1
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Nair NU, Schäffer AA, Gertz EM, Cheng K, Zerbib J, Sahu AD, Leor G, Shulman ED, Aldape KD, Ben-David U, Ruppin E. Chromosome 7 Gain Compensates for Chromosome 10 Loss in Glioma. Cancer Res 2024; 84:3464-3477. [PMID: 39078448 DOI: 10.1158/0008-5472.can-24-1366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 07/31/2024]
Abstract
The co-occurrence of chromosome 10 loss and chromosome 7 gain in gliomas is the most frequent loss-gain co-aneuploidy pair in human cancers. This phenomenon has been investigated since the late 1980s without resolution. Expanding beyond previous gene-centric studies, we investigated the co-occurrence in a genome-wide manner, taking an evolutionary perspective. Mining of large-scale tumor aneuploidy data confirmed the previous finding of a small-scale longitudinal study that the most likely order is chromosome 10 loss, followed by chromosome 7 gain. Extensive analysis of genomic and transcriptomic data from both patients and cell lines revealed that this co-occurrence can be explained by functional rescue interactions that are highly enriched on chromosome 7, which could potentially compensate for any detrimental consequences arising from the loss of chromosome 10. Transcriptomic data from various normal, noncancerous human brain tissues were analyzed to assess which tissues may be most predisposed to tolerate compensation of chromosome 10 loss by chromosome 7 gain. The analysis indicated that the preexisting transcriptomic states in the cortex and frontal cortex, where gliomas arise, are more favorable than other brain regions for compensation by rescuer genes that are active on chromosome 7. Collectively, these findings suggest that the phenomenon of chromosome 10 loss and chromosome 7 gain in gliomas is orchestrated by a complex interaction of many genes residing within these two chromosomes and provide a plausible reason why this co-occurrence happens preferentially in cancers originating in certain regions of the brain. Significance: Increased expression of multiple rescuer genes on the gained chromosome 7 could compensate for the downregulation of several vulnerable genes on the lost chromosome 10, resolving the long-standing mystery of this frequent co-occurrence in gliomas.
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Affiliation(s)
- Nishanth Ulhas Nair
- Cancer Data Science Laboratory, Computational Precision Oncology Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, Computational Precision Oncology Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - E Michael Gertz
- Cancer Data Science Laboratory, Computational Precision Oncology Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Kuoyuan Cheng
- Cancer Data Science Laboratory, Computational Precision Oncology Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- MSD, Beijing, China
| | - Johanna Zerbib
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Avinash Das Sahu
- Comprehensive Cancer Center, The University of New Mexico, Albuquerque, New Mexico
| | - Gil Leor
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Eldad D Shulman
- Cancer Data Science Laboratory, Computational Precision Oncology Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Computational Precision Oncology Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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2
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Papacocea SI, Vrinceanu D, Dumitru M, Manole F, Serboiu C, Papacocea MT. Molecular Profile as an Outcome Predictor in Glioblastoma along with MRI Features and Surgical Resection: A Scoping Review. Int J Mol Sci 2024; 25:9714. [PMID: 39273661 PMCID: PMC11395592 DOI: 10.3390/ijms25179714] [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: 07/25/2024] [Revised: 09/06/2024] [Accepted: 09/06/2024] [Indexed: 09/15/2024] Open
Abstract
Glioblastoma (GBM) is one of the most aggressive malignant tumors of the brain. We queried PubMed for articles about molecular predictor markers in GBM. This scoping review aims to analyze the most important outcome predictors in patients with GBM and to compare these factors in terms of absolute months of survival benefit and percentages. Performing a gross total resection for patients with GBM undergoing optimal chemo- and radiotherapy provides a significant benefit in overall survival compared to those patients who received a subtotal or partial resection. However, compared to IDH-Wildtype GBMs, patients with IDH-Mutant 1/2 GBMs have an increased survival. MGMT promoter methylation status is another strong outcome predictor for patients with GBM. In the reviewed literature, patients with methylated MGMT promoter lived approximately 50% to 90% longer than those with an unmethylated MGMT gene promoter. Moreover, KPS is an important predictor of survival and quality of life, demonstrating that we should refrain from aggressive surgery in important brain areas. As new therapies (such as TTFs) emerge, we are optimistic that the overall median survival will increase, even for IDH-Wildtype GBMs. In conclusion, molecular profiles are stronger outcome predictors than the extent of neurosurgical resection for GBM.
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Affiliation(s)
- Serban Iancu Papacocea
- Neurosurgery Department, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Daniela Vrinceanu
- ENT Department, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Mihai Dumitru
- ENT Department, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Felicia Manole
- ENT Department, Faculty of Medicine, University of Oradea, 410073 Oradea, Romania
| | - Crenguta Serboiu
- Cellular Biology and Histology Department, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Marius Toma Papacocea
- Neurosurgery Department, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
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3
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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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Underhill HR, Karsy M, Davidson CJ, Hellwig S, Stevenson S, Goold EA, Vincenti S, Sellers DL, Dean C, Harrison BE, Bronner MP, Colman H, Jensen RL. Subclonal Cancer Driver Mutations Are Prevalent in the Unresected Peritumoral Edema of Adult Diffuse Gliomas. Cancer Res 2024; 84:1149-1164. [PMID: 38270917 PMCID: PMC10982644 DOI: 10.1158/0008-5472.can-23-2557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/20/2023] [Accepted: 01/23/2024] [Indexed: 01/26/2024]
Abstract
Adult diffuse gliomas commonly recur regardless of therapy. As recurrence typically arises from the peritumoral edema adjacent to the resected bulk tumor, the profiling of somatic mutations from infiltrative malignant cells within this critical, unresected region could provide important insights into residual disease. A key obstacle has been the inability to distinguish between next-generation sequencing (NGS) noise and the true but weak signal from tumor cells hidden among the noncancerous brain tissue of the peritumoral edema. Here, we developed and validated True2 sequencing to reduce NGS-associated errors to <1 false positive/100 kb panel positions while detecting 97.6% of somatic mutations with an allele frequency ≥0.1%. True2 was then used to study the tumor and peritumoral edema of 22 adult diffuse gliomas including glioblastoma, astrocytoma, oligodendroglioma, and NF1-related low-grade neuroglioma. The tumor and peritumoral edema displayed a similar mutation burden, indicating that surgery debulks these cancers physically but not molecularly. Moreover, variants in the peritumoral edema included unique cancer driver mutations absent in the bulk tumor. Finally, analysis of multiple samples from each patient revealed multiple subclones with unique mutations in the same gene in 17 of 22 patients, supporting the occurrence of convergent evolution in response to patient-specific selective pressures in the tumor microenvironment that may form the molecular foundation of recurrent disease. Collectively, True2 enables the detection of ultralow frequency mutations during molecular analyses of adult diffuse gliomas, which is necessary to understand cancer evolution, recurrence, and individual response to therapy. SIGNIFICANCE True2 is a next-generation sequencing workflow that facilitates unbiased discovery of somatic mutations across the full range of variant allele frequencies, which could help identify residual disease vulnerabilities for targeted adjuvant therapies.
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Affiliation(s)
- Hunter R. Underhill
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah
- Department of Radiology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Michael Karsy
- Department of Neurological Surgery, University of Utah, Salt Lake City, Utah
| | | | | | - Samuel Stevenson
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah
| | - Eric A. Goold
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | | | - Drew L. Sellers
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Charlie Dean
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Brion E. Harrison
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah
| | - Mary P. Bronner
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Howard Colman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Neurological Surgery, University of Utah, Salt Lake City, Utah
- Department of Internal Medicine, Division of Oncology, University of Utah, Salt Lake City, Utah
| | - Randy L. Jensen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Neurological Surgery, University of Utah, Salt Lake City, Utah
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5
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Dono A, Torres J, Nunez L, Arevalo O, Rodriguez-Quinteros JC, Riascos RF, Kamali A, Tandon N, Ballester LY, Esquenazi Y. Imaging predictors of 4q12 amplified and RB1 mutated glioblastoma IDH-wildtype. J Neurooncol 2024; 167:99-109. [PMID: 38351343 PMCID: PMC11227885 DOI: 10.1007/s11060-024-04575-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/16/2024] [Indexed: 07/04/2024]
Abstract
INTRODUCTION Recent studies have identified that glioblastoma IDH-wildtype consists of different molecular subgroups with distinct prognoses. In order to accurately describe and classify gliomas, the Visually AcceSAble Rembrandt Images (VASARI) system was developed. The goal of this study was to evaluate the VASARI characteristics in molecular subgroups of IDH-wildtype glioblastoma. METHODS A retrospective analysis of glioblastoma IDH- wildtype with comprehensive next-generation sequencing and pre-operative and post-operative MRI was performed. VASARI characteristics and 205 genes were evaluated. Multiple comparison adjustment by the Bejamin-Hochberg false discovery rate (BH-FDR) was performed. A 1:3 propensity score match (PSM) with a Caliper of 0.2 was done. RESULTS 178 patients with GBM IDH-WT met the inclusion criteria. 4q12 amplified patients (n = 20) were associated with cyst presence (30% vs. 12%, p = 0.042), decreased hemorrhage (35% vs. 62%, p = 0.028), and non-restricting/mixed (35%/60%) rather than restricting diffusion pattern (5%), meanwhile, 4q12 non-amplified patients had mostly restricting (47.4%) rather than a non-restricting/mixed diffusion pattern (28.4%/23.4%). This remained statistically significant after BH-FDR adjustment (p = 0.002). PSM by 4q12 amplification showed that diffusion characteristics continued to be significantly different. Among RB1-mutant patients, 96% had well-defined enhancing margins vs. 70.6% of RB1-WT (p = 0.018), however, this was not significant after BH-FDR or PSM. CONCLUSIONS Patients with glioblastoma IDH-wildtype harboring 4q12 amplification rarely have restricting DWI patterns compared to their wildtype counterparts, in which this DWI pattern is present in ~ 50% of patients. This suggests that some phenotypic imaging characteristics can be identified among molecular subtypes of IDH-wildtype glioblastoma.
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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, 77030, Houston, TX, USA
| | - Jose Torres
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
| | - Luis Nunez
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
| | - Octavio Arevalo
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Department of Radiology, LSU Health Shreveport, 71103, Shreveport, LA, USA
| | - Juan Carlos Rodriguez-Quinteros
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
| | - Roy F Riascos
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA
| | - Arash Kamali
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA
| | - Nitin Tandon
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA
| | - Leomar Y Ballester
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 77030, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 77030, Houston, TX, USA
| | - Yoshua Esquenazi
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA.
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA.
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, 77030, Houston, TX, USA.
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6
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Nair NU, Schäffer AA, Gertz EM, Cheng K, Zerbib J, Sahu AD, Leor G, Shulman ED, Aldape KD, Ben-David U, Ruppin E. Chromosome 7 to the rescue: overcoming chromosome 10 loss in gliomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576103. [PMID: 38313282 PMCID: PMC10836086 DOI: 10.1101/2024.01.17.576103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
The co-occurrence of chromosome 10 loss and chromosome 7 gain in gliomas is the most frequent loss-gain co-aneuploidy pair in human cancers, a phenomenon that has been investigated without resolution since the late 1980s. Expanding beyond previous gene-centric studies, we investigate the co-occurrence in a genome-wide manner taking an evolutionary perspective. First, by mining large tumor aneuploidy data, we predict that the more likely order is 10 loss followed by 7 gain. Second, by analyzing extensive genomic and transcriptomic data from both patients and cell lines, we find that this co-occurrence can be explained by functional rescue interactions that are highly enriched on 7, which can possibly compensate for any detrimental consequences arising from the loss of 10. Finally, by analyzing transcriptomic data from normal, non-cancerous, human brain tissues, we provide a plausible reason why this co-occurrence happens preferentially in cancers originating in certain regions of the brain.
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7
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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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8
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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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9
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Shrestha P, Eineichner T, Wilson B, Lam NS. Intradural Intramedullary Spinal Cord Glioblastoma: A Case Report. Cureus 2023; 15:e43580. [PMID: 37593069 PMCID: PMC10430890 DOI: 10.7759/cureus.43580] [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] [Accepted: 08/16/2023] [Indexed: 08/19/2023] Open
Abstract
Primary spinal cord glioblastoma multiforme (GBM) remains uncommon and typically affects males and patients during their fifth decade of life. Our case demonstrates a 77-year-old woman who initially presented with right arm paresthesia and limited range of motion and was subsequently diagnosed with primary spinal cord GBM. Our case illustrates an atypical and nonspecific neurological presentation highlighting that spinal cord GBM can have a more indolent course, unlike what current literature suggests. It also emphasizes the importance of considering a multimodal approach when managing atypical neurological symptoms and considering an early intervention, including magnetic resonance imaging, to rule out occult neoplasm in an appropriate clinical setting, thus preventing delay in the diagnosis. This case further emphasizes the role of molecular biomarkers of tumors, including isocitrate dehydrogenase mutation as well as methylguanine-DNA methyltransferase promoter methylation status, that can independently guide and affect the treatment outcomes in this patient population.
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Affiliation(s)
| | | | | | - Naomi S Lam
- Internal Medicine, Des Moines University, Des Moines, USA
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10
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Szu JI, Tsigelny IF, Wojcinski A, Kesari S. Biological functions of the Olig gene family in brain cancer and therapeutic targeting. Front Neurosci 2023; 17:1129434. [PMID: 37274223 PMCID: PMC10232966 DOI: 10.3389/fnins.2023.1129434] [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: 12/21/2022] [Accepted: 04/26/2023] [Indexed: 06/06/2023] Open
Abstract
The Olig genes encode members of the basic helix-loop-helix (bHLH) family of transcription factors. Olig1, Olig2, and Olig3 are expressed in both the developing and mature central nervous system (CNS) and regulate cellular specification and differentiation. Over the past decade extensive studies have established functional roles of Olig1 and Olig2 in development as well as in cancer. Olig2 overexpression drives glioma proliferation and resistance to radiation and chemotherapy. In this review, we summarize the biological functions of the Olig family in brain cancer and how targeting Olig family genes may have therapeutic benefit.
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Affiliation(s)
- Jenny I. Szu
- Department of Translational Neurosciences, Providence Saint John’s Health Center, Saint John’s Cancer Institute, Santa Monica, CA, United States
| | - Igor F. Tsigelny
- San Diego Supercomputer Center, University of California, San Diego, San Diego, CA, United States
- CureScience, San Diego, CA, United States
| | - Alexander Wojcinski
- Department of Translational Neurosciences, Providence Saint John’s Health Center, Saint John’s Cancer Institute, Santa Monica, CA, United States
- Pacific Neuroscience Institute, Santa Monica, CA, United States
| | - Santosh Kesari
- Department of Translational Neurosciences, Providence Saint John’s Health Center, Saint John’s Cancer Institute, Santa Monica, CA, United States
- Pacific Neuroscience Institute, Santa Monica, CA, United States
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11
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Bonnett SA, Rosenbloom AB, Ong GT, Conner M, Rininger AB, Newhouse D, New F, Phan CQ, Ilcisin S, Sato H, Lyssand JS, Geiss G, Beechem JM. Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles. CANCER RESEARCH COMMUNICATIONS 2023; 3:763-779. [PMID: 37377888 PMCID: PMC10155752 DOI: 10.1158/2767-9764.crc-22-0396] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/20/2023] [Accepted: 04/04/2023] [Indexed: 06/29/2023]
Abstract
A deeper understanding of complex biological processes, including tumor development and immune response, requires ultra high-plex, spatial interrogation of multiple "omes". Here we present the development and implementation of a novel spatial proteogenomic (SPG) assay on the GeoMx Digital Spatial Profiler platform with next-generation sequencing readout that enables ultra high-plex digital quantitation of proteins (>100-plex) and RNA (whole transcriptome, >18,000-plex) from a single formalin-fixed paraffin-embedded (FFPE) sample. This study highlighted the high concordance, R > 0.85 and <15% change in sensitivity between the SPG assay and the single-analyte assays on various cell lines and tissues from human and mouse. Furthermore, we demonstrate that the SPG assay was reproducible across multiple users. When used in conjunction with advanced cellular neighborhood segmentation, distinct immune or tumor RNA and protein targets were spatially resolved within individual cell subpopulations in human colorectal cancer and non-small cell lung cancer. We used the SPG assay to interrogate 23 different glioblastoma multiforme (GBM) samples across four pathologies. The study revealed distinct clustering of both RNA and protein based on pathology and anatomic location. The in-depth investigation of giant cell glioblastoma multiforme (gcGBM) revealed distinct protein and RNA expression profiles compared with that of the more common GBM. More importantly, the use of spatial proteogenomics allowed simultaneous interrogation of critical protein posttranslational modifications alongside whole transcriptomic profiles within the same distinct cellular neighborhoods. Significance We describe ultra high-plex spatial proteogenomics; profiling whole transcriptome and high-plex proteomics on a single FFPE tissue section with spatial resolution. Investigation of gcGBM versus GBM revealed distinct protein and RNA expression profiles.
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Affiliation(s)
| | | | | | - Mark Conner
- NanoString Technologies, Seattle, Washington
| | | | | | - Felicia New
- NanoString Technologies, Seattle, Washington
| | - Chi Q. Phan
- NanoString Technologies, Seattle, Washington
| | | | - Hiromi Sato
- NanoString Technologies, Seattle, Washington
| | | | - Gary Geiss
- NanoString Technologies, Seattle, Washington
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12
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Wang X, Li X, Wu Y, Hong J, Zhang M. The prognostic significance of tumor-associated neutrophils and circulating neutrophils in glioblastoma (WHO CNS5 classification). BMC Cancer 2023; 23:20. [PMID: 36609243 PMCID: PMC9817270 DOI: 10.1186/s12885-022-10492-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 12/27/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Tumor-associated neutrophils (TANs) in the tumor microenvironment are prognostic biomarkers in many malignancies. However, it is unclear whether TANs can serve as a prognostic marker for clinical outcomes in patients with glioblastoma (GBM), as classified according to World Health Organization Classification of Tumors of the Central Nervous System, fifth edition (CNS5). In the present study, we analyzed correlations of TANs and peripheral blood neutrophils prior to radiotherapy with overall survival (OS) in GBM (CNS5). METHODS RNA-seq expression profiles of patients with newly diagnosed GBM (CNS5) were extracted from The Cancer Genome Atlas (TCGA), and The Chinese Glioma Genome Atlas (CGGA). TAN infiltration was inferred using CIBERSORTx algorithm. Neutrophil counts prior to radiotherapy in newly diagnosed GBM (CNS5) were obtained from the First Affiliated Hospital of Fujian Medical University. The prognostic value of TANs and peripheral blood neutrophils before radiotherapy was investigated using Kaplan-Meier analysis and Cox proportional hazards models. The robustness of these findings was evaluated by sensitivity analysis, and E values were calculated. RESULTS A total of 146 and 173 individuals with GBM (CNS5) were identified from the TCGA and CGGA cohorts, respectively. High infiltration of TANs was of prognostic of poor OS in TCGA (HR = 1.621, 95% CI: 1.004-2.619) and CGGA (HR = 1.546, 95% CI: 1.029-2.323). Levels of peripheral blood neutrophils before radiotherapy (HR = 2.073, 95% CI: 1.077-3.990) were independently associated with poor prognosis. Sensitivity analysis determined that the E-value of high TANs infiltration was 2.140 and 2.465 in the TCGA and CGGA cohorts. CONCLUSIONS TANs and peripheral blood neutrophil levels before radiotherapy are prognostic of poor outcomes in GBM (CNS5).
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Affiliation(s)
- Xuezhen Wang
- grid.412683.a0000 0004 1758 0400Department of Radiotherapy, Cancer Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China ,grid.412683.a0000 0004 1758 0400Department of Radiotherapy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiaoxia Li
- grid.412683.a0000 0004 1758 0400Department of Radiotherapy, Cancer Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China ,grid.412683.a0000 0004 1758 0400Department of Radiotherapy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yufan Wu
- grid.412683.a0000 0004 1758 0400Department of Radiotherapy, Cancer Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China ,grid.412683.a0000 0004 1758 0400Department of Radiotherapy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jinsheng Hong
- grid.412683.a0000 0004 1758 0400Department of Radiotherapy, Cancer Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China ,grid.412683.a0000 0004 1758 0400Department of Radiotherapy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China ,grid.412683.a0000 0004 1758 0400Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Mingwei Zhang
- grid.412683.a0000 0004 1758 0400Department of Radiotherapy, Cancer Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China ,grid.412683.a0000 0004 1758 0400Department of Radiotherapy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China ,grid.412683.a0000 0004 1758 0400Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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13
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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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14
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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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15
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Șerban G, Tămaș F, Bălașa R, Manu D, Tămaș C, Bălașa A. Prognostic Factors of Survival in Glioblastoma Multiforme Patients-A Retrospective Study. Diagnostics (Basel) 2022; 12:2630. [PMID: 36359474 PMCID: PMC9689032 DOI: 10.3390/diagnostics12112630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/16/2022] [Accepted: 10/28/2022] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is the most aggressive brain tumor that occurs in adults. In spite of prompt diagnosis and rapidly administered treatment, the survival expectancy is tremendously poor. Extensive research has been performed in order to establish factors to predict the outcome of GBM patients; however, worldwide accepted prognostic markers are still lacking. METHODS We retrospectively assessed all adult patients who were diagnosed with primary GBM and underwent surgical treatment during a three-year period (January 2017-December 2019) in the Neurosurgery Department of the Emergency Clinical County Hospital of Târgu Mureș, Romania. Our aim was to find any statistically relevant connections between clinical, imagistic, and histopathological characteristics and patients' survival. RESULTS A total of 75 patients were eventually included in our statistical analysis: 40 males and 35 females, with a median age of 61 years. The mean tumor dimension was 45.28 ± 15.52 mm, while the mean survival rate was 4 ± 6.75 months. A univariate analysis demonstrated a statistically significant impact of tumor size, pre-, and postoperative KPSI on survival rate. In addition, a Cox multivariate assessment strengthened previous findings regarding postoperative KPSI (regression coefficient -0.03, HR 0.97, 95% CI (HR) 0.96-0.99, p = 0.002) as a favorable prognostic factor and GBM size (regression coefficient 0.03, HR 1.03, 95% CI (HR) 1.01-1.05, p = 0.005) as a poor prognostic marker for patients' survival. CONCLUSIONS The results of our retrospective study are consistent with prior scientific results that provide evidence supporting the importance of clinical (quantified by KPSI) and imagistic (particularly tumor dimensions) features as reliable prognostic factors in GBM patients' survival.
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Affiliation(s)
- Georgiana Șerban
- Doctoral School, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania
| | - Flaviu Tămaș
- Doctoral School, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania
- Neurosurgery Clinic, Emergency Clinical County Hospital of Targu Mures, 540136 Targu Mures, Romania
- Department of Neurosurgery, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540136 Targu Mures, Romania
| | - Rodica Bălașa
- Doctoral School, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania
- 1st Neurology Clinic, Emergency Clinical County Hospital of Targu Mures, 540136 Targu Mures, Romania
- Department of Neurology, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540136 Targu Mures, Romania
| | - Doina Manu
- Center for Advanced Medical and Pharmaceutical Research, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540136 Targu Mures, Romania
| | - Corina Tămaș
- Doctoral School, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania
- Neurosurgery Clinic, Emergency Clinical County Hospital of Targu Mures, 540136 Targu Mures, Romania
| | - Adrian Bălașa
- Neurosurgery Clinic, Emergency Clinical County Hospital of Targu Mures, 540136 Targu Mures, Romania
- Department of Neurosurgery, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540136 Targu Mures, Romania
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A Head-to-Head Comparison of 18F-Fluorocholine PET/CT and Conventional MRI as Predictors of Outcome in IDH Wild-Type High-Grade Gliomas. J Clin Med 2022; 11:jcm11206065. [PMID: 36294385 PMCID: PMC9605635 DOI: 10.3390/jcm11206065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/01/2022] [Accepted: 10/06/2022] [Indexed: 01/24/2023] Open
Abstract
(1) Aim: To study the associations between imaging parameters derived from contrast-enhanced MRI (CE-MRI) and 18F-fluorocholine PET/CT and their performance as prognostic predictors in isocitrate dehydrogenase wild-type (IDH-wt) high-grade gliomas. (2) Methods: A prospective, multicenter study (FuMeGA: Functional and Metabolic Glioma Analysis) including patients with baseline CE-MRI and 18F-fluorocholine PET/CT and IDH wild-type high-grade gliomas. Clinical variables such as performance status, extent of surgery and adjuvant treatments (Stupp protocol vs others) were obtained and used to discriminate overall survival (OS) and progression-free survival (PFS) as end points. Multilesionality was assessed on the visual analysis of PET/CT and CE-MRI images. After tumor segmentation, standardized uptake value (SUV)-based variables for PET/CT and volume-based and geometrical variables for PET/CT and CE-MRI were calculated. The relationships among imaging techniques variables and their association with prognosis were evaluated using Pearson’s chi-square test and the t-test. Receiver operator characteristic, Kaplan−Meier and Cox regression were used for the survival analysis. (3) Results: 54 patients were assessed. The median PFS and OS were 5 and 11 months, respectively. Significant strong relationships between volume-dependent variables obtained from PET/CT and CE-MRI were found (r > 0.750, p < 0.05). For OS, significant associations were found with SUVmax, SUVpeak, SUVmean and sphericity (HR: 1.17, p = 0.035; HR: 1.24, p = 0.042; HR: 1.62, p = 0.040 and HR: 0.8, p = 0.022, respectively). Among clinical variables, only Stupp protocol and age showed significant associations with OS and PFS. No CE-MRI derived variables showed significant association with prognosis. In multivariate analysis, age (HR: 1.04, p = 0.002), Stupp protocol (HR: 2.81, p = 0.001), multilesionality (HR: 2.20, p = 0.013) and sphericity (HR: 0.79, p = 0.027) derived from PET/CT showed independent associations with OS. For PFS, only age (HR: 1.03, p = 0.021) and treatment protocol (HR: 2.20, p = 0.008) were significant predictors. (4) Conclusions: 18F-fluorocholine PET/CT metabolic and radiomic variables were robust prognostic predictors in patients with IDH-wt high-grade gliomas, outperforming CE-MRI derived variables.
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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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Kurdi M, Moshref RH, Katib Y, Faizo E, Najjar AA, Bahakeem B, Bamaga AK. Simple approach for the histomolecular diagnosis of central nervous system gliomas based on 2021 World Health Organization Classification. World J Clin Oncol 2022; 13:567-576. [PMID: 36157161 PMCID: PMC9346424 DOI: 10.5306/wjco.v13.i7.567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/24/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023] Open
Abstract
The classification of central nervous system (CNS) glioma went through a sequence of developments, between 2006 and 2021, started with only histological approach then has been aided with a major emphasis on molecular signatures in the 4th and 5th editions of the World Health Organization (WHO). The recent reformation in the 5th edition of the WHO classification has focused more on the molecularly defined entities with better characterized natural histories as well as new tumor types and subtypes in the adult and pediatric populations. These new subclassified entities have been incorporated in the 5th edition after the continuous exploration of new genomic, epigenomic and transcriptomic discovery. Indeed, the current guidelines of 2021 WHO classification of CNS tumors and European Association of Neuro-Oncology (EANO) exploited the molecular signatures in the diagnostic approach of CNS gliomas. Our current review presents a practical diagnostic approach for diffuse CNS gliomas and circumscribed astrocytomas using histomolecular criteria adopted by the recent WHO classification. We also describe the treatment strategies for these tumors based on EANO guidelines.
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Affiliation(s)
- Maher Kurdi
- Department of Pathology, Faculty of Medicine, King Abdulaziz University, Jeddah 213733, Saudi Arabia
| | - Rana H Moshref
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Jeddah 213733, Saudi Arabia
| | - Yousef Katib
- Department of Radiology, Faculty of Medicine, Taibah University, Almadinah Almunawwarah 213733, Saudi Arabia
| | - Eyad Faizo
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Tabuk University, Tabuk 213733, Saudi Arabia
| | - Ahmed A Najjar
- College of Medicine, Taibah University, Almadinah Almunawwarah 213733, Saudi Arabia
| | - Basem Bahakeem
- Faculty of Medicine, Umm-Alqura University, Makkah 213733, Saudi Arabia
| | - Ahmed K Bamaga
- Department of Pediatric, Neuromuscular Medicine Unit, Faculty of Medicine and King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 213733, Saudi Arabia
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19
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de Groot JF, Kim AH, Prabhu S, Rao G, Laxton AW, Fecci PE, O’Brien BJ, Sloan A, Chiang V, Tatter SB, Mohammadi AM, Placantonakis DG, Strowd RE, Chen C, Hadjipanayis C, Khasraw M, Sun D, Piccioni D, Sinicrope KD, Campian JL, Kurz SC, Williams B, Smith K, Tovar-Spinoza Z, Leuthardt EC. Efficacy of Laser Interstitial Thermal Therapy (LITT) for Newly Diagnosed and Recurrent IDH Wild-type Glioblastoma. Neurooncol Adv 2022; 4:vdac040. [PMID: 35611270 PMCID: PMC9122789 DOI: 10.1093/noajnl/vdac040] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Treatment options for unresectable new and recurrent glioblastoma remain limited. Laser ablation has demonstrated safety as a surgical approach to treat primary brain tumors. The LAANTERN prospective multicenter registry (NCT02392078) data was analyzed to determine clinical outcomes for patients with new and recurrent IDH wild-type glioblastoma.
Methods
Demographics, intraprocedural data, adverse events, KPS, health-economics, and survival data were prospectively collected then analyzed on IDH wild-type newly diagnosed and recurrent glioblastoma patients who were treated with laser ablation at 14 US centers between January 2016 and May 2019. Data was monitored for accuracy. Statistical analysis included individual variable summaries, multivariable differences in survival, and median survival numbers.
Results
A total of 29 new and 60 recurrent IDH wild-type WHO grade 4 glioblastoma patients were treated. Positive MGMT promoter methylation status was present in 5/29 of new and 23/60 of recurrent patients. Median physician-estimated extent of ablation was 91-99%. Median overall-survival was 9.73 months (95% confidence interval: 5.16, 15.91) for newly diagnosed patients and median post-procedure survival was 8.97 (6.94, 12.36) months for recurrent patients. Median overall-survival for newly diagnosed patients receiving post-LITT chemo/radiation was 16.14 months (6.11, not reached). Factors associated with improved survival were MGMT promoter methylation, adjuvant chemotherapy within 12 weeks, and tumor volume <3cc.
Conclusions
Laser ablation is a viable option for patients with new and recurrent glioblastoma. Median overall survival for IDH wild type newly diagnosed glioblastoma is comparable to outcomes observed in other tumor resection studies when those patients undergo radiation and chemotherapy following LITT.
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Affiliation(s)
- John F de Groot
- Department of Neuro-Oncology
- UCSF Weill Institute for Neurosciences, San Francisco, CA
| | - Albert H Kim
- Department of Neurosurgery
- Washington University School of Medicine, St. Louis, MO
| | - Sujit Prabhu
- Department of Neurosurgery
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ganesh Rao
- Department of Neurosurgery
- Baylor College of Medicine, Houston, TX
| | - Adrian W Laxton
- Department of Neurosurgery
- Wake Forest Baptist Health, Winston-Salem, NC
| | - Peter E Fecci
- Department of Neurosurgery
- Duke University Medical Center, Durham, NC
| | - Barbara J O’Brien
- Department of Neuro-Oncology
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Sloan
- Department of Neurosurgery
- University Hospitals – Cleveland Medical Center & Seidman Cancer Center, Cleveland, OH
| | - Veronica Chiang
- Department of Neurosurgery
- Yale School of Medicine, New Haven, CT
| | - Stephen B Tatter
- Department of Neurosurgery
- Wake Forest Baptist Health, Winston-Salem, NC
| | - Alireza M Mohammadi
- Department of Neurosurgery
- Cleveland Clinic Lerner College of Medicine at CWRU, Cleveland, OH
| | | | - Roy E Strowd
- Department of Neuro-Oncology
- Wake Forest Baptist Health, Winston-Salem, NC
| | - Clark Chen
- Department of Neurosurgery
- University of Minnesota Medical Center, Minneapolis, MN
| | | | - Mustafa Khasraw
- Department of Neuro-Oncology
- Duke University Medical Center, Durham, NC
| | - David Sun
- Department of Neurosurgery
- Norton Neuroscience Institute, Louisville, KY
| | - David Piccioni
- Department of Neuro-Oncology
- University of California San Diego Health, La Jolla, CA
| | - Kaylyn D Sinicrope
- Department of Neuro-Oncology
- Norton Neuroscience Institute, Louisville, KY
| | | | - Sylvia C Kurz
- Department of Neuro-Oncology
- NYU Langone Perlmutter Cancer Center, New York, NY
| | - Brian Williams
- Department of Neurosurgery
- University of Louisville Health, Louisville, KY
| | - Kris Smith
- Department of Neurosurgery
- Barrow Neurological Institute, Phoenix, AZ
| | | | - Eric C Leuthardt
- Department of Neurosurgery
- Washington University School of Medicine, St. Louis, MO
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20
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Abdelsayed N, Bondranko Z, Montesano P. Schwannomatosis Presenting With a Grade IV Glioblastoma: A Case Report and Literature Review. Cureus 2022; 14:e23381. [PMID: 35475061 PMCID: PMC9022045 DOI: 10.7759/cureus.23381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 11/17/2022] Open
Abstract
Schwannomatosis is a rare subset of neurofibromatosis. It is a disease process with a predisposition to schwannomas in the absence of bilateral vestibular schwannomas, which differentiates it from neurofibromatosis 2 (NF2). It is occasionally associated with certain tumors such as malignant peripheral nerve sheath tumors or rhabdoid tumors. Currently, there is limited literature to suggest an association between schwannomatosis and glioblastoma (GB). We present a case of a 55-year-old female with a history significant for schwannomatosis who presented after a witnessed first-time seizure with left facial weakness and slurred speech. She was found to have a 3 cm right-sided ring-enhancing lesion that was excised and found to be a grade IV Isocitrate dehydrogenase (IDH) wildtype GB.
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21
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Tian W, Yan G, Chen K, Han X, Zhang W, Sun L, Zhang Q, Zhang Y, Li Y, Liu M, Zhang Q. Development and Validation of a Novel Prognostic Model for Lower-Grade Glioma Based on Enhancer RNA-Regulated Prognostic Genes. Front Oncol 2022; 12:714338. [PMID: 35299740 PMCID: PMC8921558 DOI: 10.3389/fonc.2022.714338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 02/01/2022] [Indexed: 12/19/2022] Open
Abstract
Enhancer RNAs (eRNAs) are present specifically in tumors, where they affect the expression of eRNA-regulated genes (ERGs). Owing to this characteristic, ERGs were hypothesized to improve prognosis of overall survival in heterogeneous low-grade and intermediate-grade gliomas. This study aimed to construct and validate an ERG prognostic tool to facilitate clinical management, and offer more effective diagnostic and therapeutic biomarkers for glioma. Survival-related eRNAs were identified, and their ERGs were selected based on eRNA and target gene information. The ERG prognostic model was constructed and validated using internal and external validation cohorts. Finally, biological differences related to the ERG signature were analysed to explore the potential mechanisms influencing survival outcomes. Thirteen ERGs were identified and used to build an ERG risk signature, which included five super-enhancer RNA (seRNA)-regulated genes and five LGG-specific eRNA-regulated genes. The prognostic nomogram established based on combining the ERG score, age, and sex was evaluated by calibration curves, clinical utility, Harrell’s concordance index (0.86; 95% CI: 0.83-0.90), and time-dependent receiver operator characteristic curves. We also explored potential immune-related mechanisms that might cause variation in survival. The established prognostic model displayed high validity and robustness. Several immune-related genes regulated by seRNAs or specific eRNAs were identified, indicating that these transcripts or their genes were potential targets for improving immunotherapeutic/therapeutic outcomes. The functions of an important specific eRNA-regulated gene (USP28) were validated in robust vitro experiments. In addition, the ERG risk signature was significantly associated with the immune microenvironment and other immune-related features.
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Affiliation(s)
- Wei Tian
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Guangcan Yan
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Kegong Chen
- Department of Cardio-Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinhao Han
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Wei Zhang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Lin Sun
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Qi Zhang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Yafeng Zhang
- Department of Health Management, School of Health Management, Harbin Medical University, Harbin, China
| | - Yan Li
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Meina Liu
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Qiuju Zhang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
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22
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Liu Y, Sathe AA, Abdullah KG, McBrayer SK, Adams SH, Brenner AJ, Hatanpaa KJ, Viapiano MS, Xing C, Walker JM, Richardson TE. Global DNA methylation profiling reveals chromosomal instability in IDH-mutant astrocytomas. Acta Neuropathol Commun 2022; 10:32. [PMID: 35264242 PMCID: PMC8908645 DOI: 10.1186/s40478-022-01339-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/24/2022] [Indexed: 12/21/2022] Open
Abstract
Diffusely infiltrating gliomas are among the most common central nervous system tumors in adults. Over the past decade, the subcategorization of these tumors has changed to include both traditional histologic features and more recently identified molecular factors. However, one molecular feature that has yet to be integrated is the presence/absence of chromosomal instability (CIN). Herein, we use global methylation profiling to evaluate a reference cohort of IDH-mutant astrocytomas with and without prior evidence of CIN (n = 42), and apply the resulting methylation-based characteristics to a larger test cohort of publicly-available IDH-mutant astrocytomas (n = 245). We demonstrate that IDH-mutant astrocytomas with evidence of CIN cluster separately from their chromosomally-stable counterparts. CIN cases were associated with higher initial histologic grade, altered expression patterns of genes related to CIN in other cancers, elevated initial total copy number burden, and significantly worse progression-free and overall survival. In addition, in a grade-for-grade analysis, patients with CIN-positive WHO grade 2 and 3 tumors had significantly worse survival. These results suggest that global methylation profiling can be used to discriminate between chromosomally stable and unstable IDH-mutant astrocytomas, and may therefore provide a reliable and cost-effective method for identifying gliomas with chromosomal instability and resultant poor clinical outcome.
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Affiliation(s)
- Yan Liu
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Adwait Amod Sathe
- Eugene McDermott Center for Human Growth & Development, 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
| | - 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
| | - Steven H. Adams
- Department of Pathology, Stony Brook University Hospital, Stony Brook, NY 11794 USA
| | - Andrew J. Brenner
- Department of Internal Medicine, Division of Hematology & Oncology, University of Texas Health San Antonio, San Antonio, TX 78229 USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX 78229 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
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Jamie M. Walker
- Department of Pathology and Laboratory Medicine, Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Disease, University of Texas Health San Antonio, 7703 Floyd Curl Dr., MC 8070, San Antonio, TX 78229 USA
| | - Timothy E. Richardson
- Department of Pathology and Laboratory Medicine, Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Disease, University of Texas Health San Antonio, 7703 Floyd Curl Dr., MC 8070, San Antonio, TX 78229 USA
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23
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Tian W, Chen K, Yan G, Han X, Liu Y, Zhang Q, Liu M. A Novel Prognostic Tool for Glioma Based on Enhancer RNA-Regulated Immune Genes. Front Cell Dev Biol 2022; 9:798445. [PMID: 35127714 PMCID: PMC8811171 DOI: 10.3389/fcell.2021.798445] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Gliomas are the most malignant tumors of the nervous system. Even though their survival outcome is closely affected by immune-related genes (IRGs) in the tumor microenvironment (TME), the corresponding regulatory mechanism remains poorly characterized. Methods: Specific enhancer RNAs (eRNAs) can be found in tumors, where they control downstream genes. The present study aimed to identify eRNA-regulated IRGs, evaluate their influence on the TME, and use them to construct a novel prognostic model for gliomas. Results: Thirteen target genes (ADCYAP1R1, BMP2, BMPR1A, CD4, DDX17, ELN, FGF13, MAPT, PDIA2, PSMB8, PTPN6, SEMA6C, and SSTR5) were identified and integrated into a comprehensive risk signature, which distinguished two risk subclasses. Discrepancies between these subclasses were compared to explore potential mechanisms attributed to eRNA-regulated genes, including immune cell infiltration, clinicopathological features, survival outcomes, and chemotherapeutic drug sensitivity. Furthermore, the risk signature was used to construct a prognostic tool that was evaluated by calibration curve, clinical utility, Harrell’s concordance index (0.87; 95% CI: 0.84–0.90), and time-dependent receiver operator characteristic curves (AUCs: 0.93 and 0.89 at 3 and 5 years, respectively). The strong reliability and robustness of the established prognostic tool were validated in another independent cohort. Finally, potential subtypes were explored in patients with grade III tumors. Conclusion: Overall, eRNAs were associated with immune-related dysfunctions in the TME. Targeting of IRGs regulated by eRNAs could improve immunotherapeutic/therapeutic outcomes.
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Affiliation(s)
- Wei Tian
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Kegong Chen
- Department of Cardio-Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guangcan Yan
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Xinhao Han
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Qiuju Zhang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Meina Liu
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
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24
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Nuechterlein N, Shapiro LG, Holland EC, Cimino PJ. Machine learning modeling of genome-wide copy number alteration signatures reliably predicts IDH mutational status in adult diffuse glioma. Acta Neuropathol Commun 2021; 9:191. [PMID: 34863298 PMCID: PMC8645099 DOI: 10.1186/s40478-021-01295-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022] Open
Abstract
Knowledge of 1p/19q-codeletion and IDH1/2 mutational status is necessary to interpret any investigational study of diffuse gliomas in the modern era. While DNA sequencing is the gold standard for determining IDH mutational status, genome-wide methylation arrays and gene expression profiling have been used for surrogate mutational determination. Previous studies by our group suggest that 1p/19q-codeletion and IDH mutational status can be predicted by genome-wide somatic copy number alteration (SCNA) data alone, however a rigorous model to accomplish this task has yet to be established. In this study, we used SCNA data from 786 adult diffuse gliomas in The Cancer Genome Atlas (TCGA) to develop a two-stage classification system that identifies 1p/19q-codeleted oligodendrogliomas and predicts the IDH mutational status of astrocytic tumors using a machine-learning model. Cross-validated results on TCGA SCNA data showed near perfect classification results. Furthermore, our astrocytic IDH mutation model validated well on four additional datasets (AUC = 0.97, AUC = 0.99, AUC = 0.95, AUC = 0.96) as did our 1p/19q-codeleted oligodendroglioma screen on the two datasets that contained oligodendrogliomas (MCC = 0.97, MCC = 0.97). We then retrained our system using data from these validation sets and applied our system to a cohort of REMBRANDT study subjects for whom SCNA data, but not IDH mutational status, is available. Overall, using genome-wide SCNAs, we successfully developed a system to robustly predict 1p/19q-codeletion and IDH mutational status in diffuse gliomas. This system can assign molecular subtype labels to tumor samples of retrospective diffuse glioma cohorts that lack 1p/19q-codeletion and IDH mutational status, such as the REMBRANDT study, recasting these datasets as validation cohorts for diffuse glioma research.
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Affiliation(s)
- Nicholas Nuechterlein
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Linda G Shapiro
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Patrick J Cimino
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, Division of Neuropathology, University of Washington, 325 9th Avenue, Box 359791, Seattle, WA, 98104, USA.
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25
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Kukreja L, Li CJ, Ezhilan S, Iyer VR, Kuo JS. Emerging Epigenetic Therapies for Brain Tumors. Neuromolecular Med 2021; 24:41-49. [PMID: 34677796 DOI: 10.1007/s12017-021-08691-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/14/2021] [Indexed: 01/30/2023]
Abstract
Malignant brain tumors are among the most intractable cancers, including malignancies such as glioblastoma, diffuse midline glioma, medulloblastoma, and ependymoma. Unfortunately, treatment options for these brain tumors have been inadequate and complex, leading to poor prognoses and creating a need for new treatment modalities. Aberrant epigenetics define these types of tumors, with underlying changes in DNA methylation, histone modifications, chromatin structure and noncoding RNAs. Epigenetic-targeted therapies are an alternative that have the potential to reverse the epigenetic deregulation underpinning brain malignancies. Various drugs targeting epigenetic regulators have shown promise in preclinical and clinical testing. In this review, we highlight some of the recent emerging epigenetic targeted therapies for brain tumors being evaluated in the discovery phase and in clinical trials.
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Affiliation(s)
- Lokesh Kukreja
- Department of Neurosurgery, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Catherine J Li
- Department of Neurosurgery, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Sathyapriya Ezhilan
- Department of Neurosurgery, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Vishwanath R Iyer
- Department of Molecular Biosciences, LIVESTRONG Cancer Institutes and Department of Oncology, Dell Medical School, The University of Texas, Austin, TX, USA
| | - John S Kuo
- Department of Neurosurgery, Mulva Clinic for the Neurosciences and LIVESTRONG Cancer Institutes and Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA. .,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
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26
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Richardson TE, Raghunathan A, Abdullah KG, Hatanpaa KJ, Walker JM. Prognostic Value of Isolated TERT Promoter Mutation in Grade 2 and 3 IDH-Wildtype Astrocytomas. J Neuropathol Exp Neurol 2021; 80:885-886. [PMID: 34343326 DOI: 10.1093/jnen/nlab067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Timothy E Richardson
- From the Department of Pathology and Laboratory Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA (TER, JMW); Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas, USA (TER, JMW); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (AR); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA (KGA); and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA (KJH)
| | - Aditya Raghunathan
- From the Department of Pathology and Laboratory Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA (TER, JMW); Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas, USA (TER, JMW); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (AR); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA (KGA); and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA (KJH)
| | - Kalil G Abdullah
- From the Department of Pathology and Laboratory Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA (TER, JMW); Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas, USA (TER, JMW); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (AR); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA (KGA); and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA (KJH)
| | - Kimmo J Hatanpaa
- From the Department of Pathology and Laboratory Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA (TER, JMW); Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas, USA (TER, JMW); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (AR); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA (KGA); and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA (KJH)
| | - Jamie M Walker
- From the Department of Pathology and Laboratory Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA (TER, JMW); Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas, USA (TER, JMW); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (AR); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA (KGA); and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA (KJH)
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27
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18F-FET PET Uptake Characteristics of Long-Term IDH-Wildtype Diffuse Glioma Survivors. Cancers (Basel) 2021; 13:cancers13133163. [PMID: 34202726 PMCID: PMC8268019 DOI: 10.3390/cancers13133163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 11/28/2022] Open
Abstract
Simple Summary IDH-wildtype (IDHwt) gliomas represent a tumor entity with poor overall survival. Only rare cases have an overall survival over several years. Dynamic and static 18F-FET PET is recommended as valuable complementary tool for glioma imaging in gliomas. This study shows that, besides molecular genetic prognosticators, long survival (≥36 months survival) in IDHwt gliomas is associated with a longer time-to-peak and smaller volume on 18F-FET PET at initial diagnosis compared to glioma patients with a short-term survival (≤15 months survival). 18F-FET uptake intensity and MRI-derived tumor size do not differ in patients with long-term survival compared to patient with a short-term survival. Abstract Background: IDHwt diffuse gliomas represent the tumor entity with one of the worst clinical outcomes. Only rare cases present with a long-term survival of several years. Here we aimed at comparing the uptake characteristics on dynamic 18F-FET PET, clinical and molecular genetic parameters of long-term survivors (LTS) versus short-term survivors (STS): Methods: Patients with de-novo IDHwt glioma (WHO grade III/IV) and 18F-FET PET prior to any therapy were stratified into LTS (≥36 months survival) and STS (≤15 months survival). Static and dynamic 18F-FET PET parameters (mean/maximal tumor-to-background ratio (TBRmean/max), biological tumor volume (BTV), minimal time-to-peak (TTPmin)), diameter and volume of contrast-enhancement on MRI, clinical parameters (age, sex, Karnofksy-performance-score), mode of surgery; initial treatment and molecular genetics were assessed and compared between LTS and STS. Results: Overall, 75 IDHwt glioma patients were included (26 LTS, 49 STS). LTS were significantly younger (p < 0.001), had a higher rate of WHO grade III glioma (p = 0.032), of O(6)-Methylguanine-DNA methyltransferase (MGMT) promoter methylation (p < 0.001) and missing Telomerase reverse transcriptase promoter (TERTp) mutations (p = 0.004) compared to STS. On imaging, LTS showed a smaller median BTV (p = 0.017) and a significantly longer TTPmin (p = 0.008) on 18F-FET PET than STS, while uptake intensity (TBRmean/max) did not differ. In contrast to the tumor-volume on PET, MRI-derived parameters such as tumor size as well as all other above-mentioned parameters did not differ between LTS and STS (p > 0.05 each). Conclusion: Besides molecular genetic prognosticators, a long survival time in IDHwt glioma patients is associated with a longer TTPmin as well as a smaller BTV on 18F-FET PET at initial diagnosis. 18F-FET uptake intensity as well as the MRI-derived tumor size (volume and maximal diameter) do not differ in patients with long-term survival.
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28
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Richardson TE, Hatanpaa KJ, Walker JM. Molecular Characterization of "True" Low-Grade IDH-Wildtype Astrocytomas. J Neuropathol Exp Neurol 2021; 80:431-435. [PMID: 33829259 DOI: 10.1093/jnen/nlab023] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Numerous recent studies have demonstrated that the vast majority of IDH-wildtype astrocytomas with WHO grade II/III histology have clinical outcomes equivalent to IDH-wildtype glioblastomas. This has called into question the existence of an IDH-wildtype lower-grade astrocytoma (LGA) category, and the cIMPACT-NOW study group has suggested 3 molecular features which, if present, warrant upgrading IDH-wildtype LGA to glioblastoma: EGFR amplification, 7+/10-, and TERT promoter mutation. Herein, we evaluate the clinical, histologic, and molecular features of IDH-wildtype low-grade astrocytomas, defined here as infiltrative adult astrocytoma lacking histologic features of glioblastoma (microvascular proliferation and/or necrosis), IDH1/2 mutation, and all 3 of the cIMPACT-NOW update 3 factors. Compared with their counterparts with cIMPACT-NOW features of glioblastoma (LGA-C+; n = 108), IDH-wildtype LGAs lacking these features (LGA-C0; n = 36) occur in significantly younger patients, are more frequently WHO grade II, have less total copy number variation distributed across the entire genome, less frequent homozygous deletion of CDKN2A, less frequent PTEN and PIK3CA alterations, and more frequent NF1 alterations. These results suggest that although rare, a "true" IDH-wildtype LGA category does exist, and has distinct clinical and molecular features consistent with relatively beneficial clinical outcomes in these patients.
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Affiliation(s)
- Timothy E Richardson
- From the Department of Pathology and Laboratory Medicine and Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jamie M Walker
- From the Department of Pathology and Laboratory Medicine and Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas, USA
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Richardson TE, Sathe AA, Xing C, Mirchia K, Viapiano MS, Snuderl M, Abdullah KG, Hatanpaa KJ, Walker JM. Molecular Signatures of Chromosomal Instability Correlate With Copy Number Variation Patterns and Patient Outcome in IDH-Mutant and IDH-Wildtype Astrocytomas. J Neuropathol Exp Neurol 2021; 80:354-365. [PMID: 33755138 DOI: 10.1093/jnen/nlab008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Chromosomal instability due to mutations in genes guarding the stability of the genome is a well-known mechanism underlying tumorigenesis and malignant progression in numerous cancers. The effect of this process in gliomas is mostly unknown with relatively little research examining the effects of chromosomal instability on patient outcome and therapeutic efficacy, although studies have shown that overall/total copy number variation (CNV) is elevated in higher histologic grades and in cases with more rapid progression and shorter patient survival. Herein, we examine a 70-gene mRNA expression signature (CIN70), which has been previously shown to correlate tightly with chromosomal instability, in 2 independent cohorts of IDH-mutant astrocytomas (total n = 241), IDH-wildtype astrocytomas (n = 228), and oligodendrogliomas (n = 128). Our results show that CIN70 expression levels correlate with total CNV, as well as higher grade, progression-free survival, and overall survival in both IDH-mutant and IDH-wildtype astrocytomas. In oligodendrogliomas, these mRNA signatures correlate with total CNV but not consistently with clinical outcome. These data suggest that chromosomal instability is an underlying factor in aggressive behavior and progression of a subset of diffuse astrocytomas. In addition, chromosomal instability may in part explain the poor response of diffuse gliomas to treatment and may serve as a future therapeutic target.
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Affiliation(s)
- Timothy E Richardson
- From the Department of Pathology and Laboratory Medicine; University of Texas Health San Antonio, San Antonio, Texas, USA.,Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Adwait Amod Sathe
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kanish Mirchia
- Department of Pathology, State University of New York, Upstate Medical University, Syracuse, 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
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York City, New York, USA
| | - Kalil G Abdullah
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jamie M Walker
- From the Department of Pathology and Laboratory Medicine; University of Texas Health San Antonio, San Antonio, Texas, USA.,Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas, USA
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30
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Kalita O, Sporikova Z, Hajduch M, Megova Houdova M, Slavkovsky R, Hrabalek L, Halaj M, Klementova Y, Dolezel M, Drabek J, Tuckova L, Ehrmann J, Vrbkova J, Trojanec R, Vaverka M. The Influence of Gene Aberrations on Survival in Resected IDH Wildtype Glioblastoma Patients: A Single-Institution Study. ACTA ACUST UNITED AC 2021; 28:1280-1293. [PMID: 33801093 PMCID: PMC8025822 DOI: 10.3390/curroncol28020122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/17/2021] [Indexed: 12/18/2022]
Abstract
This prospective population-based study on a group of 132 resected IDH-wildtype (IDH-wt) glioblastoma (GBM) patients assesses the prognostic and predictive value of selected genetic biomarkers and clinical factors for GBM as well as the dependence of these values on the applied therapeutic modalities. The patients were treated in our hospital between June 2006 and June 2015. Clinical data and tumor samples were analyzed to determine the frequencies of TP53, MDM2, EGFR, RB1, BCR, and CCND1 gene aberrations and the duplication/deletion statuses of the 9p21.3, 1p36.3, 19q13.32, and 10p11.1 chromosome regions. Cut-off values distinguishing low (LCN) and high (HCN) copy number status for each marker were defined. Additionally, MGMT promoter methylation and IDH1/2 mutation status were investigated retrospectively. Young age, female gender, Karnofsky scores (KS) above 80, chemoradiotherapy, TP53 HCN, and CCND1 HCN were identified as positive prognostic factors, and smoking was identified as a negative prognostic factor. Cox proportional regression models of the chemoradiotherapy patient group revealed TP53 HCN and CCND1 HCN to be positive prognostic factors for both progression-free survival and overall survival. These results confirmed the influence of key clinical factors (age, KS, adjuvant oncotherapy, and smoking) on survival in GBM IDH-wt patients and demonstrated the prognostic and/or predictive importance of CCND1, MDM2, and 22q12.2 aberrations.
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Affiliation(s)
- Ondrej Kalita
- Department of Neurosurgery, University Hospital Olomouc, I.P. Pavlova 6, 779 00 Olomouc, Czech Republic
| | - Zuzana Sporikova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Hnevotinska 5, 779 00 Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Hnevotinska 5, 779 00 Olomouc, Czech Republic
| | - Magdalena Megova Houdova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Hnevotinska 5, 779 00 Olomouc, Czech Republic
| | - Rastislav Slavkovsky
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Hnevotinska 5, 779 00 Olomouc, Czech Republic
| | - Lumir Hrabalek
- Department of Neurosurgery, University Hospital Olomouc, I.P. Pavlova 6, 779 00 Olomouc, Czech Republic
| | - Matej Halaj
- Department of Neurosurgery, University Hospital Olomouc, I.P. Pavlova 6, 779 00 Olomouc, Czech Republic
| | - Yvona Klementova
- Department of Oncology, University Hospital Olomouc, I.P. Pavlova 6, 779 00 Olomouc, Czech Republic
| | - Martin Dolezel
- Department of Oncology, University Hospital Olomouc, I.P. Pavlova 6, 779 00 Olomouc, Czech Republic
| | - Jiri Drabek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Hnevotinska 5, 779 00 Olomouc, Czech Republic
| | - Lucie Tuckova
- Department of Pathology and Laboratory of Molecular Pathology, University Hospital Olomouc, Hnevotinska 3, 779 00 Olomouc, Czech Republic
| | - Jiri Ehrmann
- Department of Pathology and Laboratory of Molecular Pathology, University Hospital Olomouc, Hnevotinska 3, 779 00 Olomouc, Czech Republic
| | - Jana Vrbkova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Hnevotinska 5, 779 00 Olomouc, Czech Republic
| | - Radek Trojanec
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Hnevotinska 5, 779 00 Olomouc, Czech Republic
| | - Miroslav Vaverka
- Department of Neurosurgery, University Hospital Olomouc, I.P. Pavlova 6, 779 00 Olomouc, Czech Republic
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31
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Richardson TE, Kumar A, Xing C, Hatanpaa KJ, Walker JM. Overcoming the Odds: Toward a Molecular Profile of Long-Term Survival in Glioblastoma. J Neuropathol Exp Neurol 2021; 79:1031-1037. [PMID: 32954439 DOI: 10.1093/jnen/nlaa102] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
For over a century, gliomas were characterized solely by histologic features. With the publication of the WHO Classification of Tumours of the Central Nervous System, Revised 4th Edition in 2016, integrated histologic and molecular diagnosis became the norm, providing improved tumor grading and prognosis with IDH1/2 (isocitrate dehydrogenase 1 and 2) mutation being the most significant prognostic feature in all grades of adult diffuse glioma. Since then, much work has been done to identify additional molecular prognostic features, but the bulk of the progress has been made in defining aggressive features in lower grade astrocytoma. Although there have been several large case series of glioblastomas with long-term survival (LTS; overall survival ≥36 months), less is known about the clinical and molecular features of these cases. Herein, we review 19 studies examining LTS glioblastoma patients from 2009 to 2020 that include variable molecular analysis, including 465 cases with survival of 36 months or more (total n = 2328). These studies suggest that while there is no definitive molecular signature of long survival, younger age, IDH mutation, and MGMT (methyl guanine methyl transferase) promoter hypermethylation are associated with longer overall survival, and in IDH-wildtype tumors, chromosome 19/20 co-gain and lack of EGFR amplification, chromosome 7 gain/10 loss, and TERT promoter mutation are associated with LTS.
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Affiliation(s)
- Timothy E Richardson
- Department of Pathology, State University of New York, Upstate Medical University, Syracuse, New York
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth & Development
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development.,Department of Bioinformatics and Department of Population and Data Sciences
| | | | - Jamie M Walker
- University of Texas Southwestern Medical Center, Dallas, Texas; and Department of Pathology and Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, Texas
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32
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Dono A, Ramesh AV, Wang E, Shah M, Tandon N, Ballester LY, Esquenazi Y. The role of RB1 alteration and 4q12 amplification in IDH-WT glioblastoma. Neurooncol Adv 2021; 3:vdab050. [PMID: 34131647 PMCID: PMC8193911 DOI: 10.1093/noajnl/vdab050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Recent studies have identified that glioblastoma IDH-wildtype (GBM IDH-WT) might be comprised of molecular subgroups with distinct prognoses. Therefore, we investigated the correlation between genetic alterations and survival in 282 GBM IDH-WT patients, to identify subgroups with distinct outcomes. METHODS We reviewed characteristics of GBM IDH-WT (2009-2019) patients analyzed by next-generation sequencing interrogating 205 genes and 26 rearrangements. Progression-free survival (PFS) and overall survival (OS) were evaluated with the log-rank test and Cox regression models. We validated our results utilizing data from cBioPortal (MSK-IMPACT dataset). RESULTS Multivariable analysis of GBM IDH-WT revealed that treatment with chemoradiation and RB1-mutant status correlated with improved PFS (hazard ratio [HR] 0.25, P < .001 and HR 0.47, P = .002) and OS (HR 0.24, P < .001 and HR 0.49, P = .016). In addition, younger age (<55 years) was associated with improved OS. Karnofsky performance status less than 80 (HR 1.44, P = .024) and KDR amplification (HR 2.51, P = .008) were predictors of worse OS. KDR-amplified patients harbored coexisting PDGFRA and KIT amplification (P < .001) and TP53 mutations (P = .04). RB1-mutant patients had less frequent CDKN2A/B and EGFR alterations (P < .001). Conversely, RB1-mutant patients had more frequent TP53 (P < .001) and SETD2 (P = .006) mutations. Analysis of the MSK-IMPACT dataset (n = 551) validated the association between RB1 mutations and improved PFS (11.0 vs 8.7 months, P = .009) and OS (34.7 vs 21.7 months, P = .016). CONCLUSIONS RB1-mutant GBM IDH-WT is a molecular subgroup with improved PFS and OS. Meanwhile, 4q12 amplification (KDR/PDGFRA/KIT) denoted patients with worse OS. Identifying subgroups of GBM IDH-WT with distinct survival is important for optimal clinical trial design, incorporation of targeted therapies, and personalized neuro-oncological care.
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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
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | | | - Mauli Shah
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, 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
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Memorial Hermann Hospital-TMC, 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
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Memorial Hermann Hospital-TMC, Houston, Texas, USA
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33
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Mirchia K, Richardson TE. Beyond IDH-Mutation: Emerging Molecular Diagnostic and Prognostic Features in Adult Diffuse Gliomas. Cancers (Basel) 2020; 12:E1817. [PMID: 32640746 PMCID: PMC7408495 DOI: 10.3390/cancers12071817] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 12/19/2022] Open
Abstract
Diffuse gliomas are among the most common adult central nervous system tumors with an annual incidence of more than 16,000 cases in the United States. Until very recently, the diagnosis of these tumors was based solely on morphologic features, however, with the publication of the WHO Classification of Tumours of the Central Nervous System, revised 4th edition in 2016, certain molecular features are now included in the official diagnostic and grading system. One of the most significant of these changes has been the division of adult astrocytomas into IDH-wildtype and IDH-mutant categories in addition to histologic grade as part of the main-line diagnosis, although a great deal of heterogeneity in the clinical outcome still remains to be explained within these categories. Since then, numerous groups have been working to identify additional biomarkers and prognostic factors in diffuse gliomas to help further stratify these tumors in hopes of producing a more complete grading system, as well as understanding the underlying biology that results in differing outcomes. The field of neuro-oncology is currently in the midst of a "molecular revolution" in which increasing emphasis is being placed on genetic and epigenetic features driving current diagnostic, prognostic, and predictive considerations. In this review, we focus on recent advances in adult diffuse glioma biomarkers and prognostic factors and summarize the state of the field.
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Affiliation(s)
- Kanish Mirchia
- Department of Pathology, State University of New York, Upstate Medical University, Syracuse, NY 13210, USA;
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