfer Imaging and Diffusion MRI. Cancers (Basel) 2022; 14:cancers14081907. [PMID: 35454814 PMCID: PMC9031574 DOI: 10.3390/cancers14081907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Glioblastoma (GBM), the most frequent and malignant histological type of glioma, is associated with a very high mortality rate. MRI is a useful method for the evaluation of tumor growth. However, there are few studies that have quantitatively evaluated the changes in disease state after TMZ treatment against GBM, and it is not fully understood how the effects of treatment are reflected in the quantitative values measured on MRI. We used the C6 glioma rat model to evaluate the tumor changes due to chemotherapy at different doses of TMZ in terms of quantitative values measured by neurite orientation dispersion and density imaging (NODDI) and amide proton transfer (APT) imaging using 7T-MRI. These methods can evaluate the microstructural changes caused by TMZ-induced tumor growth inhibition. Abstract This study aimed to evaluate tumor changes due to chemotherapy with temozolomide (TMZ) in terms of quantitative values measured by APT imaging and NODDI. We performed TMZ treatment (administered orally by gavage to the TMZ-40 mg and TMZ-60 mg groups) on 7-week-old male Wistar rats with rat glioma C6 implanted in the right brain. T2WI, APT imaging, diffusion tensor imaging (DTI), and NODDI were performed on days 7 and 14 after implantation using 7T-MRI, and the calculated quantitative values were statistically compared. Then, HE staining was performed on brain tissue at day 7 and day 14 for each group to compare the results with the MR images. TMZ treatment inhibited tumor growth and necrotic area formation. The necrotic areas observed upon hematoxylin and eosin (HE) staining were consistent with the MTR low-signal areas observed upon APT imaging. The intracellular volume fraction (ICVF) map of the NODDI could best show the microstructure of the tumor, and its value could significantly highlight the difference in treatment effects at different TMZ doses. APT imaging and NODDI can be used to detect the microstructural changes caused by TMZ-induced tumor growth inhibition. The ICVF may be useful as a parameter for determining the effect of TMZ.
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26
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Wolter M, Felsberg J, Malzkorn B, Kaulich K, Reifenberger G. Droplet digital PCR-based analyses for robust, rapid, and sensitive molecular diagnostics of gliomas. Acta Neuropathol Commun 2022; 10:42. [PMID: 35361262 PMCID: PMC8973808 DOI: 10.1186/s40478-022-01335-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/20/2022] [Indexed: 11/10/2022] Open
Abstract
Classification of gliomas involves the combination of histological features with molecular biomarkers to establish an integrated histomolecular diagnosis. Here, we report on the application and validation of a set of molecular assays for glioma diagnostics based on digital PCR technology using the QX200™ Droplet Digital™ PCR (ddPCR) system. The investigated ddPCR-based assays enable the detection of diagnostically relevant glioma-associated mutations in the IDH1, IDH2, H3-3A, BRAF, and PRKCA genes, as well as in the TERT promoter. In addition, ddPCR-based assays assessing diagnostically relevant copy number alterations were studied, including 1p/19q codeletion, gain of chromosome 7 and loss of chromosome 10 (+ 7/-10), EGFR amplification, duplication of the BRAF locus, and CDKN2A homozygous deletion. Results obtained by ddPCR were validated by other methods, including immunohistochemistry, Sanger sequencing, pyrosequencing, microsatellite analyses for loss of heterozygosity, as well as real-time PCR- or microarray-based copy number assays. Particular strengths of the ddPCR approach are (1) its high analytical sensitivity allowing for reliable detection of mutations even with low mutant allele frequencies, (2) its quantitative determination of mutant allele frequencies and copy number changes, and (3) its rapid generation of results within a single day. Thus, in line with other recent studies our findings support ddPCR analysis as a valuable approach for molecular glioma diagnostics in a fast, quantitative and highly sensitive manner.
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27
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Hasanau T, Pisarev E, Kisil O, Nonoguchi N, Le Calvez-Kelm F, Zvereva M. Detection of TERT Promoter Mutations as a Prognostic Biomarker in Gliomas: Methodology, Prospects, and Advances. Biomedicines 2022; 10:728. [PMID: 35327529 PMCID: PMC8945783 DOI: 10.3390/biomedicines10030728] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/13/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
This article reviews the existing approaches to determining the TERT promoter mutational status in patients with various tumoral diseases of the central nervous system. The operational characteristics of the most common methods and their transferability in medical practice for the selection or monitoring of personalized treatments based on the TERT status and other related molecular biomarkers in patients with the most common tumors, such as glioblastoma, oligodendroglioma, and astrocytoma, are compared. The inclusion of new molecular markers in the course of CNS clinical management requires their rapid and reliable assessment. Availability of molecular evaluation of gliomas facilitates timely decisions regarding patient follow-up with the selection of the most appropriate treatment protocols. Significant progress in the inclusion of molecular biomarkers for their subsequent clinical application has been made since 2016 when the WHO CNS classification first used molecular markers to classify gliomas. In this review, we consider the methodological approaches used to determine mutations in the promoter region of the TERT gene in tumors of the central nervous system. In addition to classical molecular genetical methods, other methods for determining TERT mutations based on mass spectrometry, magnetic resonance imaging, next-generation sequencing, and nanopore sequencing are reviewed with an assessment of advantages and disadvantages. Beyond that, noninvasive diagnostic methods based on the determination of the mutational status of the TERT promoter are discussed.
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Affiliation(s)
- Tsimur Hasanau
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Eduard Pisarev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia;
- Chair of Chemistry of Natural Compounds, Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga Kisil
- Gause Institute of New Antibiotics, 119021 Moscow, Russia;
| | - Naosuke Nonoguchi
- Department of Neurosurgery, Osaka Medical and Pharmaceutical University, Takatsuki 569-8686, Japan;
| | - Florence Le Calvez-Kelm
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC), 69372 Lyon, France;
| | - Maria Zvereva
- Chair of Chemistry of Natural Compounds, Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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28
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Persano F, Gigli G, Leporatti S. Natural Compounds as Promising Adjuvant Agents in The Treatment of Gliomas. Int J Mol Sci 2022; 23:3360. [PMID: 35328780 PMCID: PMC8955269 DOI: 10.3390/ijms23063360] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 02/07/2023] Open
Abstract
In humans, glioblastoma is the most prevalent primary malignant brain tumor. Usually, glioblastoma has specific characteristics, such as aggressive cell proliferation and rapid invasion of surrounding brain tissue, leading to a poor patient prognosis. The current therapy-which provides a multidisciplinary approach with surgery followed by radiotherapy and chemotherapy with temozolomide-is not very efficient since it faces clinical challenges such as tumor heterogeneity, invasiveness, and chemoresistance. In this respect, natural substances in the diet, integral components in the lifestyle medicine approach, can be seen as potential chemotherapeutics. There are several epidemiological studies that have shown the chemopreventive role of natural dietary compounds in cancer progression and development. These heterogeneous compounds can produce anti-glioblastoma effects through upregulation of apoptosis and autophagy; allowing the promotion of cell cycle arrest; interfering with tumor metabolism; and permitting proliferation, neuroinflammation, chemoresistance, angiogenesis, and metastasis inhibition. Although these beneficial effects are promising, the efficacy of natural compounds in glioblastoma is limited due to their bioavailability and blood-brain barrier permeability. Thereby, further clinical trials are necessary to confirm the in vitro and in vivo anticancer properties of natural compounds. In this article, we overview the role of several natural substances in the treatment of glioblastoma by considering the challenges to be overcome and future prospects.
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Affiliation(s)
- Francesca Persano
- Department of Mathematics and Physics, University of Salento, Via Per Arnesano, 73100 Lecce, Italy;
- CNR Nanotec-Istituto di Nanotecnologia, Via Monteroni, 73100 Lecce, Italy
| | - Giuseppe Gigli
- Department of Mathematics and Physics, University of Salento, Via Per Arnesano, 73100 Lecce, Italy;
- CNR Nanotec-Istituto di Nanotecnologia, Via Monteroni, 73100 Lecce, Italy
| | - Stefano Leporatti
- CNR Nanotec-Istituto di Nanotecnologia, Via Monteroni, 73100 Lecce, Italy
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29
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Tirrò E, Massimino M, Broggi G, Romano C, Minasi S, Gianno F, Antonelli M, Motta G, Certo F, Altieri R, Manzella L, Caltabiano R, Barbagallo GMV, Buttarelli FR, Magro G, Giangaspero F, Vigneri P. A Custom DNA-Based NGS Panel for the Molecular Characterization of Patients With Diffuse Gliomas: Diagnostic and Therapeutic Applications. Front Oncol 2022; 12:861078. [PMID: 35372034 PMCID: PMC8969903 DOI: 10.3389/fonc.2022.861078] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
The management of patients with Central Nervous System (CNS) malignancies relies on the appropriate classification of these tumors. Recently, the World Health Organization (WHO) has published new criteria underlining the importance of an accurate molecular characterization of CNS malignancies, in order to integrate the information generated by histology. Next generation sequencing (NGS) allows single step sequencing of multiple genes, generating a comprehensive and specific mutational profile of the tumor tissue. We developed a custom NGS-based multi-gene panel (Glio-DNA panel) for the identification of the correct glioma oncotype and the detection of its essential molecular aberrations. Specifically, the Glio-DNA panel targets specific genetic and chromosomal alterations involving ATRX chromatin remodeler (ATRX), cyclin dependent kinase inhibitor 2A (CDKN2A), isocitrate dehydrogenase (NADP+) 1 (IDH1) and the telomerase reverse transcriptase (TERT) promoter while also recognizing the co-deletion of 1p/19q, loss of chromosome 10 and gain of chromosome 7. Furthermore, the Glio-DNA panel also evaluates the methylation level of the O-6-methylguanine-DNA methyltransferase (MGMT) gene promoter that predicts temozolomide efficacy. As knowledge of the mutational landscape of each glioma is mandatory to define a personalized therapeutic strategy, the Glio-DNA panel also identifies alterations involving “druggable” or “actionable” genes. To test the specificity of our panel, we used two reference mutated DNAs verifying that NGS allele frequency measurement was highly accurate and sensitive. Subsequently, we performed a comparative analysis between conventional techniques - such as immunohistochemistry or fluorescence in situ hybridization - and NGS on 60 diffuse glioma samples that had been previously characterized. The comparison between conventional testing and NGS showed high concordance, suggesting that the Glio-DNA panel may replace multiple time-consuming tests. Finally, the identification of alterations involving different actionable genes matches glioma patients with potential targeted therapies available through clinical trials. In conclusion, our analysis demonstrates NGS efficacy in simultaneously detecting different genetic alterations useful for the diagnosis, prognosis and treatment of adult patients with diffuse glioma.
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Affiliation(s)
- Elena Tirrò
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
- Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
- *Correspondence: Elena Tirrò,
| | - Michele Massimino
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giuseppe Broggi
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Anatomic Pathology, University of Catania, Catania, Italy
| | - Chiara Romano
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Simone Minasi
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, La Sapienza University, Rome, Italy
| | - Francesca Gianno
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, La Sapienza University, Rome, Italy
| | - Manila Antonelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, La Sapienza University, Rome, Italy
| | - Gianmarco Motta
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
| | - Francesco Certo
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Neurological Surgery, Policlinico “G. Rodolico - San Marco” University Hospital, University of Catania, Catania, Italy
| | - Roberto Altieri
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Neurological Surgery, Policlinico “G. Rodolico - San Marco” University Hospital, University of Catania, Catania, Italy
| | - Livia Manzella
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Anatomic Pathology, University of Catania, Catania, Italy
| | - Giuseppe Maria Vincenzo Barbagallo
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Neurological Surgery, Policlinico “G. Rodolico - San Marco” University Hospital, University of Catania, Catania, Italy
| | - Francesca Romana Buttarelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, La Sapienza University, Rome, Italy
| | - Gaetano Magro
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Anatomic Pathology, University of Catania, Catania, Italy
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, La Sapienza University, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Paolo Vigneri
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
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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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Sporikova Z, Slavkovsky R, Tuckova L, Kalita O, Megova Houdova M, Ehrmann J, Hajduch M, Hrabalek L, Vaverka M. IDH1/2 Mutations in Patients With Diffuse Gliomas: A Single Centre Retrospective Massively Parallel Sequencing Analysis. Appl Immunohistochem Mol Morphol 2022; 30:178-183. [PMID: 35262523 PMCID: PMC8920008 DOI: 10.1097/pai.0000000000000997] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/26/2021] [Indexed: 12/05/2022]
Abstract
Patients below 55 years were genetically studied because the prevalence of isocitrate dehydrogenase 1 (IDH1) decreases in older patients and on grounds of cost-effectiveness, as suggested by the World Health Organization (WHO) in 2016. The aim of our study was to use novel massively parallel sequencing (MPS) approaches to examine rare variants of IDH1/2 in Czech diffuse astrocytic and oligodendroglial tumors (gliomas) patients below 55 years of age who had been immunohistochemically (IHC) diagnosed as IDH1 R132H negative. The IHC IDH1 status (wild type or mutant) of 275 tissue samples was analyzed using antibodies against the IDH1 R132H protein. Sixty-three samples of 55 years old patients with IHC IDH1 WT status were genotyped using two different MPS technologies to detect rare IDH1 and IDH2 variants. The tiered IHC (60 positive) and molecular (10 positive) approach thus revealed that 70 of the 275 samples (25%) bore IDH1/IDH2 mutations. The combined molecular and IHC approach thus revealed that 70 of the 275 samples (25%) considered in the study bore IDH1/IDH2 mutations. IHC detection of the IDH1 R132H variant should be routinely complemented with MPS to detect rare IDH1/2 variants in glioma patients below 55 years of age with negative IHC result of IDH R132H variant.
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Affiliation(s)
| | | | | | - Ondrej Kalita
- Neurosurgery, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc
- Department of Health Care Science, Faculty of Humanities, T. Bata University in Zlin, the Czech Republic
| | | | | | | | - Lumir Hrabalek
- Neurosurgery, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc
| | - Miroslav Vaverka
- Neurosurgery, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc
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32
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Mawrin C, Koch R, Waldt N, Sandalcioglu IE, Braunsdorf WEK, Warnke JP, Goehre F, Meisel HJ, Ewald C, Neyazii S, Schüller U, Kirches E. A new amplicon-based gene panel for next generation sequencing characterization of meningiomas. Brain Pathol 2022; 32:e13046. [PMID: 35213080 PMCID: PMC8877726 DOI: 10.1111/bpa.13046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/03/2021] [Indexed: 12/20/2022] Open
Abstract
Meningiomas are the most frequent primary intracranial tumors. The considerable variety of histological subtypes has been expanded by the definition of molecular alterations, which can improve both diagnostic accuracy and determination of individual patient's outcome. According to the upcoming WHO classification of brain tumors, the in‐time analysis of frequent molecular events in meningiomas may become mandatory to define meningioma subtypes. We have compiled a custom‐made amplicon‐based next generation sequencing (NGS) meningioma panel covering the most frequent known recurrent mutations in 15 different genes. In an unselected consecutive meningioma cohort (109 patients) analyzed over a period of 12 months, we detected mutations in 11 different genes, with most frequent alterations in NF2 (43%), AKT1E17K (15%), and TRAF7 (13%). In 39 tumors (36%), two different mutations were detected, with NF2 and SUFU (n = 5) and KLF4 and TRAF7 (n = 5) being the most frequent combinations. No alterations were found in POLR2A, CDKN2A, CDKN2B, and BAP1, and no homozygous CDKN2A/B deletion was detected. NF2 mutations were found in tumors of all WHO grades, whereas mutations in KLF4, TRAF7, and SMO were restricted to WHO grade I meningiomas. In contrast, SMARCE1 and TERT mutations were associated with WHO grade II meningiomas (according to the WHO classification 2016). The distribution of mutations across histological subtypes or tumor localization was in line with the existing literature, with typical combinations like KLF4K409Q/TRAF7 for secretory meningiomas and preferential skull base localization of meningiomas harboring SMO and AKT1E17K mutations. Thus, we present a custom‐made NGS meningioma panel providing a time and cost‐efficient reliable detection of relevant somatic molecular alterations in meningiomas suitable for daily routine.
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Affiliation(s)
- Christian Mawrin
- Department of Neuropathology, Otto-von-Guericke-University, Magdeburg, Germany
| | - Ralf Koch
- Department of Neuropathology, Otto-von-Guericke-University, Magdeburg, Germany
| | - Natalie Waldt
- Department of Neuropathology, Otto-von-Guericke-University, Magdeburg, Germany
| | - I Erol Sandalcioglu
- Department of Neurosurgery, Otto-von-Guericke-University, Magdeburg, Germany
| | | | - Jan-Peter Warnke
- Department of Neurosurgery, Paracelsus-Hospital Zwickau, Zwickau, Germany
| | - Felix Goehre
- Department of Neurosurgery, Bergmannstrost Hospital Halle/Saale, Halle/Saale, Germany
| | - Hans-Jürgen Meisel
- Department of Neurosurgery, Bergmannstrost Hospital Halle/Saale, Halle/Saale, Germany
| | - Christian Ewald
- Department of Neurosurgery, Brandenburg Medical School, Brandenburg an der Havel, Germany
| | - Sina Neyazii
- Department of Pediatric Hematology and Oncology, University Hospital Hamburg, Hamburg, Germany.,Research Institute Children's Cancer Center, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Hospital Hamburg, Hamburg, Germany.,Research Institute Children's Cancer Center, Hamburg, Germany.,Department of Neuropathology, University Hospital Hamburg, Hamburg, Germany
| | - Elmar Kirches
- Department of Neuropathology, Otto-von-Guericke-University, Magdeburg, Germany
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Kassem NM, Kassem HA, Selim H, Hafez M. Targeted next generation sequencing provides insight for the genetic alterations in liquid biopsy of Egyptian brain tumor patients. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00214-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Abstract
Background
Glioblastoma (GBM) is the commonest primary malignant cerebral tumor in adults. Detection of genetic mutations in liquid biopsy is endorsed rapidly throughout several solid neoplasms but still limited in GBM. Our study provides insight for the genetic alterations in liquid biopsy of the newly diagnosed GBM patients using next generation sequencing technology together with identification of the microsatellite instability (MSI) status in those patients.
Results
Eighteen variants detected in 15 genes which were (4, 12 and 2) missense, coding silent and intronic mutations, respectively. The 4 substitution–missense mutations were as follows: Drug responsive TP53 (p.Pro72Arg) variant was detected in 6 patients (85.7%). KDR (p.Gln472His) variant was noted in 4 patients (57.1%) as a result of substitution at c.1416A > T. Two patients revealed KIT (p.Met541Leu) variant which result from substitution at c.1621A > C. Only one patient showed mutation in JAK3 gene which was (p.Val718Leu) variant resulting from c.2152G > C substitution. Regarding MSI status, four cases (57.1%) were MSI-Low and three cases (42.9%) were MSI-High.
Conclusions
This study identifies the molecular landscape and microsatellite instability alternations in Egyptian brain tumor patients, which may have an important role in improving the outcome, survival and may help in evolving a characteristic individual therapy.
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Chen C, Du X, Liu H, Lu X, Li D, Qi J. Construction of a prognostic classifier and prediction of the immune landscape and immunosuppressive molecules in gliomas based on combination of inflammatory response-related genes and angiogenesis-associated genes. EUR J INFLAMM 2022. [DOI: 10.1177/1721727x221133708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Objective:We aimed to combine inflammatory response-related genes (IRRGs) and angiogenesis-associated genes (AAGs) to build a prognostic classifier and to predict immune landscapes and immunosuppressive molecules in gliomas. Introduction: Gliomas, the commonest primary brain tumors, account for about 80% of cancerous tumors in the central nervous system (CNS), featuring rapid progression, high malignancy, and extremely poor prognosis. The induction of inflammatory responses and angiogenesis have been considered to be closely related to tumors. However, there are little publications systematically elaborating on their impacts on gliomas. Methods: We downloaded the data of IRRGs and AAGs from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases, and retrieved 68 differentially expressed genes (DEGs), of which 13 DEGs pertained to the prognosis of glioma cases. Next, 9 DEGs were screened from the 13 major DEGs with predictive significance and utilized to build a 9-gene signature as a prognostic risk score model (PRSM) with the aid of univariate Cox regression analyses (CRA) and least absolute shrinkage and selection operator (LASSO)-CRA. On this basis, glioma patients fell into high-risk (HR) group and low-risk (LR) group. Later, we implemented Gene Set Enrichment Analysis (GSEA, Gene Set: WP_ANGIOGENESIS) and calculate the scores of cell infiltration and immune-associated function by harnessing single-sample GSEA (ssGSEA). Results: The prognosis was compared between the two groups by introducing Kaplan-Meier (KM) analysis, which yielded that HR group exhibited poorer prognosis. Additionally, the predictive capacity and independent characteristics were proven by the receiver operating characteristic curve (ROC) and multivariate CRA. Further, We took an evaluation of immune profiles, which unraveled that immunosuppressive cell count was distinctively larger in HS group. Finally, a protein-protein interaction (PPI) network of DEGs was built, and 10 hub genes were obtained, of which epidermal growth factor receptor (EGFR) was closely related to poor prognosis. Conclusion: A 9-gene signature was established on the strength of IRRGs and AAGs for predicting glioma prognosis, tumor microenvironment (TME), immune landscapes and immunosuppressive molecules. However, the molecular mechanism developed by this signature to function in tumor immunity needs further experimental research in the future and is expected to be a research target for glioma immunotherapy strategies.
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Affiliation(s)
- Chunbao Chen
- Department of Neurosurgery, Affiliated Hospital of North Sichuan Medical College, Nanchong City, People’s Republic of China
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong City, People’s Republic of China
| | - Xue Du
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong City, People’s Republic of China
| | - Hongjun Liu
- Department of Neurosurgery, Affiliated Hospital of North Sichuan Medical College, Nanchong City, People’s Republic of China
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong City, People’s Republic of China
| | - Xingyu Lu
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong City, People’s Republic of China
| | - Dong Li
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong City, People’s Republic of China
| | - Jian Qi
- Department of Neurosurgery, Affiliated Hospital of North Sichuan Medical College, Nanchong City, People’s Republic of China
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong City, People’s Republic of China
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Stapińska-Syniec A, Grabiec M, Rylski M, Acewicz A, Sobstyl M. DNA hydroxymethylation in high-grade gliomas. J Neurol Surg A Cent Eur Neurosurg 2021; 83:568-572. [PMID: 34872125 DOI: 10.1055/a-1713-7699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Background and Study Aims Since the new WHO classification of nervous system tumors (2016 revised 4th edition) has been released, gliomas are classified depending on molecular and genetic markers in connection with histopathology, instead of histopathology itself as it was in the previous classification. Over the last years, epigenetic analysis has taken on increased importance in the diagnosis and treatment of different cancers. Multiple studies confirmed that DNA methylation and hydroxymethylation play an important role in the regulation of gene expression during carcinogenesis. In this review, we aim to present the current state of knowledge on DNA hydroxymethylation in human high-grade gliomas (WHO grade III and IV). Results The correlation of DNA hydroxymethylation and survival in glioblastoma patients was evaluated by different studies. The majority of them showed that the expression of 5-hydroxymethylcytosine (5-hmC) and Ten-eleven translocation (TET) enzymes were significantly reduced, sometimes almost undetectable in high-grade gliomas in comparison with the control brain. A decreased level of 5-hmC was associated with poor survival in patients, but high expression of the TET3 enzyme was related to a better prognosis for GBM patients. This points to the relevance of DNA hydroxymethylation in molecular diagnostics of human gliomas, including survival estimation or differentiating patients in terms of response to the treatment. Conclusion Future studies may shed some more light on this epigenetic mechanism involved in the pathogenesis of human high-grade gliomas and help to develop new targeted therapies.
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Affiliation(s)
| | - Marta Grabiec
- Department of Clinical Cytology, Centrum Medyczne Ksztalcenia Podyplomowego, Warszawa, Poland
| | - Marcin Rylski
- Department of Clinical Cytology, Centrum Medyczne Ksztalcenia Podyplomowego, Warszawa, Poland.,Department of Neuroradiology, Instytut Psychiatrii i Neurologii, Warsaw, Poland
| | - Albert Acewicz
- Department of Neuropathology, Instytut Psychiatrii i Neurologii, Warsaw, Poland
| | - Michał Sobstyl
- Department of Neurosurgery, Instytut Psychiatrii i Neurologii, Warsaw, Poland
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Nuechterlein N, Shapiro LG, Holland EC, Cimino PJ. Machine learning modeling of genome-wide copy number alteration signatures reliably predicts IDH mutational status in adult diffuse glioma. Acta Neuropathol Commun 2021; 9:191. [PMID: 34863298 PMCID: PMC8645099 DOI: 10.1186/s40478-021-01295-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022] Open
Abstract
Knowledge of 1p/19q-codeletion and IDH1/2 mutational status is necessary to interpret any investigational study of diffuse gliomas in the modern era. While DNA sequencing is the gold standard for determining IDH mutational status, genome-wide methylation arrays and gene expression profiling have been used for surrogate mutational determination. Previous studies by our group suggest that 1p/19q-codeletion and IDH mutational status can be predicted by genome-wide somatic copy number alteration (SCNA) data alone, however a rigorous model to accomplish this task has yet to be established. In this study, we used SCNA data from 786 adult diffuse gliomas in The Cancer Genome Atlas (TCGA) to develop a two-stage classification system that identifies 1p/19q-codeleted oligodendrogliomas and predicts the IDH mutational status of astrocytic tumors using a machine-learning model. Cross-validated results on TCGA SCNA data showed near perfect classification results. Furthermore, our astrocytic IDH mutation model validated well on four additional datasets (AUC = 0.97, AUC = 0.99, AUC = 0.95, AUC = 0.96) as did our 1p/19q-codeleted oligodendroglioma screen on the two datasets that contained oligodendrogliomas (MCC = 0.97, MCC = 0.97). We then retrained our system using data from these validation sets and applied our system to a cohort of REMBRANDT study subjects for whom SCNA data, but not IDH mutational status, is available. Overall, using genome-wide SCNAs, we successfully developed a system to robustly predict 1p/19q-codeletion and IDH mutational status in diffuse gliomas. This system can assign molecular subtype labels to tumor samples of retrospective diffuse glioma cohorts that lack 1p/19q-codeletion and IDH mutational status, such as the REMBRANDT study, recasting these datasets as validation cohorts for diffuse glioma research.
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Affiliation(s)
- Nicholas Nuechterlein
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Linda G Shapiro
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Patrick J Cimino
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, Division of Neuropathology, University of Washington, 325 9th Avenue, Box 359791, Seattle, WA, 98104, USA.
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37
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Nickel AC, Picard D, Qin N, Wolter M, Kaulich K, Hewera M, Pauck D, Marquardt V, Torga G, Muhammad S, Zhang W, Schnell O, Steiger HJ, Hänggi D, Fritsche E, Her NG, Nam DH, Carro MS, Remke M, Reifenberger G, Kahlert UD. Longitudinal stability of molecular alterations and drug response profiles in tumor spheroid cell lines enables reproducible analyses. Biomed Pharmacother 2021; 144:112278. [PMID: 34628166 DOI: 10.1016/j.biopha.2021.112278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
The utility of patient-derived tumor cell lines as experimental models for glioblastoma has been challenged by limited representation of the in vivo tumor biology and low clinical translatability. Here, we report on longitudinal epigenetic and transcriptional profiling of seven glioblastoma spheroid cell line models cultured over an extended period. Molecular profiles were associated with drug response data obtained for 231 clinically used drugs. We show that the glioblastoma spheroid models remained molecularly stable and displayed reproducible drug responses over prolonged culture times of 30 in vitro passages. Integration of gene expression and drug response data identified predictive gene signatures linked to sensitivity to specific drugs, indicating the potential of gene expression-based prediction of glioblastoma therapy response. Our data thus empowers glioblastoma spheroid disease modeling as a useful preclinical assay that may uncover novel therapeutic vulnerabilities and associated molecular alterations.
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Affiliation(s)
- A C Nickel
- Department of Neurosurgery, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany
| | - D Picard
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany; Institute of Neuropathology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Düsseldorf, Germany
| | - N Qin
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany; Institute of Neuropathology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Düsseldorf, Germany
| | - M Wolter
- Institute of Neuropathology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany
| | - K Kaulich
- Institute of Neuropathology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany
| | - M Hewera
- Department of Neurosurgery, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany
| | - D Pauck
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany; Institute of Neuropathology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany
| | - V Marquardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany; Institute of Neuropathology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany
| | - G Torga
- Drug Development Unit, Sarah Cannon Research Institute, London, UK
| | - S Muhammad
- Department of Neurosurgery, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany
| | - W Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - O Schnell
- Department of Neurosurgery, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - H-J Steiger
- Department of Neurosurgery, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany
| | - D Hänggi
- Department of Neurosurgery, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany
| | - E Fritsche
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - N-G Her
- R&D Center, AIMEDBIO Inc., Seoul, South Korea
| | - D-H Nam
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University, Seoul 06351, South Korea
| | - M S Carro
- Department of Neurosurgery, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - M Remke
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany; Institute of Neuropathology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Düsseldorf, Germany
| | - G Reifenberger
- Institute of Neuropathology, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Düsseldorf, Germany
| | - U D Kahlert
- Department of Neurosurgery, University Hospital Düsseldorf and Medical Faculty, Heinrich Heine University Düsseldorf, Germany; Molecular and Experimental Surgery, Department of General, Visceral, Vascular, and Transplant Surgery, University Hospital Magdeburg, Magdeburg, Germany.
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Sun Y, Jing Y, Zhang Y. Serum lncRNA-ANRIL and SOX9 expression levels in glioma patients and their relationship with poor prognosis. World J Surg Oncol 2021; 19:287. [PMID: 34556140 PMCID: PMC8461887 DOI: 10.1186/s12957-021-02392-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/03/2021] [Indexed: 01/16/2023] Open
Abstract
Background lncRNA-CDKN2B antisense RNA 1 (ANRIL) and SRY-box transcription factor 9 (SOX9) has abnormal expression in many tumors including glioma, but the underlying molecular mechanism is unclear. This study set out to investigate the serum lncRNA-ANRIL and SOX9 levels in glioma patients and their effects on prognosis. Methods We enrolled 142 glioma patients admitted to our hospital from May 2014 to May 2016 into the research group (RG) and 120 healthy subjects receiving concurrent physical examinations into the control group (CG). Fasting peripheral blood (4 mL each) was sampled from subjects from the two groups. Using the quantitative real-time polymerase chain reaction (qRT-PCR), lncRNA-ANRIL and SOX9 were measured to explore their values in the early diagnosis of glioma. Patients from RG were followed up for 3 years to analyze the influence of lncRNA-ANRIL and SOX9 on patient prognosis. We purchased glioma cell lines U251 and U87 and grouped them according to the transfection of different plasmids. We conducted CCK8 assay to test cell proliferation, Transwell assay to test cell invasion, the flow cytometry to test cell apoptosis, and Western Blot assay to measure bcl-2 and bax protein levels. Results ANRIL and SOX9 were evidently higher in RG than in CG (P<0.01). The receiver operating characteristic (ROC) curve revealed that the diagnostic sensitivity of ANRIL combined with SOX9 for glioma was 81.62%, and the specificity was 90.83% (P<0.01). ANRIL and SOX9 were closely related to tumor grade, tumor diameter, distant metastasis, and family history of glioma (P<0.01). In total, 135 patients were successfully followed up (95.07%). Patients with high levels of ANRIL and SOX9 had a markedly poorer prognosis than those with low levels (P<0.05). ANRIL and SOX9 were markedly higher in glioma cell lines (U251 and U87) than in normal brain cells (P<0.01). The proliferation and invasion of U251 cells were notably reduced after the transfection of ANRIL and SOX9 inhibitory sequences (P<0.01), but the apoptosis was notably increased (P<0.01). Bcl-2 expression was markedly increased in lncRNA-ANRIL-inhibitor and SOX9-inhibitor (P<0.01), while bax expression was markedly reduced in lncRNA-ANRIL-inhibitor and SOX9-inhibitor (P<0.01). Conclusion lncRNA-ANRIL and SOX9 levels were higher in glioma patients than in healthy people. High-lncRNA-ANRIL and SOX9 levels were strongly associated with unfavorable prognosis of patients. The testing of biological behaviors revealed that lncRNA-ANRIL and SOX9 worked as tumor-promoting genes in glioma.
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Affiliation(s)
- Youlu Sun
- Department of Neurosurgery, Guangrao County People's Hospital, No. 180 Huayuan Road, Dongying, Guangrao County, 257300, P.R. China
| | - Yuesong Jing
- Department of Neurosurgery, The Second People's Hospital Of Dongying, Dongying, 257335, P.R. China
| | - Yuxin Zhang
- Department of Neurosurgery, Guangrao County People's Hospital, No. 180 Huayuan Road, Dongying, Guangrao County, 257300, P.R. China.
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Cardona AF, Jaramillo-Velásquez D, Ruiz-Patiño A, Polo C, Jiménez E, Hakim F, Gómez D, Ramón JF, Cifuentes H, Mejía JA, Salguero F, Ordoñez C, Muñoz Á, Bermúdez S, Useche N, Pineda D, Ricaurte L, Zatarain-Barrón ZL, Rodríguez J, Avila J, Rojas L, Jaller E, Sotelo C, Garcia-Robledo JE, Santoyo N, Rolfo C, Rosell R, Arrieta O. Efficacy of osimertinib plus bevacizumab in glioblastoma patients with simultaneous EGFR amplification and EGFRvIII mutation. J Neurooncol 2021; 154:353-364. [PMID: 34498213 DOI: 10.1007/s11060-021-03834-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Amplification of EGFR and its active mutant EGFRvIII are common in glioblastoma (GB). While EGFR and EGFRvIII play critical roles in pathogenesis, targeted therapy with EGFR-tyrosine kinase inhibitors or antibodies has shown limited efficacy. To improve the likelihood of effectiveness, we targeted adult patients with recurrent GB enriched for simultaneous EGFR amplification and EGFRvIII mutation, with osimertinib/bevacizumab at doses described for non-small cell lung cancer. METHODS We retrospectively explored whether previously described EGFRvIII mutation in association with EGFR gene amplification could predict response to osimertinib/bevacizumab combination in a subset of 15 patients treated at recurrence. The resistance pattern in a subgroup of subjects is described using a commercial next-generation sequencing panel in liquid biopsy. RESULTS There were ten males (66.7%), and the median patient's age was 56 years (range 38-70 years). After their initial diagnosis, 12 patients underwent partial (26.7%) or total resection (53.3%). Subsequently, all cases received IMRT and concurrent and adjuvant temozolomide (TMZ; the median number of cycles 9, range 6-12). The median follow-up after recurrence was 17.1 months (95% CI 12.3-22.6). All patients received osimertinib/bevacizumab as a second-line intervention with a median progression-free survival (PFS) of 5.1 months (95% CI 2.8-7.3) and overall survival of 9.0 months (95% CI 3.9-14.0). The PFS6 was 46.7%, and the overall response rate was 13.3%. After exposure to the osimertinib/bevacizumab combination, the main secondary alterations were MET amplification, STAT3, IGF1R, PTEN, and PDGFR. CONCLUSIONS While the osimertinib/bevacizumab combination was marginally effective in most GB patients with simultaneous EGFR amplification plus EGFRvIII mutation, a subgroup experienced a long-lasting meaningful benefit. The findings of this brief cohort justify the continuation of the research in a clinical trial. The pattern of resistance after exposure to osimertinib/bevacizumab includes known mechanisms in the regulation of EGFR, findings that contribute to the understanding and targeting in a stepwise rational this pathway.
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Affiliation(s)
- Andrés F Cardona
- Clinical and Translational Oncology Group, Brain Tumor Unit, Clínica del Country, Calle 116 No. 9 - 72, c. 318, Bogotá, Colombia. .,Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia. .,Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia. .,Thoracic Oncology Unit, Clínica del Country, Bogotá, Colombia.
| | | | - Alejandro Ruiz-Patiño
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Carolina Polo
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Enrique Jiménez
- Neurosurgery Department, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Fernando Hakim
- Neurosurgery Department, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Diego Gómez
- Neurosurgery Department, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | | | | | | | - Fernando Salguero
- Neurosurgery Department, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Camila Ordoñez
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Álvaro Muñoz
- Radio-Oncology Department, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Sonia Bermúdez
- Neuroradiology Section, Radiology Department, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Nicolas Useche
- Neuroradiology Section, Radiology Department, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Diego Pineda
- Neuroradiology Section, Radiology Department, Clínica del Country, Bogotá, Colombia
| | | | | | - July Rodríguez
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Jenny Avila
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Leonardo Rojas
- Clinical and Translational Oncology Group, Brain Tumor Unit, Clínica del Country, Calle 116 No. 9 - 72, c. 318, Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia.,Clinical Oncology Department, Clínica Colsanitas, Bogotá, Colombia
| | - Elvira Jaller
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Carolina Sotelo
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | | | - Nicolas Santoyo
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cáncer Center, Mount Sinai Hospital System & Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Rafael Rosell
- Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Oscar Arrieta
- Laboratory of Personalized Medicine, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
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40
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Zeng C, Wang J, Li M, Wang H, Lou F, Cao S, Lu C. Comprehensive Molecular Characterization of Chinese Patients with Glioma by Extensive Next-Generation Sequencing Panel Analysis. Cancer Manag Res 2021; 13:3573-3588. [PMID: 33953611 PMCID: PMC8092857 DOI: 10.2147/cmar.s291681] [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: 11/25/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Background Tremendous efforts have been made to explore biomarkers for classifying and grading glioma. However, the majority of the current understanding is based on public databases that might not accurately reflect the Asian population. Here, we investigated the genetic landscape of Chinese glioma patients using a validated multigene next-generation sequencing (NGS) panel to provide a strong rationale for the future classification and prognosis of glioma in this population. Methods We analyzed 83 samples, consisting of 71 initial treatments and 12 recurrent surgical tumors, from 81 Chinese patients with gliomas by performing multigene NGS with an Acornmed panel targeting 808 cancer-related hotspot genes, including genes related to glioma (hotspots, selected exons or complete coding sequences) and full-length SNPs located on chromosomes 1 and 19. Results A total of 76 (91.57%) glioma samples had at least one somatic mutation. The most commonly mutated genes were TP53, TERT, IDH1, PTEN, ATRX, and EGFR. Approximately one-third of cases exhibited more than one copy number variation. Of note, this study identified the amplification of genes, such as EGFR and PDGFRA, which were significantly associated with glioblastoma but had not been previously used for clinical classification (P<0.05). Significant differences in genomic profiles between different pathological subtypes and WHO grade were observed. Compared to the MSKCC database primarily comprised of Caucasians, H3F3A mutations and MET amplifications exhibited higher mutation rates, whereas TERT mutations and EGFR and CDKN2A/B copy number variations presented a lower mutation rate in Chinese patients with glioma (P<0.05). Conclusion Our multigene NGS in the simultaneous evaluation of multiple relevant markers revealed several novel genetic alterations in Chinese patients with glioma. NGS-based molecular analysis is a reliable and effective method for diagnosing brain tumors, assisting clinicians in evaluating additional potential therapeutic options, such as targeted therapy, for glioma patients in different racial/ethnic groups.
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Affiliation(s)
- Chun Zeng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China.,China National Clinical Research Center for Neurological Diseases, Beijing, People's Republic of China
| | - Jing Wang
- Department of Neurosurgery, Peking University International Hospital, Beijing, People's Republic of China
| | - Mingwei Li
- Acornmed Biotechnology Co., Ltd, Beijing, People's Republic of China
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd, Beijing, People's Republic of China
| | - Feng Lou
- Acornmed Biotechnology Co., Ltd, Beijing, People's Republic of China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd, Beijing, People's Republic of China
| | - Changyu Lu
- Department of Neurosurgery, Peking University International Hospital, Beijing, People's Republic of China
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41
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Gramatzki D, Felsberg J, Roth P, Kaulich K, von Deimling A, Rushing EJ, Reifenberger G, Weller M. The molecular evolution of glioblastoma treated by gross total resection alone. Neuro Oncol 2021; 23:334-336. [PMID: 33173940 DOI: 10.1093/neuonc/noaa261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Dorothee Gramatzki
- Department of Neurology and Brain Tumor Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Jörg Felsberg
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, Düsseldorf, Germany
| | - Patrick Roth
- Department of Neurology and Brain Tumor Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Kerstin Kaulich
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, Düsseldorf, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Heidelberg and Clinical Cooperation Unit Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - Elisabeth Jane Rushing
- Department of Neuropathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, Düsseldorf, Germany.,German Cancer Consortium, partner site Essen/Düsseldorf, German Cancer Research Center, Heidelberg, Germany
| | - Michael Weller
- Department of Neurology and Brain Tumor Center, University Hospital and University of Zurich, Zurich, Switzerland
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da Silva EM, Selenica P, Vahdatinia M, Pareja F, Da Cruz Paula A, Ferrando L, Gazzo AM, Dopeso H, Ross DS, Bakhteri A, Riaz N, Chandarlapaty S, Razavi P, Norton L, Wen HY, Brogi E, Weigelt B, Zhang H, Reis-Filho JS. TERT promoter hotspot mutations and gene amplification in metaplastic breast cancer. NPJ Breast Cancer 2021; 7:43. [PMID: 33863915 PMCID: PMC8052452 DOI: 10.1038/s41523-021-00250-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/15/2021] [Indexed: 12/22/2022] Open
Abstract
Metaplastic breast cancers (MBCs) are characterized by complex genomes, which seem to vary according to their histologic subtype. TERT promoter hotspot mutations and gene amplification are rare in common forms of breast cancer, but present in a subset of phyllodes tumors. Here, we sought to determine the frequency of genetic alterations affecting TERT in a cohort of 60 MBCs with distinct predominant metaplastic components (squamous, 23%; spindle, 27%; osseous, 8%; chondroid, 42%), and to compare the repertoire of genetic alterations of MBCs according to the presence of TERT promoter hotspot mutations or gene amplification. Forty-four MBCs were subjected to: whole-exome sequencing (WES; n = 27) or targeted sequencing of 341-468 cancer-related genes (n = 17); 16 MBCs were subjected to Sanger sequencing of the TERT promoter, TP53 and selected exons of PIK3CA, HRAS, and BRAF. TERT promoter hotspot mutations (n = 9) and TERT gene amplification (n = 1) were found in 10 of the 60 MBCs analyzed, respectively. These TERT alterations were less frequently found in MBCs with predominant chondroid differentiation than in other MBC subtypes (p = 0.01, Fisher's exact test) and were mutually exclusive with TP53 mutations (p < 0.001, CoMEt). In addition, a comparative analysis of the MBCs subjected to WES or targeted cancer gene sequencing (n = 44) revealed that MBCs harboring TERT promoter hotspot mutations or gene amplification (n = 6) more frequently harbored PIK3CA than TERT wild-type MBCs (n = 38; p = 0.001; Fisher's exact test). In conclusion, TERT somatic genetic alterations are found in a subset of TP53 wild-type MBCs with squamous/spindle differentiation, highlighting the genetic diversity of these cancers.
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Affiliation(s)
- Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mahsa Vahdatinia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenzo Ferrando
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Internal Medicine, University of Genoa, Genova, Italy
| | - Andrea M Gazzo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Higinio Dopeso
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dara S Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ariya Bakhteri
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hong Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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43
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Next generation sequencing impacts the classification and management of primary brain tumours. Pathology 2021; 53:780-782. [PMID: 33858664 DOI: 10.1016/j.pathol.2020.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 01/04/2023]
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44
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Wang Z, Wang Y, Yang T, Xing H, Wang Y, Gao L, Guo X, Xing B, Wang Y, Ma W. Machine learning revealed stemness features and a novel stemness-based classification with appealing implications in discriminating the prognosis, immunotherapy and temozolomide responses of 906 glioblastoma patients. Brief Bioinform 2021; 22:6220175. [PMID: 33839757 PMCID: PMC8425448 DOI: 10.1093/bib/bbab032] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant and lethal intracranial tumor, with extremely limited treatment options. Immunotherapy has been widely studied in GBM, but none can significantly prolong the overall survival (OS) of patients without selection. Considering that GBM cancer stem cells (CSCs) play a non-negligible role in tumorigenesis and chemoradiotherapy resistance, we proposed a novel stemness-based classification of GBM and screened out certain population more responsive to immunotherapy. The one-class logistic regression algorithm was used to calculate the stemness index (mRNAsi) of 518 GBM patients from The Cancer Genome Atlas (TCGA) database based on transcriptomics of GBM and pluripotent stem cells. Based on their stemness signature, GBM patients were divided into two subtypes via consensus clustering, and patients in Stemness Subtype I presented significantly better OS but poorer progression-free survival than Stemness Subtype II. Genomic variations revealed patients in Stemness Subtype I had higher somatic mutation loads and copy number alteration burdens. Additionally, two stemness subtypes had distinct tumor immune microenvironment patterns. Tumor Immune Dysfunction and Exclusion and subclass mapping analysis further demonstrated patients in Stemness Subtype I were more likely to respond to immunotherapy, especially anti-PD1 treatment. The pRRophetic algorithm also indicated patients in Stemness Subtype I were more resistant to temozolomide therapy. Finally, multiple machine learning algorithms were used to develop a 7-gene Stemness Subtype Predictor, which were further validated in two external independent GBM cohorts. This novel stemness-based classification could provide a promising prognostic predictor for GBM and may guide physicians in selecting potential responders for preferential use of immunotherapy.
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Affiliation(s)
- Zihao Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yaning Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Tianrui Yang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Hao Xing
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yuekun Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lu Gao
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaopeng Guo
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Bing Xing
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yu Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Wenbin Ma
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Casar-Borota O, Boldt H, Engström B, Andersen MS, Baussart B, Bengtsson D, Berinder K, Ekman B, Feldt-Rasmussen U, Höybye C, Jørgensen JOL, Kolnes AJ, Korbonits M, Rasmussen ÅK, Lindsay JR, Loughrey PB, Maiter D, Manojlovic-Gacic E, Pahnke J, Poliani PL, Popovic V, Ragnarsson O, Schalin-Jäntti C, Scheie D, Tóth M, Villa C, Wirenfeldt M, Kunicki J, Burman P. Corticotroph Aggressive Pituitary Tumors and Carcinomas Frequently Harbor ATRX Mutations. J Clin Endocrinol Metab 2021; 106:1183-1194. [PMID: 33106857 PMCID: PMC7993578 DOI: 10.1210/clinem/dgaa749] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 12/13/2022]
Abstract
CONTEXT Aggressive pituitary tumors (APTs) are characterized by unusually rapid growth and lack of response to standard treatment. About 1% to 2% develop metastases being classified as pituitary carcinomas (PCs). For unknown reasons, the corticotroph tumors are overrepresented among APTs and PCs. Mutations in the alpha thalassemia/mental retardation syndrome X-linked (ATRX) gene, regulating chromatin remodeling and telomere maintenance, have been implicated in the development of several cancer types, including neuroendocrine tumors. OBJECTIVE To study ATRX protein expression and mutational status of the ATRX gene in APTs and PCs. DESIGN We investigated ATRX protein expression by using immunohistochemistry in 30 APTs and 18 PCs, mostly of Pit-1 and T-Pit cell lineage. In tumors lacking ATRX immunolabeling, mutational status of the ATRX gene was explored. RESULTS Nine of the 48 tumors (19%) demonstrated lack of ATRX immunolabelling with a higher proportion in patients with PCs (5/18; 28%) than in those with APTs (4/30;13%). Lack of ATRX was most common in the corticotroph tumors, 7/22 (32%), versus tumors of the Pit-1 lineage, 2/24 (8%). Loss-of-function ATRX mutations were found in all 9 ATRX immunonegative cases: nonsense mutations (n = 4), frameshift deletions (n = 4), and large deletions affecting 22-28 of the 36 exons (n = 3). More than 1 ATRX gene defect was identified in 2 PCs. CONCLUSION ATRX mutations occur in a subset of APTs and are more common in corticotroph tumors. The findings provide a rationale for performing ATRX immunohistochemistry to identify patients at risk of developing aggressive and potentially metastatic pituitary tumors.
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Affiliation(s)
- Olivera Casar-Borota
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Clinical Pathology, Uppsala University Hospital, Uppsala, Sweden
- Correspondence and Reprint Requests: Olivera Casar-Borota, MD, PhD, Department of Immunology, Genetics and Pathology, Uppsala University and Department of Clinical Pathology, Uppsala University Hospital, Dag Hammarskjölds väg 20, 75851 Uppsala, Sweden. E-mail:
| | - Henning Bünsow Boldt
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Britt Edén Engström
- Department of Medical Sciences, Endocrinology and Mineral Metabolism, Uppsala University, Uppsala, Sweden
- Department of Endocrinology and Diabetology, Uppsala University Hospital, Uppsala, Sweden
| | - Marianne Skovsager Andersen
- Department of Endocrinology, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | | | - Daniel Bengtsson
- Department of Internal Medicine, Kalmar, Region of Kalmar County, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Katarina Berinder
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Department of Endocrinology, Karolinska University Hospital, Stockholm, Sweden
| | - Bertil Ekman
- Department of Endocrinology, University Hospital, Linköping, Sweden
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Ulla Feldt-Rasmussen
- Department of Medical Endocrinology and Metabolism, Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Health Research Sciences, Copenhagen University, Copenhagen, Denmark
| | - Charlotte Höybye
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Department of Endocrinology, Karolinska University Hospital, Stockholm, Sweden
| | - Jens Otto L Jørgensen
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Anders Jensen Kolnes
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Márta Korbonits
- Centre for Endocrinology, William Harvey Research Institute, Barts, UK
- The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Åse Krogh Rasmussen
- Department of Endocrinology and Metabolism, Copenhagen University Hospital, Copenhagen, Denmark
| | - John R Lindsay
- Mater Infirmorum Hospital, Belfast Health & Social Care Trust (BHSCT), UK
- Regional Centre for Endocrinology and Diabetes, Royal Victoria Hospital, Belfast Health & Social Care Trust, UK
| | - Paul Benjamin Loughrey
- Regional Centre for Endocrinology and Diabetes, Royal Victoria Hospital, Belfast Health & Social Care Trust, UK
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast, UK
| | - Dominique Maiter
- Department of Endocrinology and Nutrition, UCL Cliniques universitaires Saint-Luc, 1200 Brussels, Belgium
| | | | - Jens Pahnke
- University of Oslo (UiO) and Oslo University Hospital (OUS), Department of Pathology, Translational Neurodegeneration Research and Neuropathology Lab, Oslo, Norway
- LIED, University of Lübeck, Lübeck, Germany
- Department of Pharmacology, Medical Faculty, University of Latvia, Riga, Latvia
| | - Pietro Luigi Poliani
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia Medical School, Brescia, Italy
| | | | - Oskar Ragnarsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Endocrinology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Camilla Schalin-Jäntti
- Endocrinology, Abdominal Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Miklós Tóth
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Chiara Villa
- Department of Pathological Cytology and Anatomy, Foch Hospital, Suresnes, France
- INSERM U1016, Institut Cochin, Paris, France; Université Paris Descartes-Université de Paris, Paris, France
- Department of Endocrinology, Sart Tilman B35, 4000 Liège, Belgium
| | - Martin Wirenfeldt
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jacek Kunicki
- Department of Neurosurgery, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Pia Burman
- Department of Endocrinology, Skåne University Hospital, Malmö, Lund University, Sweden
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The multi-target small-molecule inhibitor SB747651A shows in vitro and in vivo anticancer efficacy in glioblastomas. Sci Rep 2021; 11:6066. [PMID: 33727611 PMCID: PMC7966768 DOI: 10.1038/s41598-021-85536-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/01/2021] [Indexed: 02/08/2023] Open
Abstract
Glioblastoma multiforme is the most common primary brain tumor and among the most lethal types of cancer. Several mono-target small molecule-inhibitors have been investigated as novel therapeutics, thus far with poor success. In this study we investigated the anticancer effects of SB747651A, a multi-target small-molecule inhibitor, in three well characterized patient-derived glioblastoma spheroid cultures and a murine orthotopic xenograft model. Concentrations of 5–10 µM SB747651A reduced cell proliferation, spheroid formation, migration and chemoresistance, while apoptotic cell death increased. Investigation of oncogenic kinase signaling showed decreased phosphorylation levels of mTOR, CREB, GSK3 and GYS1 leading to altered glycogen metabolism and formation of intracellular reactive oxygen species. Expression levels of cancer stemness marker SOX2 were reduced in treated tumor cells and SB747651A treatment significantly prolonged survival of mice with intracranial glioblastoma xenografts, while no adverse effects were observed in vivo at doses of 25 mg/kg administered 5 days/week for 8 weeks. These findings suggest that SB747651A has anticancer effects in glioblastoma. The cancer-related pathophysiological mechanisms targeted by SB747651A are shared among many types of cancer; however, an in-depth clarification of the mechanisms of action in cancer cells is important before further potential application of SB747651A as an anticancer agent can be considered.
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Meta R, Boldt HB, Kristensen BW, Sahm F, Sjursen W, Torp SH. The Prognostic Value of Methylation Signatures and NF2 Mutations in Atypical Meningiomas. Cancers (Basel) 2021; 13:cancers13061262. [PMID: 33809258 PMCID: PMC8001619 DOI: 10.3390/cancers13061262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/02/2021] [Accepted: 03/08/2021] [Indexed: 01/01/2023] Open
Abstract
Simple Summary The WHO 2016 classification of human meningiomas is debated due to the subjective evaluation of the histopathological diagnostics and grading. However, meningioma classification based on genome-wide DNA methylation profiling has become useful in classification of these tumors by being a better prognostic tool. The current pilot study was designed to test out genome-wide DNA methylation profiling on atypical meningiomas as these tumors have a highly variable risk of recurrence. Although we found that it had diagnostic value, further refinements on the methylation profile procedure are required. With this study we aim to motivate and impact researchers to continue to work and debate towards an improved meningioma classification including molecular and genetic biomarkers, which will benefit patients with such diagnoses. Abstract Background: Due to the solely subjective histopathological assessment, the WHO 2016 classification of human meningiomas is subject to interobserver variation. Consequently, the need for more reliable and objective markers are highly needed. The aim of this pilot study was to apply genome-wide DNA methylation analysis on a series of atypical meningiomas to evaluate the practical utility of this approach, examine whether prognostic subclasses are achieved and investigate whether there is an association between the methylation subclasses with poor prognosis and time to recurrence. NF1/2 mutation analyses were also performed to explore the prognostic value of such mutations in these atypical meningiomas. Methods: Twenty intracranial WHO grade II atypical meningiomas from adult patients were included. They consisted of 10 cases with recurrence (group I), and 10 cases without recurrence (group II). The formalin-fixed and paraffin-embedded tissues underwent standardized genome-wide DNA methylation analysis, and the profiles were matched with the reference library and tumor classifier from Heidelberg. NF1/2 somatic mutation analyses were performed using the CNSv1panel from Düsseldorf. Results: Eighteen out of 20 cases matched to the meningioma class using the common brain tumor classifier (v11b4). Four of these cases matched to a methylation subclass related to a prognostic subgroup based on a cut-off of 0.9. NF2 mutations were detected in 55% of cases across both groups, and the most prominent copy number alterations were chromosomal losses of 22q, 1p and 14q. No significant NF1 mutations were identified. Conclusions: Genome-wide DNA methylation profiling represents a useful tool in the diagnostics of meningiomas, however, methodological adjustments need to be addressed.
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Affiliation(s)
- Rahmina Meta
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; (W.S.); (S.H.T.)
- Correspondence:
| | - Henning B. Boldt
- Department of Pathology, Odense University Hospital, 5000 Odense, Denmark; (H.B.B.); (B.W.K.)
- Research Unit of Pathology, Department of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Bjarne W. Kristensen
- Department of Pathology, Odense University Hospital, 5000 Odense, Denmark; (H.B.B.); (B.W.K.)
- Department of Pathology, The Bartholin Institute, Rigshospitalet, Copenhagen University Hospital, 2100 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC) and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Copenhagen, Denmark
- Department of Oncology, Odense University Hospital, 5000 Odense, Denmark
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany;
- German Cancer Research Centre CCU Neuropathology (DKFZ), 69120 Heidelberg, Germany
| | - Wenche Sjursen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; (W.S.); (S.H.T.)
- Department of Medical Genetics, St. Olavs Hospital, 7030 Trondheim, Norway
| | - Sverre H. Torp
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; (W.S.); (S.H.T.)
- Department of Pathology, St. Olavs Hospital, 7030 Trondheim, Norway
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TERT Promoter Alterations in Glioblastoma: A Systematic Review. Cancers (Basel) 2021; 13:cancers13051147. [PMID: 33800183 PMCID: PMC7962450 DOI: 10.3390/cancers13051147] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Glioblastoma is the most common malignant primary brain tumor in adults. Glioblastoma accounts for 2 to 3 cases per 100,000 persons in North America and Europe. Glioblastoma classification is now based on histopathological and molecular features including isocitrate dehydrogenase (IDH) mutations. At the end of the 2000s, genome-wide sequencing of glioblastoma identified recurrent somatic genetic alterations involved in oncogenesis. Among them, the alterations in the promoter region of the telomerase reverse transcriptase (TERTp) gene are highly recurrent and occur in 70% to 80% of all glioblastomas, including glioblastoma IDH wild type and glioblastoma IDH mutated. This review focuses on recent advances related to physiopathological mechanisms, diagnosis, and clinical implications. Abstract Glioblastoma, the most frequent and aggressive primary malignant tumor, often presents with alterations in the telomerase reverse transcriptase promoter. Telomerase is responsible for the maintenance of telomere length to avoid cell death. Telomere lengthening is required for cancer cell survival and has led to the investigation of telomerase activity as a potential mechanism that enables cancer growth. The aim of this systematic review is to provide an overview of the available data concerning TERT alterations and glioblastoma in terms of incidence, physiopathological understanding, and potential therapeutic implications.
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Franceschi E, De Biase D, Di Nunno V, Pession A, Tosoni A, Gatto L, Tallini G, Visani M, Lodi R, Bartolini S, Brandes AA. IDH1 Non-Canonical Mutations and Survival in Patients with Glioma. Diagnostics (Basel) 2021; 11:diagnostics11020342. [PMID: 33669525 PMCID: PMC7922632 DOI: 10.3390/diagnostics11020342] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Non-canonical mutations of the isocitrate dehydrogenase (IDH) genes have been described in about 20-25% and 5-12% of patients with WHO grade II and III gliomas, respectively. To date, the prognostic value of these rare mutations is still a topic of debate. METHODS We selected patients with WHO grade II and III gliomas and IDH1 mutations with available tissue samples for next-generation sequencing. The clinical outcomes and baseline behaviors of patients with canonical IDH1 R132H and non-canonical IDH1 mutations were compared. RESULTS We evaluated 433 patients harboring IDH1 mutations. Three hundred and ninety patients (90.1%) had a canonical IDH1 R132H mutation while 43 patients (9.9%) had a non-canonical IDH1 mutation. Compared to those with the IDH1 canonical mutation, patients with non-canonical mutations were younger (p < 0.001) and less frequently presented the 1p19q codeletion (p = 0.017). Multivariate analysis confirmed that the extension of surgery (p = 0.003), the presence of the 1p19q codeletion (p = 0.001), and the presence of a non-canonical mutation (p = 0.041) were variables correlated with improved overall survival. CONCLUSION the presence of non-canonical IDH1 mutations could be associated with improved survival among patients with IDH1 mutated grade II-III glioma.
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Affiliation(s)
- Enrico Franceschi
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
- Correspondence: ; Tel.: +39-05-1622-5697
| | - Dario De Biase
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie)-Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, 40126 Bologna, Italy; (D.D.B.); (A.P.)
| | - Vincenzo Di Nunno
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie)-Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, 40126 Bologna, Italy; (D.D.B.); (A.P.)
| | - Alicia Tosoni
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
| | - Lidia Gatto
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale)-Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, 40126 Bologna, Italy; (G.T.); (M.V.)
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale)-Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, 40126 Bologna, Italy; (G.T.); (M.V.)
| | - Raffaele Lodi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy;
| | - Stefania Bartolini
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
| | - Alba Ariela Brandes
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
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Ghiaseddin A, Hoang Minh LB, Janiszewska M, Shin D, Wick W, Mitchell DA, Wen PY, Grossman SA. Adult precision medicine: learning from the past to enhance the future. Neurooncol Adv 2021; 3:vdaa145. [PMID: 33543142 PMCID: PMC7846182 DOI: 10.1093/noajnl/vdaa145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Despite therapeutic advances for other malignancies, gliomas remain challenging solid tumors to treat. Complete surgical resection is nearly impossible due to gliomas’ diffuse infiltrative nature, and treatment is hampered by restricted access to the tumors due to limited transport across the blood–brain barrier. Recent advances in genomic studies and next-generation sequencing techniques have led to a better understanding of gliomas and identification of potential aberrant signaling pathways. Targeting the specific genomic abnormalities via novel molecular therapies has opened a new avenue in the management of gliomas, with encouraging results in preclinical studies and early clinical trials. However, molecular characterization of gliomas revealed significant heterogeneity, which poses a challenge for targeted therapeutic approaches. In this context, leading neuro-oncology researchers and clinicians, industry innovators, and patient advocates convened at the inaugural annual Remission Summit held in Orlando, FL in February 2019 to discuss the latest advances in immunotherapy and precision medicine approaches for the treatment of adult and pediatric brain tumors and outline the unanswered questions, challenges, and opportunities that lay ahead for advancing the duration and quality of life for patients with brain tumors. Here, we provide historical context for precision medicine in other cancers, present emerging approaches for gliomas, discuss their limitations, and outline the steps necessary for future success. We focus on the advances in small molecule targeted therapy, as the use of immunotherapy as an emerging precision medicine modality for glioma treatment has recently been reviewed by our colleagues.
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Affiliation(s)
- Ashley Ghiaseddin
- Department of Neurosurgery, University of Florida, Gainesville, Florida, USA
| | - Lan B Hoang Minh
- Department of Neurosurgery, University of Florida, Gainesville, Florida, USA
| | | | - David Shin
- Department of Neurosurgery, University of Florida, Gainesville, Florida, USA
| | - Wolfgang Wick
- Neurology Clinic, Heidelberg University Medical Center, Heidelberg, Germany
| | - Duane A Mitchell
- Department of Neurosurgery, University of Florida, Gainesville, Florida, USA
| | - Patrick Y Wen
- Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA.,Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Stuart A Grossman
- Department of Oncology, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, USA
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