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Lee B, Hwang S, Bae H, Choi KH, Suh YL. Diagnostic utility of genetic alterations in distinguishing IDH-wildtype glioblastoma from lower-grade gliomas: Insight from next-generation sequencing analysis of 479 cases. Brain Pathol 2024; 34:e13234. [PMID: 38217295 PMCID: PMC11328351 DOI: 10.1111/bpa.13234] [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: 08/08/2023] [Accepted: 12/20/2023] [Indexed: 01/15/2024] Open
Abstract
The accurate diagnosis and classification of gliomas are essential for appropriate treatment planning and prognosis prediction. This study aimed to investigate the molecular diagnostics of IDH-wildtype diffuse astrocytic gliomas and identify potential genetic variants that could differentiate glioblastoma (GBM) from lower-grade gliomas when DNA methylation analysis is not feasible. In total, 479 H3-and IDH-wildtype diffuse astrocytic gliomas were included in this study. All the cases were diagnosed according to the 2021 World Health Organization (WHO) classification of central nervous system (CNS) tumors. Panel sequencing data were collected, and clinicopathological information was retrieved from medical records. Genetic alterations and histological findings were analyzed to determine their diagnostic utility and prognostic implications. Out of 479 cases, 439 (91.6%) were diagnosed with GBM, including 28 cases that were molecularly diagnosed as GBM. However, 40 (8.4%) cases could not be classified according to the 2021 WHO classification and were diagnosed as lower-grade diffuse astrocytic glioma, IDH-wildtype, not elsewhere classified (LGNEC). In addition to the three genetic alterations included in the diagnostic criteria of GBM, PTEN and EGFR mutations were found to be enriched in GBM. Patients harboring mTOR pathway mutations demonstrated a more favorable prognosis and often exhibited morphology resembling subependymal giant cell astrocytoma, along with a high tumor mutational burden. Among patients with mTOR pathway mutations, those lacking molecular diagnostic features of GBM exhibited outstanding survival outcomes, even in the presence of grade 4 histology. Integration of molecular features enhanced the diagnostic accuracy of IDH-wildtype gliomas. Some molecular alterations enriched in GBM offer valuable insights for molecular diagnosis and glioma classification. Furthermore, high-grade diffuse astrocytic gliomas featuring mTOR pathway mutations in the absence of molecular diagnostic features of GBM could represent more favorable tumor types distinct from GBM.
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Affiliation(s)
- Boram Lee
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Soohyun Hwang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyunsik Bae
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Pathology center, Seegene Medical Foundation, Seoul 04805, Republic of Korea
| | - Kyue-Hee Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yeon-Lim Suh
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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2
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Latzer P, Zelba H, Battke F, Reinhardt A, Shao B, Bartsch O, Rabsteyn A, Harter J, Schulze M, Okech T, Golf A, Kyzirakos-Feger C, Kayser S, Pieper N, Feldhahn M, Wünsche J, Seitz C, Hadaschik D, Garbe C, Hauser TK, la Fougère C, Biskup D, Brooke D, Parker D, Martens UM, Illerhaus G, Blumenthal DT, Merrell R, Lorenzo LS, Hidvégi M, de Robles P, Kebir S, Li WW, Li VW, Williams M, Miller AM, Kesari S, Castro M, Desjardins A, Ashley DM, Friedman HS, Wen PY, Neil EC, Iwamoto FM, Sipos B, Geletneky K, Zender L, Glas M, Reardon DA, Biskup S. A real-world observation of patients with glioblastoma treated with a personalized peptide vaccine. Nat Commun 2024; 15:6870. [PMID: 39127809 PMCID: PMC11316744 DOI: 10.1038/s41467-024-51315-8] [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: 02/29/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024] Open
Abstract
Current treatment outcome of patients with glioblastoma (GBM) remains poor. Following standard therapy, recurrence is universal with limited survival. Tumors from 173 GBM patients are analysed for somatic mutations to generate a personalized peptide vaccine targeting tumor-specific neoantigens. All patients were treated within the scope of an individual healing attempt. Among all vaccinated patients, including 70 treated prior to progression (primary) and 103 treated after progression (recurrent), the median overall survival from first diagnosis is 31.9 months (95% CI: 25.0-36.5). Adverse events are infrequent and are predominantly grade 1 or 2. A vaccine-induced immune response to at least one of the vaccinated peptides is detected in blood samples of 87 of 97 (90%) monitored patients. Vaccine-specific T-cell responses are durable in most patients. Significantly prolonged survival is observed for patients with multiple vaccine-induced T-cell responses (53 months) compared to those with no/low induced responses (27 months; P = 0.03). Altogether, our results highlight that the application of personalized neoantigen-targeting peptide vaccine is feasible and represents a promising potential treatment option for GBM patients.
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Affiliation(s)
| | - Henning Zelba
- Zentrum für Humangenetik Tübingen, Tübingen, Germany
| | | | | | - Borong Shao
- Zentrum für Humangenetik Tübingen, Tübingen, Germany
| | | | | | | | | | - Thomas Okech
- MVZ Zentrum für ambulante Onkologie GmbH, Tübingen, Germany
| | - Alexander Golf
- MVZ Zentrum für ambulante Onkologie GmbH, Tübingen, Germany
| | | | - Simone Kayser
- Zentrum für Humangenetik Tübingen, Tübingen, Germany
| | | | | | - Julian Wünsche
- Zentrum für Humangenetik Tübingen, Tübingen, Germany
- MVZ Zentrum für ambulante Onkologie GmbH, Tübingen, Germany
| | - Christian Seitz
- Universitätsklinikum Heidelberg, KiTZ, Hopp Children's Cancer Center, Heidelberg, Germany
| | | | - Claus Garbe
- Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | | | - Christian la Fougère
- Nuklearmedizin und Klinische Molekulare Bildgebung, Universitätsklinikum Tübingen, Tübingen, Germany
| | | | - Dawn Brooke
- Provenance Precision Medicine Foundation, Wilmette, IL, USA
| | | | - Uwe M Martens
- Department of Hematology and Oncology, Cancer Center Heilbronn-Franken, SLK Kliniken GmbH, Heilbronn, Germany
| | | | | | - Ryan Merrell
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Máté Hidvégi
- Jewish Theological Seminary-University of Jewish Studies (OR-ZSE), Budapest, Hungary
| | - Paula de Robles
- Department of Clinical Neurosciences, University of Calgary, Calgary, AB, Canada
- Tom Baker Cancer Centre, Calgary, AB, Canada
| | - Sied Kebir
- Universitätsklinikum Essen, Essen, Germany
| | | | - Vincent W Li
- Angiogenesis Foundation, Cambridge, MA, USA
- Harvard Medical School Dermatology, Boston, MA, USA
| | | | - Alexandra M Miller
- Brain and Spine Tumor Center, NYU Langone Health's Perlmutter Cancer Center, New York, NY, USA
| | - Santosh Kesari
- Pacific Neuroscience Institute, Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Michael Castro
- Cellworks Group Inc, South San Francisco, CA, USA
- Personalized Cancer Medicine, PLLC, Santa Monica, CA, USA
| | - Annick Desjardins
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - David M Ashley
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
- Preston Robert Tisch Brain Tumor Centre, Duke University, Durham, NC, USA
| | - Henry S Friedman
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Elisabeth C Neil
- Department of Neurology, University of Minnesota Health, Minneapolis, MN, USA
| | | | - Bence Sipos
- BAG für Pathologie und Molekularpathologie Stuttgart, Molekularpathologie Baden-Württemberg GbR, Stuttgart, Germany
| | | | - Lars Zender
- University Hospital Tübingen, Internal Medicine VIII, Tübingen, Germany
| | - Martin Glas
- Division of Clinical Neurooncology, Department of Neurology, Universitätsklinikum Essen Klinik für Neurologie, Essen, Germany
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Saskia Biskup
- Zentrum für Humangenetik Tübingen, Tübingen, Germany.
- CeGaT GmbH, Tübingen, Germany.
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Chen WF, Chuang JMJ, Yang SN, Chen NF, Bhattacharya M, Liu HT, Dhama K, Chakraborty C, Wen ZH. Gene expression profiling and the isocitrate dehydrogenase mutational landscape of temozolomide‑resistant glioblastoma. Oncol Lett 2024; 28:378. [PMID: 38939621 PMCID: PMC11209862 DOI: 10.3892/ol.2024.14511] [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: 09/21/2023] [Accepted: 04/09/2024] [Indexed: 06/29/2024] Open
Abstract
Glioblastoma multiforme (GBM) is an aggressive brain cancer that occurs more frequently than other brain tumors. The present study aimed to reveal a novel mechanism of temozolomide resistance in GBM using bioinformatics and wet lab analyses, including meta-Z analysis, Kaplan-Meier survival analysis, protein-protein interaction (PPI) network establishment, cluster analysis of co-expressed gene networks, and hierarchical clustering of upregulated and downregulated genes. Next-generation sequencing and quantitative PCR analyses revealed downregulated [tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1 (TIE1), calcium voltage-gated channel auxiliary subunit α2Δ1 (CACNA2D1), calpain 6 (CAPN6) and a disintegrin and metalloproteinase with thrombospondin motifs 6 (ADAMTS6)] and upregulated [serum amyloid (SA)A1, SAA2, growth differentiation factor 15 (GDF15) and ubiquitin specific peptidase 26 (USP26)] genes. Different statistical models were developed for these genes using the Z-score for P-value conversion, and Kaplan-Meier plots were constructed using several patient cohorts with brain tumors. The highest number of nodes was observed in the PPI network was for ADAMTS6 and TIE1. The PPI network model for all genes contained 35 nodes and 241 edges. Immunohistochemical staining was performed using isocitrate dehydrogenase (IDH)-wild-type or IDH-mutant GBM samples from patients and a significant upregulation of TIE1 (P<0.001) and CAPN6 (P<0.05) protein expression was demonstrated in IDH-mutant GBM in comparison with IDH-wild-type GBM. Structural analysis revealed an IDH-mutant model demonstrating the mutant residues (R132, R140 and R172). The findings of the present study will help the future development of novel biomarkers and therapeutics for brain tumors.
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Affiliation(s)
- Wu-Fu Chen
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan, R.O.C
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, R.O.C
| | - Jimmy Ming-Jung Chuang
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan, R.O.C
| | - San-Nan Yang
- Department of Pediatrics, E-DA Hospital, School of Medicine, College of Medicine I-Shou University, Kaohsiung 82445, Taiwan, R.O.C
- School of Medicine for International Students, College of Medicine, I-Shou University, Kaohsiung 82445, Taiwan, R.O.C
| | - Nan-Fu Chen
- Division of Neurosurgery, Department of Surgery, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan, R.O.C
- Center for General Education, Cheng Shiu University, Kaohsiung 833301, Taiwan, R.O.C
| | | | - Hsin-Tzu Liu
- Department of Medical Research, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien 970374, Taiwan, R.O.C
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agriculture Research-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India
| | - Zhi-Hong Wen
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, R.O.C
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Metellus P, Camilla C, Bialecki E, Beaufils N, Vellutini C, Pellegrino E, Tomasini P, Ahluwalia MS, Mansouri A, Nanni I, Ouafik L. The landscape of cancer-associated transcript fusions in adult brain tumors: a longitudinal assessment in 140 patients with cerebral gliomas and brain metastases. Front Oncol 2024; 14:1382394. [PMID: 39087020 PMCID: PMC11288828 DOI: 10.3389/fonc.2024.1382394] [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: 02/05/2024] [Accepted: 06/17/2024] [Indexed: 08/02/2024] Open
Abstract
Background Oncogenic fusions of neurotrophic receptor tyrosine kinase NTRK1, NTRK2, or NTRK3 genes have been found in different types of solid tumors. The treatment of patients with TRK fusion cancer with a first-generation TRK inhibitor (such as larotrectinib or entrectinib) is associated with high response rates (>75%), regardless of tumor histology and presence of metastases. Due to the efficacy of TRK inhibitor therapy of larotrectinib and entrectinib, it is clinically important to identify patients accurately and efficiently with TRK fusion cancer. In this retrospective study, we provide unique data on the incidence of oncogenic NTRK gene fusions in patients with brain metastases (BM) and gliomas. Methods 140 samples fixed and paraffin-embedded tissue (FFPE) of adult patients (59 of gliomas [17 of WHO grade II, 20 of WHO grade III and 22 glioblastomas] and 81 of brain metastasis (BM) of different primary tumors) are analyzed. Identification of NTRK gene fusions is performed using next-generation sequencing (NGS) technology using Focus RNA assay kit (Thermo Fisher Scientific). Results We identified an ETV6 (5)::NTRK3 (15) fusion event using targeted next-generation sequencing (NGS) in one of 59 glioma patient with oligodendroglioma-grade II, IDH-mutated and 1p19q co-deleted at incidence of 1.69%. Five additional patients harboring TMPRSS (2)::ERG (4) were identified in pancreatic carcinoma brain metastasis (BM), prostatic carcinoma BM, endometrium BM and oligodendroglioma (grade II), IDH-mutated and 1p19q co-deleted. A FGFR3 (17)::TACC3 (11) fusion was identified in one carcinoma breast BM. Aberrant splicing to produce EGFR exons 2-7 skipping mRNA, and MET exon 14 skipping mRNA were identified in glioblastoma and pancreas carcinoma BM, respectively. Conclusions This study provides data on the incidence of NTRK gene fusions in brain tumors, which could strongly support the relevance of innovative clinical trials with specific targeted therapies (larotrectinib, entrectinib) in this population of patients. FGFR3 (17)::TACC3 (11) rearrangement was detected in breast carcinoma BM with the possibility of using some specific targeted therapies and TMPRSS (2)::ERG (4) rearrangements occur in a subset of patients with, prostatic carcinoma BM, endometrium BM, and oligodendroglioma (grade II), IDH-mutated and 1p19q co-deleted, where there are yet no approved ERG-directed therapies.
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Affiliation(s)
- Philippe Metellus
- Aix Marseille Univ, Centre national de Recherche Scientifique (CNRS), INP, Inst Neurophysiopathol, Marseille, France
- Ramsay Santé, Hôpital Privé Clairval, Département de Neurochirurgie, Marseille, France
| | - Clara Camilla
- Aix Marseille Univ, Centre national de Recherche Scientifique (CNRS), INP, Inst Neurophysiopathol, Marseille, France
- Aix Marseille Univ, APHM, CHU Timone, Service d’OncoBiologie, Marseille, France
| | - Emilie Bialecki
- Ramsay Santé, Hôpital Privé Clairval, Département de Neurochirurgie, Marseille, France
| | - Nathalie Beaufils
- Aix Marseille Univ, APHM, CHU Timone, Service d’OncoBiologie, Marseille, France
| | - Christine Vellutini
- Aix Marseille Univ, Centre national de Recherche Scientifique (CNRS), INP, Inst Neurophysiopathol, Marseille, France
| | - Eric Pellegrino
- Aix Marseille Univ, APHM, CHU Timone, Service d’OncoBiologie, Marseille, France
| | - Pascale Tomasini
- Aix Marseille Univ, APHM, Oncologie multidisciplinaire et innovations thérapeutiques, Marseille, France
- Aix-Marseille Univ, Centre national de Recherche Scientifique (CNRS), Inserm, CRCM, Marseille, France
| | - Manmeet S. Ahluwalia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL, United States
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
| | - Alireza Mansouri
- Department of Neurosurgery, Penn State Cancer Institute, Hershey, PA, United States
| | - Isabelle Nanni
- Aix Marseille Univ, APHM, CHU Timone, Service d’OncoBiologie, Marseille, France
| | - L’Houcine Ouafik
- Aix Marseille Univ, Centre national de Recherche Scientifique (CNRS), INP, Inst Neurophysiopathol, Marseille, France
- Aix Marseille Univ, APHM, CHU Timone, Service d’OncoBiologie, Marseille, France
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5
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Richardson TE, Walker JM, Hambardzumyan D, Brem S, Hatanpaa KJ, Viapiano MS, Pai B, Umphlett M, Becher OJ, Snuderl M, McBrayer SK, Abdullah KG, Tsankova NM. Genetic and epigenetic instability as an underlying driver of progression and aggressive behavior in IDH-mutant astrocytoma. Acta Neuropathol 2024; 148:5. [PMID: 39012509 PMCID: PMC11252228 DOI: 10.1007/s00401-024-02761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/17/2024]
Abstract
In recent years, the classification of adult-type diffuse gliomas has undergone a revolution, wherein specific molecular features now represent defining diagnostic criteria of IDH-wild-type glioblastomas, IDH-mutant astrocytomas, and IDH-mutant 1p/19q-codeleted oligodendrogliomas. With the introduction of the 2021 WHO CNS classification, additional molecular alterations are now integrated into the grading of these tumors, given equal weight to traditional histologic features. However, there remains a great deal of heterogeneity in patient outcome even within these established tumor subclassifications that is unexplained by currently codified molecular alterations, particularly in the IDH-mutant astrocytoma category. There is also significant intercellular genetic and epigenetic heterogeneity and plasticity with resulting phenotypic heterogeneity, making these tumors remarkably adaptable and robust, and presenting a significant barrier to the design of effective therapeutics. Herein, we review the mechanisms and consequences of genetic and epigenetic instability, including chromosomal instability (CIN), microsatellite instability (MSI)/mismatch repair (MMR) deficits, and epigenetic instability, in the underlying biology, tumorigenesis, and progression of IDH-mutant astrocytomas. We also discuss the contribution of recent high-resolution transcriptomics studies toward defining tumor heterogeneity with single-cell resolution. While intratumoral heterogeneity is a well-known feature of diffuse gliomas, the contribution of these various processes has only recently been considered as a potential driver of tumor aggressiveness. CIN has an independent, adverse effect on patient survival, similar to the effect of histologic grade and homozygous CDKN2A deletion, while MMR mutation is only associated with poor overall survival in univariate analysis but is highly correlated with higher histologic/molecular grade and other aggressive features. These forms of genomic instability, which may significantly affect the natural progression of these tumors, response to therapy, and ultimately clinical outcome for patients, are potentially measurable features which could aid in diagnosis, grading, prognosis, and development of personalized therapeutics.
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Affiliation(s)
- Timothy E Richardson
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA.
| | - Jamie M Walker
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Neurosurgery, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mariano S Viapiano
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Neurosurgery, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Balagopal Pai
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa Umphlett
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
| | - Oren J Becher
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Samuel K McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Nadejda M Tsankova
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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6
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Nasser AM, Melamed L, Wetzel EA, Chang JCC, Nagashima H, Kitagawa Y, Muzyka L, Wakimoto H, Cahill DP, Miller JJ. CDKN2A/B Homozygous Deletion Sensitizes IDH-Mutant Glioma to CDK4/6 Inhibition. Clin Cancer Res 2024; 30:2996-3005. [PMID: 38718141 PMCID: PMC11250907 DOI: 10.1158/1078-0432.ccr-24-0562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/10/2024] [Accepted: 05/06/2024] [Indexed: 07/16/2024]
Abstract
PURPOSE Treatment paradigms for isocitrate dehydrogenase (IDH)-mutant gliomas are rapidly evolving. Although typically indolent and responsive to initial treatment, these tumors invariably recur at a higher grade and require salvage treatment. Homozygous deletion of the tumor suppressor gene CDKN2A/B frequently emerges at recurrence in these tumors, driving poor patient outcomes. We investigated the effect of CDK-Rb pathway blockade on IDH-mutant glioma growth in vitro and in vivo using CDK4/6 inhibitors (CDKi). EXPERIMENTAL DESIGN Cell viability, proliferation assays, and flow cytometry were used to examine the pharmacologic effect of two distinct CDKi, palbociclib and abemaciclib, in multiple patient-derived IDH-mutant glioma lines. Isogenic models were used to directly investigate the influence of CDKN2A/B status on CDKi sensitivity. Orthotopic xenograft tumor models were used to examine the efficacy and tolerability of CDKi in vivo. RESULTS CDKi treatment leads to decreased cell viability and proliferative capacity in patient-derived IDH-mutant glioma lines, coupled with enrichment of cells in the G1 phase. CDKN2A inactivation sensitizes IDH-mutant glioma to CDKi in both endogenous and isogenic models with engineered CDKN2A deletion. CDK4/6 inhibitor administration improves survival in orthotopically implanted IDH-mutant glioma models. CONCLUSIONS IDH-mutant gliomas with deletion of CDKN2A/B are sensitized to CDK4/6 inhibitors. These results support the investigation of the use of these agents in a clinical setting.
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Affiliation(s)
- Ali M. Nasser
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Lisa Melamed
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Ethan A. Wetzel
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Jenny Chia-Chen Chang
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Hiroaki Nagashima
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yosuke Kitagawa
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Logan Muzyka
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Hiroaki Wakimoto
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Daniel P. Cahill
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Julie J. Miller
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
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7
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Abecunas C, Kidd AD, Jiang Y, Zong H, Fallahi-Sichani M. Multivariate analysis of metabolic state vulnerabilities across diverse cancer contexts reveals synthetically lethal associations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.28.569098. [PMID: 38076921 PMCID: PMC10705426 DOI: 10.1101/2023.11.28.569098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Targeting the distinct metabolic needs of tumor cells has recently emerged as a promising strategy for cancer therapy. The heterogeneous, context-dependent nature of cancer cell metabolism, however, poses challenges in identifying effective therapeutic interventions. Here, we utilize various unsupervised and supervised multivariate modeling approaches to systematically pinpoint recurrent metabolic states within hundreds of cancer cell lines, elucidate their association with tumor lineage and growth environments, and uncover vulnerabilities linked to their metabolic states across diverse genetic and tissue contexts. We validate key findings via analysis of data from patient-derived tumors and pharmacological screens, and by performing new genetic and pharmacological experiments. Our analysis uncovers new synthetically lethal associations between the tumor metabolic state (e.g., oxidative phosphorylation), driver mutations (e.g., loss of tumor suppressor PTEN), and actionable biological targets (e.g., mitochondrial electron transport chain). Investigating the mechanisms underlying these relationships can inform the development of more precise and context-specific, metabolism-targeted cancer therapies.
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Affiliation(s)
- Cara Abecunas
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
- Present address: Novartis Institutes for BioMedical Research, Cambridge, MA 02139
| | - Audrey D. Kidd
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908
| | - Ying Jiang
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908
| | - Hui Zong
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908
| | - Mohammad Fallahi-Sichani
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908
- Lead contact
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8
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Dono A, Zhu P, Takayasu T, Arevalo O, Riascos R, Tandon N, Ballester LY, Esquenazi Y. Extent of Resection Thresholds in Molecular Subgroups of Newly Diagnosed Isocitrate Dehydrogenase-Wildtype Glioblastoma. Neurosurgery 2024:00006123-990000000-01153. [PMID: 38687046 DOI: 10.1227/neu.0000000000002964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/05/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Maximizing the extent of resection (EOR) improves outcomes in glioblastoma (GBM). However, previous GBM studies have not addressed the EOR impact in molecular subgroups beyond IDH1/IDH2 status. In the current article, we evaluate whether EOR confers a benefit in all GBM subtypes or only in particular molecular subgroups. METHODS A retrospective cohort of newly diagnosed GBM isocitrate dehydrogenase (IDH)-wildtype undergoing resection were prospectively included in a database (n = 138). EOR and residual tumor volume (RTV) were quantified with semiautomated software. Formalin-fixed paraffin-embedded tumor tissues were analyzed by targeted next-generation sequencing. The association between recurrent genomic alterations and EOR/RTV was evaluated using a recursive partitioning analysis to identify thresholds of EOR or RTV that may predict survival. The Kaplan-Meier methods and multivariable Cox proportional hazards regression methods were applied for survival analysis. RESULTS Patients with EOR ≥88% experienced 44% prolonged overall survival (OS) in multivariable analysis (hazard ratio: 0.56, P = .030). Patients with alterations in the TP53 pathway and EOR <89% showed reduced OS compared to TP53 pathway altered patients with EOR>89% (10.5 vs 18.8 months; HR: 2.78, P = .013); however, EOR/RTV was not associated with OS in patients without alterations in the TP53 pathway. Meanwhile, in all patients with EOR <88%, PTEN-altered had significantly worse OS than PTEN-wildtype (9.5 vs 15.4 months; HR: 4.53, P < .001). CONCLUSION Our results suggest that a subset of molecularly defined GBM IDH-wildtype may benefit more from aggressive resections. Re-resections to optimize EOR might be beneficial in a subset of molecularly defined GBMs. Molecular alterations should be taken into consideration for surgical treatment decisions in GBM IDH-wildtype.
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Affiliation(s)
- Antonio Dono
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ping Zhu
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | - Octavio Arevalo
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Roy Riascos
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
- Memorial Hermann Hospital - TMC, Houston, Texas, USA
| | - Nitin Tandon
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
- Memorial Hermann Hospital - TMC, Houston, Texas, USA
| | - Leomar Y Ballester
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yoshua Esquenazi
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, Texas, USA
- Memorial Hermann Hospital - TMC, Houston, Texas, USA
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, Texas, USA
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9
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Ebrahimi A, Waha A, Schittenhelm J, Gohla G, Schuhmann MU, Pietsch T. BCOR::CREBBP fusion in malignant neuroepithelial tumor of CNS expands the spectrum of methylation class CNS tumor with BCOR/BCOR(L1)-fusion. Acta Neuropathol Commun 2024; 12:60. [PMID: 38637838 PMCID: PMC11025138 DOI: 10.1186/s40478-024-01780-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Methylation class "CNS tumor with BCOR/BCOR(L1)-fusion" was recently defined based on methylation profiling and tSNE analysis of a series of 21 neuroepithelial tumors with predominant presence of a BCOR fusion and/or characteristic CNV breakpoints at chromosome 22q12.31 and chromosome Xp11.4. Clear diagnostic criteria are still missing for this tumor type, specially that BCOR/BCOR(L1)-fusion is not a consistent finding in these tumors despite being frequent and that none of the Heidelberger classifier versions is able to clearly identify these cases, in particular tumors with alternative fusions other than those involving BCOR, BCORL1, EP300 and CREBBP. In this study, we introduce a BCOR::CREBBP fusion in an adult patient with a right temporomediobasal tumor, for the first time in association with methylation class "CNS tumor with BCOR/BCOR(L1)-fusion" in addition to 35 cases of CNS neuroepithelial tumors with molecular and histopathological characteristics compatible with "CNS tumor with BCOR/BCOR(L1)-fusion" based on a comprehensive literature review and data mining in the repository of 23 published studies on neuroepithelial brain Tumors including 7207 samples of 6761 patients. Based on our index case and the 35 cases found in the literature, we suggest the archetypical histological and molecular features of "CNS tumor with BCOR/BCOR(L1)-fusion". We also present four adult diffuse glioma cases including GBM, IDH-Wildtype and Astrocytoma, IDH-Mutant with CREBBP fusions and describe the necessity of complementary molecular analysis in "CNS tumor with BCOR/BCOR(L1)-alterations for securing a final diagnosis.
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Affiliation(s)
- Azadeh Ebrahimi
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany.
| | - Andreas Waha
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany
| | - Jens Schittenhelm
- Institute of Neuropathology, University Hospital of Tübingen, Tübingen, Germany
| | - Georg Gohla
- Department of Diagnostic and Interventional Radiology, University Hospital of Tübingen, Tübingen, Germany
| | - Martin U Schuhmann
- Department of Neurosurgery, University Hospital of Tübingen, Tübingen, Germany
| | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany
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10
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Zhang C, Yang Y, Cui Q, Zhao D, Cui C. Identification and Analysis of Sex-Biased Copy Number Alterations. HEALTH DATA SCIENCE 2024; 4:0121. [PMID: 39011274 PMCID: PMC11249066 DOI: 10.34133/hds.0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/16/2024] [Indexed: 07/17/2024]
Abstract
Background: Sex difference has long been recognized at cancer incidence, outcomes, and responses to therapy. Analyzing the somatic mutation profiles of large-scale cancer samples between the sexes have revealed several potential drivers of cancer with sex difference. However, it is still a demand for in-depth scrutinizing the sex-biased characteristics of genome instability to link the clinical differences for individual cancer type. Methods: Here, we utilized a published framework devised to specifically compare the copy number profiles between 2 groups to identify the sex-biased copy number alterations (CNAs) across 16 cancer types from the The Cancer Genome Atlas Program database, and dissected the impact of those CNAs. Results: Totally, 81 male-biased CNA regions and 23 female-biased CNA regions in 16 cancer types were found. Functional annotation analysis showed that several critical biological functions associated with sex-biased CNAs are shared in multiple cancer types, including immune-related pathways and regulation of cellular signaling. Most sex-biased CNAs have a substantial effect on transcriptional consequence, where the average of over 68% of genes have a linear relationship with CNAs across cancer types, and 14% of those genes are affected by the combination of the sex and copy number. Furthermore, 29 sex-biased CNA regions show latent capacity to be sex-specific prognostic biomarker such as CNA on 11q13.4 for head and neck cancer and lung cancer. Conclusions: This analysis offers new insights into the role of sex in cancer etiology and prognosis through a detailed characterization of sex differences in genome instability of diverse cancers.
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Affiliation(s)
- Chenhao Zhang
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing 100191, China
| | - Yang Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Qinghua Cui
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing 100191, China
- School of Sports Medicine, Wuhan Institute of Physical Education, No.461 Luoyu Rd. Wuchang District, Wuhan 430079, Hubei Province, China
| | - Dongyu Zhao
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing 100191, China
| | - Chunmei Cui
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing 100191, China
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11
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Aryal B, Bizhanova Z, Joseph EA, Yin Y, Wagner PL, Dalton E, LaFramboise WA, Bartlett DL, Allen CJ. Navigating Precision Oncology: Insights from an Integrated Clinical Data and Biobank Repository Initiative across a Network Cancer Program. Cancers (Basel) 2024; 16:760. [PMID: 38398150 PMCID: PMC10886699 DOI: 10.3390/cancers16040760] [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: 01/09/2024] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Advancing cancer treatment relies on the rapid translation of new scientific discoveries to patient care. To facilitate this, an oncology biobank and data repository program, also referred to as the "Moonshot" program, was launched in 2021 within the Integrated Network Cancer Program of the Allegheny Health Network. A clinical data program (CDP) and biospecimen repository were established, and patient data and blood and tissue samples have been collected prospectively. To date, the study has accrued 2920 patients, predominantly female (61%) and Caucasian (90%), with a mean age of 64 ± 13 years. The most common cancer sites were the endometrium/uterus (12%), lung/bronchus (12%), breast (11%), and colon/rectum (11%). Of patients diagnosed with cancer, 34% were diagnosed at stage I, 25% at stage II, 26% at stage III, and 15% at stage IV. The CDP is designed to support our initiative in advancing personalized cancer research by providing a comprehensive array of patient data, encompassing demographic characteristics, diagnostic details, and treatment responses. The "Moonshot" initiative aims to predict therapy responses and clinical outcomes through cancer-related biomarkers. The CDP facilitates this initiative by fostering data sharing, enabling comparative analyses, and informing the development of novel diagnostic and therapeutic methods.
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Affiliation(s)
- Bibek Aryal
- Allegheny Singer Research Institute, Allegheny Health Network, Pittsburgh, PA 15212, USA; (B.A.); (Z.B.); (E.A.J.); (Y.Y.)
| | - Zhadyra Bizhanova
- Allegheny Singer Research Institute, Allegheny Health Network, Pittsburgh, PA 15212, USA; (B.A.); (Z.B.); (E.A.J.); (Y.Y.)
| | - Edward A. Joseph
- Allegheny Singer Research Institute, Allegheny Health Network, Pittsburgh, PA 15212, USA; (B.A.); (Z.B.); (E.A.J.); (Y.Y.)
| | - Yue Yin
- Allegheny Singer Research Institute, Allegheny Health Network, Pittsburgh, PA 15212, USA; (B.A.); (Z.B.); (E.A.J.); (Y.Y.)
| | - Patrick L. Wagner
- Division of Surgical Oncology, Institute of Surgery, Allegheny Health Network, Pittsburgh, PA 15212, USA;
| | | | | | - David L. Bartlett
- Allegheny Health Network Cancer Institute, Pittsburgh, PA 15212, USA;
| | - Casey J. Allen
- Division of Surgical Oncology, Institute of Surgery, Allegheny Health Network, Pittsburgh, PA 15212, USA;
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12
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Al-Ghabkari A, Huang B, Park M. Aberrant MET Receptor Tyrosine Kinase Signaling in Glioblastoma: Targeted Therapy and Future Directions. Cells 2024; 13:218. [PMID: 38334610 PMCID: PMC10854665 DOI: 10.3390/cells13030218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/27/2023] [Accepted: 01/12/2024] [Indexed: 02/10/2024] Open
Abstract
Brain tumors represent a heterogeneous group of neoplasms characterized by a high degree of aggressiveness and a poor prognosis. Despite recent therapeutic advances, the treatment of brain tumors, including glioblastoma (GBM), an aggressive primary brain tumor associated with poor prognosis and resistance to therapy, remains a significant challenge. Receptor tyrosine kinases (RTKs) are critical during development and in adulthood. Dysregulation of RTKs through activating mutations and gene amplification contributes to many human cancers and provides attractive therapeutic targets for treatment. Under physiological conditions, the Met RTK, the hepatocyte growth factor/scatter factor (HGF/SF) receptor, promotes fundamental signaling cascades that modulate epithelial-to-mesenchymal transition (EMT) involved in tissue repair and embryogenesis. In cancer, increased Met activity promotes tumor growth and metastasis by providing signals for proliferation, survival, and migration/invasion. Recent clinical genomic studies have unveiled multiple mechanisms by which MET is genetically altered in GBM, including focal amplification, chromosomal rearrangements generating gene fusions, and a splicing variant mutation (exon 14 skipping, METex14del). Notably, MET overexpression contributes to chemotherapy resistance in GBM by promoting the survival of cancer stem-like cells. This is linked to distinctive Met-induced pathways, such as the upregulation of DNA repair mechanisms, which can protect tumor cells from the cytotoxic effects of chemotherapy. The development of MET-targeted therapies represents a major step forward in the treatment of brain tumours. Preclinical studies have shown that MET-targeted therapies (monoclonal antibodies or small molecule inhibitors) can suppress growth and invasion, enhancing the efficacy of conventional therapies. Early-phase clinical trials have demonstrated promising results with MET-targeted therapies in improving overall survival for patients with recurrent GBM. However, challenges remain, including the need for patient stratification, the optimization of treatment regimens, and the identification of mechanisms of resistance. This review aims to highlight the current understanding of mechanisms underlying MET dysregulation in GBM. In addition, it will focus on the ongoing preclinical and clinical assessment of therapies targeting MET dysregulation in GBM.
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Affiliation(s)
- Abdulhameed Al-Ghabkari
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
| | - Bruce Huang
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
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13
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Briceno N, Vera E, Komlodi-Pasztor E, Abdullaev Z, Choi A, Grajkowska E, Kunst T, Levine J, Lindsley M, Fernandez K, Reyes J, Boris L, Burton E, Panzer M, Polskin L, Penas-Prado M, Pillai T, Theeler BJ, Wu J, Wall K, Papanicolau-Sengos A, Quezado M, Smirniotopoulos J, Aldape K, Armstrong TS, Gilbert MR. Long-term survivors of glioblastoma: Tumor molecular, clinical, and imaging findings. Neurooncol Adv 2024; 6:vdae019. [PMID: 38420614 PMCID: PMC10901543 DOI: 10.1093/noajnl/vdae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
Background Glioblastoma (GBM) is the most aggressive primary brain malignancy with <45% living a year beyond diagnosis. Previously published investigations of long-term survivors (LTS) provided clinical data but rarely incorporated a comprehensive clinical and molecular analysis. Herein, we identify clinical, imaging, molecular, and outcome features for 23 GBM-LTS patients and compare them with a matched cohort of short-term survivors (STS). Methods Molecularly confirmed Isocitrate Dehydrogenase (IDH) wildtype GBM patients living ≥3 years post-diagnosis (NLTS = 23) or <3 years (NSTS = 75) were identified from our Natural History study. Clinical and demographic characteristics were compared. Tumor tissue was analyzed with targeted next generation sequencing (NGS) (NLTS = 23; NSTS = 74) and methylation analysis (NLTS = 18; NSTS = 28). Pre-surgical MRI scans for a subset of LTS (N = 14) and STS control (N = 28) matched on sex, age, and extent of resection were analyzed. Results LTS tended to be younger. Diagnostic MRIs showed more LTS with T1 tumor hypointensity. LTS tumors were enriched for MGMTp methylation and tumor protein 53 (TP53) mutation. Three patients with classic GBM histology were reclassified based on NGS and methylation testing. Additionally, there were LTS with typical poor prognostic molecular markers. Conclusions Our findings emphasize that generalized predictions of prognosis are inaccurate for individual patients and underscore the need for complete clinical evaluation including molecular work-up to confirm the diagnosis. Continued accrual of patients to LTS registries that containcomprehensive clinical, imaging, tumor molecular data, and outcomes measures may pro\vide important insights about individual patient prognosis.
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Affiliation(s)
- Nicole Briceno
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Elizabeth Vera
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Edina Komlodi-Pasztor
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zied Abdullaev
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anna Choi
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ewa Grajkowska
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tricia Kunst
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason Levine
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Matthew Lindsley
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kelly Fernandez
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jennifer Reyes
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa Boris
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Eric Burton
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Marissa Panzer
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lily Polskin
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Marta Penas-Prado
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tina Pillai
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Brett J Theeler
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jing Wu
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kathleen Wall
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Martha Quezado
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - James Smirniotopoulos
- George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
- MedPix, National Library of Medicine, Bethesda, Maryland, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Terri S Armstrong
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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14
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Nuechterlein N, Shelbourn A, Cimino PJ. Whole gain of chromosome 19, not co-gain of chromosomes 19 and 20, characterizes a class of glioblastomas with more favorable outcomes. J Neuropathol Exp Neurol 2023; 83:53-57. [PMID: 37964704 PMCID: PMC10746695 DOI: 10.1093/jnen/nlad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Affiliation(s)
- Nicholas Nuechterlein
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Allison Shelbourn
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Patrick J Cimino
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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15
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Wang Y, Song Y, Liu Z, Li J, Wang G, Pan H, Zheng Z. miR‑149‑3p suppresses the proliferation and metastasis of glioma cells by targeting the CBX2/Wnt/β‑catenin pathway. Exp Ther Med 2023; 26:562. [PMID: 37954123 PMCID: PMC10632954 DOI: 10.3892/etm.2023.12261] [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: 04/23/2023] [Accepted: 09/11/2023] [Indexed: 11/14/2023] Open
Abstract
The present study aimed to investigate the role of miR-149-3p/chromobox 2 (CBX2)/Wnt/β-catenin pathway in the proliferation and metastasis of glioma cells. The expression and clinical significance of miR-149-3p and CBX2 were analyzed using data from public databases. Cell Counting Kit-8 and colony formation assays were performed to measure cell proliferation. Transwell assays were used to assess cell invasion. The results showed that miR-149-3p was downregulated and CBX2 was upregulated in glioma, and that the downregulated expression of miR-149-3p promoted the proliferation and invasion of glioma cells. In addition, downregulated expression of CBX2 suppressed the proliferation and invasion of glioma cells. Dual-luciferase assay indicated that CBX2 is a target gene of miR149-3p. The possible molecular mechanism of CBX2 was probed by western blotting, which showed that it may further affect the Wnt/β-catenin pathway. These present findings demonstrated that miR-149-3p may function as a tumor suppressor miRNA by directly regulating CBX2 and serve important roles in the malignancy of glioma.
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Affiliation(s)
- Yanjun Wang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Yanqun Song
- Department of Neurosurgery, The Third People's Hospital of Heze City, Heze, Shandong 274031, P.R. China
| | - Zhongcheng Liu
- Department of Neurosurgery, The First People's Hospital of Tai'an, Tai'an, Shandong 271000, P.R. China
| | - Junmin Li
- Department of Obstetrics and Gynecology, Jinan Maternity and Child Care Hospital, Jinan, Shandong 250021, P.R. China
| | - Guodong Wang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Hong Pan
- Department of Ophthalmology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
- Department of Ophthalmology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Zhiming Zheng
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, P.R. China
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16
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Tateishi K, Miyake Y, Nakamura T, Iwashita H, Hayashi T, Oshima A, Honma H, Hayashi H, Sugino K, Kato M, Satomi K, Fujii S, Komori T, Yamamoto T, Cahill DP, Wakimoto H. Genetic alterations that deregulate RB and PDGFRA signaling pathways drive tumor progression in IDH2-mutant astrocytoma. Acta Neuropathol Commun 2023; 11:186. [PMID: 38012788 PMCID: PMC10680361 DOI: 10.1186/s40478-023-01683-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023] Open
Abstract
In IDH-mutant astrocytoma, IDH2 mutation is quite rare and biological mechanisms underlying tumor progression in IDH2-mutant astrocytoma remain elusive. Here, we report a unique case of IDH2 mutant astrocytoma, CNS WHO grade 3 that developed tumor progression. We performed a comprehensive genomic and epigenomic analysis for primary and recurrent tumors and found that both tumors harbored recurrent IDH2R172K and TP53R248W mutation with CDKN2A/B hemizygous deletion. We also found amplifications of CDK4 and MDM2 with PDGFRA gain in the recurrent tumor and upregulated protein expressions of these genes. We further developed, for the first time, a xenograft mouse model of IDH2R172K and TP53R248W mutant astrocytoma from the recurrent tumor, but not from the primary tumor. Consistent with parent recurrent tumor cells, amplifications of CDK4 and MDM2 and PDGFRA gain were found, while CDKN2A/B was identified as homozygous deletion in the xenografts, qualifying for integrated diagnosis of astrocytoma, IDH2-mutant, CNS WHO grade 4. Cell viability assay found that CDK4/6 inhibitor and PDGFR inhibitor potently decreased cell viability in recurrent tumor cells, as compared to primary tumor cells. These findings suggest that gene alterations that activate retinoblastoma (RB) signaling pathways and PDGFR may drive tumor progression and xenograft formation in IDH2-mutant astrocytoma, which is equivalent to progressive IDH1-mutant astrocytoma. Also, our findings suggest that these genomic alterations may represent therapeutic targets in IDH2-mutant astrocytoma.
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Affiliation(s)
- Kensuke Tateishi
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama, 2360004, Japan.
- Laboratory of Biopharmaceutical and Regenerative Science, Graduate School of Medical Science, Yokohama City University, Yokohama, Japan.
- Neurosurgical-Oncology Laboratory, Yokohama City University, Yokohama, Japan.
| | - Yohei Miyake
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama, 2360004, Japan
- Neurosurgical-Oncology Laboratory, Yokohama City University, Yokohama, Japan
| | - Taishi Nakamura
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama, 2360004, Japan
- Neurosurgical-Oncology Laboratory, Yokohama City University, Yokohama, Japan
| | - Hiromichi Iwashita
- Department of Pathology, Yokohama City University Hospital, Yokohama, Japan
- Department of Diagnostic Pathology, Yokohama City University Hospital, Yokohama, Japan
| | - Takahiro Hayashi
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama, 2360004, Japan
- Neurosurgical-Oncology Laboratory, Yokohama City University, Yokohama, Japan
| | - Akito Oshima
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama, 2360004, Japan
- Neurosurgical-Oncology Laboratory, Yokohama City University, Yokohama, Japan
| | - Hirokuni Honma
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama, 2360004, Japan
- Neurosurgical-Oncology Laboratory, Yokohama City University, Yokohama, Japan
| | - Hiroaki Hayashi
- Neurosurgical-Oncology Laboratory, Yokohama City University, Yokohama, Japan
- Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Kyoka Sugino
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama, 2360004, Japan
- Laboratory of Biopharmaceutical and Regenerative Science, Graduate School of Medical Science, Yokohama City University, Yokohama, Japan
- Neurosurgical-Oncology Laboratory, Yokohama City University, Yokohama, Japan
| | - Miyui Kato
- Laboratory of Biopharmaceutical and Regenerative Science, Graduate School of Medical Science, Yokohama City University, Yokohama, Japan
- Neurosurgical-Oncology Laboratory, Yokohama City University, Yokohama, Japan
| | - Kaishi Satomi
- Department of Pathology, Kyorin University School of Medicine, Tokyo, Japan
| | - Satoshi Fujii
- Department of Diagnostic Pathology, Yokohama City University Hospital, Yokohama, Japan
- Department of Molecular Pathology, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Takashi Komori
- Department of Laboratory Medicine and Pathology (Neuropathology), Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Tetsuya Yamamoto
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama, 2360004, Japan
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
- Translational-Neurooncology Laboratory, Brain Tumor Research Center, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
- Translational-Neurooncology Laboratory, Brain Tumor Research Center, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
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17
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Golub D, Lynch DG, Pan PC, Liechty B, Slocum C, Bale T, Pisapia DJ, Juthani R. Polymorphous low-grade neuroepithelial tumor of the young with FGFR3-TACC3 fusion mimicking high-grade glioma: case report and series of high-grade correlates. Front Oncol 2023; 13:1307591. [PMID: 38074682 PMCID: PMC10698862 DOI: 10.3389/fonc.2023.1307591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024] Open
Abstract
Background Polymorphous low-grade neuroepithelial tumor of the young (PLNTY) is a recently described entity that can mimic high-grade glioma (HGG) in histologic and molecular features; however, factors predicting aggressive behavior in these tumors are unclear. Methods We present an indolent neuroepithelial neoplasm in a 59-year-old female with imaging initially suggestive of HGG, and a series of adult patients with HGG harboring FGFR3-TACC3 fusions are also presented for comparison. Results Pathology in the case patient revealed low-grade cytomorphology, microcalcifications, unusual neovascularization, and a low proliferation index. The lesion was diffusely CD34+ and harbored an FGFR3-TACC3 fusion and TERT promoter mutation. A diagnosis of PLNTY was therefore favored and the patient was observed with no progression at 15-month follow-up. In patients with HGG with FGFR3-TACC3 fusions, molecular findings included IDH-wildtype status, absence of 1p19q codeletion, CDKN2A loss, TERT promoter mutations and lack of MGMT promoter methylation. These patients demonstrated a median 15-month overall survival and a 6-month progression-free survival. Conclusion PLNTY is a rare low-grade entity that can display characteristics of HGG, particularly in adults. Presence of FGFR3-TACC3 fusions and other high-grade features should raise concern for a more malignant precursor lesion when a diagnosis of PLNTY is considered.
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Affiliation(s)
- Danielle Golub
- Department of Neurosurgery, Weill Cornell Medicine, New York, NY, United States
- Department of Neurosurgery, Northwell Health, Manhasset, NY, United States
| | - Daniel G. Lynch
- Zucker School of Medicine at Hofstra/Northwell Health, Hempstead, NY, United States
| | - Peter C. Pan
- Department of Neurology, Weill Cornell Medicine, New York, NY, United States
- Department of Neurology, Columbia University, New York, NY, United States
| | - Benjamin Liechty
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Cheyanne Slocum
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Tejus Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David J. Pisapia
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Rupa Juthani
- Department of Neurosurgery, Weill Cornell Medicine, New York, NY, United States
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18
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Rautajoki KJ, Jaatinen S, Hartewig A, Tiihonen AM, Annala M, Salonen I, Valkonen M, Simola V, Vuorinen EM, Kivinen A, Rauhala MJ, Nurminen R, Maass KK, Lahtela SL, Jukkola A, Yli-Harja O, Helén P, Pajtler KW, Ruusuvuori P, Haapasalo J, Zhang W, Haapasalo H, Nykter M. Genomic characterization of IDH-mutant astrocytoma progression to grade 4 in the treatment setting. Acta Neuropathol Commun 2023; 11:176. [PMID: 37932833 PMCID: PMC10629206 DOI: 10.1186/s40478-023-01669-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
As the progression of low-grade diffuse astrocytomas into grade 4 tumors significantly impacts patient prognosis, a better understanding of this process is of paramount importance for improved patient care. In this project, we analyzed matched IDH-mutant astrocytomas before and after progression to grade 4 from six patients (discovery cohort) with genome-wide sequencing, 21 additional patients with targeted sequencing, and 33 patients from Glioma Longitudinal AnalySiS cohort for validation. The Cancer Genome Atlas data from 595 diffuse gliomas provided supportive information. All patients in our discovery cohort received radiation, all but one underwent chemotherapy, and no patient received temozolomide (TMZ) before progression to grade 4 disease. One case in the discovery cohort exhibited a hypermutation signature associated with the inactivation of the MSH2 and DNMT3A genes. In other patients, the number of chromosomal rearrangements and deletions increased in grade 4 tumors. The cell cycle checkpoint gene CDKN2A, or less frequently RB1, was most commonly inactivated after receiving both chemo- and radiotherapy when compared to other treatment groups. Concomitant activating PDGFRA/MET alterations were detected in tumors that acquired a homozygous CDKN2A deletion. NRG3 gene was significantly downregulated and recurrently altered in progressed tumors. Its decreased expression was associated with poorer overall survival in both univariate and multivariate analysis. We also detected progression-related alterations in RAD51B and other DNA repair pathway genes associated with the promotion of error-prone DNA repair, potentially facilitating tumor progression. In our retrospective analysis of patient treatment and survival timelines (n = 75), the combination of postoperative radiation and chemotherapy (mainly TMZ) outperformed radiation, especially in the grade 3 tumor cohort, in which it was typically given after primary surgery. Our results provide further insight into the contribution of treatment and genetic alterations in cell cycle, growth factor signaling, and DNA repair-related genes to tumor evolution and progression.
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Affiliation(s)
- Kirsi J Rautajoki
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland.
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland.
| | - Serafiina Jaatinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Aliisa M Tiihonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Iida Salonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Masi Valkonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Vili Simola
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Elisa M Vuorinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Anni Kivinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Minna J Rauhala
- Department of Neurosurgery, Tampere University Hospital and Tampere University, Tampere, Finland
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Riikka Nurminen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Kendra K Maass
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro Oncology, German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Sirpa-Liisa Lahtela
- Department of Oncology, Tampere University Hospital and Tays Cancer Centre, Tampere, Finland
| | - Arja Jukkola
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Department of Oncology, Tampere University Hospital and Tays Cancer Centre, Tampere, Finland
| | - Olli Yli-Harja
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Pauli Helén
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro Oncology, German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Pekka Ruusuvuori
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Joonas Haapasalo
- Department of Neurosurgery, Tampere University Hospital and Tampere University, Tampere, Finland
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Hannu Haapasalo
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
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19
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Venneti S, Kawakibi AR, Ji S, Waszak SM, Sweha SR, Mota M, Pun M, Deogharkar A, Chung C, Tarapore RS, Ramage S, Chi A, Wen PY, Arrillaga-Romany I, Batchelor TT, Butowski NA, Sumrall A, Shonka N, Harrison RA, de Groot J, Mehta M, Hall MD, Daghistani D, Cloughesy TF, Ellingson BM, Beccaria K, Varlet P, Kim MM, Umemura Y, Garton H, Franson A, Schwartz J, Jain R, Kachman M, Baum H, Burant CF, Mottl SL, Cartaxo RT, John V, Messinger D, Qin T, Peterson E, Sajjakulnukit P, Ravi K, Waugh A, Walling D, Ding Y, Xia Z, Schwendeman A, Hawes D, Yang F, Judkins AR, Wahl D, Lyssiotis CA, de la Nava D, Alonso MM, Eze A, Spitzer J, Schmidt SV, Duchatel RJ, Dun MD, Cain JE, Jiang L, Stopka SA, Baquer G, Regan MS, Filbin MG, Agar NY, Zhao L, Kumar-Sinha C, Mody R, Chinnaiyan A, Kurokawa R, Pratt D, Yadav VN, Grill J, Kline C, Mueller S, Resnick A, Nazarian J, Allen JE, Odia Y, Gardner SL, Koschmann C. Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways. Cancer Discov 2023; 13:2370-2393. [PMID: 37584601 PMCID: PMC10618742 DOI: 10.1158/2159-8290.cd-23-0131] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/30/2023] [Accepted: 08/10/2023] [Indexed: 08/17/2023]
Abstract
Patients with H3K27M-mutant diffuse midline glioma (DMG) have no proven effective therapies. ONC201 has recently demonstrated efficacy in these patients, but the mechanism behind this finding remains unknown. We assessed clinical outcomes, tumor sequencing, and tissue/cerebrospinal fluid (CSF) correlate samples from patients treated in two completed multisite clinical studies. Patients treated with ONC201 following initial radiation but prior to recurrence demonstrated a median overall survival of 21.7 months, whereas those treated after recurrence had a median overall survival of 9.3 months. Radiographic response was associated with increased expression of key tricarboxylic acid cycle-related genes in baseline tumor sequencing. ONC201 treatment increased 2-hydroxyglutarate levels in cultured H3K27M-DMG cells and patient CSF samples. This corresponded with increases in repressive H3K27me3 in vitro and in human tumors accompanied by epigenetic downregulation of cell cycle regulation and neuroglial differentiation genes. Overall, ONC201 demonstrates efficacy in H3K27M-DMG by disrupting integrated metabolic and epigenetic pathways and reversing pathognomonic H3K27me3 reduction. SIGNIFICANCE The clinical, radiographic, and molecular analyses included in this study demonstrate the efficacy of ONC201 in H3K27M-mutant DMG and support ONC201 as the first monotherapy to improve outcomes in H3K27M-mutant DMG beyond radiation. Mechanistically, ONC201 disrupts integrated metabolic and epigenetic pathways and reverses pathognomonic H3K27me3 reduction. This article is featured in Selected Articles from This Issue, p. 2293.
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Affiliation(s)
| | | | - Sunjong Ji
- University of Michigan, Ann Arbor, Michigan
| | - Sebastian M. Waszak
- University of California, San Francisco, San Francisco, California
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
- Laboratory of Computational Neuro-Oncology, Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stefan R. Sweha
- University of Michigan, Ann Arbor, Michigan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | - Chan Chung
- University of Michigan, Ann Arbor, Michigan
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | | | | | | | - Patrick Y. Wen
- Center for Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts
| | | | | | | | | | | | | | - John de Groot
- University of California, San Francisco, San Francisco, California
| | | | | | | | | | | | - Kevin Beccaria
- Department of Neurosurgery, Necker Sick Children's University Hospital and Paris Descartes University, Paris, France
| | - Pascale Varlet
- Department of Neuropathology, Sainte-Anne Hospital and Paris Descartes University, Paris, France
| | | | | | | | | | | | | | | | - Heidi Baum
- University of Michigan, Ann Arbor, Michigan
| | | | - Sophie L. Mottl
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | | | | | | | | | | | | | | | | | - Yujie Ding
- University of Michigan, Ann Arbor, Michigan
| | - Ziyun Xia
- University of Michigan, Ann Arbor, Michigan
| | | | - Debra Hawes
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Fusheng Yang
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander R. Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | | | - Daniel de la Nava
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain
- Solid Tumor Program, Cima Universidad de Navarra, Pamplona, Spain
- Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Marta M. Alonso
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain
- Solid Tumor Program, Cima Universidad de Navarra, Pamplona, Spain
- Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Augustine Eze
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC
| | - Jasper Spitzer
- Institute of Innate Immunity, AG Immunogenomics, University Hospital Bonn, Bonn, Germany
- Institute of Clinical Chemistry and Clinical Pharmacology, AG Immunmonitoring and Genomics, University Hospital Bonn, Bonn, Germany
| | - Susanne V. Schmidt
- Institute of Innate Immunity, AG Immunogenomics, University Hospital Bonn, Bonn, Germany
- Institute of Clinical Chemistry and Clinical Pharmacology, AG Immunmonitoring and Genomics, University Hospital Bonn, Bonn, Germany
| | - Ryan J. Duchatel
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- Paediatric Program, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, NSW, Australia
| | - Matthew D. Dun
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- Paediatric Program, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, NSW, Australia
| | - Jason E. Cain
- Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Sylwia A. Stopka
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gerard Baquer
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael S. Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mariella G. Filbin
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Nathalie Y.R. Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lili Zhao
- University of Michigan, Ann Arbor, Michigan
| | | | - Rajen Mody
- University of Michigan, Ann Arbor, Michigan
| | | | - Ryo Kurokawa
- University of Michigan, Ann Arbor, Michigan
- The University of Tokyo, Tokyo, Japan
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Viveka N. Yadav
- Department of Pediatrics at Children's Mercy Research Institute, Kansas City, Missouri
| | - Jacques Grill
- Department of Pediatric and Adolescent Oncology and INSERM Unit 981, Gustave Roussy and University Paris-Saclay, Villejuif, France
| | - Cassie Kline
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Sabine Mueller
- University of California, San Francisco, San Francisco, California
- Department of Oncology, Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Adam Resnick
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Javad Nazarian
- Department of Pediatrics, Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
- Research Center for Genetic Medicine, Children's National Hospital, Washington, DC
- George Washington University School of Medicine and Health Sciences, Washington, DC
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20
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Kinslow CJ, Rae AI, Taparra K, Kumar P, Siegelin MD, Grinband J, Gill BJA, McKhann GM, Sisti MB, Bruce JN, Canoll PD, Iwamoto FM, Horowitz DP, Kachnic LA, Neugut AI, Yu JB, Cheng SK, Wang TJC. MGMT Promoter Methylation Predicts Overall Survival after Chemotherapy for 1p/19q-Codeleted Gliomas. Clin Cancer Res 2023; 29:4399-4407. [PMID: 37611077 PMCID: PMC10872921 DOI: 10.1158/1078-0432.ccr-23-1295] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/12/2023] [Accepted: 08/22/2023] [Indexed: 08/25/2023]
Abstract
PURPOSE While MGMT promoter methylation (mMGMT) is predictive of response to alkylating chemotherapy and guides treatment decisions in glioblastoma, its role in grade 2 and 3 glioma remains unclear. Recent data suggest that mMGMT is prognostic of progression-free survival in 1p/19q-codeleted oligodendrogliomas, but an effect on overall survival (OS) has not been demonstrated. EXPERIMENTAL DESIGN We identified patients with newly diagnosed 1p/19q-codeleted gliomas and known MGMT promoter status in the National Cancer Database from 2010 to 2019. Multivariable Cox proportional hazards regression modeling was used to assess the effect of mMGMT on OS after adjusting for age, sex, race, comorbidity, grade, extent of resection, chemotherapy, and radiotherapy. RESULTS We identified 1,297 eligible patients, 938 (72.3%) of whom received chemotherapy in their initial course of treatment. The MGMT promoter was methylated in 1,009 (77.8%) patients. Unmethylated MGMT (uMGMT) was associated with worse survival compared with mMGMT [70% {95% confidence interval (CI), 64%-77%} vs. 81% (95% CI, 78%-85%); P < 0.001; adjusted HR (aHR), 2.35 (95% CI, 1.77-3.14)]. uMGMT was associated with worse survival in patients who received chemotherapy [63% (95% CI, 55-73%) vs. 80% (95% CI, 76%-84%); P < 0.001; aHR, 2.61 (95% CI, 1.89-3.60)] but not in patients who did not receive chemotherapy [P = 0.38; HR, 1.31 (95% CI, 0.71-2.42)]. Similar results were observed regardless of World Health Organization grade and after single- or multiagent chemotherapy. CONCLUSIONS Our study demonstrates an association between mMGMT and OS in 1p/19q-codeleted gliomas. MGMT promoter status should be considered as a stratification factor in future clinical trials of 1p/19q-codeleted gliomas that use OS as an endpoint.
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Affiliation(s)
- Connor J. Kinslow
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 622 West 168th Street, BNH B011, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
| | - Ali I. Rae
- Department of Neurological Surgery, Oregon Health & Sciences University, 3181 SW Sam Jackson Pkwy, Portland, OR 97239
| | - Kekoa Taparra
- Department of Radiation Oncology, Stanford University, 875 Blake Wilbur Drive, Stanford, CA 94305
| | - Prashanth Kumar
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 622 West 168th Street, BNH B011, New York, NY 10032
| | - Markus D. Siegelin
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
- Departments of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St. Nicholas Ave Rm. 1001 New York, NY 10032
| | - Jack Grinband
- Program in Imaging and Cognitive Sciences, Columbia University, New York, New York 10032, USA
- David Mahoney Center for Brain and Behavior Research, Columbia University, New York, New York 10032, USA
| | - Brian J. A. Gill
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
- Department of Neurological Surgery, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 710 West 168th Street, New York, NY 10032
| | - Guy M. McKhann
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
- Department of Neurological Surgery, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 710 West 168th Street, New York, NY 10032
| | - Michael B. Sisti
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
- Department of Neurological Surgery, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 710 West 168th Street, New York, NY 10032
| | - Jeffrey N. Bruce
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
- Department of Neurological Surgery, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 710 West 168th Street, New York, NY 10032
| | - Peter D. Canoll
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
- Department of Radiation Oncology, Stanford University, 875 Blake Wilbur Drive, Stanford, CA 94305
| | - Fabio M. Iwamoto
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 710 West 168th Street, New York, NY 10032
| | - David P. Horowitz
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 622 West 168th Street, BNH B011, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
| | - Lisa A. Kachnic
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 622 West 168th Street, BNH B011, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
| | - Alfred I. Neugut
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
- Department of Medicine, Vagelos College of Physicians and Surgeons, and Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th St, New York, NY 10032
| | - James B. Yu
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 622 West 168th Street, BNH B011, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
| | - Simon K. Cheng
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 622 West 168th Street, BNH B011, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
| | - Tony J. C. Wang
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 622 West 168th Street, BNH B011, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032
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21
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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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22
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Mu Q, Chai R, Pang B, Yang Y, Liu H, Zhao Z, Bao Z, Song D, Zhu Z, Yan M, Jiang B, Mo Z, Tang J, Sa JK, Cho HJ, Chang Y, Chan KHY, Loi DSC, Tam SST, Chan AKY, Wu AR, Liu Z, Poon WS, Ng HK, Chan DTM, Iavarone A, Nam DH, Jiang T, Wang J. Identifying predictors of glioma evolution from longitudinal sequencing. Sci Transl Med 2023; 15:eadh4181. [PMID: 37792958 DOI: 10.1126/scitranslmed.adh4181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Clonal evolution drives cancer progression and therapeutic resistance. Recent studies have revealed divergent longitudinal trajectories in gliomas, but early molecular features steering posttreatment cancer evolution remain unclear. Here, we collected sequencing and clinical data of initial-recurrent tumor pairs from 544 adult diffuse gliomas and performed multivariate analysis to identify early molecular predictors of tumor evolution in three diffuse glioma subtypes. We found that CDKN2A deletion at initial diagnosis preceded tumor necrosis and microvascular proliferation that occur at later stages of IDH-mutant glioma. Ki67 expression at diagnosis was positively correlated with acquiring hypermutation at recurrence in the IDH-wild-type glioma. In all glioma subtypes, MYC gain or MYC-target activation at diagnosis was associated with treatment-induced hypermutation at recurrence. To predict glioma evolution, we constructed CELLO2 (Cancer EvoLution for LOngitudinal data version 2), a machine learning model integrating features at diagnosis to forecast hypermutation and progression after treatment. CELLO2 successfully stratified patients into subgroups with distinct prognoses and identified a high-risk patient group featured by MYC gain with worse post-progression survival, from the low-grade IDH-mutant-noncodel subtype. We then performed chronic temozolomide-induction experiments in glioma cell lines and isogenic patient-derived gliomaspheres and demonstrated that MYC drives temozolomide resistance by promoting hypermutation. Mechanistically, we demonstrated that, by binding to open chromatin and transcriptionally active genomic regions, c-MYC increases the vulnerability of key mismatch repair genes to treatment-induced mutagenesis, thus triggering hypermutation. This study reveals early predictors of cancer evolution under therapy and provides a resource for precision oncology targeting cancer dynamics in diffuse gliomas.
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Affiliation(s)
- Quanhua Mu
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
- SIAT-HKUST Joint Laboratory of Cell Evolution and Digital Health, Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, Guangdong 518045, China
| | - Ruichao Chai
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Bo Pang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Yingxi Yang
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Hanjie Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Zheng Zhao
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Zhaoshi Bao
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Dong Song
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Zhihan Zhu
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Mengli Yan
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Biaobin Jiang
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Zongchao Mo
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Jihong Tang
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Jason K Sa
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul 06351, Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Hee Jin Cho
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul 06351, Korea
| | - Yuzhou Chang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Kaitlin Hao Yi Chan
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Danson Shek Chun Loi
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Sindy Sing Ting Tam
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Aden Ka Yin Chan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, SAR 999077, China
| | - Angela Ruohao Wu
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Zhaoqi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Wai Sang Poon
- CUHK Otto Wong Brain Tumour Centre, Department of Surgery, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ho Keung Ng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, SAR 999077, China
| | - Danny Tat Ming Chan
- CUHK Otto Wong Brain Tumour Centre, Department of Surgery, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Antonio Iavarone
- Department of Neurological Surgery, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Do-Hyun Nam
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul 06351, Korea
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 110745, Korea
- Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University School of Medicine, Seoul 110745, Korea
- Chinese Glioma Genome Atlas (CGGA) and Asian Glioma Genome Atlas (AGGA) Research Networks
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Chinese Glioma Genome Atlas (CGGA) and Asian Glioma Genome Atlas (AGGA) Research Networks
- Research Unit of Accurate Diagnosis, Treatment, and Translational Medicine of Brain Tumors, Chinese Academy of Medical Sciences, Beijing 100070, China
| | - Jiguang Wang
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
- SIAT-HKUST Joint Laboratory of Cell Evolution and Digital Health, Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, Guangdong 518045, China
- Chinese Glioma Genome Atlas (CGGA) and Asian Glioma Genome Atlas (AGGA) Research Networks
- Hong Kong Center for Neurodegenerative Diseases, InnoHK, Hong Kong, SAR 999077, China
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23
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Fontana D, Crespiatico I, Crippa V, Malighetti F, Villa M, Angaroni F, De Sano L, Aroldi A, Antoniotti M, Caravagna G, Piazza R, Graudenzi A, Mologni L, Ramazzotti D. Evolutionary signatures of human cancers revealed via genomic analysis of over 35,000 patients. Nat Commun 2023; 14:5982. [PMID: 37749078 PMCID: PMC10519956 DOI: 10.1038/s41467-023-41670-3] [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: 03/29/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
Recurring sequences of genomic alterations occurring across patients can highlight repeated evolutionary processes with significant implications for predicting cancer progression. Leveraging the ever-increasing availability of cancer omics data, here we unveil cancer's evolutionary signatures tied to distinct disease outcomes, representing "favored trajectories" of acquisition of driver mutations detected in patients with similar prognosis. We present a framework named ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) to extract such signatures from sequencing experiments generated by different technologies such as bulk and single-cell sequencing data. We apply ASCETIC to (i) single-cell data from 146 myeloid malignancy patients and bulk sequencing from 366 acute myeloid leukemia patients, (ii) multi-region sequencing from 100 early-stage lung cancer patients, (iii) exome/genome data from 10,000+ Pan-Cancer Atlas samples, and (iv) targeted sequencing from 25,000+ MSK-MET metastatic patients, revealing subtype-specific single-nucleotide variant signatures associated with distinct prognostic clusters. Validations on several datasets underscore the robustness and generalizability of the extracted signatures.
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Affiliation(s)
- Diletta Fontana
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Ilaria Crespiatico
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Valentina Crippa
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Federica Malighetti
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Matteo Villa
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Fabrizio Angaroni
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
- Center of Computational Biology, Human Technopole, Milano, Italy
| | - Luca De Sano
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
| | - Andrea Aroldi
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- Hematology and Clinical Research Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Marco Antoniotti
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre-B4, Milan, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Alex Graudenzi
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy.
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre-B4, Milan, Italy.
- Institute of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche (IBFM-CNR), Segrate, Milan, Italy.
| | - Luca Mologni
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
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24
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Yokoda RT, Cobb WS, Yong RL, Crary JF, Viapiano MS, Walker JM, Umphlett M, Tsankova NM, Richardson TE. CDKN2A mutations have equivalent prognostic significance to homozygous deletion in IDH-mutant astrocytoma. J Neuropathol Exp Neurol 2023; 82:845-852. [PMID: 37550258 DOI: 10.1093/jnen/nlad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023] Open
Abstract
Homozygous deletion of CDKN2A/B is currently considered a molecular signature for grade 4 in IDH-mutant astrocytomas, irrespective of tumor histomorphology. The 2021 WHO Classification of CNS Tumors does not currently include grading recommendations for histologically lower-grade (grade 2-3) IDH-mutant astrocytoma with CDKN2A mutation or other CDKN2A alterations, and little is currently known about the prognostic implications of these alternative CDKN2A inactivating mechanisms. To address this, we evaluated a cohort of institutional and publicly available IDH-mutant astrocytomas, 15 with pathogenic mutations in CDKN2A, 47 with homozygous CDKN2A deletion, and 401 with retained/wildtype CDKN2A. The IDH-mutant astrocytomas with mutant and deleted CDKN2A had significantly higher overall copy number variation compared to those with retained/wildtype CDKN2A, consistent with more aggressive behavior. Astrocytoma patients with CDKN2A mutation had significantly worse progression-free (p = 0.0025) and overall survival (p < 0.0001) compared to grade-matched patients with wildtype CDKN2A, but statistically equivalent progression-free survival and overall survival outcomes to patients with CDKN2A deletion. No significant survival difference was identified between CDKN2A mutant cases with or without loss of the second allele. These findings suggest that CDKN2A mutation has a detrimental effect on survival in otherwise lower-grade IDH-mutant astrocytomas, similar to homozygous CDKN2A deletion, and should be considered for future grading schemes.
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Affiliation(s)
- Raquel T Yokoda
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Raymund L Yong
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John F Crary
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mariano S Viapiano
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, New York, USA
- Department of Neurosurgery, State University of New York, Upstate Medical University, Syracuse, New York, USA
| | - Jamie M Walker
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Melissa Umphlett
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nadejda M Tsankova
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Timothy E Richardson
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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25
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Machado GC, Ferrer VP. MUC17 mutations and methylation are associated with poor prognosis in adult-type diffuse glioma patients. J Neurol Sci 2023; 452:120762. [PMID: 37562166 DOI: 10.1016/j.jns.2023.120762] [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: 02/10/2023] [Revised: 07/03/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Diffuse gliomas are tumors that arise from glial or glial progenitor cells. They are currently classified as astrocytoma isocitrate dehydrogenase (IDH)-mutant or oligodendroglioma IDH-mutant, and 1p/19q-codeleted, both slower-growing tumors, or glioblastoma (GBM), a more aggressive tumor. Despite advances in the diagnosis and treatment of gliomas, the median survival time after diagnosis of GBM remains low, approximately 15 months, with a 5-year overall survival rate of only 6.8%. Therefore, new biomarkers that could support the earlier diagnosis and prognosis of these tumors would be of great value. MUC17, a membrane-bound mucin, has been identified as a potential biomarker for several tumors. However, the role of this mucin in adult gliomas has not yet been explored. Here, we show for the first time, in a retrospective study and by in silico analysis that MUC17 is one of the relevant mutant genes in adult gliomas. Moreover, that an increase in MUC17 methylation correlates with an increase in glioma malignancy grade. Patients with MUC17 mutations had a poorer prognosis than their wild-type counterparts in both GBM and non-GBM glioma cohorts. We also analyzed mutational profiles that correlated strongly with poor survival. Therefore, in this study, we present a new potential biomarker for further investigation, especially for the prognosis of adult diffuse gliomas.
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Affiliation(s)
- Gabriel Cardoso Machado
- Laboratory of Cell and Molecular Biology of Tumors, Department of Cell and Molecular Biology, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil; Graduate Program in Pathological Anatomy, Faculty of Medicine, Rio de Janeiro Federal University, Rio de Janeiro, Brazil
| | - Valéria Pereira Ferrer
- Laboratory of Cell and Molecular Biology of Tumors, Department of Cell and Molecular Biology, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil; Graduate Program in Pathological Anatomy, Faculty of Medicine, Rio de Janeiro Federal University, Rio de Janeiro, Brazil.
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26
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Kocakavuk E, Johnson KC, Sabedot TS, Reinhardt HC, Noushmehr H, Verhaak RGW. Hemizygous CDKN2A deletion confers worse survival outcomes in IDHmut-noncodel gliomas. Neuro Oncol 2023; 25:1721-1723. [PMID: 37329568 PMCID: PMC10479907 DOI: 10.1093/neuonc/noad095] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023] Open
Affiliation(s)
- Emre Kocakavuk
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center (WTZ), National Center for Tumor Diseases (NCT) West, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kevin C Johnson
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA
| | - Thais S Sabedot
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Hospital, Detroit, Michigan, USA
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center (WTZ), National Center for Tumor Diseases (NCT) West, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Houtan Noushmehr
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Hospital, Detroit, Michigan, USA
| | - Roel G W Verhaak
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Neurosurgery, Amsterdam University Medical Center, Amsterdam, The Netherlands
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27
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Yu P, Qu N, Zhu R, Hu J, Han P, Wu J, Tan L, Gan H, He C, Fang C, Lei Y, Li J, He C, Lan F, Shi X, Wei W, Wang Y, Ji Q, Yu FX, Wang YL. TERT accelerates BRAF mutant-induced thyroid cancer dedifferentiation and progression by regulating ribosome biogenesis. SCIENCE ADVANCES 2023; 9:eadg7125. [PMID: 37647391 PMCID: PMC10468137 DOI: 10.1126/sciadv.adg7125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023]
Abstract
TERT reactivation occurs frequently in human malignancies, especially advanced cancers. However, in vivo functions of TERT reactivation in cancer progression and the underlying mechanism are not fully understood. In this study, we expressed TERT and/or active BRAF (BRAF V600E) specifically in mouse thyroid epithelium. While BRAF V600E alone induced papillary thyroid cancer (PTC), coexpression of BRAF V600E and TERT resulted in poorly differentiated thyroid carcinoma (PDTC). Spatial transcriptome analysis revealed that tumors from mice coexpressing BRAF V600E and TERT were highly heterogeneous, and cell dedifferentiation was positively correlated with ribosomal biogenesis. Mechanistically, TERT boosted ribosomal RNA (rRNA) expression and protein synthesis by interacting with multiple proteins involved in ribosomal biogenesis. Furthermore, we found that CX-5461, an rRNA transcription inhibitor, effectively blocked proliferation and induced redifferentiation of thyroid cancer. Thus, TERT promotes thyroid cancer progression by inducing cancer cell dedifferentiation, and ribosome inhibition represents a potential strategy to treat TERT-reactivated cancers.
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Affiliation(s)
- Pengcheng Yu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ning Qu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Rui Zhu
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaqian Hu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peizhen Han
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiahao Wu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Licheng Tan
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hualei Gan
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Cong He
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chuantao Fang
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yubin Lei
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian Li
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chenxi He
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Lan
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Shi
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenjun Wei
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qinghai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fa-Xing Yu
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Long Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Navickas SM, Giles KA, Brettingham-Moore KH, Taberlay PC. The role of chromatin remodeler SMARCA4/BRG1 in brain cancers: a potential therapeutic target. Oncogene 2023:10.1038/s41388-023-02773-9. [PMID: 37433987 PMCID: PMC10374441 DOI: 10.1038/s41388-023-02773-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/16/2023] [Accepted: 06/29/2023] [Indexed: 07/13/2023]
Abstract
The chromatin remodeler SMARCA4/BRG1 is a key epigenetic regulator with diverse roles in coordinating the molecular programs that underlie brain tumour development. BRG1 function in brain cancer is largely specific to the tumour type and varies further between tumour subtypes, highlighting its complexity. Altered SMARCA4 expression has been linked to medulloblastoma, low-grade gliomas such as oligodendroglioma, high-grade gliomas such as glioblastoma and atypical/teratoid rhabdoid tumours. SMARCA4 mutations in brain cancer predominantly occur in the crucial catalytic ATPase domain, which is associated with tumour suppressor activity. However, SMARCA4 is opposingly seen to promote tumourigenesis in the absence of mutation and through overexpression in other brain tumours. This review explores the multifaceted interaction between SMARCA4 and various brain cancer types, highlighting its roles in tumour pathogenesis, the pathways it regulates, and the advances that have been made in understanding the functional relevance of mutations. We discuss developments made in targeting SMARCA4 and the potential to translate these to adjuvant therapies able to enhance current methods of brain cancer treatment.
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Affiliation(s)
- Sophie M Navickas
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Katherine A Giles
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- Children's Medical Research Institute, 214 Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Kate H Brettingham-Moore
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
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29
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Kinslow CJ, Mercurio A, Kumar P, Rae AI, Siegelin MD, Grinband J, Taparra K, Upadhyayula PS, McKhann GM, Sisti MB, Bruce JN, Canoll PD, Iwamoto FM, Kachnic LA, Yu JB, Cheng SK, Wang TJC. Association of MGMT Promoter Methylation With Survival in Low-grade and Anaplastic Gliomas After Alkylating Chemotherapy. JAMA Oncol 2023; 9:919-927. [PMID: 37200021 PMCID: PMC10196932 DOI: 10.1001/jamaoncol.2023.0990] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/13/2023] [Indexed: 05/19/2023]
Abstract
Importance O6-methylguanine-DNA methyltransferase (MGMT [OMIM 156569]) promoter methylation (mMGMT) is predictive of response to alkylating chemotherapy for glioblastomas and is routinely used to guide treatment decisions. However, the utility of MGMT promoter status for low-grade and anaplastic gliomas remains unclear due to molecular heterogeneity and the lack of sufficiently large data sets. Objective To evaluate the association of mMGMT for low-grade and anaplastic gliomas with chemotherapy response. Design, Setting, and Participants This cohort study aggregated grade II and III primary glioma data from 3 prospective cohort studies with patient data collected from August 13, 1995, to August 3, 2022, comprising 411 patients: MSK-IMPACT, EORTC (European Organization of Research and Treatment of Cancer) 26951, and Columbia University. Statistical analysis was performed from April 2022 to January 2023. Exposure MGMT promoter methylation status. Main Outcomes and Measures Multivariable Cox proportional hazards regression modeling was used to assess the association of mMGMT status with progression-free survival (PFS) and overall survival (OS) after adjusting for age, sex, molecular class, grade, chemotherapy, and radiotherapy. Subgroups were stratified by treatment status and World Health Organization 2016 molecular classification. Results A total of 411 patients (mean [SD] age, 44.1 [14.5] years; 283 men [58%]) met the inclusion criteria, 288 of whom received alkylating chemotherapy. MGMT promoter methylation was observed in 42% of isocitrate dehydrogenase (IDH)-wild-type gliomas (56 of 135), 53% of IDH-mutant and non-codeleted gliomas (79 of 149), and 74% of IDH-mutant and 1p/19q-codeleted gliomas (94 of 127). Among patients who received chemotherapy, mMGMT was associated with improved PFS (median, 68 months [95% CI, 54-132 months] vs 30 months [95% CI, 15-54 months]; log-rank P < .001; adjusted hazard ratio [aHR] for unmethylated MGMT, 1.95 [95% CI, 1.39-2.75]; P < .001) and OS (median, 137 months [95% CI, 104 months to not reached] vs 61 months [95% CI, 47-97 months]; log-rank P < .001; aHR, 1.65 [95% CI, 1.11-2.46]; P = .01). After adjusting for clinical factors, MGMT promoter status was associated with chemotherapy response in IDH-wild-type gliomas (aHR for PFS, 2.15 [95% CI, 1.26-3.66]; P = .005; aHR for OS, 1.69 [95% CI, 0.98-2.91]; P = .06) and IDH-mutant and codeleted gliomas (aHR for PFS, 2.99 [95% CI, 1.44-6.21]; P = .003; aHR for OS, 4.21 [95% CI, 1.25-14.2]; P = .02), but not IDH-mutant and non-codeleted gliomas (aHR for PFS, 1.19 [95% CI, 0.67-2.12]; P = .56; aHR for OS, 1.07 [95% CI, 0.54-2.12]; P = .85). Among patients who did not receive chemotherapy, mMGMT status was not associated with PFS or OS. Conclusions and Relevance This study suggests that mMGMT is associated with response to alkylating chemotherapy for low-grade and anaplastic gliomas and may be considered as a stratification factor in future clinical trials of patients with IDH-wild-type and IDH-mutant and codeleted tumors.
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Affiliation(s)
- Connor J. Kinslow
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Ann Mercurio
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Prashanth Kumar
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Ali I. Rae
- Department of Neurological Surgery, Oregon Health & Sciences University, Portland
| | - Markus D. Siegelin
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Department of Pathology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Department of Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Jack Grinband
- Department of Psychiatry, Columbia University, New York, New York
- Department of Radiology, Columbia University, New York, New York
| | - Kekoa Taparra
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Pavan S. Upadhyayula
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Guy M. McKhann
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Michael B. Sisti
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Jeffrey N. Bruce
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Peter D. Canoll
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Department of Pathology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Department of Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Fabio M. Iwamoto
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Lisa A. Kachnic
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - James B. Yu
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Simon K. Cheng
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Tony J. C. Wang
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
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Hollon T, Jiang C, Chowdury A, Nasir-Moin M, Kondepudi A, Aabedi A, Adapa A, Al-Holou W, Heth J, Sagher O, Lowenstein P, Castro M, Wadiura LI, Widhalm G, Movahed-Ezazi M, Neuschmelting V, Reinecke D, von Spreckelsen N, Berger M, Hervey-Jumper S, Golfinos J, Camelo-Piragua S, Freudiger C, Lee H, Orringer D. Artificial-intelligence-based molecular classification of diffuse gliomas using rapid, label-free optical imaging. Nat Med 2023; 29:828-832. [PMID: 36959422 PMCID: PMC10445531 DOI: 10.1038/s41591-023-02252-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/08/2023] [Indexed: 03/25/2023]
Abstract
Molecular classification has transformed the management of brain tumors by enabling more accurate prognostication and personalized treatment. However, timely molecular diagnostic testing for patients with brain tumors is limited, complicating surgical and adjuvant treatment and obstructing clinical trial enrollment. In this study, we developed DeepGlioma, a rapid (<90 seconds), artificial-intelligence-based diagnostic screening system to streamline the molecular diagnosis of diffuse gliomas. DeepGlioma is trained using a multimodal dataset that includes stimulated Raman histology (SRH); a rapid, label-free, non-consumptive, optical imaging method; and large-scale, public genomic data. In a prospective, multicenter, international testing cohort of patients with diffuse glioma (n = 153) who underwent real-time SRH imaging, we demonstrate that DeepGlioma can predict the molecular alterations used by the World Health Organization to define the adult-type diffuse glioma taxonomy (IDH mutation, 1p19q co-deletion and ATRX mutation), achieving a mean molecular classification accuracy of 93.3 ± 1.6%. Our results represent how artificial intelligence and optical histology can be used to provide a rapid and scalable adjunct to wet lab methods for the molecular screening of patients with diffuse glioma.
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Affiliation(s)
- Todd Hollon
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Cheng Jiang
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Asadur Chowdury
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Mustafa Nasir-Moin
- Department of Neurosurgery, New York University, Street, City, 10587, State, Country
| | - Akhil Kondepudi
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Alexander Aabedi
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Arjun Adapa
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Wajd Al-Holou
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Jason Heth
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Oren Sagher
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Pedro Lowenstein
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Maria Castro
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Lisa Irina Wadiura
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Georg Widhalm
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Misha Movahed-Ezazi
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Volker Neuschmelting
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - David Reinecke
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Niklas von Spreckelsen
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Mitchell Berger
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Shawn Hervey-Jumper
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - John Golfinos
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Sandra Camelo-Piragua
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Christian Freudiger
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Honglak Lee
- Machine Learning in Neurosurgery Laboratory, Department of Neurosurgery, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, 48105, MI, USA
| | - Daniel Orringer
- Department of Neurosurgery, New York University, Street, City, 10587, State, Country
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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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Yamaguchi J, Ohka F, Kitano Y, Maeda S, Motomura K, Aoki K, Takeuchi K, Nagata Y, Hattori H, Tsujiuchi T, Motomura A, Nishikawa T, Kibe Y, Shinjo K, Kondo Y, Saito R. Rapid detection of the MYD88 L265P mutation for pre- and intra-operative diagnosis of primary central nervous system lymphoma. Cancer Sci 2023. [PMID: 36859777 DOI: 10.1111/cas.15762] [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: 10/26/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 03/03/2023] Open
Abstract
The myeloid differentiation primary response gene 88 (MYD88) L265P mutation is a disease-specific mutation of primary central nervous system lymphoma (PCNSL) among the central nervous system tumors. Accordingly, this mutation is considered a reliable diagnostic molecular marker of PCNSL. As the intra-operative diagnosis of PCNSL is sometimes difficult to achieve using histological examinations alone, intra-operative detection of the MYD88 L265P mutation could be effective for the accurate diagnosis of PCNSL. Herein, we aimed to develop a novel rapid genotyping system (GeneSoC) using real-time polymerase chain reaction (PCR) based on microfluidic thermal cycling technology. This real-time PCR system shortened the analysis time, which enabled the detection of the MYD88 L265P mutation within 15 min. Rapid detection of the MYD88 L265P mutation was performed intra-operatively using GeneSoC in 24 consecutive cases with suspected malignant brain tumors, including 10 cases with suspected PCNSL before surgery. The MYD88 L265P mutation was detected in eight cases in which tumors were pathologically diagnosed as PCNSL after the operation, while wild-type MYD88 was detected in 16 cases. Although two of the 16 cases with wild-type MYD88 were pathologically diagnosed as PCNSL after the operation, MYD88 L265P could be detected in all eight PCNSL cases harboring MYD88 L265P. The MYD88 L265P mutation could also be detected using cell-free DNA derived from the cerebrospinal fluid of two PCNSL cases. Detection of the MYD88 L265P mutation using GeneSoC might not only improve the accuracy of intra-operative diagnosis of PCNSL but also help the future pre-operative diagnosis through liquid biopsy of cerebrospinal fluid.
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Affiliation(s)
- Junya Yamaguchi
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yotaro Kitano
- Department of Neurosurgery, Mie University Graduate School of Medicine, Tsu, Japan
| | - Sachi Maeda
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuya Motomura
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kosuke Aoki
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhito Takeuchi
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichi Nagata
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hikaru Hattori
- Department of Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | | | - Ayako Motomura
- Department of Neurosurgery, Daido Hospital, Nagoya, Japan
| | - Tomohide Nishikawa
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuji Kibe
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keiko Shinjo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Li L, Leng W, Chen J, Li S, Lei B, Zhang H, Zhao H. Identification of a copper metabolism-related gene signature for predicting prognosis and immune response in glioma. Cancer Med 2023; 12:10123-10137. [PMID: 36856182 PMCID: PMC10166918 DOI: 10.1002/cam4.5688] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/06/2023] [Accepted: 02/01/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Gliomas are highly refractory intracranial cancers characterized by genetic and transcriptional heterogeneity. However, therapeutic options are limited. In the last years, copper-induced cell death is becoming a prospective treatment strategy for gliomas and other solid tumors, but copper metabolism-related genes associated with cancer development remain unclear. METHODS We first collected gene expression data from The Cancer Genome Atlas (TCGA) to identify significantly differentially expressed copper metabolism-related genes in gliomas. Using these genes, we performed COX regression and Least Absolute Shrinkage and Selection Operator (LASSO) regression to construct the prognostic model. The prognostic value of the model was further validated by CGGA testing set. Subsequently, functional analyses were carried out, including gene set enrichment analysis (GSEA), immune infiltration analysis, and mutation analysis. Finally, the expression levels of these genes were verified by immunohistochemical analysis. RESULTS The prognostic model consisted of 7 genes: CDK1, LOXL2, LOXL3, NFE2L2, SLC31A1, SUMF1 and FDX1. According to this prognosis model, glioma patients could be split into the high-risk group or low-risk group, and the low-risk group showed significantly better prognostic survival (p < 0.001). Moreover, the high-risk group had higher levels of immune cell infiltration, immune checkpoint genes expression, and higher tumor mutational burden (TMB), which indicates that they might benefit more from immunotherapy. Finally, we confirmed the expression level of FDX1, SUMF1, and SLC31A1 protein as significantly different in glioblastoma, lower-grade glioma, and non-tumor brain tissues by immunohistochemical analysis, and the high expression of FDX1 and SLC31A1 protein was related to poor survival in glioma patients. CONCLUSIONS Our study could contribute to the prognosis prediction and decision-making in patients with gliomas.
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Affiliation(s)
- Ling Li
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenyuan Leng
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Junying Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shaoying Li
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bingxi Lei
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huasong Zhang
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Otolaryngology, Longgang E.N.T hospital & Shenzhen Key Laboratory of E.N.T, Institute of E.N.T, Shenzhen, China
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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Abstract
Importance Malignant primary brain tumors cause more than 15 000 deaths per year in the United States. The annual incidence of primary malignant brain tumors is approximately 7 per 100 000 individuals and increases with age. Five-year survival is approximately 36%. Observations Approximately 49% of malignant brain tumors are glioblastomas, and 30% are diffusely infiltrating lower-grade gliomas. Other malignant brain tumors include primary central nervous system (CNS) lymphoma (7%) and malignant forms of ependymomas (3%) and meningiomas (2%). Symptoms of malignant brain tumors include headache (50%), seizures (20%-50%), neurocognitive impairment (30%-40%), and focal neurologic deficits (10%-40%). Magnetic resonance imaging before and after a gadolinium-based contrast agent is the preferred imaging modality for evaluating brain tumors. Diagnosis requires tumor biopsy with consideration of histopathological and molecular characteristics. Treatment varies by tumor type and often includes a combination of surgery, chemotherapy, and radiation. For patients with glioblastoma, the combination of temozolomide with radiotherapy improved survival when compared with radiotherapy alone (2-year survival, 27.2% vs 10.9%; 5-year survival, 9.8% vs 1.9%; hazard ratio [HR], 0.6 [95% CI, 0.5-0.7]; P < .001). In patients with anaplastic oligodendroglial tumors with 1p/19q codeletion, probable 20-year overall survival following radiotherapy without vs with the combination of procarbazine, lomustine, and vincristine was 13.6% vs 37.1% (80 patients; HR, 0.60 [95% CI, 0.35-1.03]; P = .06) in the EORTC 26951 trial and 14.9% vs 37% in the RTOG 9402 trial (125 patients; HR, 0.61 [95% CI, 0.40-0.94]; P = .02). Treatment of primary CNS lymphoma includes high-dose methotrexate-containing regimens, followed by consolidation therapy with myeloablative chemotherapy and autologous stem cell rescue, nonmyeloablative chemotherapy regimens, or whole brain radiation. Conclusions and Relevance The incidence of primary malignant brain tumors is approximately 7 per 100 000 individuals, and approximately 49% of primary malignant brain tumors are glioblastomas. Most patients die from progressive disease. First-line therapy for glioblastoma is surgery followed by radiation and the alkylating chemotherapeutic agent temozolomide.
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Affiliation(s)
- Lauren R Schaff
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Neurology, Weill Cornell Medicine, New York, New York
| | - Ingo K Mellinghoff
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Neurology, Weill Cornell Medicine, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pharmacology, Weill Cornell Medicine, New York, New York
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35
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Miller JJ, Gonzalez Castro LN, McBrayer S, Weller M, Cloughesy T, Portnow J, Andronesi O, Barnholtz-Sloan JS, Baumert BG, Berger MS, Bi WL, Bindra R, Cahill DP, Chang SM, Costello JF, Horbinski C, Huang RY, Jenkins RB, Ligon KL, Mellinghoff IK, Nabors LB, Platten M, Reardon DA, Shi DD, Schiff D, Wick W, Yan H, von Deimling A, van den Bent M, Kaelin WG, Wen PY. Isocitrate dehydrogenase (IDH) mutant gliomas: A Society for Neuro-Oncology (SNO) consensus review on diagnosis, management, and future directions. Neuro Oncol 2023; 25:4-25. [PMID: 36239925 PMCID: PMC9825337 DOI: 10.1093/neuonc/noac207] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Isocitrate dehydrogenase (IDH) mutant gliomas are the most common adult, malignant primary brain tumors diagnosed in patients younger than 50, constituting an important cause of morbidity and mortality. In recent years, there has been significant progress in understanding the molecular pathogenesis and biology of these tumors, sparking multiple efforts to improve their diagnosis and treatment. In this consensus review from the Society for Neuro-Oncology (SNO), the current diagnosis and management of IDH-mutant gliomas will be discussed. In addition, novel therapies, such as targeted molecular therapies and immunotherapies, will be reviewed. Current challenges and future directions for research will be discussed.
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Affiliation(s)
- Julie J Miller
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - L Nicolas Gonzalez Castro
- Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Samuel McBrayer
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, Texas, 75235, USA
| | - Michael Weller
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091 Zurich, Switzerland
| | | | - Jana Portnow
- Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Ovidiu Andronesi
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Jill S Barnholtz-Sloan
- Informatics and Data Science (IDS), Center for Biomedical Informatics and Information Technology (CBIIT), Trans-Divisional Research Program (TDRP), Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Bethesda, MD, USA
| | - Brigitta G Baumert
- Cantonal Hospital Graubunden, Institute of Radiation-Oncology, Chur, Switzerland
| | - Mitchell S Berger
- Department of Neurosurgery, University of California-San Francisco, San Francisco, California, USA
| | - Wenya Linda Bi
- Harvard Medical School, Boston, MA, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ranjit Bindra
- Department of Therapeutic Radiology, Brain Tumor Center, Yale School of Medicine, New Haven, CT, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Susan M Chang
- Department of Neurosurgery, University of California-San Francisco, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurosurgery, University of California-San Francisco, San Francisco, California, USA
| | - Craig Horbinski
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Raymond Y Huang
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Robert B Jenkins
- Individualized Medicine Research, Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, Minnesota 55901, USA
| | - Keith L Ligon
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Ingo K Mellinghoff
- Department of Neurology, Evnin Family Chair in Neuro-Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - L Burt Nabors
- Department of Neurology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael Platten
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - David A Reardon
- Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Diana D Shi
- Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - David Schiff
- Division of Neuro-Oncology, Department of Neurology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Wolfgang Wick
- Neuro-Oncology at the German Cancer Research Center (DKFZ), Program Chair of Neuro-Oncology at the National Center for Tumor Diseases (NCT), and Neurology and Chairman at the Neurology Clinic in Heidelberg, Heidelberg, Germany
| | - Hai Yan
- Genetron Health Inc, Gaithersburg, Maryland 20879, USA
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, and, Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), and, DKTK, INF 224, 69120 Heidelberg, Germany
| | - Martin van den Bent
- Brain Tumour Centre, Erasmus MC Cancer Institute, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - William G Kaelin
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Patrick Y Wen
- Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
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Fortin Ensign SP, Jenkins RB, Giannini C, Sarkaria JN, Galanis E, Kizilbash SH. Translational significance of CDKN2A/B homozygous deletion in isocitrate dehydrogenase-mutant astrocytoma. Neuro Oncol 2023; 25:28-36. [PMID: 35973817 PMCID: PMC9825307 DOI: 10.1093/neuonc/noac205] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Indexed: 01/26/2023] Open
Abstract
Isocitrate dehydrogenase (IDH) 1 or 2 mutations confer a favorable prognosis compared to IDH-wildtype in astrocytoma, frequently denoting a lower grade malignancy. However, recent molecular profiling has identified specific aggressive tumor subgroups with clear clinical prognostic implications that are independent of histologic grading. The homozygous deletion of CDKN2A/B is the strongest implicated independent indicator of the poor prognosis within IDH-mutant astrocytoma, and the identification of this alteration in these lower histologic grade tumors transforms their biology toward an aggressive grade 4 phenotype clinically. CDKN2A/B homozygous deletion is now sufficient to define a grade 4 tumor in IDH-mutant astrocytomas regardless of histologic appearance, yet there are currently no effective molecularly informed targeted therapies for these tumors. The biological impact of CDKN2A/B homozygous deletion in IDH-mutant tumors and the optimal treatment strategy for this molecular subgroup remains insufficiently explored. Here we review the current understanding of the translational significance of homozygous deletion of CDKN2A/B gene expression in IDH-mutant astrocytoma and associated diagnostic and therapeutic implications.
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Affiliation(s)
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
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Richardson TE, Yokoda RT, Rashidipour O, Vij M, Snuderl M, Brem S, Hatanpaa KJ, McBrayer SK, Abdullah KG, Umphlett M, Walker JM, Tsankova NM. Mismatch repair protein mutations in isocitrate dehydrogenase (IDH)-mutant astrocytoma and IDH-wild-type glioblastoma. Neurooncol Adv 2023; 5:vdad085. [PMID: 37554222 PMCID: PMC10406418 DOI: 10.1093/noajnl/vdad085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Mutations in mismatch repair (MMR) genes (MSH2, MSH6, MLH1, and PMS2) are associated with microsatellite instability and a hypermutator phenotype in numerous systemic cancers, and germline MMR mutations have been implicated in multi-organ tumor syndromes. In gliomas, MMR mutations can function as an adaptive response to alkylating chemotherapy, although there are well-documented cases of germline and sporadic mutations, with detrimental effects on patient survival. METHODS The clinical, pathologic, and molecular features of 18 IDH-mutant astrocytomas and 20 IDH-wild-type glioblastomas with MMR mutations in the primary tumor were analyzed in comparison to 361 IDH-mutant and 906 IDH-wild-type tumors without MMR mutations. In addition, 12 IDH-mutant astrocytomas and 18 IDH-wild-type glioblastomas that developed MMR mutations between initial presentation and tumor recurrence were analyzed in comparison to 50 IDH-mutant and 104 IDH-wild-type cases that remained MMR-wild-type at recurrence. RESULTS In both IDH-mutant astrocytoma and IDH-wild-type glioblastoma cohorts, the presence of MMR mutation in primary tumors was associated with significantly higher tumor mutation burden (TMB) (P < .0001); however, MMR mutations only resulted in worse overall survival in the IDH-mutant astrocytomas (P = .0069). In addition, gain of MMR mutation between the primary and recurrent surgical specimen occurred more frequently with temozolomide therapy (P = .0073), and resulted in a substantial increase in TMB (P < .0001), higher grade (P = .0119), and worse post-recurrence survival (P = .0022) in the IDH-mutant astrocytoma cohort. CONCLUSIONS These results suggest that whether present initially or in response to therapy, MMR mutations significantly affect TMB but appear to only influence the clinical outcome in IDH-mutant astrocytoma subsets.
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Affiliation(s)
- Timothy E Richardson
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Raquel T Yokoda
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Omid Rashidipour
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Meenakshi Vij
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York, New York, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Samuel K McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Melissa Umphlett
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jamie M Walker
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nadejda M Tsankova
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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38
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Vij M, Yokoda RT, Rashidipour O, Tran I, Vasudevaraja V, Snuderl M, Yong RL, Cobb WS, Umphlett M, Walker JM, Tsankova NM, Richardson TE. The prognostic impact of subclonal IDH1 mutation in grade 2-4 astrocytomas. Neurooncol Adv 2023; 5:vdad069. [PMID: 37324217 PMCID: PMC10263115 DOI: 10.1093/noajnl/vdad069] [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] [Indexed: 06/17/2023] Open
Abstract
Background Isocitrate dehydrogenase (IDH) mutations are thought to represent an early oncogenic event in glioma evolution, found with high penetrance across tumor cells; however, in rare cases, IDH mutation may exist only in a small subset of the total tumor cells (subclonal IDH mutation). Methods We present 2 institutional cases with subclonal IDH1 R132H mutation. In addition, 2 large publicly available cohorts of IDH-mutant astrocytomas were mined for cases harboring subclonal IDH mutations (defined as tumor cell fraction with IDH mutation ≤0.67) and the clinical and molecular features of these subclonal cases were compared to clonal IDH-mutant astrocytomas. Results Immunohistochemistry (IHC) performed on 2 institutional World Health Organization grade 4 IDH-mutant astrocytomas revealed only a minority of tumor cells in each case with IDH1 R132H mutant protein, and next-generation sequencing (NGS) revealed remarkably low IDH1 variant allele frequencies compared to other pathogenic mutations, including TP53 and/or ATRX. DNA methylation classified the first tumor as high-grade IDH-mutant astrocytoma with high confidence (0.98 scores). In the publicly available datasets, subclonal IDH mutation was present in 3.9% of IDH-mutant astrocytomas (18/466 tumors). Compared to clonal IDH-mutant astrocytomas (n = 156), subclonal cases demonstrated worse overall survival in grades 3 (P = .0106) and 4 (P = .0184). Conclusions While rare, subclonal IDH1 mutations are present in a subset of IDH-mutant astrocytomas of all grades, which may lead to a mismatch between IHC results and genetic/epigenetic classification. These findings suggest a possible prognostic role of IDH mutation subclonality, and highlight the potential clinical utility of quantitative IDH1 mutation evaluation by IHC and NGS.
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Affiliation(s)
- Meenakshi Vij
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Raquel T Yokoda
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Omid Rashidipour
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ivy Tran
- Department of Pathology, NYU Langone Health, New York, New York, USA
| | | | - Matija Snuderl
- Department of Pathology, NYU Langone Health, New York, New York, USA
| | - Raymund L Yong
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Melissa Umphlett
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jamie M Walker
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nadejda M Tsankova
- Nadejda M. Tsankova, MD, PhD, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Icahn Building, 9-20E, New York, NY 10029, USA ()
| | - Timothy E Richardson
- Corresponding Authors: Timothy E. Richardson, DO, PhD, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.58, New York, NY 10029, USA ()
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Dono A, El Achi H, Bundrant BE, Goli PS, Zhu P, Ozkizilkaya HI, Esquenazi Y, Ballester LY. Infiltrating gliomas with FGFR alterations: Histologic features, genetic alterations, and potential clinical implications. Cancer Biomark 2022; 36:117-131. [PMID: 36530080 DOI: 10.3233/cbm-220041] [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] [Indexed: 12/15/2022]
Abstract
BACKGROUND Fibroblast growth factor receptors (FGFRs) are frequently altered in cancers and present a potential therapeutic avenue. However, the type and prevalence of FGFR alterations in infiltrating gliomas (IGs) needs further investigation. OBJECTIVE To understand the prevalence/type of FGFR alterations in IGs. METHODS We reviewed clinicopathologic and genomic alterations of FGFR-mutant gliomas in a cohort of 387 patients. Tumors were examined by DNA next-generation sequencing for somatic mutations with a panel interrogating 205-genes. For comparison, cBioPortal databases were queried to identify FGFR-altered IGs. RESULTS Fourteen patients (3.6%) with FGFR-mutant tumors were identified including 11 glioblastomas, Isocitrate dehydrogenase (IDH) - wildtype (GBM-IDH-WT), 2 oligodendrogliomas, and 1 astrocytoma IDH-mutant. FGFR-altered IGs showed endocrinoid capillaries, microvascular proliferation, necrosis, oligodendroglioma-like cells, fibrin thrombi, microcalcifications, and nodular growth. FGFR3 was the most commonly altered FGFR gene (64.3%). The most common additional mutations in FGFR-altered IGs were TERTp, CDKN2A/B, PTEN, CDK4, MDM2, and TP53. FGFR3 alterations were only observed in GBM-IDH-WT. EGFR alterations were rarely identified in FGFR3-altered gliomas. CONCLUSIONS Histologic features correlate with FGFR alterations in IGs. FGFR3-TACC3 fusion and FGFR3 amplification are the most common FGFR alterations in IGs. FGFR alterations are a rare, but potentially viable, therapeutic target in asubset of IGs.
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Affiliation(s)
- Antonio Dono
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hanadi El Achi
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bethany E Bundrant
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Ping Zhu
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hanim I Ozkizilkaya
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yoshua Esquenazi
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Memorial Hermann Hospital-TMC, Houston, TX, USA.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Leomar Y Ballester
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Lin B, Ziebro J, Smithberger E, Skinner KR, Zhao E, Cloughesy TF, Binder ZA, O’Rourke DM, Nathanson DA, Furnari FB, Miller CR. EGFR, the Lazarus target for precision oncology in glioblastoma. Neuro Oncol 2022; 24:2035-2062. [PMID: 36125064 PMCID: PMC9713527 DOI: 10.1093/neuonc/noac204] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Lazarus effect is a rare condition that happens when someone seemingly dead shows signs of life. The epidermal growth factor receptor (EGFR) represents a target in the fatal neoplasm glioblastoma (GBM) that through a series of negative clinical trials has prompted a vocal subset of the neuro-oncology community to declare this target dead. However, an argument can be made that the core tenets of precision oncology were overlooked in the initial clinical enthusiasm over EGFR as a therapeutic target in GBM. Namely, the wrong drugs were tested on the wrong patients at the wrong time. Furthermore, new insights into the biology of EGFR in GBM vis-à-vis other EGFR-driven neoplasms, such as non-small cell lung cancer, and development of novel GBM-specific EGFR therapeutics resurrects this target for future studies. Here, we will examine the distinct EGFR biology in GBM, how it exacerbates the challenge of treating a CNS neoplasm, how these unique challenges have influenced past and present EGFR-targeted therapeutic design and clinical trials, and what adjustments are needed to therapeutically exploit EGFR in this devastating disease.
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Affiliation(s)
- Benjamin Lin
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Julia Ziebro
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Erin Smithberger
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Pathobiology and Translational Sciences Program, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kasey R Skinner
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Neurosciences Curriculum, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Eva Zhao
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Timothy F Cloughesy
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Zev A Binder
- Department of Neurosurgery and Glioblastoma Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Donald M O’Rourke
- Department of Neurosurgery and Glioblastoma Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David A Nathanson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Frank B Furnari
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, San Diego, California, USA
- Ludwig Cancer Research, San Diego, California, USA
| | - C Ryan Miller
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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He Q, Chen J, Xie Z, Chen Z. Wild-Type Isocitrate Dehydrogenase-Dependent Oxidative Decarboxylation and Reductive Carboxylation in Cancer and Their Clinical Significance. Cancers (Basel) 2022; 14:cancers14235779. [PMID: 36497259 PMCID: PMC9741289 DOI: 10.3390/cancers14235779] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
The human isocitrate dehydrogenase (IDH) gene encodes for the isoenzymes IDH1, 2, and 3, which catalyze the conversion of isocitrate and α-ketoglutarate (α-KG) and are required for normal mammalian metabolism. Isocitrate dehydrogenase 1 and 2 catalyze the reversible conversion of isocitrate to α-KG. Isocitrate dehydrogenase 3 is the key enzyme that mediates the production of α-KG from isocitrate in the tricarboxylic acid (TCA) cycle. In the TCA cycle, the decarboxylation reaction catalyzed by isocitrate dehydrogenase mediates the conversion of isocitrate to α-KG accompanied by dehydrogenation, a process commonly known as oxidative decarboxylation. The formation of 6-C isocitrate from α-KG and CO2 catalyzed by IDH is termed reductive carboxylation. This IDH-mediated reversible reaction is of great importance in tumor cells. We outline the role of the various isocitrate dehydrogenase isoforms in cancer, discuss the metabolic implications of interference with IDH, summarize therapeutic interventions targeting changes in IDH expression, and highlight areas for future research.
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von Knebel Doeberitz N, Paech D, Sturm D, Pusch S, Turcan S, Saunthararajah Y. Changing paradigms in oncology: Toward noncytotoxic treatments for advanced gliomas. Int J Cancer 2022; 151:1431-1446. [PMID: 35603902 PMCID: PMC9474618 DOI: 10.1002/ijc.34131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022]
Abstract
Glial-lineage malignancies (gliomas) recurrently mutate and/or delete the master regulators of apoptosis p53 and/or p16/CDKN2A, undermining apoptosis-intending (cytotoxic) treatments. By contrast to disrupted p53/p16, glioma cells are live-wired with the master transcription factor circuits that specify and drive glial lineage fates: these transcription factors activate early-glial and replication programs as expected, but fail in their other usual function of forcing onward glial lineage-maturation-late-glial genes have constitutively "closed" chromatin requiring chromatin-remodeling for activation-glioma-genesis disrupts several epigenetic components needed to perform this work, and simultaneously amplifies repressing epigenetic machinery instead. Pharmacologic inhibition of repressing epigenetic enzymes thus allows activation of late-glial genes and terminates glioma self-replication (self-replication = replication without lineage-maturation), independent of p53/p16/apoptosis. Lineage-specifying master transcription factors therefore contrast with p53/p16 in being enriched in self-replicating glioma cells, reveal a cause-effect relationship between aberrant epigenetic repression of late-lineage programs and malignant self-replication, and point to specific epigenetic targets for noncytotoxic glioma-therapy.
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Affiliation(s)
| | - Daniel Paech
- Division of RadiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of NeuroradiologyBonn University HospitalBonnGermany
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ) HeidelbergHeidelbergGermany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)HeidelbergGermany
- Department of Pediatric Oncology, Hematology & ImmunologyHeidelberg University HospitalHeidelbergGermany
| | - Stefan Pusch
- Department of NeuropathologyInstitute of Pathology, Ruprecht‐Karls‐University HeidelbergHeidelbergGermany
- German Cancer Consortium (DKTK), Clinical Cooperation Unit (CCU) Neuropathology, German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Sevin Turcan
- Department of NeurologyHeidelberg University HospitalHeidelbergGermany
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology ResearchTaussig Cancer Institute, Cleveland ClinicClevelandOhioUSA
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Sherman MA, Yaari AU, Priebe O, Dietlein F, Loh PR, Berger B. Genome-wide mapping of somatic mutation rates uncovers drivers of cancer. Nat Biotechnol 2022; 40:1634-1643. [PMID: 35726091 PMCID: PMC9646522 DOI: 10.1038/s41587-022-01353-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 05/10/2022] [Indexed: 01/12/2023]
Abstract
Identification of cancer driver mutations that confer a proliferative advantage is central to understanding cancer; however, searches have often been limited to protein-coding sequences and specific non-coding elements (for example, promoters) because of the challenge of modeling the highly variable somatic mutation rates observed across tumor genomes. Here we present Dig, a method to search for driver elements and mutations anywhere in the genome. We use deep neural networks to map cancer-specific mutation rates genome-wide at kilobase-scale resolution. These estimates are then refined to search for evidence of driver mutations under positive selection throughout the genome by comparing observed to expected mutation counts. We mapped mutation rates for 37 cancer types and applied these maps to identify putative drivers within intronic cryptic splice regions, 5' untranslated regions and infrequently mutated genes. Our high-resolution mutation rate maps, available for web-based exploration, are a resource to enable driver discovery genome-wide.
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Affiliation(s)
- Maxwell A Sherman
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology Program, Cambridge, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam U Yaari
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Center for Brains, Minds and Machines of MIT and Harvard, Cambridge, MA, USA
| | - Oliver Priebe
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Physics, University of Pennsylvania, Philadelphia, PA, USA
| | - Felix Dietlein
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard-MIT Health Sciences and Technology Program, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Ge X, Xu M, Cheng T, Hu N, Sun P, Lu B, Wang Z, Li J. TP53I13 promotes metastasis in glioma via macrophages, neutrophils, and fibroblasts and is a potential prognostic biomarker. Front Immunol 2022; 13:974346. [PMID: 36275718 PMCID: PMC9585303 DOI: 10.3389/fimmu.2022.974346] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Background TP53I13 is a protein coding tumor suppression gene encoded by the tumor protein p53. Overexpression of TP53I13 impedes tumor cell proliferation. Nevertheless, TP53I13 role and expression in the emergence and progression of glioma (low-grade glioma and glioblastoma) are yet to be identified. Thus, we aim to use comprehensive bioinformatics analyses to investigate TP53I13 and its prognostic value in gliomas. Methods Multiple databases were consulted to evaluate and assess the expression of TP53I13, such as the Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), GeneMANIA, and Gene Expression Profiling Interactive. TP53I13 expression was further explored using immunohistochemistry (IHC) and multiplex immunohistochemistry (mIHC). Through Gene Set Enrichment Analysis (GSEA), the biological functions of TP53I13 and metastatic processes associated with it were studied. Results The expression of TP53I13 was higher in tumor samples compared to normal samples. In samples retrieved from the TCGA and CGGA databases, high TP53I13 expression was associated with poor survival outcomes. The analysis of multivariate Cox showed that TP53I13 might be an independent prognostic marker of glioma. It was also found that increased expression of TP53I13 was significantly correlated with PRS type, status, 1p/19q codeletion status, IDH mutation status, chemotherapy, age, and tumor grade. According to CIBERSORT (Cell-type Identification by Estimating Relative Subsets of RNA Transcript), the expression of TP53I13 correlates with macrophages, neutrophils, and dendritic cells. GSEA shows a close correlation between TP53I13 and p53 signaling pathways, DNA replication, and the pentose phosphate pathway. Conclusion Our results reveal a close correlation between TP53I13 and gliomas. Further, TP53I13 expression could affect the survival outcomes in glioma patients. In addition, TP53I13 was an independent marker that was crucial in regulating the infiltration of immune cells into tumors. As a result of these findings, TP53I13 might represent a new biomarker of immune infiltration and prognosis in patients with gliomas.
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Affiliation(s)
- Xinqi Ge
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Manyu Xu
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Tong Cheng
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Nan Hu
- Medical School of Nantong University, Nantong, China
| | - Pingping Sun
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Bing Lu
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Ziheng Wang
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
- *Correspondence: Jian Li, ; Ziheng Wang,
| | - Jian Li
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- *Correspondence: Jian Li, ; Ziheng Wang,
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Abstract
Standard treatment for patients with IDH-mutant gliomas with radiation therapy and chemotherapy is non-curative and associated with long-term neurotoxicity. This has created intense interest in targeted therapeutic strategies that are specifically designed of IDH-mutant tumors. Much progress has been made in understanding the unique biology of IDH-mutant gliomas, and now various IDH-mutant-specific targeting strategies are in various phases of development. Here, we will review a range of IDH-mutant targeting treatments being explored, including direct IDH inhibitors, as well as strategies that take advantage of IDH-mutant-specific vulnerabilities.
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Affiliation(s)
- Julie J Miller
- Department of Neurology, Pappas Center for Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Richardson TE, Walker JM, Abdullah KG, McBrayer SK, Viapiano MS, Mussa ZM, Tsankova NM, Snuderl M, Hatanpaa KJ. Chromosomal instability in adult-type diffuse gliomas. Acta Neuropathol Commun 2022; 10:115. [PMID: 35978439 PMCID: PMC9386991 DOI: 10.1186/s40478-022-01420-w] [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: 07/12/2022] [Accepted: 08/04/2022] [Indexed: 11/14/2022] Open
Abstract
Chromosomal instability (CIN) is a fundamental property of cancer and a key underlying mechanism of tumorigenesis and malignant progression, and has been documented in a wide variety of cancers, including colorectal carcinoma with mutations in genes such as APC. Recent reports have demonstrated that CIN, driven in part by mutations in genes maintaining overall genomic stability, is found in subsets of adult-type diffusely infiltrating gliomas of all histologic and molecular grades, with resulting elevated overall copy number burden, chromothripsis, and poor clinical outcome. Still, relatively few studies have examined the effect of this process, due in part to the difficulty of routinely measuring CIN clinically. Herein, we review the underlying mechanisms of CIN, the relationship between chromosomal instability and malignancy, the prognostic significance and treatment potential in various cancers, systemic disease, and more specifically, in diffusely infiltrating glioma subtypes. While still in the early stages of discovery compared to other solid tumor types in which CIN is a known driver of malignancy, the presence of CIN as an early factor in gliomas may in part explain the ability of these tumors to develop resistance to standard therapy, while also providing a potential molecular target for future therapies.
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Affiliation(s)
- Timothy E. Richardson
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
| | - Jamie M. Walker
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Kalil G. Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA 15213 USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA 15232 USA
| | - Samuel K. McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Mariano S. Viapiano
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY 13210 USA
- Department of Neurosurgery, State University of New York, Upstate Medical University, Syracuse, NY 13210 USA
| | - Zarmeen M. Mussa
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
| | - Nadejda M. Tsankova
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York City, NY 10016 USA
| | - Kimmo J. Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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Yu Z, Liu Z, Lian X, Cheng X, Liu B, Zhang B, Wang H, Wang J, Li A, Ren Z, Pang B, Qian R, Gao Y. High expression of HOXA4 in patients with glioma indicates unfavorable clinical outcomes. Cell Cycle 2022; 21:2387-2402. [PMID: 35852388 DOI: 10.1080/15384101.2022.2096715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Zhenghong Yu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan Province Intelligent Orthopedic Technology Innovation and Transformation International Joint Laboratory, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Zhengzhou, China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan Province Intelligent Orthopedic Technology Innovation and Transformation International Joint Laboratory, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Zhengzhou, China
| | - Xiaoyu Lian
- Department of Surgery of Spine and Spinal Cord, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Henan Zhengzhou, China
| | - Xingbo Cheng
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan Province Intelligent Orthopedic Technology Innovation and Transformation International Joint Laboratory, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Zhengzhou, China
| | - Binfeng Liu
- Department of Surgery of Spine and Spinal Cord, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Henan Zhengzhou, China
| | - Bo Zhang
- Department of Surgery of Spine and Spinal Cord, Henan University People’s Hospital, Henan Provincial People’s Hospital, Henan Zhengzhou, China
| | - Hongbo Wang
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan Province Intelligent Orthopedic Technology Innovation and Transformation International Joint Laboratory, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Zhengzhou, China
| | - Jialin Wang
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan Province Intelligent Orthopedic Technology Innovation and Transformation International Joint Laboratory, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Zhengzhou, China
| | - Ang Li
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan Province Intelligent Orthopedic Technology Innovation and Transformation International Joint Laboratory, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Zhengzhou, China
| | - Zhishuai Ren
- Department of Surgery of Spine and Spinal Cord, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Henan Zhengzhou, China
| | - Bo Pang
- Department of Neurosurgery, The Fourth Medical Center of Chinese PLA General Hospital, Beijing, P.R.China
| | - Rongjun Qian
- Department of Neurosurgery, Henan Provincial People’s Hospital, People’s Hospital of Henan University, People’s Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanzheng Gao
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan Province Intelligent Orthopedic Technology Innovation and Transformation International Joint Laboratory, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Zhengzhou, China
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Gatto L, Franceschi E, Tosoni A, Nunno VD, Bartolini S, Brandes AA. Hypermutation as a potential predictive biomarker of immunotherapy efficacy in high-grade gliomas: a broken dream? Immunotherapy 2022; 14:799-813. [PMID: 35670093 DOI: 10.2217/imt-2021-0277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A high tumor mutational burden and mismatch repair deficiency are observed in 'hypermutated' high-grade gliomas (HGGs); however, the molecular characterization of this distinct subtype and whether it predicts the response to immune checkpoint inhibitors (ICIs) are largely unknown. Pembrolizumab is a valid therapeutic option for the treatment of hypermutated cancers of diverse origin, but only a few clinical trials have explored the activity of ICIs in hypermutated HGGs. HGGs appear to differ from other cancers, likely due to the prevalence of subclonal versus clonal neoantigens, which are unable to elicit an immune response with ICIs. The main aim of this review is to summarize the current knowledge on hypermutation in HGGs, focusing on the broken promises of tumor mutational burden and mismatch repair deficiency as potential biomarkers of response to ICIs.
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Affiliation(s)
- Lidia Gatto
- Department of Oncology, AUSL Bologna, Bologna, Italy
| | - Enrico Franceschi
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Alicia Tosoni
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | - Stefania Bartolini
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Alba Ariela Brandes
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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Lassman AB, Sepúlveda-Sánchez JM, Cloughesy TF, Gil-Gil MJ, Puduvalli VK, Raizer JJ, De Vos FY, Wen PY, Butowski NA, Clement PM, Groves MD, Belda-Iniesta C, Giglio P, Soifer HS, Rowsey S, Xu C, Avogadri F, Wei G, Moran S, Roth P. Infigratinib in Patients with Recurrent Gliomas and FGFR Alterations: A Multicenter Phase II Study. Clin Cancer Res 2022; 28:2270-2277. [PMID: 35344029 PMCID: PMC9167702 DOI: 10.1158/1078-0432.ccr-21-2664] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/04/2021] [Accepted: 03/17/2022] [Indexed: 01/09/2023]
Abstract
PURPOSE FGFR genomic alterations (amplification, mutations, and/or fusions) occur in ∼8% of gliomas, particularly FGFR1 and FGFR3. We conducted a multicenter open-label, single-arm, phase II study of a selective FGFR1-3 inhibitor, infigratinib (BGJ398), in patients with FGFR-altered recurrent gliomas. PATIENTS AND METHODS Adults with recurrent/progressive gliomas harboring FGFR alterations received oral infigratinib 125 mg on days 1 to 21 of 28-day cycles. The primary endpoint was investigator-assessed 6-month progression-free survival (PFS) rate by Response Assessment in Neuro-Oncology criteria. Comprehensive genomic profiling was performed on available pretreatment archival tissue to explore additional molecular correlations with efficacy. RESULTS Among 26 patients, the 6-month PFS rate was 16.0% [95% confidence interval (CI), 5.0-32.5], median PFS was 1.7 months (95% CI, 1.1-2.8), and objective response rate was 3.8%. However, 4 patients had durable disease control lasting longer than 1 year. Among these, 3 had tumors harboring activating point mutations at analogous positions of FGFR1 (K656E; n = 2) or FGFR3 (K650E; n = 1) in pretreatment tissue; an FGFR3-TACC3 fusion was detected in the other. Hyperphosphatemia was the most frequently reported treatment-related adverse event (all-grade, 76.9%; grade 3, 3.8%) and is a known on-target toxicity of FGFR inhibitors. CONCLUSIONS FGFR inhibitor monotherapy with infigratinib had limited efficacy in a population of patients with recurrent gliomas and different FGFR genetic alterations, but durable disease control lasting more than 1 year was observed in patients with tumors harboring FGFR1 or FGFR3 point mutations or FGFR3-TACC3 fusions. A follow-up study with refined biomarker inclusion criteria and centralized FGFR testing is warranted.
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Affiliation(s)
- Andrew B. Lassman
- Division of Neuro-Oncology, Department of Neurology and Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons and NewYork-Presbyterian, New York, New York
- Corresponding Author: Andrew B. Lassman, Columbia University Irving Medical Center, 710 W 168th St, New York, NY 10032. Phone: 212-342-0871; Fax: 212-342-1246; E-mail:
| | | | | | - Miguel J. Gil-Gil
- Institut Català d'Oncologia, Hospitalet de Llobregat, Barcelona, Spain
| | - Vinay K. Puduvalli
- Division of Neuro-Oncology, Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Jeffrey J. Raizer
- Northwestern University, Department of Neurology, Section of Neuro-Oncology, Chicago, Illinois
| | - Filip Y.F. De Vos
- Department Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Patrick Y. Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | | | | | - Pierre Giglio
- Division of Neuro-Oncology, Ohio State University Wexner Medical Center, Columbus, Ohio
| | | | | | - Cindy Xu
- QED Therapeutics, San Francisco, California
| | | | - Ge Wei
- QED Therapeutics, San Francisco, California
| | | | - Patrick Roth
- Department of Neurology & Brain Tumor Center, University Hospital and University of Zurich, Zurich, Switzerland
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Kannan S, Kannan Murugan A, Balasubramaniam S, Kannan Munirajan A, Alzahrani AS. Gliomas: Genetic alterations, mechanisms of metastasis, recurrence, drug resistance, and recent trends in molecular therapeutic options. Biochem Pharmacol 2022; 201:115090. [PMID: 35577014 DOI: 10.1016/j.bcp.2022.115090] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 12/15/2022]
Abstract
Glioma is the most common intracranial tumor with poor treatment outcomes and has high morbidity and mortality. Various studies on genomic analyses of glioma found a variety of deregulated genes with somatic mutations including TERT, TP53, IDH1, ATRX, TTN, etc. The genetic alterations in the key genes have been demonstrated to play a crucial role in gliomagenesis by modulating important signaling pathways that alter the fundamental intracellular functions such as DNA damage and repair, cell proliferation, metabolism, growth, wound healing, motility, etc. The SPRK1, MMP2, MMP9, AKT, mTOR, etc., genes, and noncoding RNAs (miRNAs, lncRNAs, circRNAs, etc) were shown mostly to be implicated in the metastases of glioma. Despite advances in the current treatment strategies, a low-grade glioma is a uniformly fatal disease with overall median survival of ∼5-7 years while the patients bearing high-grade tumors display poorer median survival of ∼9-10 months mainly due to aggressive metastasis and therapeutic resistance. This review discusses the spectrum of deregulated genes, molecular and cellular mechanisms of metastasis, recurrence, and its management, the plausible causes for the development of therapy resistance, current treatment options, and the recent trends in malignant gliomas. Understanding the pathogenic mechanisms and advances in molecular genetics would aid in the novel diagnosis, prognosis, and translation of pathogenesis-based treatment opportunities which could pave the way for precision medicine in glioma.
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Affiliation(s)
- Siddarth Kannan
- School of Medicine, University of Central Lancashire, Preston PR1 2HE UK
| | - Avaniyapuram Kannan Murugan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh - 11211 Saudi Arabia.
| | | | - Arasambattu Kannan Munirajan
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113 India
| | - Ali S Alzahrani
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh - 11211 Saudi Arabia; Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh - 11211 Saudi Arabia
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