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Thirimanne HN, Almiron-Bonnin D, Nuechterlein N, Arora S, Jensen M, Parada CA, Qiu C, Szulzewsky F, English CW, Chen WC, Sievers P, Nassiri F, Wang JZ, Klisch TJ, Aldape KD, Patel AJ, Cimino PJ, Zadeh G, Sahm F, Raleigh DR, Shendure J, Ferreira M, Holland EC. Meningioma transcriptomic landscape demonstrates novel subtypes with regional associated biology and patient outcome. CELL GENOMICS 2024; 4:100566. [PMID: 38788713 DOI: 10.1016/j.xgen.2024.100566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/16/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
Meningiomas, although mostly benign, can be recurrent and fatal. World Health Organization (WHO) grading of the tumor does not always identify high-risk meningioma, and better characterizations of their aggressive biology are needed. To approach this problem, we combined 13 bulk RNA sequencing (RNA-seq) datasets to create a dimension-reduced reference landscape of 1,298 meningiomas. The clinical and genomic metadata effectively correlated with landscape regions, which led to the identification of meningioma subtypes with specific biological signatures. The time to recurrence also correlated with the map location. Further, we developed an algorithm that maps new patients onto this landscape, where the nearest neighbors predict outcome. This study highlights the utility of combining bulk transcriptomic datasets to visualize the complexity of tumor populations. Further, we provide an interactive tool for understanding the disease and predicting patient outcomes. This resource is accessible via the online tool Oncoscape, where the scientific community can explore the meningioma landscape.
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Affiliation(s)
| | - Damian Almiron-Bonnin
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas Nuechterlein
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Matt Jensen
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Seattle Translational Tumor Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Carolina A Parada
- Department of Neurological Surgery, University of Washington Medical Center, Seattle, WA, USA
| | - Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Collin W English
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - William C Chen
- Departments of Radiation Oncology, Neurological Surgery, and Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Farshad Nassiri
- Department of Surgery, Division of Neurosurgery, University of Toronto, Toronto, ON, Canada
| | - Justin Z Wang
- Department of Surgery, Division of Neurosurgery, University of Toronto, Toronto, ON, Canada
| | - Tiemo J Klisch
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Akash J Patel
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Patrick J Cimino
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Gelareh Zadeh
- Department of Surgery, Division of Neurosurgery, University of Toronto, Toronto, ON, Canada
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David R Raleigh
- Departments of Radiation Oncology, Neurological Surgery, and Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington Medical Center, Seattle, WA, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Seattle Translational Tumor Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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2
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Yokogami K, Watanabe T, Yamashita S, Mizuguchi A, Takeshima H. Inhibition of BMP signaling pathway induced senescence and calcification in anaplastic meningioma. J Neurooncol 2024; 167:455-465. [PMID: 38446374 PMCID: PMC11096233 DOI: 10.1007/s11060-024-04625-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
PURPOSE Meningiomas are the most common type of brain tumors and are generally benign, but malignant atypical meningiomas and anaplastic meningiomas frequently recur with poor prognosis. The metabolism of meningiomas is little known, so few effective treatment options other than surgery and radiation are available, and the targets for treatment of recurrence are not well defined. The Aim of this paper is to find the therapeutic target. METHODS The effects of bone morphogenetic protein (BMP) signal inhibitor (K02288) and upstream regulator Gremlin2 (GREM2) on meningioma's growth and senescence were examined. In brief, we examined as follows: 1) Proliferation assay by inhibiting BMP signaling. 2) Comprehensive analysis of forced expression GREM2.3) Correlation between GREM2 mRNA expression and proliferation marker in 87 of our clinical samples. 4) Enrichment analysis between GREM2 high/low expressed groups using RNA-seq data (42 cases) from the public database GREIN. 5) Changes in metabolites and senescence markers associated with BMP signal suppression. RESULTS Inhibitors of BMP receptor (BMPR1A) and forced expression of GREM2 shifted tryptophan metabolism from kynurenine/quinolinic acid production to serotonin production in malignant meningiomas, reduced NAD + /NADH production, decreased gene cluster expression involved in oxidative phosphorylation, and caused decrease in ATP. Finally, malignant meningiomas underwent cellular senescence, decreased proliferation, and eventually formed psammoma bodies. Reanalyzed RNA-seq data of clinical samples obtained from GREIN showed that increased expression of GREM2 decreased the expression of genes involved in oxidative phosphorylation, similar to our experimental results. CONCLUSIONS The GREM2-BMPR1A-tryptophan metabolic pathway in meningiomas is a potential new therapeutic target.
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Affiliation(s)
- Kiyotaka Yokogami
- Department of Neurosurgery, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan.
| | - Takashi Watanabe
- Department of Neurosurgery, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Shinji Yamashita
- Department of Neurosurgery, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Asako Mizuguchi
- Department of Neurosurgery, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Hideo Takeshima
- Department of Neurosurgery, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
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3
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Zakimi N, Nguyen MP, Raleigh DR. Gene transcript fusions are associated with clinical outcomes and molecular groups of meningiomas. Acta Neuropathol 2024; 147:57. [PMID: 38509407 PMCID: PMC10954959 DOI: 10.1007/s00401-024-02708-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Affiliation(s)
- Naomi Zakimi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Minh P Nguyen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
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4
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Qin Q, Popic V, Yu H, White E, Khorgade A, Shin A, Wienand K, Dondi A, Beerenwinkel N, Vazquez F, Al’Khafaji AM, Haas BJ. CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581862. [PMID: 38464114 PMCID: PMC10925146 DOI: 10.1101/2024.02.24.581862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Gene fusions are found as cancer drivers in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential in cancer clinical diagnostics, prognostics, and for guiding therapeutic development. Most currently available methods for fusion transcript detection are compatible with Illumina RNA-seq involving highly accurate short read sequences. Recent advances in long read isoform sequencing enable the detection of fusion transcripts at unprecedented resolution in bulk and single cell samples. Here we developed a new computational tool CTAT-LR-fusion to detect fusion transcripts from long read RNA-seq with or without companion short reads, with applications to bulk or single cell transcriptomes. We demonstrate that CTAT-LR-fusion exceeds fusion detection accuracy of alternative methods as benchmarked with simulated and real long read RNA-seq. Using short and long read RNA-seq, we further apply CTAT-LR-fusion to bulk transcriptomes of nine tumor cell lines, and to tumor single cells derived from a melanoma sample and three metastatic high grade serous ovarian carcinoma samples. In both bulk and in single cell RNA-seq, long isoform reads yielded higher sensitivity for fusion detection than short reads with notable exceptions. By combining short and long reads in CTAT-LR-fusion, we are able to further maximize detection of fusion splicing isoforms and fusion-expressing tumor cells. CTAT-LR-fusion is available at https://github.com/TrinityCTAT/CTAT-LR-fusion/wiki.
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Affiliation(s)
- Qian Qin
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Victoria Popic
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Houlin Yu
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Emily White
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Akanksha Khorgade
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Asa Shin
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Kirsty Wienand
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Arthur Dondi
- ETH Zurich, Department of Biosystems Science and Engineering, Schanzenstrasse 44, 4056 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Schanzenstrasse 44, 4056 Basel, Switzerland
| | - Niko Beerenwinkel
- ETH Zurich, Department of Biosystems Science and Engineering, Schanzenstrasse 44, 4056 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Schanzenstrasse 44, 4056 Basel, Switzerland
| | - Francisca Vazquez
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Aziz M. Al’Khafaji
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Brian J. Haas
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
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5
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Yamashita M, Kuroha M, Kinowawki Y, Kashiwagi N, Watanabe K, Nagase M, Niizato D, Mitsuiki N, Isoda T, Kamiya T, Arisaka A, Inaji M, Ohashi K, Imai K, Kanegane H, Morio T, Takagi M. A SAMD5-SASH1 fusion in solitary infantile myofibromatosis. Pediatr Blood Cancer 2023; 70:e30278. [PMID: 36861442 DOI: 10.1002/pbc.30278] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/08/2023] [Indexed: 03/03/2023]
Affiliation(s)
- Motoi Yamashita
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masae Kuroha
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuko Kinowawki
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Nao Kashiwagi
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kotaro Watanabe
- Department of Pediatrics, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Mika Nagase
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Daiki Niizato
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Noriko Mitsuiki
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takeshi Isoda
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takahiro Kamiya
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Atsuko Arisaka
- Department of Pediatrics, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Motoki Inaji
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kenichi Ohashi
- Department of Human Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kohsuke Imai
- Department of Community Pediatrics, Perinatal and Maternal Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Pediatrics, National Defense Medical College, Tokorozawa, Japan
| | - Hirokazu Kanegane
- Department of Child Health and Development, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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6
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Pereira BJA, Marcondes Lerario A, Sola PR, Laurentino TDS, Mohan DR, de Almeida AN, Pires de Aguiar PH, da Silva Paiva W, Wakamatsu A, Teixeira MJ, Oba-Shinjo SM, Marie SKN. Impact of a cell cycle and an extracellular matrix remodeling transcriptional signature on tumor progression and correlation with EZH2 expression in meningioma. J Neurosurg 2023; 138:649-662. [PMID: 36029259 DOI: 10.3171/2022.7.jns22953] [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: 04/22/2022] [Accepted: 07/06/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE The authors searched for genetic and transcriptional signatures associated with tumor progression and recurrence in their cohort of patients with meningiomas, combining the analysis of targeted exome, NF2-LOH, transcriptome, and protein expressions. METHODS The authors included 91 patients who underwent resection of intracranial meningioma at their institution between June 2000 and November 2007. The search of somatic mutations was performed by Next Generation Sequencing through a customized panel and multiplex ligation-dependent probe amplification for NF2 loss of heterozygosity. The transcriptomic profile was analyzed by QuantSeq 3' mRNA-Seq. The differentially expressed genes of interest were validated at the protein level analysis by immunohistochemistry. RESULTS The transcriptomic analysis identified an upregulated set of genes related to metabolism and cell cycle and downregulated genes related to immune response and extracellular matrix remodeling in grade 2 (atypical) meningiomas, with a significant difference in recurrent compared with nonrecurrent cases. EZH2 nuclear positivity associated with grade 2, particularly with recurrent tumors and EZH2 gene expression level, correlated positively with the expression of genes related to cell cycle and negatively to genes related to immune response and regulation of cell motility. CONCLUSIONS The authors identified modules of dysregulated genes in grade 2 meningiomas related to the activation of oxidative metabolism, cell division, cell motility due to extracellular remodeling, and immune evasion that were predictive of survival and exhibited significant correlations with EZH2 expression.
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Affiliation(s)
| | - Antonio Marcondes Lerario
- 2Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan
| | - Paula Rodrigues Sola
- 1Department of Neurology, Laboratory of Molecular and Cellular Biology, University of São Paulo, São Paulo, Brazil
| | - Talita de Sousa Laurentino
- 1Department of Neurology, Laboratory of Molecular and Cellular Biology, University of São Paulo, São Paulo, Brazil
| | - Dipika R Mohan
- 3Medical Scientist Training Program, and Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan
| | | | - Paulo Henrique Pires de Aguiar
- 5Medical Research ABC Medical School, Santo André, Brazil.,6Pontifice Catholic University of São Paulo, Sorocaba, Brazil; and
| | | | - Alda Wakamatsu
- 7Department of Pathology, Hepatic Pathology Laboratory, University of São Paulo, São Paulo, Brazil
| | | | - Sueli Mieko Oba-Shinjo
- 1Department of Neurology, Laboratory of Molecular and Cellular Biology, University of São Paulo, São Paulo, Brazil
| | - Suely Kazue Nagahashi Marie
- 1Department of Neurology, Laboratory of Molecular and Cellular Biology, University of São Paulo, São Paulo, Brazil
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7
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Paths of Evolution of Progressive Anaplastic Meningiomas: A Clinical and Molecular Pathology Study. J Pers Med 2023; 13:jpm13020206. [PMID: 36836440 PMCID: PMC9965923 DOI: 10.3390/jpm13020206] [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: 01/04/2023] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Grade 3 meningiomas are rare malignant tumors that can originate de novo or from the progression of lower grade meningiomas. The molecular bases of anaplasia and progression are poorly known. We aimed to report an institutional series of grade 3 anaplastic meningiomas and to investigate the evolution of molecular profile in progressive cases. Clinical data and pathologic samples were retrospectively collected. VEGF, EGFR, EGFRvIII, PD-L1; and Sox2 expression; MGMT methylation status; and TERT promoter mutation were assessed in paired meningioma samples collected from the same patient before and after progression using immunohistochemistry and PCR. Young age, de novo cases, origin from grade 2 in progressive cases, good clinical status, and unilateral side, were associated with more favorable outcomes. In ten progressive meningiomas, by comparing molecular profile before and after progression, we identified two subgroups of patients, one defined by Sox2 increase, suggesting a stem-like, mesenchymal phenotype, and another defined by EGFRvIII gain, suggesting a committed progenitor, epithelial phenotype. Interestingly, cases with Sox2 increase had a significantly shortened survival compared to those with EGFRvIII gain. PD-L1 increase at progression was also associated with worse prognosis, portending immune escape. We thus identified the key drivers of meningioma progression, which can be exploited for personalized treatments.
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8
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Vaubel RA, Kumar R, Weiskittel TM, Jenkins S, Dasari S, Uhm JH, Lachance DH, Brown PD, Van Gompel JJ, Jenkins RB, Kipp BR, Sukov WR, Giannini C, Johnson DR, Raghunathan A. Genomic markers of recurrence risk in atypical meningioma following gross total resection. Neurooncol Adv 2023; 5:vdad004. [PMID: 36845294 PMCID: PMC9950854 DOI: 10.1093/noajnl/vdad004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background Meningiomas are the most common primary central nervous system (CNS) tumor in adults and CNS World Health Organization grade 2 (atypical) meningiomas show an intermediate risk of recurrence/progression. Molecular parameters are needed to better inform management following gross total resection (GTR). Methods We performed comprehensive genomic analysis of tumor tissue from 63 patients who underwent radiologically confirmed GTR of a primary grade 2 meningioma, including a CLIA-certified target next-generation sequencing panel (n = 61), chromosomal microarray (n = 63), genome-wide methylation profiling (n = 62), H3K27me3 immunohistochemistry (n = 62), and RNA-sequencing (n = 19). Genomic features were correlated with long-term clinical outcomes (median follow-up: 10 years) using Cox proportional hazards regression modeling and published molecular prognostic signatures were evaluated. Results The presence of specific copy number variants (CNVs), including -1p, -10q, -7p, and -4p, was the strongest predictor of decreased recurrence-free survival (RFS) within our cohort (P < .05). NF2 mutations were frequent (51%) but did not show a significant association with RFS. DNA methylation-based classification assigned tumors to DKFZ Heidelberg benign (52%) or intermediate (47%) meningioma subclasses and was not associated with RFS. H3K27 trimethylation (H3K27me3) was unequivocally lost in 4 tumors, insufficient for RFS analysis. Application of published integrated histologic/molecular grading systems did not improve prediction of recurrence risk over the presence of -1p or -10q alone. Conclusions CNVs are strong predictors of RFS in grade 2 meningiomas following GTR. Our study supports incorporation of CNV profiling into clinical evaluation to better guide postoperative patient management, which can be readily implemented using existing, clinically validated technologies.
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Affiliation(s)
- Rachael A Vaubel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Rahul Kumar
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Taylor M Weiskittel
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah Jenkins
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Surendra Dasari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Joon H Uhm
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Paul D Brown
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jamie J Van Gompel
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Derek R Johnson
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Aditya Raghunathan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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9
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Malta TM, Snyder J, Noushmehr H, Castro AV. Advances in Central Nervous System Tumor Classification. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1416:121-135. [PMID: 37432624 DOI: 10.1007/978-3-031-29750-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Historically, the classification of tumors of the central nervous system (CNS) relies on the histologic appearance of cells under a microscope; however, the molecular era of medicine has resulted in new diagnostic paradigms anchored in the intrinsic biology of disease. The 2021 World Health Organization (WHO) reformulated the classification of CNS tumors to incorporate molecular parameters, in addition to histology, to define many tumor types. A contemporary classification system with integrated molecular features aims to provide an unbiased tool to define tumor subtype, the risk of tumor progression, and even the response to certain therapeutic agents. Meningiomas are heterogeneous tumors as depicted by the current 15 distinct variants defined by histology in the 2021 WHO classification, which also incorporated the first moelcular critiera for meningioma grading: homozygous loss of CDKN2A/B and TERT promoter mutation as criteria for a WHO grade 3 meningioma. The proper classification and clinical management of meningioma patients requires a multidisciplinary approach, which in addition to the information on microscopic (histology) and macroscopic (Simpson grade and imaging), should also include molecular alterations. In this chapter, we present the most up-to-date knowledge in CNS tumor classification, particularly in meningioma, in the molecular era and how it could affect their future classification and clinical management of patients with these diseases.
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Affiliation(s)
- Tathiane M Malta
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - James Snyder
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA.
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10
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Multi-instance learning based on spatial continuous category representation for case-level meningioma grading in MRI images. APPL INTELL 2022. [DOI: 10.1007/s10489-022-04114-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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11
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Maier AD, Meddis A, Mirian C, Haslund-Vinding J, Bartek J, Krog SM, Nguyen TUP, Areškevičiūtė A, Melchior LC, Heegaard S, Kristensen BW, Munch TN, Fugleholm K, Ziebell M, Raleigh DR, Poulsen FR, Gerds TA, Litman T, Scheie D, Mathiesen T. Gene expression analysis during progression of malignant meningioma compared to benign meningioma. J Neurosurg 2022; 138:1302-1312. [PMID: 36115056 DOI: 10.3171/2022.7.jns22585] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/22/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Meningioma is the most common primary intracranial neoplasm. Only 1%-3% of meningiomas are malignant according to the 2016 WHO criteria (WHO grade III). High-grade meningiomas present specific gene expression signatures indicating aggressive growth or recurrence. However, changes in gene expression and in neuroinflammatory gene expression signatures in WHO grade III meningiomas and during progression from WHO grade I or II to grade III are unknown. METHODS The authors used a NanoString targeted gene expression panel with focus on 787 genes relevant in meningioma pathology and neuroinflammatory pathways to investigate patients with grade III meningiomas treated at Rigshospitalet from 2000 to 2020 (n = 51). A temporal dimension was added to the investigation by including samples from patients' earlier grade I and II meningiomas and grade III recurrences (n = 139 meningiomas). The authors investigated changes in neuroinflammatory gene expression signatures in 1) grade I meningiomas that later transformed into grade III meningiomas, and 2) grade III meningiomas compared with nonrecurrent grade I meningiomas. RESULTS The authors' data indicate that FOXM1, TOP2A, BIRC5, and MYBL2 were enriched and the HOTAIR regulatory pathway was enriched in grade III meningiomas compared with nonrecurrent grade I meningiomas. They discovered a separation of malignant and benign meningiomas based only on genes involved in microglia regulation with enrichment of P2RY12 in grade I compared with grade III meningiomas. Interestingly, FOXM1 was upregulated in premalignant grade I meningioma years before the grade III transformation. CONCLUSIONS The authors found gene expression changes in low-grade meningiomas that predated histological transformation to grade III meningiomas. Neuroinflammation genes distinguished grade III from grade I meningiomas.
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Affiliation(s)
- Andrea D Maier
- Departments of1Neurosurgery and.,2Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Alessandra Meddis
- 3Section of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Jiri Bartek
- Departments of1Neurosurgery and.,4Department of Neurosurgery, Karolinska University Hospital, Solna, Stockholm, Sweden.,5Department of Clinical Neuroscience, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Sebastian M Krog
- 6Department of Oncology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Aušrinė Areškevičiūtė
- 7Department of Pathology, Danish Reference Center for Prion Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Linea C Melchior
- 2Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Steffen Heegaard
- 2Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,8Department of Ophthalmology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Bjarne W Kristensen
- 9Department of Clinical Medicine and Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark.,10Department of Pathology, The Bartholin Institute, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Tina N Munch
- Departments of1Neurosurgery and.,11Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,17Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | | | - David R Raleigh
- Departments of12Neurological Surgery and.,13Radiation Oncology, University of California, San Francisco, California
| | - Frantz R Poulsen
- 14Department of Neurosurgery, Odense University Hospital, Odense, Denmark.,15Clinical Institute and BRIDGE, University of Southern Denmark, Odense, Denmark; and
| | - Thomas A Gerds
- 3Section of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | | | - David Scheie
- 2Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Tiit Mathiesen
- Departments of1Neurosurgery and.,17Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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12
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Gadot R, Khan AB, Patel R, Goethe E, Shetty A, Hadley CC, V JCB, Harmanci AS, Klisch TJ, Yoshor D, Sheth SA, Patel AJ. Predictors of postoperative seizure outcome in supratentorial meningioma. J Neurosurg 2022; 137:515-524. [PMID: 35099915 DOI: 10.3171/2021.9.jns211738] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/01/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Meningiomas are the most common primary intracranial tumor. Seizures are common sequelae of meningioma development. Meningioma patients with seizures can be effectively treated with resection, with reports of seizure freedom of 60%-90%. Still, many patients manifest persistent epilepsy. Determining factors associated with worsened seizure outcomes remains critical in improving the quality of life for these patients. The authors sought to identify clinical, radiological, and histological factors associated with worse seizure outcomes in patients with supratentorial meningioma and preoperative seizures. METHODS The authors retrospectively reviewed the charts of 384 patients who underwent meningioma resection from 2008 to 2020. The charts of patients with a documented history of preoperative seizures were further reviewed for clinical, radiological, operative, perioperative, histological, and postoperative factors associated with seizures. Engel class at last follow-up was retrospectively assigned by the authors and further grouped into favorable (class I) and worse (class II-IV) outcomes. Factors were subsequently compared by group using comparative statistics. Univariable and multivariable regression models were utilized to identify independent predictors of worse seizure outcome. RESULTS Fifty-nine patients (15.4%) were found to have preoperative seizures, of whom 57 had sufficient postoperative data to determine Engel class outcome. Forty-two patients (74%) had Engel class I outcomes. The median follow-up was 17 months. Distinct margins on preoperative imaging (p = 0.012), Simpson grade I resection (p = 0.004), postresection ischemia (p = 0.019), WHO grade (p = 0.019), and recurrent disease (p = 0.015) were found to be the strongest predictors of Engel class outcome in univariable logistic regression. MIB-1 index (p = 0.001) and residual volume (p = 0.014) at last follow-up were found to be the strongest predictors of Engel class outcome in univariable generalized linear regression. Postresection ischemia (p = 0.012), WHO grade (p = 0.022), recurrent disease (p = 0.038), and MIB-1 index (p = 0.002) were found to be the strongest independent predictors of Engel class outcomes in multivariable analysis. CONCLUSIONS Postresection ischemia, higher WHO grade, elevated MIB-1 index, and disease recurrence independently predict postresection seizure persistence in patients with supratentorial meningioma. Further understanding of the etiology of these markers may aid in elucidation of this complex disease process and guide management to prevent worse outcomes.
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Affiliation(s)
- Ron Gadot
- 1Department of Neurosurgery, Baylor College of Medicine, Houston
| | - A Basit Khan
- 1Department of Neurosurgery, Baylor College of Medicine, Houston
| | - Rajan Patel
- 1Department of Neurosurgery, Baylor College of Medicine, Houston
| | - Eric Goethe
- 1Department of Neurosurgery, Baylor College of Medicine, Houston
| | - Arya Shetty
- 1Department of Neurosurgery, Baylor College of Medicine, Houston
| | | | - James C Bayley V
- 1Department of Neurosurgery, Baylor College of Medicine, Houston
| | - Akdes S Harmanci
- 1Department of Neurosurgery, Baylor College of Medicine, Houston
| | - Tiemo J Klisch
- 2Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
| | - Daniel Yoshor
- 3Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania; and
| | - Sameer A Sheth
- 1Department of Neurosurgery, Baylor College of Medicine, Houston
| | - Akash J Patel
- 1Department of Neurosurgery, Baylor College of Medicine, Houston
- 2Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
- 4Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, Texas
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13
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Bayley JC, Hadley CC, Harmanci AO, Harmanci AS, Klisch TJ, Patel AJ. Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies. SCIENCE ADVANCES 2022; 8:eabm6247. [PMID: 35108039 DOI: 10.1126/sciadv.abm6247] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
One-fifth of meningiomas classified as benign by World Health Organization (WHO) histopathological grading will behave malignantly. To better diagnose these tumors, several groups turned to DNA methylation, whereas we combined RNA-sequencing (RNA-seq) and cytogenetics. Both approaches were more accurate than histopathology in identifying aggressive tumors, but whether they revealed similar tumor types was unclear. We therefore performed unbiased DNA methylation, RNA-seq, and cytogenetic profiling on 110 primary meningiomas WHO grade I and II). Each technique distinguished the same three groups (two benign and one malignant) as our previous molecular classification; integrating these methods into one classifier further improved accuracy. Computational modeling revealed strong correlations between transcription and cytogenetic changes, particularly loss of chromosome 1p, in malignant tumors. Applying our classifier to data from previous studies also resolved certain anomalies entailed by grouping tumors by WHO grade. Accurate classification will therefore elucidate meningioma biology as well as improve diagnosis and prognosis.
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Affiliation(s)
- James C Bayley
- Department of Neurosurgery, Baylor College of Medicine, Houston , TX 77030, USA
| | - Caroline C Hadley
- Department of Neurosurgery, Baylor College of Medicine, Houston , TX 77030, USA
| | - Arif O Harmanci
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center , Houston , TX 77030, USA
| | - Akdes S Harmanci
- Department of Neurosurgery, Baylor College of Medicine, Houston , TX 77030, USA
| | - Tiemo J Klisch
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston , TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Akash J Patel
- Department of Neurosurgery, Baylor College of Medicine, Houston , TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston , TX 77030, USA
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston , TX 77030, USA
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14
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Bim LV, Carneiro TNR, Buzatto VC, Colozza-Gama GA, Koyama FC, Thomaz DMD, de Jesus Paniza AC, Lee EA, Galante PAF, Cerutti JM. Molecular Signature Expands the Landscape of Driver Negative Thyroid Cancers. Cancers (Basel) 2021; 13:5184. [PMID: 34680332 PMCID: PMC8534197 DOI: 10.3390/cancers13205184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/12/2021] [Indexed: 12/04/2022] Open
Abstract
Thyroid cancer is the most common endocrine malignancy. However, the cytological diagnosis of follicular thyroid carcinoma (FTC), Hürthle cell carcinoma (HCC), and follicular variant of papillary thyroid carcinoma (FVPTC) and their benign counterparts is a challenge for preoperative diagnosis. Nearly 20-30% of biopsied thyroid nodules are classified as having indeterminate risk of malignancy and incur costs to the health care system. Based on that, 120 patients were screened for the main driver mutations previously described in thyroid cancer. Subsequently, 14 mutation-negative cases that are the main source of diagnostic errors (FTC, HCC, or FVPTC) underwent RNA-Sequencing analysis. Somatic variants in candidate driver genes (ECD, NUP98,LRP1B, NCOR1, ATM, SOS1, and SPOP) and fusions were described. NCOR1 and SPOP variants underwent validation. Moreover, expression profiling of driver-negative samples was compared to 16 BRAF V600E, RAS, or PAX8-PPARg positive samples. Negative samples were separated in two clusters, following the expression pattern of the RAS/PAX8-PPARg or BRAF V600E positive samples. Both negative groups showed distinct BRS, ERK, and TDS scores, tumor mutation burden, signaling pathways and immune cell profile. Altogether, here we report novel gene variants and describe cancer-related pathways that might impact preoperative diagnosis and provide insights into thyroid tumor biology.
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Affiliation(s)
- Larissa Valdemarin Bim
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
| | - Thaise Nayane Ribeiro Carneiro
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
| | - Vanessa Candiotti Buzatto
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Rua Professor Daher Cutait 69, Bela Vista, São Paulo 01308-060, SP, Brazil; (V.C.B.); (F.C.K.); (P.A.F.G.)
| | - Gabriel Avelar Colozza-Gama
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
| | - Fernanda C. Koyama
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Rua Professor Daher Cutait 69, Bela Vista, São Paulo 01308-060, SP, Brazil; (V.C.B.); (F.C.K.); (P.A.F.G.)
| | - Debora Mota Dias Thomaz
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
| | - Ana Carolina de Jesus Paniza
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115, USA;
| | - Pedro Alexandre Favoretto Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Rua Professor Daher Cutait 69, Bela Vista, São Paulo 01308-060, SP, Brazil; (V.C.B.); (F.C.K.); (P.A.F.G.)
| | - Janete Maria Cerutti
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
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15
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Maggio I, Franceschi E, Di Nunno V, Gatto L, Tosoni A, Angelini D, Bartolini S, Lodi R, Brandes AA. Discovering the Molecular Landscape of Meningioma: The Struggle to Find New Therapeutic Targets. Diagnostics (Basel) 2021; 11:1852. [PMID: 34679551 PMCID: PMC8534341 DOI: 10.3390/diagnostics11101852] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/27/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Meningiomas are the most common primary CNS tumors. They are usually benign but can present aggressive behavior in about 20% of cases. The genetic landscape of meningioma is characterized by the presence (in about 60% of cases) or absence of NF2 mutation. Low-grade meningiomas can also present other genetic alterations, particularly affecting SMO, TRAF7, KLF4 AKT1 and PI3KCA. In higher grade meningiomas, mutations of TERT promoter and deletion of CDKN2A/B seem to have a prognostic value. Furthermore, other genetic alterations have been identified, such as BAP1, DMD and PBRM1. Different subgroups of DNA methylation appear to be correlated with prognosis. In this review, we explored the genetic landscape of meningiomas and the possible therapeutic implications.
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Affiliation(s)
- Ilaria Maggio
- Medical Oncology Department, Azienda USL, Via Altura n. 3, 40139 Bologna, Italy; (I.M.); (V.D.N.); (L.G.)
| | - Enrico Franceschi
- Nervous System Medical Oncology Department, IRCSS Istituto di Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (A.T.); (D.A.); (S.B.); (A.A.B.)
| | - Vincenzo Di Nunno
- Medical Oncology Department, Azienda USL, Via Altura n. 3, 40139 Bologna, Italy; (I.M.); (V.D.N.); (L.G.)
- Nervous System Medical Oncology Department, IRCSS Istituto di Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (A.T.); (D.A.); (S.B.); (A.A.B.)
| | - Lidia Gatto
- Medical Oncology Department, Azienda USL, Via Altura n. 3, 40139 Bologna, Italy; (I.M.); (V.D.N.); (L.G.)
- Nervous System Medical Oncology Department, IRCSS Istituto di Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (A.T.); (D.A.); (S.B.); (A.A.B.)
| | - Alicia Tosoni
- Nervous System Medical Oncology Department, IRCSS Istituto di Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (A.T.); (D.A.); (S.B.); (A.A.B.)
| | - Daniele Angelini
- Nervous System Medical Oncology Department, IRCSS Istituto di Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (A.T.); (D.A.); (S.B.); (A.A.B.)
| | - Stefania Bartolini
- Nervous System Medical Oncology Department, IRCSS Istituto di Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (A.T.); (D.A.); (S.B.); (A.A.B.)
| | - Raffaele Lodi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; or
| | - Alba Ariela Brandes
- Nervous System Medical Oncology Department, IRCSS Istituto di Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (A.T.); (D.A.); (S.B.); (A.A.B.)
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16
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Ijare OB, Hambarde S, Brasil da Costa FH, Lopez S, Sharpe MA, Helekar SA, Hangel G, Bogner W, Widhalm G, Bachoo RM, Baskin DS, Pichumani K. Glutamine anaplerosis is required for amino acid biosynthesis in human meningiomas. Neuro Oncol 2021; 24:556-568. [PMID: 34515312 DOI: 10.1093/neuonc/noab219] [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: 11/13/2022] Open
Abstract
BACKGROUND We postulate that meningiomas undergo distinct metabolic reprogramming in tumorigenesis and unravelling their metabolic phenotypes provide new therapeutic insights. Glutamine catabolism is key to the growth and proliferation of tumors. Here, we investigated the metabolomics of freshly resected meningiomas and glutamine metabolism in patient-derived meningioma cells. METHODS 1H NMR spectroscopy of tumor tissues from 33 meningioma patients was used to differentiate the metabolite profiles of grade-I and grade-II meningiomas. Glutamine metabolism was examined using 13C/ 15N glutamine tracer, in five patient-derived meningioma cells. RESULTS Alanine, lactate, glutamate, glutamine, and glycine were predominantly elevated only in grade-II meningiomas by 74%, 76%, 35%, 75% and 33% respectively, with alanine, and glutamine being statistically significant (p ≤ 0.02). 13C/ 15N glutamine tracer experiments revealed that both grade-I and -II meningiomas actively metabolize glutamine to generate various key carbon intermediates including alanine and proline that are necessary for the tumor growth. Also, it is shown that glutaminase (GLS1) inhibitor, CB-839 is highly effective in downregulating glutamine metabolism and decreasing proliferation in meningioma cells. CONCLUSION Alanine and glutamine/glutamate are mainly elevated in grade-II meningiomas. Grade-I meningiomas possess relatively higher glutamine metabolism providing carbon/nitrogen for the biosynthesis of key nonessential amino acids. GLS1 inhibitor (CB-839) would be very effective in downregulating glutamine metabolic pathways in grade-I meningiomas leading to decreased cellular proliferation.
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Affiliation(s)
- Omkar B Ijare
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX, USA
| | - Shashank Hambarde
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX, USA
| | - Fabio Henrique Brasil da Costa
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX, USA
| | - Sophie Lopez
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX, USA
| | - Martyn A Sharpe
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX, USA
| | - Santosh A Helekar
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Gilbert Hangel
- High-field MR Center, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria.,Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Bogner
- High-field MR Center, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Georg Widhalm
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Robert M Bachoo
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, Dallas, TX, USA
| | - David S Baskin
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Kumar Pichumani
- Kenneth R. Peak Brain and Pituitary Tumor Treatment Center, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital and Research Institute, Houston, TX, USA.,Weill Cornell Medical College, New York, NY, USA
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17
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Abstract
PURPOSE OF REVIEW To discuss recent advances in the meningioma biology and their clinical implications. RECENT FINDINGS Meningioma is the most common primary intracranial tumor. Mostly benign, 20% of cases display an aggressive behavior despite best standard of care. The genetic landscape of meningiomas is divided according to NF2 mutational status. Although about 60% of meningiomas display NF2 mutations, the other share is more heterogenous. Mutations in TRAF7, SMO, v-akt murine thymoma viral oncogene homolog 1 (AKT1), PI3KCA and KLF4 are seen mostly in WHO grade 1 meningiomas. In higher grade meningiomas, mutations of the TERT promoter and deletions of CDKN2A/B emerge and have prognostic value. Moreover, mutations in DMD, BAP1 and PBRM1 have recently been discovered and are being further explored. DNA methylation subgroups offer valuable insight into meningioma prognosis and its implementation in clinical setting is under evaluation. Moreover, the study of distinct meningioma populations such as radiation-induced meningioma and progestin-associated meningioma may provide further insight into meningioma oncogenesis and potential therapeutic targets. SUMMARY The mutational landscape of meningioma has expanded following the use of the new genetic sequencing approaches. Novel mutations have been characterized and reveal their prognostic and therapeutic applications. This improved understanding of meningioma biology has promising implications for novel treatment strategies.
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18
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MPscore: A Novel Predictive and Prognostic Scoring for Progressive Meningioma. Cancers (Basel) 2021; 13:cancers13051113. [PMID: 33807688 PMCID: PMC7961759 DOI: 10.3390/cancers13051113] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Subtyping for meningioma is urgently required to stratify the patients with high risks of recurrence and progression due to the intertumoral heterogeneity in meningioma. Here, we performed a consensus clustering of 179 meningiomas and identified progressive subtype (subtype 3) based the transcriptome profiles. Loss of chromosome 1q along with Neurofibromin 2 (NF2) mutation or loss of chromosome 22p is exclusively presented in subtype 3 meningioma. DNA methylation analyses of meningioma subtypes also suggested hypermethylation was observed in subtype 3 meningioma. Our findings identified low expression of Alkaline Phosphatase (ALPL) is the most significant feature in progressive subtype of meningioma. We constructed and validated a meningioma progression score (MPscore) to characterize the progressive phenotype in meningioma. The predictive accuracy has also been validated in three independent cohorts. Therefore, MPscore can be potentially useful for meningioma recurrence prediction and stratification. Abstract Meningioma is the most common tumor in central nervous system (CNS). Although most cases of meningioma are benign (WHO grade I) and curable by surgical resection, a few tumors remain diagnostically and therapeutically challenging due to the frequent recurrence and progression. The heterogeneity of meningioma revealed by DNA methylation profiling suggests the demand of subtyping for meningioma. Therefore, we performed a clustering analyses to characterize the progressive features of meningioma and constructed a meningioma progression score to predict the risk of the recurrence. A total of 179 meningioma transcriptome from RNA sequencing was included for progression subtype clustering. Four biologically distinct subtypes (subtype 1, subtype 2, subtype 3 and subtype 4) were identified. Copy number alternation and genomewide DNA methylation of each subtype was also characterized. Immune cell infiltration was examined by the microenvironment cell populations counter. All anaplastic meningiomas (7/7) and most atypical meningiomas (24/32) are enriched in subtype 3 while no WHO II or III meningioma presents in subtype 1, suggesting subtype 3 meningioma is a progressive subtype. Stemness index and immune response are also heterogeneous across four subtypes. Monocytic lineage is the most immune cell type in all meningiomas, except for subtype 1. CD8 positive T cells are predominantly observed in subtype 3. To extend the clinical utility of progressive meningioma subtyping, we constructed the meningioma progression score (MPscore) by the signature genes in subtype 3. The predictive accuracy and prognostic capacity of MPscore has also been validated in three independent cohort. Our study uncovers four biologically distinct subtypes in meningioma and the MPscore is potentially helpful in the recurrence risk prediction and response to treatments stratification in meningioma.
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19
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Takei J, Tanaka T, Teshigawara A, Tochigi S, Hasegawa Y, Murayama Y. Alteration of FOXM1 expression and macrophage polarization in refractory meningiomas during long-term follow-up. Transl Cancer Res 2021; 10:553-566. [PMID: 35116285 PMCID: PMC8797451 DOI: 10.21037/tcr-20-1896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022]
Abstract
Malignant progression of grade I meningioma with a long latency period is rare. We experienced grade II/III meningiomas with refractoriness and recurrence from grade I meningiomas through multiple surgeries. Three patients with atypical/anaplastic meningioma experienced long-latent recurrence after initial surgery for grade I (meningothelial) meningioma without following adjuvant radiotherapy were included in the present study. Histological findings of the initial tumors in all cases (case 1, 2, and 3) revealed meningothelial meningioma with 1%, 5%, and 0.1% MIB-1 positive cells, respectively. Surprisingly, magnetic resonance imaging (MRI) detected a recurrent tumor 2, 12, and 12 years after the initial operation, respectively. Case 1 was atypical meningioma after third recurrence, and case 2 and 3 were anaplastic meningioma after second and third recurrence, respectively. The patient in case 2 received adjuvant radiotherapy. In case 2, the tumor recurred intracranial and distant metastasis to the lung with huge substantial pleural effusion was detected. To investigate the pathogenesis of malignant progression from benign to malignant meningioma, CD163/CD68 expression by immunohistochemically and FOXM1 mRNA expression by RT-PCR were compared using surgical specimens from initial and recurrent tumors in all three patients. The ratio of CD163/CD68 positivity and FOXM1 mRNA expression were increased in recurrent tumors compared with matched initial tumors. CD163 and FOXM1 expression levels were induced even in recurrent grade I meningioma, suggesting that macrophage polarization and pro-mitotic transcriptional factor might be associated with clinical behavior of meningioma and be useful as a prediction marker for malignant progression. Careful long-term follow-up is important for early diagnosis of malignant progression in meningiomas, even if grade I meningioma is completely resected. Development of a multidisciplinary approach including radiation and novel molecular targeted therapy is expected for recurrent and malignant meningiomas.
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Affiliation(s)
- Jun Takei
- Department of Neurosurgery, Jikei University School of Medicine Kashiwa Hospital, Chiba, Japan.,Department of Neurosurgery, Jikei University School of Medicine, Tokyo, Japan
| | - Toshihide Tanaka
- Department of Neurosurgery, Jikei University School of Medicine Kashiwa Hospital, Chiba, Japan
| | - Akihiko Teshigawara
- Department of Neurosurgery, Jikei University School of Medicine Kashiwa Hospital, Chiba, Japan
| | - Satoru Tochigi
- Department of Neurosurgery, Jikei University School of Medicine Kashiwa Hospital, Chiba, Japan
| | - Yuzuru Hasegawa
- Department of Neurosurgery, Jikei University School of Medicine Kashiwa Hospital, Chiba, Japan
| | - Yuichi Murayama
- Department of Neurosurgery, Jikei University School of Medicine, Tokyo, Japan
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20
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Dunn J, Lenis VP, Hilton DA, Warta R, Herold-Mende C, Hanemann CO, Futschik ME. Integration and Comparison of Transcriptomic and Proteomic Data for Meningioma. Cancers (Basel) 2020; 12:E3270. [PMID: 33167358 PMCID: PMC7694371 DOI: 10.3390/cancers12113270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/03/2020] [Indexed: 12/17/2022] Open
Abstract
Meningioma are the most frequent primary intracranial tumour. Management of aggressive meningioma is complex, and development of effective biomarkers or pharmacological interventions is hampered by an incomplete knowledge of molecular landscape. Here, we present an integrated analysis of two complementary omics studies to investigate alterations in the "transcriptome-proteome" profile of high-grade (III) compared to low-grade (I) meningiomas. We identified 3598 common transcripts/proteins and revealed concordant up- and downregulation in grade III vs. grade I meningiomas. Concordantly upregulated genes included FABP7, a fatty acid binding protein and the monoamine oxidase MAOB, the latter of which we validated at the protein level and established an association with Food and Drug Administration (FDA)-approved drugs. Notably, we derived a plasma signature of 21 discordantly expressed genes showing positive changes in protein but negative in transcript levels of high-grade meningiomas, including the validated genes CST3, LAMP2, PACS1 and HTRA1, suggesting the acquisition of these proteins by tumour from plasma. Aggressive meningiomas were enriched in processes such as oxidative phosphorylation and RNA metabolism, whilst concordantly downregulated genes were related to reduced cellular adhesion. Overall, our study provides the first transcriptome-proteome characterisation of meningioma, identifying several novel and previously described transcripts/proteins with potential grade III biomarker and therapeutic significance.
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Affiliation(s)
- Jemma Dunn
- Faculty of Health: Medicine, Dentistry and Human Sciences, The Institute of Translational and Stratified Medicine, University of Plymouth, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK;
| | - Vasileios P. Lenis
- School of Health & Life Sciences, Centuria Building, Teesside University, Middlesbrough, Tees Valley TS1 3BX, UK;
| | - David A. Hilton
- Cellular and Anatomical Pathology, Plymouth Hospitals NHS Trust, Derriford Road, Plymouth PL6 8BU, UK;
| | - Rolf Warta
- Department of Neurosurgery, Division of Experimental Neurosurgery, Heidelberg University Hospital, 69120 Heidelberg, Germany; (R.W.); (C.H.-M.)
| | - Christel Herold-Mende
- Department of Neurosurgery, Division of Experimental Neurosurgery, Heidelberg University Hospital, 69120 Heidelberg, Germany; (R.W.); (C.H.-M.)
| | - C. Oliver Hanemann
- Faculty of Health: Medicine, Dentistry and Human Sciences, The Institute of Translational and Stratified Medicine, University of Plymouth, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK;
| | - Matthias E. Futschik
- Faculty of Medicine, School of Public Health, Imperial College London, Medical School, St Mary’s Hospital, Praed Street, London W2 1NY, UK
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21
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Liu J, Xia C, Wang G. Multi-Omics Analysis in Initiation and Progression of Meningiomas: From Pathogenesis to Diagnosis. Front Oncol 2020; 10:1491. [PMID: 32983987 PMCID: PMC7484374 DOI: 10.3389/fonc.2020.01491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/13/2020] [Indexed: 12/31/2022] Open
Abstract
Meningiomas are common intracranial tumors that can be cured by surgical resection in most cases. However, the most disconcerting is high-grade meningiomas, which frequently recur despite initial successful treatment, eventually conferring poor prognosis. Therefore, the early diagnosis and classification of meningioma is necessary for the subsequent intervention and an improved prognosis. A growing body of evidence demonstrates the potential of multi-omics study (including genomics, transcriptomics, epigenomics, proteomics) for meningioma diagnosis and mechanistic links to potential pathological mechanism. This thesis addresses a neglected aspect of recent advances in the field of meningiomas at multiple omics levels, highlighting that the integration of multi-omics can reveal the mechanism of meningiomas, which provides a timely and necessary scientific basis for the treatment of meningiomas.
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Affiliation(s)
- Jiachen Liu
- Clinical Medicine, Xiangya Medical College of Central South University, Changsha, China
| | - Congcong Xia
- Clinical Medicine, Xiangya Medical College of Central South University, Changsha, China
| | - Gaiqing Wang
- Department of Neurology, Sanya Central Hospital (The Third People's Hospital of Hainan Province), Sanya, China
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22
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Zhang H, Mo J, Jiang H, Li Z, Hu W, Zhang C, Wang Y, Wang X, Liu C, Zhao B, Zhang J, Zhang K. Deep Learning Model for the Automated Detection and Histopathological Prediction of Meningioma. Neuroinformatics 2020; 19:393-402. [PMID: 32974873 DOI: 10.1007/s12021-020-09492-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 01/12/2023]
Abstract
The volumetric assessment and accurate grading of meningiomas before surgery are highly relevant for therapy planning and prognosis prediction. This study was to design a deep learning algorithm and evaluate the performance in detecting meningioma lesions and grade classification. In total, 5088 patients with histopathologically confirmed meningioma were retrospectively included. The pyramid scene parsing network (PSPNet) was trained to automatically detect and delineate the meningiomas. The results were compared to manual segmentations by evaluating the mean intersection over union (mIoU). The performance of grade classification was evaluated by accuracy. For the automated detection and segmentation of meningiomas, the mean pixel accuracy, tumor accuracy, background accuracy and mIoU were 99.68%, 81.36%, 99.88% and 81.36% for all patients; 99.52%, 84.86%, 99.93% and 84.86% for grade I meningiomas; 99.57%, 80.11%, 99.92% and 80.12% for grade II meningiomas; and 99.75%, 78.40%, 99.99% and 78.40% for grade III meningiomas, respectively. For grade classification, the accuracy values of the training and test datasets were 99.93% and 81.52% for all patients; 99.98% and 98.51% for grade I meningiomas; 99.91% and 66.67% for grade II meningiomas; and 99.88% and 73.91% for grade III meningiomas, respectively. The automated detection, segmentation and grade classification of meningiomas based on deep learning were accurate and reliable and may improve the monitoring and treatment of this frequently occurring tumor entity. Furthermore, the method could function as a useful tool for preassessment and preselection for radiologists, offering auxiliary information for clinical decision making in presurgical evaluation.
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Affiliation(s)
- Hua Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jiajie Mo
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Han Jiang
- OpenBayes Joint Laboratory For Artificial Intelligence, Tianjin University, Tianjin, China
| | - Zhuyun Li
- OpenBayes Joint Laboratory For Artificial Intelligence, Tianjin University, Tianjin, China.,Graduate School of IPS, Waseda University, Fukuoka, Japan
| | - Wenhan Hu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Chao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yao Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Xiu Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Chang Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Baotian Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jianguo Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China. .,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China. .,China National Clinical Research Center for Neurological Diseases, Beijing, China.
| | - Kai Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China. .,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China. .,China National Clinical Research Center for Neurological Diseases, Beijing, China.
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23
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Multiplatform genomic profiling and magnetic resonance imaging identify mechanisms underlying intratumor heterogeneity in meningioma. Nat Commun 2020; 11:4803. [PMID: 32968068 PMCID: PMC7511976 DOI: 10.1038/s41467-020-18582-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 09/02/2020] [Indexed: 12/13/2022] Open
Abstract
Meningiomas are the most common primary intracranial tumors, but the molecular drivers of meningioma tumorigenesis are poorly understood. We hypothesized that investigating intratumor heterogeneity in meningiomas would elucidate biologic drivers and reveal new targets for molecular therapy. To test this hypothesis, here we perform multiplatform molecular profiling of 86 spatially-distinct samples from 13 human meningiomas. Our data reveal that regional alterations in chromosome structure underlie clonal transcriptomic, epigenomic, and histopathologic signatures in meningioma. Stereotactic co-registration of sample coordinates to preoperative magnetic resonance images further suggest that high apparent diffusion coefficient (ADC) distinguishes meningioma regions with proliferating cells enriched for developmental gene expression programs. To understand the function of these genes in meningioma, we develop a human cerebral organoid model of meningioma and validate the high ADC marker genes CDH2 and PTPRZ1 as potential targets for meningioma therapy using live imaging, single cell RNA sequencing, CRISPR interference, and pharmacology.
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24
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Khan AB, Gadot R, Shetty A, Bayley JC, Hadley CC, Cardenas MF, Jalali A, Harmanci AS, Harmanci AO, Wheeler DA, Klisch TJ, Patel AJ. Identification of novel fusion transcripts in meningioma. J Neurooncol 2020; 149:219-230. [PMID: 32949309 DOI: 10.1007/s11060-020-03599-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/08/2020] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Meningiomas are the most common primary intracranial tumor. Recent next generation sequencing analyses have elaborated the molecular drivers of this disease. We aimed to identify and characterize novel fusion genes in meningiomas. METHODS We performed a secondary analysis of our RNA sequencing data of 145 primary meningioma from 140 patients to detect fusion genes. Semi-quantitative rt-PCR was performed to confirm transcription of the fusion genes in the original tumors. Whole exome sequencing was performed to identify copy number variations within each tumor sample. Comparative RNA seq analysis was performed to assess the clonality of the fusion constructs within the tumor. RESULTS We detected six fusion events (NOTCH3-SETBP1, NF2-SPATA13, SLC6A3-AGBL3, PHF19-FOXP2 in two patients, and ITPK1-FBP2) in five out of 145 tumor samples. All but one event (NF2-SPATA13) led to extremely short reading frames, making these events de facto null alleles. Three of the five patients had a history of childhood radiation. Four out of six fusion events were detected in expression type C tumors, which represent the most aggressive meningioma. We validated the presence of the RNA transcripts in the tumor tissue by semi-quantitative RT PCR. All but the two PHF19-FOXP2 fusions demonstrated high degrees of clonality. CONCLUSIONS Fusion genes occur infrequently in meningiomas and are more likely to be found in tumors with greater degree of genomic instability (expression type C) or in patients with history of cranial irradiation.
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Affiliation(s)
- A Basit Khan
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - Ron Gadot
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - Arya Shetty
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - James C Bayley
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - Caroline C Hadley
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - Maria F Cardenas
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ali Jalali
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA
| | - Akdes S Harmanci
- School of Biomedical Informatics, Center for Computational Systems Medicine, University of Texas Health Science Center At Houston, Houston, TX, 77030, USA
| | - Arif O Harmanci
- School of Biomedical Informatics, Center for Computational Systems Medicine, University of Texas Health Science Center At Houston, Houston, TX, 77030, USA
| | - David A Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tiemo J Klisch
- Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Akash J Patel
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA.
- Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA.
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA.
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25
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Ma J, Hong Y, Chen W, Li D, Tian K, Wang K, Yang Y, Zhang Y, Chen Y, Song L, Chen L, Zhang L, Du J, Zhang J, Wu Z, Zhang D, Wang L. High Copy-Number Variation Burdens in Cranial Meningiomas From Patients With Diverse Clinical Phenotypes Characterized by Hot Genomic Structure Changes. Front Oncol 2020; 10:1382. [PMID: 32923390 PMCID: PMC7457130 DOI: 10.3389/fonc.2020.01382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022] Open
Abstract
Meningiomas, as the most common primary tumor of the central nervous system, are known to harbor genomic aberrations that associate with clinical phenotypes. Here we performed genome-wide genotyping for cranial meningiomas in 383 Chinese patients and identified 9,821 copy-number variations (CNVs). Particularly, patients with diverse clinical features had distinct tumor CNV profiles. CNV burdens were greater in high-grade (WHO grade II and III) samples, recurrent lesions, large tumors (diameter >4.3 cm), and those collected from male patients. Nevertheless, the level of CNV burden did not relate to tumor locations, peritumoral brain edema, bone invasion, or multiple lesions. Overall, the most common tumor CNVs were the copy-number gain (CNG) at 22q11.1 and the copy-number losses (CNLs) at 22q13.2, 14q11.2, 1p34.3, and 1p31.3. Recurrent lesions were featured by the CNLs at 1p31.3, 6q22.31, 9p21.3, and 11p12, and high-grade samples had more CNVs at 4q13.3 and 6q22.31. Meanwhile, large tumors were more likely to have the CNVs at 1p31.3 and 1p34.3. Additionally, recurrence prediction indicated the CNLs at 4p16.3 (p = 0.009, hazard ratio = 5.69) and 10p11.22 (p = 0.037, hazard ratio = 4.53) were candidate independent risk factors.
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Affiliation(s)
- Junpeng Ma
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yaqiang Hong
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wei Chen
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Da Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Kaibing Tian
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ke Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yang Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuan Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yujia Chen
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lairong Song
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Liangpeng Chen
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Liwei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China.,Beijing Key Laboratory of Brain Tumor, Beijing, China
| | - Jiang Du
- Department of Neuropathology, Beijing Neurological Institute, Capital Medical University, Beijing, China
| | - Junting Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China.,Beijing Key Laboratory of Brain Tumor, Beijing, China
| | - Zhen Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China.,Beijing Key Laboratory of Brain Tumor, Beijing, China
| | - Dake Zhang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Liang Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
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26
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Helgager J, Driver J, Hoffman S, Bi WL. Molecular Advances in Central Nervous System Mesenchymal Tumors. Surg Pathol Clin 2020; 13:291-303. [PMID: 32389268 DOI: 10.1016/j.path.2020.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mesenchymal tumors of the central nervous system (CNS) comprise an array of neoplasms that may arise from or secondarily affect the CNS and its immediate surroundings. This review focuses on meningiomas and solitary fibrous tumors, the most common primary CNS mesenchymal tumors, and discusses recent advances in unveiling the molecular landscapes of these neoplasms. An effort is made to underscore those molecular findings most relevant to tumor diagnostics and prognostication from a practical perspective. As molecular techniques become more readily used at the clinical level, such alterations may strengthen formal grading schemes and lend themselves to treatment with targeted therapies.
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Affiliation(s)
- Jeffrey Helgager
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph Driver
- Center for Skull Base and Pituitary Surgery, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Samantha Hoffman
- Center for Skull Base and Pituitary Surgery, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wenya Linda Bi
- Center for Skull Base and Pituitary Surgery, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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27
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Adams CL, Ercolano E, Ferluga S, Sofela A, Dave F, Negroni C, Kurian KM, Hilton DA, Hanemann CO. A Rapid Robust Method for Subgrouping Non-NF2 Meningiomas According to Genotype and Detection of Lower Levels of M2 Macrophages in AKT1 E17K Mutated Tumours. Int J Mol Sci 2020; 21:E1273. [PMID: 32070062 PMCID: PMC7073007 DOI: 10.3390/ijms21041273] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 12/19/2022] Open
Abstract
The majority of meningiomas are grade I, but some grade I tumours are clinically more aggressive. Recent advances in the genetic study of meningiomas has allowed investigation into the influence of genetics on the tumour microenvironment, which is important for tumorigenesis. We have established that the endpoint genotyping method Kompetitive Allele Specific PCR (KASP™) is a fast, reliable method for the screening of meningioma samples into different non-NF2 mutational groups using a standard real-time PCR instrument. This genotyping method and four-colour flow cytometry has enabled us to assess the variability in the largest immune cell infiltrate population, M2 macrophages (CD45+HLA-DR+CD14+CD163+) in 42 meningioma samples, and to suggest that underlying genetics is relevant. Further immunohistochemistry analysis comparing AKT1 E17K mutants to WHO grade I NF2-negative samples showed significantly lower levels of CD163-positive activated M2 macrophages in meningiomas with mutated AKT1 E17K, signifying a more immunosuppressive tumour microenvironment in NF2 meningiomas. Our data suggested that underlying tumour genetics play a part in the development of the immune composition of the tumour microenvironment. Stratifying meningiomas by mutational status and correlating this with their cellular composition will aid in the development of new immunotherapies for patients.
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Affiliation(s)
- Claire L. Adams
- Faculty of Health: Medicine, Dentistry and Human Sciences, The Institute of Translational and Stratified Medicine, University of Plymouth, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK (C.N.)
| | - Emanuela Ercolano
- Faculty of Health: Medicine, Dentistry and Human Sciences, The Institute of Translational and Stratified Medicine, University of Plymouth, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK (C.N.)
| | - Sara Ferluga
- Faculty of Health: Medicine, Dentistry and Human Sciences, The Institute of Translational and Stratified Medicine, University of Plymouth, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK (C.N.)
| | - Agbolahan Sofela
- Faculty of Health: Medicine, Dentistry and Human Sciences, The Institute of Translational and Stratified Medicine, University of Plymouth, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK (C.N.)
- Department of Neurosurgery, University Hospitals Plymouth NHS Trust, Derriford Road, Plymouth PL6 8DH, UK
| | - Foram Dave
- Faculty of Health: Medicine, Dentistry and Human Sciences, The Institute of Translational and Stratified Medicine, University of Plymouth, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK (C.N.)
| | - Caterina Negroni
- Faculty of Health: Medicine, Dentistry and Human Sciences, The Institute of Translational and Stratified Medicine, University of Plymouth, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK (C.N.)
| | - Kathreena M. Kurian
- Institute of Clinical Neuroscience, University of Bristol and Southmead Hospital, North Bristol Trust, Bristol BS8 1QU, UK
| | - David A. Hilton
- Cellular and Anatomical Pathology, University Hospitals Plymouth NHS Trust, Derriford Road, Plymouth PL6 8DH, UK
| | - C. Oliver Hanemann
- Faculty of Health: Medicine, Dentistry and Human Sciences, The Institute of Translational and Stratified Medicine, University of Plymouth, The John Bull Building, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK (C.N.)
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