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Hoang DT, Shulman ED, Turakulov R, Abdullaev Z, Singh O, Campagnolo EM, Lalchungnunga H, Stone EA, Nasrallah MP, Ruppin E, Aldape K. Prediction of DNA methylation-based tumor types from histopathology in central nervous system tumors with deep learning. Nat Med 2024:10.1038/s41591-024-02995-8. [PMID: 38760587 DOI: 10.1038/s41591-024-02995-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 04/11/2024] [Indexed: 05/19/2024]
Abstract
Precision in the diagnosis of diverse central nervous system (CNS) tumor types is crucial for optimal treatment. DNA methylation profiles, which capture the methylation status of thousands of individual CpG sites, are state-of-the-art data-driven means to enhance diagnostic accuracy but are also time consuming and not widely available. Here, to address these limitations, we developed Deep lEarning from histoPathoLOgy and methYlation (DEPLOY), a deep learning model that classifies CNS tumors to ten major categories from histopathology. DEPLOY integrates three distinct components: the first classifies CNS tumors directly from slide images ('direct model'), the second initially generates predictions for DNA methylation beta values, which are subsequently used for tumor classification ('indirect model'), and the third classifies tumor types directly from routinely available patient demographics. First, we find that DEPLOY accurately predicts beta values from histopathology images. Second, using a ten-class model trained on an internal dataset of 1,796 patients, we predict the tumor categories in three independent external test datasets including 2,156 patients, achieving an overall accuracy of 95% and balanced accuracy of 91% on samples that are predicted with high confidence. These results showcase the potential future use of DEPLOY to assist pathologists in diagnosing CNS tumors within a clinically relevant short time frame.
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Affiliation(s)
- Danh-Tai Hoang
- Biological Data Science Institute, College of Science, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eldad D Shulman
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Rust Turakulov
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Omkar Singh
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Emma M Campagnolo
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - H Lalchungnunga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Eric A Stone
- Biological Data Science Institute, College of Science, Australian National University, Canberra, Australian Capital Territory, Australia
| | - MacLean P Nasrallah
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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2
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Rogers JL, Wall T, Acquaye-Mallory AA, Boris L, Kim Y, Aldape K, Quezado MM, Butman JA, Smirniotopoulos JG, Chaudhry H, Tsien CI, Chittiboina P, Zaghloul K, Aboud O, Avgeropoulos NG, Burton EC, Cachia DM, Dixit KS, Drappatz J, Dunbar EM, Forsyth P, Komlodi-Pasztor E, Mandel J, Ozer BH, Lee EQ, Ranjan S, Lukas RV, Raygada M, Salacz ME, Smith-Cohn MA, Snyder J, Soldatos A, Theeler BJ, Widemann BC, Camphausen KA, Heiss JD, Armstrong TS, Gilbert MR, Penas-Prado M. Virtual multi-institutional tumor board: a strategy for personalized diagnoses and management of rare CNS tumors. J Neurooncol 2024; 167:349-359. [PMID: 38427131 PMCID: PMC11023967 DOI: 10.1007/s11060-024-04613-6] [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: 12/29/2023] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
PURPOSE Multidisciplinary tumor boards (MTBs) integrate clinical, molecular, and radiological information and facilitate coordination of neuro-oncology care. During the COVID-19 pandemic, our MTB transitioned to a virtual and multi-institutional format. We hypothesized that this expansion would allow expert review of challenging neuro-oncology cases and contribute to the care of patients with limited access to specialized centers. METHODS We retrospectively reviewed records from virtual MTBs held between 04/2020-03/2021. Data collected included measures of potential clinical impact, including referrals to observational or therapeutic studies, referrals for specialized neuropathology analysis, and whether molecular findings led to a change in diagnosis and/or guided management suggestions. RESULTS During 25 meetings, 32 presenters discussed 44 cases. Approximately half (n = 20; 48%) involved a rare central nervous system (CNS) tumor. In 21% (n = 9) the diagnosis was changed or refined based on molecular profiling obtained at the NIH and in 36% (n = 15) molecular findings guided management. Clinical trial suggestions were offered to 31% (n = 13), enrollment in the observational NCI Natural History Study to 21% (n = 9), neuropathology review and molecular testing at the NIH to 17% (n = 7), and all received management suggestions. CONCLUSION Virtual multi-institutional MTBs enable remote expert review of CNS tumors. We propose them as a strategy to facilitate expert opinions from specialized centers, especially for rare CNS tumors, helping mitigate geographic barriers to patient care and serving as a pre-screening tool for studies. Advanced molecular testing is key to obtaining a precise diagnosis, discovering potentially actionable targets, and guiding management.
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Affiliation(s)
- James L Rogers
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Thomas Wall
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Alvina A Acquaye-Mallory
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Lisa Boris
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Yeonju Kim
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
- Wayne State University School of Medicine, 540 E Canfield St, Detroit, MI, 48201, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Martha M Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - John A Butman
- Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - James G Smirniotopoulos
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Huma Chaudhry
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Christina I Tsien
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
- Proton Therapy Center, Sibley Memorial Hospital, Johns Hopkins Medicine, 5255 Loughboro Rd NW, Washington, DC, 20016, USA
| | - Prashant Chittiboina
- Surgical Neurology Branch,, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Kareem Zaghloul
- Surgical Neurology Branch,, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Orwa Aboud
- Department of Neurology and Neurological Surgery, UC Davis Comprehensive Cancer Center, 4860 Y Street, Sacramento, CA, 95817, USA
| | - Nicholas G Avgeropoulos
- Brain and Spine Tumor Program, Orlando Health Cancer Institute, 1400 S. Orange Ave, Orlando, FL, 32806, USA
- Global Medical Affairs, Novocure GmbH, D4 Pk. 6, 6039, Root, Switzerland
| | - Eric C Burton
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - David M Cachia
- Department of Hematology/Oncology, University of Massachusetts, 55 Lake Ave, Worcester, MA, 01655, USA
| | - Karan S Dixit
- Lou and Jean Malnati Brain Tumor Institute, Northwestern University Feinberg School of Medicine, 675 N St Clair St, Chicago, IL, 60611, USA
| | - Jan Drappatz
- Department of Neurology, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Erin M Dunbar
- Piedmont Brain Tumor Center, Piedmont Atlanta Hospital, Atlanta, GA, 2001 Peachtree St30309, USA
| | - Peter Forsyth
- Department of Neuro-Oncology, Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA
| | - Edina Komlodi-Pasztor
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
- Department of Neurology, MedStar Georgetown University Hospital, 3800 Reservoir Road Washington, Washington DC, 20007, USA
| | - Jacob Mandel
- Department of Neurology, Baylor College of Medicine, 7200 Cambridge St, Houston, TX, 77030, USA
| | - Byram H Ozer
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Eudocia Q Lee
- Center for Neuro-Oncology, Dana Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Surabhi Ranjan
- Department of Neurology, Cleveland Clinic Florida, Weston Hospital, 2950 Cleveland Clinic Boulevard, Weston, FL, 33331, US
| | - Rimas V Lukas
- Lou and Jean Malnati Brain Tumor Institute, Northwestern University Feinberg School of Medicine, 675 N St Clair St, Chicago, IL, 60611, USA
| | - Margarita Raygada
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 1 Center Dr, Bethesda, MD, 20892, USA
| | - Michael E Salacz
- Department of Hematology and Medical Oncology, MD Anderson Cancer Center at Cooper, Cooper University Health Care, Two Cooper Plaza, Camden, NJ, 08103, USA
| | - Matthew A Smith-Cohn
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
- Benefis Sletten Cancer Institute, 1117 29Th St. S, Great Falls, MT, 59405, USA
| | - James Snyder
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, 2800 W Grand Blvd, Detroit, MI, 48202, USA
| | - Ariane Soldatos
- National Institute of Neurological Disorders and Stroke,, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Brett J Theeler
- School of Medicine, Uniformed Services University, 4301 Jones Bridge Rd, Bethesda, MD, 20814, USA
| | - Brigitte C Widemann
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Kevin A Camphausen
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - John D Heiss
- Surgical Neurology Branch,, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Terri S Armstrong
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Marta Penas-Prado
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA.
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Andreiuolo F, Ferrone CK, Rajan S, Perry A, Guney E, Cham E, Giannini C, Toland A, Willard N, de Souza AS, Dazelle K, Chung HJ, Singh O, Conway K, Coley N, Dampier C, Abdullaev Z, Pratt D, Cimino PJ, Quezado M, Aldape K. Molecular and clinicopathologic characteristics of CNS embryonal tumors with BRD4::LEUTX fusion. Acta Neuropathol Commun 2024; 12:42. [PMID: 38500181 PMCID: PMC10946093 DOI: 10.1186/s40478-024-01746-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Central nervous system (CNS) embryonal tumors are a heterogeneous group of high-grade malignancies, and the increasing clinical use of methylation profiling and next-generation sequencing has led to the identification of molecularly distinct subtypes. One proposed tumor type, CNS tumor with BRD4::LEUTX fusion, has been described. As only a few CNS tumors with BRD4::LEUTX fusions have been described, we herein characterize a cohort of 9 such cases (4 new, 5 previously published) to further describe their clinicopathologic and molecular features. We demonstrate that CNS embryonal tumor with BRD4::LEUTX fusion comprises a well-defined methylation class/cluster. We find that patients are young (4 years or younger), with large tumors at variable locations, and frequently with evidence of leptomeningeal/cerebrospinal fluid (CSF) dissemination. Histologically, tumors were highly cellular with high-grade embryonal features. Immunohistochemically, 5/5 cases showed synaptophysin and 4/5 showed OLIG2 expression, thus overlapping with CNS neuroblastoma, FOXR2-activated. DNA copy number profiles were generally flat; however, two tumors had chromosome 1q gains. No recurring genomic changes, besides the presence of the fusion, were found. The LEUTX portion of the fusion transcript was constant in all cases assessed, while the BRD4 portion varied but included a domain with proto-oncogenic activity in all cases. Two patients with clinical follow up available had tumors with excellent response to chemotherapy. Two of our patients were alive without evidence of recurrence or progression after gross total resection and chemotherapy at 16 and 33 months. One patient relapsed, and the last of our four patients died of disease one month after diagnosis. Overall, this case series provides additional evidence for this as a distinct tumor type defined by the presence of a specific fusion as well as a distinct DNA methylation signature. Studies on larger series are required to further characterize these tumors.
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Affiliation(s)
- Felipe Andreiuolo
- Department of Pathology, Rede D'Or, Rio de Janeiro, RJ, Brazil
- D'Or Institute for Research and Education, Rio de Janeiro, RJ, Brazil
- Department of Pathology, Instituto Estadual Do Cérebro Paulo Niemeyer, Rio de Janeiro, RJ, Brazil
| | - Christina K Ferrone
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Sharika Rajan
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Arie Perry
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Ekin Guney
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Elaine Cham
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angus Toland
- Department of Pathology, University of Colorado Hospital, Aurora, CO, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Hospital, Aurora, CO, USA
| | | | - Karen Dazelle
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Hye-Jung Chung
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Omkar Singh
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Kyle Conway
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas Coley
- Diagnostic Pathology Medical Group, Inc., Sacramento, CA, USA
| | - Christopher Dampier
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Patrick J Cimino
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA.
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4
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Walsh JR, Sun G, Balan J, Hardcastle J, Vollenweider J, Jerde C, Rumilla K, Koellner C, Koleilat A, Hasadsri L, Kipp B, Jenkinson G, Klee E. A supervised learning method for classifying methylation disorders. BMC Bioinformatics 2024; 25:66. [PMID: 38347515 PMCID: PMC10863277 DOI: 10.1186/s12859-024-05673-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND DNA methylation is one of the most stable and well-characterized epigenetic alterations in humans. Accordingly, it has already found clinical utility as a molecular biomarker in a variety of disease contexts. Existing methods for clinical diagnosis of methylation-related disorders focus on outlier detection in a small number of CpG sites using standardized cutoffs which differentiate healthy from abnormal methylation levels. The standardized cutoff values used in these methods do not take into account methylation patterns which are known to differ between the sexes and with age. RESULTS Here we profile genome-wide DNA methylation from blood samples drawn from within a cohort composed of healthy controls of different age and sex alongside patients with Prader-Willi syndrome (PWS), Beckwith-Wiedemann syndrome, Fragile-X syndrome, Angelman syndrome, and Silver-Russell syndrome. We propose a Generalized Additive Model to perform age and sex adjusted outlier analysis of around 700,000 CpG sites throughout the human genome. Utilizing z-scores among the cohort for each site, we deployed an ensemble based machine learning pipeline and achieved a combined prediction accuracy of 0.96 (Binomial 95% Confidence Interval 0.868[Formula: see text]0.995). CONCLUSION We demonstrate a method for age and sex adjusted outlier detection of differentially methylated loci based on a large cohort of healthy individuals. We present a custom machine learning pipeline utilizing this outlier analysis to classify samples for potential methylation associated congenital disorders. These methods are able to achieve high accuracy when used with machine learning methods to classify abnormal methylation patterns.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Alaa Koleilat
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
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5
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Satomi K, Ichimura K, Shibahara J. Decoding the DNA methylome of central nervous system tumors: An emerging modality for integrated diagnosis. Pathol Int 2024; 74:51-67. [PMID: 38224248 DOI: 10.1111/pin.13402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024]
Abstract
The definitive diagnosis and classification of individual cancers are crucial for patient care and cancer research. To achieve a robust diagnosis of central nervous system (CNS) tumors, a genotype-phenotype integrated diagnostic approach was introduced in recent versions of the World Health Organization classification, followed by the incorporation of a genome-wide DNA methylome-based classification. Microarray-based platforms are widely used to obtain DNA methylome data, and the German Cancer Research Center (Deutsches Krebsforschungszentrum [DKFZ]) has a webtool for a DNA methylation-based classifier (DKFZ classifier). Integration of DNA methylome will further enhance the precision of CNS tumor classification, especially in diagnostically challenging cases. However, in the clinical application of DNA methylome-based classification, challenges related to data interpretation persist, in addition to technical caveats, regulations, and limited accessibility. Dimensionality reduction (DMR) can complement integrated diagnosis by visualizing a profile and comparing it with other known samples. Therefore, DNA methylome-based classification is a highly useful research tool for auxiliary analysis in challenging diagnostic and rare disease cases, and for establishing novel tumor concepts. Decoding the DNA methylome, especially by DMR in addition to DKFZ classifier, emphasizes the capability of grasping the fundamental biological principles that provide new perspectives on CNS tumors.
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Affiliation(s)
- Kaishi Satomi
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
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6
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Mackinnon AC, Chandrashekar DS, Suster DI. Molecular pathology as basis for timely cancer diagnosis and therapy. Virchows Arch 2024; 484:155-168. [PMID: 38012424 DOI: 10.1007/s00428-023-03707-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/16/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023]
Abstract
Precision and personalized therapeutics have witnessed significant advancements in technology, revolutionizing the capabilities of laboratories to generate vast amounts of genetic data. Coupled with computational resources for analysis and interpretation, and integrated with various other types of data, including genomic data, electronic medical health (EMH) data, and clinical knowledge, these advancements support optimized health decisions. Among these technologies, next-generation sequencing (NGS) stands out as a transformative tool in the field of cancer treatment, playing a crucial role in precision oncology. NGS-based workflows are employed across a range of applications, including gene panels, exome sequencing, and whole-genome sequencing, supporting comprehensive analysis of the entire cancer genome, including mutations, copy number variations, gene expression profiles, and epigenetic modifications. By utilizing the power of NGS, these workflows contribute to enhancing our understanding of disease mechanisms, diagnosis confirmation, identifying therapeutic targets, and guiding personalized treatment decisions. This manuscript explores the diverse applications of NGS in cancer treatment, highlighting its significance in guiding diagnosis and treatment decisions, identifying therapeutic targets, monitoring disease progression, and improving patient outcomes.
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Affiliation(s)
- A Craig Mackinnon
- Department of Pathology, University of Alabama at Birmingham, 619 19Th Street South, Birmingham, AL, 35249, USA.
| | | | - David I Suster
- Department of Pathology, Rutgers University New Jersey Medical School, 150 Bergen Street, Newark, NJ, 07103, USA.
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7
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Singh J, Sahu S, Mohan T, Mahajan S, Sharma MC, Sarkar C, Suri V. Current status of DNA methylation profiling in neuro-oncology as a diagnostic support tool: A review. Neurooncol Pract 2023; 10:518-526. [PMID: 38009119 PMCID: PMC10666812 DOI: 10.1093/nop/npad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023] Open
Abstract
Over the last 2 decades, high throughput genome-wide molecular profiling has revealed characteristic genetic and epigenetic alterations associated with different types of central nervous system (CNS) tumors. DNA methylation profiling has emerged as an important molecular platform for CNS tumor classification with improved diagnostic accuracy and patient risk stratification in comparison to the standard of care histopathological analysis and any single molecular tests. The emergence of DNA methylation arrays have also played a crucial role in refining existing types and the discovery of new tumor types or subtypes. The adoption of methylation data into neuro-oncology has been greatly aided by the development of a freely accessible machine learning-based classifier. In this review, we discuss methylation workflow, address the utility of DNA methylation profiling in CNS tumors in a routine diagnostic setting, and provide an overview of the methylation-based tumor types and new types or subtypes identified with this platform.
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Affiliation(s)
- Jyotsna Singh
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Saumya Sahu
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Trishala Mohan
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Swati Mahajan
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Mehar C Sharma
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Vaishali Suri
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
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8
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Yoda RA, Cimino PJ. Classification and Grading of Central Nervous System Tumors According to the World Health Organization 5th Edition. Semin Neurol 2023; 43:833-844. [PMID: 37949117 DOI: 10.1055/s-0043-1776793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The World Health Organization (WHO) released the 5th edition of its classification of central nervous system (CNS) tumors in 2021. Advances in the landscape of molecular tumor pathophysiology prompted major revisions to the previous edition released in 2016, some of which were first introduced by the Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy-Not Official WHO (cIMPACT-NOW). The 2021 classification system integrates newly gained molecular insights to guide changes in tumor taxonomy and nomenclature, introduces several new types of tumors, and expands the use of molecular testing for diagnosis and grading, with a particular impact on adult-type and pediatric-type gliomas, ependymomas, and embryonal tumors. These updates aim to promote clear and accurate diagnoses, yield more reliable prognostic information, and enable the selection of optimal therapies. Familiarity with these changes will be of great importance for clinicians involved in the management of CNS tumor patients.
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Affiliation(s)
- Rebecca A Yoda
- Division of Neuropathology, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Patrick J Cimino
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
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9
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Pratt D, Penas-Prado M, Gilbert MR. Clinical impact of molecular profiling in rare brain tumors. Curr Opin Neurol 2023; 36:579-586. [PMID: 37973025 DOI: 10.1097/wco.0000000000001211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to describe the commonly used molecular diagnostics and illustrate the prognostic importance to the more accurate diagnosis that also may uncover therapeutic targets. RECENT FINDINGS The most recent WHO Classification of Central Nervous System Tumours (2021) lists over 100 distinct tumor types. While traditional histology continues to be an important component, molecular testing is increasingly being incorporated as requisite diagnostic criteria. Specific molecular findings such as co-deletion of the short arm of chromosome 1 (1p) and long arm of chromosome 19 (19q) now define IDH-mutant gliomas as oligodendroglioma. In recent years, DNA methylation profiling has emerged as a dynamic tool with high diagnostic accuracy. The integration of specific genetic (mutations, fusions) and epigenetic (CpG methylation) alterations has led to diagnostic refinement and the discovery of rare brain tumor types with distinct clinical outcomes. Molecular profiling is anticipated to play an increasing role in routine surgical neuropathology, although costs, access, and logistical concerns remain challenging. SUMMARY This review summarizes the current state of molecular testing in neuro-oncology highlighting commonly used and developing technologies, while also providing examples of new tumor types/subtypes that have emerged as a result of improved diagnostic precision.
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Affiliation(s)
| | - Marta Penas-Prado
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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10
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Park JW, Lee K, Kim EE, Kim SI, Park SH. Brain Tumor Classification by Methylation Profile. J Korean Med Sci 2023; 38:e356. [PMID: 37935168 PMCID: PMC10627723 DOI: 10.3346/jkms.2023.38.e356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/12/2023] [Indexed: 11/09/2023] Open
Abstract
The goal of the methylation classifier in brain tumor classification is to accurately classify tumors based on their methylation profiles. Accurate brain tumor diagnosis is the first step for healthcare professionals to predict tumor prognosis and establish personalized treatment plans for patients. The methylation classifier can be used to perform classification on tumor samples with diagnostic difficulties due to ambiguous histology or mismatch between histopathology and molecular signatures, i.e., not otherwise specified (NOS) cases or not elsewhere classified (NEC) cases, aiding in pathological decision-making. Here, the authors elucidate upon the application of a methylation classifier as a tool to mitigate the inherent complexities associated with the pathological evaluation of brain tumors, even when pathologists are experts in histopathological diagnosis and have access to enough molecular genetic information. Also, it should be emphasized that methylome cannot classify all types of brain tumors, and it often produces erroneous matches even with high matching scores, so, excessive trust is prohibited. The primary issue is the considerable difficulty in obtaining reference data regarding the methylation profile of each type of brain tumor. This challenge is further amplified when dealing with recently identified novel types or subtypes of brain tumors, as such data are not readily accessible through open databases or authors of publications. An additional obstacle arises from the fact that methylation classifiers are primarily research-based, leading to the unavailability of charging patients. It is important to note that the application of methylation classifiers may require specialized laboratory techniques and expertise in DNA methylation analysis.
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Affiliation(s)
- Jin Woo Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Kwanghoon Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Eric Eunshik Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Seong-Ik Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Institute of Neuroscience, Seoul National University College of Medicine, Seoul, Korea.
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11
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Drexler R, Sauvigny T, Schüller U, Eckhardt A, Maire CL, Khatri R, Hausmann F, Hänzelmann S, Huber TB, Bonn S, Bode H, Lamszus K, Westphal M, Dührsen L, Ricklefs FL. Epigenetic profiling reveals a strong association between lack of 5-ALA fluorescence and EGFR amplification in IDH-wildtype glioblastoma. Neurooncol Pract 2023; 10:462-471. [PMID: 37720395 PMCID: PMC10502788 DOI: 10.1093/nop/npad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023] Open
Abstract
Background 5-aminolevulinic acid (5-ALA) fluorescence-guided resection increases the percentage of complete CNS tumor resections and improves the progression-free survival of IDH-wildtype glioblastoma patients. A small subset of IDH-wildtype glioblastoma shows no 5-ALA fluorescence. An explanation for these cases is missing. In this study, we used DNA methylation profiling to further characterize non-fluorescent glioblastomas. Methods Patients with newly diagnosed and recurrent IDH-wildtype glioblastoma that underwent surgery were analyzed. The intensity of intraoperative 5-ALA fluorescence was categorized as non-visible or visible. DNA was extracted from tumors and genome-wide DNA methylation patterns were analyzed using Illumina EPIC (850k) arrays. Furthermore, 5-ALA intensity was measured by flow cytometry on human gliomasphere lines (BT112 and BT145). Results Of 74 included patients, 12 (16.2%) patients had a non-fluorescent glioblastoma, which were compared to 62 glioblastomas with 5-ALA fluorescence. Clinical characteristics were equally distributed between both groups. We did not find significant differences between DNA methylation subclasses and 5-ALA fluorescence (P = .24). The distribution of cells of the tumor microenvironment was not significantly different between the non-fluorescent and fluorescent tumors. Copy number variations in EGFR and simultaneous EGFRvIII expression were strongly associated with 5-ALA fluorescence since all non-fluorescent glioblastomas were EGFR-amplified (P < .01). This finding was also demonstrated in recurrent tumors. Similarly, EGFR-amplified glioblastoma cell lines showed no 5-ALA fluorescence after 24 h of incubation. Conclusions Our study demonstrates an association between non-fluorescent IDH-wildtype glioblastomas and EGFR gene amplification which should be taken into consideration for recurrent surgery and future studies investigating EGFR-amplified gliomas.
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Affiliation(s)
- Richard Drexler
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Sauvigny
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, Research Institute Children’s Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Alicia Eckhardt
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Lab of Radiobiology & Experimental Radiation Oncology, University Cancer Center Hamburg, Hamburg, Germany
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Cecile L Maire
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Robin Khatri
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabian Hausmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sonja Hänzelmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Helena Bode
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franz L Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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12
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Hickman RA, Miller AM, Arcila ME. Cerebrospinal fluid: A unique source of circulating tumor DNA with broad clinical applications. Transl Oncol 2023; 33:101688. [PMID: 37196447 DOI: 10.1016/j.tranon.2023.101688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
Malignancies involving the central nervous system present unique challenges for diagnosis and monitoring due to the difficulties and risks of direct biopsies and the low specificity and/or sensitivity of other techniques for assessment. In recent years, liquid biopsy of the cerebrospinal fluid (CSF) has emerged as a convenient alternative that combines minimal invasiveness with the ability to detect disease-defining or therapeutically actionable genetic alterations from circulating tumor DNA (ctDNA). Since CSF can be obtained by lumbar puncture, or an established ventricular access device at multiple time points, ctDNA analysis enables initial molecular characterization and longitudinal monitoring throughout a patient's disease course, promoting optimization of treatment regimens. This review outlines some of the key aspects of ctDNA from CSF as a highly suitable approach for clinical assessment, the benefits and drawbacks, testing methods, as well as potential future advancements in this field. We anticipate wider adoption of this practice as technologies and pipelines improve and envisage significant improvements for cancer care.
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Affiliation(s)
- Richard A Hickman
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, New York, NY, United States; Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Alexandra M Miller
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, New York, NY, United States; Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, United States.
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13
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Otani Y, Satomi K, Suruga Y, Ishida J, Fujii K, Ichimura K, Date I. Utility of genome-wide DNA methylation profiling for pediatric-type diffuse gliomas. Brain Tumor Pathol 2023; 40:56-65. [PMID: 37004583 DOI: 10.1007/s10014-023-00457-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/14/2023] [Indexed: 04/04/2023]
Abstract
Despite the current progress of treatment, pediatric-type diffuse glioma is one of the most lethal primary malignant tumors in the central nervous system (CNS). Since pediatric-type CNS tumors are rare disease entities and highly heterogeneous, the diagnosis is challenging. An accurate diagnosis is essential for the choice of optimal treatment, which leads to precision oncology and improvement of the patient's outcome. Genome-wide DNA methylation profiling recently emerged as one of the most important tools for the diagnosis of CNS tumors, and the utility of this novel assay has been reported in both pediatric and adult patients. In the current World Health Organization classification published in 2021, several new entities are recognized in pediatric-type diffuse gliomas, some of which require methylation profiling. In this review, we investigated the utility of genome-wide DNA methylation profiling in pediatric-type diffuse glioma, as well as issues in the clinical application of this assay. Furthermore, the combination of genome-wide DNA methylation profiling and other comprehensive genomic assays, which may improve diagnostic accuracy and detection of the actionable target, will be discussed.
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Affiliation(s)
- Yoshihiro Otani
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1 Shikata-Cho, Kita-Ku, Okayama, 700-8558, Japan.
| | - Kaishi Satomi
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka-Shi, Tokyo, 181-8611, Japan
| | - Yasuki Suruga
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1 Shikata-Cho, Kita-Ku, Okayama, 700-8558, Japan
| | - Joji Ishida
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1 Shikata-Cho, Kita-Ku, Okayama, 700-8558, Japan
| | - Kentaro Fujii
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1 Shikata-Cho, Kita-Ku, Okayama, 700-8558, Japan
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Isao Date
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1 Shikata-Cho, Kita-Ku, Okayama, 700-8558, Japan
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14
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Sievers P, Sill M, Schrimpf D, Abdullaev Z, Donson AM, Lake JA, Friedel D, Scheie D, Tynninen O, Rauramaa T, Vepsäläinen KL, Samuel D, Chapman R, Grundy RG, Pajtler KW, Tauziède-Espariat A, Métais A, Varlet P, Snuderl M, Jacques TS, Aldape K, Reuss DE, Korshunov A, Wick W, Pfister SM, von Deimling A, Sahm F, Jones DTW. Pediatric-type high-grade neuroepithelial tumors with CIC gene fusion share a common DNA methylation signature. NPJ Precis Oncol 2023; 7:30. [PMID: 36964296 PMCID: PMC10039012 DOI: 10.1038/s41698-023-00372-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
Pediatric neoplasms in the central nervous system (CNS) show extensive clinical and molecular heterogeneity and are fundamentally different from those occurring in adults. Molecular genetic testing contributes to accurate diagnosis and enables an optimal clinical management of affected children. Here, we investigated a rare, molecularly distinct type of pediatric high-grade neuroepithelial tumor (n = 18), that was identified through unsupervised visualization of genome-wide DNA methylation array data, together with copy number profiling, targeted next-generation DNA sequencing, and RNA transcriptome sequencing. DNA and/or RNA sequencing revealed recurrent fusions involving the capicua transcriptional repressor (CIC) gene in 10/10 tumor samples analyzed, with the most common fusion being CIC::LEUTX (n = 9). In addition, a CIC::NUTM1 fusion was detected in one of the tumors. Apart from the detected fusion events, no additional oncogenic alteration was identified in these tumors. The histopathological review demonstrated a morphologically heterogeneous group of high-grade neuroepithelial tumors with positive immunostaining for markers of glial differentiation in combination with weak and focal expression of synaptophysin, CD56 and CD99. All tumors were located in the supratentorial compartment, occurred during childhood (median age 8.5 years) and typically showed early relapses. In summary, we expand the spectrum of pediatric-type tumors of the CNS by reporting a previously uncharacterized group of rare high-grade neuroepithelial tumors that share a common DNA methylation signature and recurrent gene fusions involving the transcriptional repressor CIC. Downstream functional consequences of the fusion protein CIC::LEUTX and potential therapeutic implications need to be further investigated.
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Affiliation(s)
- 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.
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- 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
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jessica A Lake
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA
| | - Dennis Friedel
- 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 Scheie
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Olli Tynninen
- Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tuomas Rauramaa
- Department of Pathology, Kuopio University Hospital, University of Kuopio, Kuopio, Finland
- Unit of Pathology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Kaisa L Vepsäläinen
- Department of Pediatrics, Kuopio University Hospital, University of Kuopio, Kuopio, Finland
| | - David Samuel
- Department of Hematology/Oncology, Valley Children's Hospital, Madera, CA, USA
| | - Rebecca Chapman
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Arnault Tauziède-Espariat
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, Paris, France
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Alice Métais
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, Paris, France
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, Paris, France
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center, New York, NY, USA
| | - Thomas S Jacques
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David E Reuss
- 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
| | - Andrey Korshunov
- 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
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- 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
| | - 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
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
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15
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Gubbiotti MA, Santi M, Storm PB, Li M, Xu F, Abdullaev Z, Aldape K, Viaene AN. First-time identification of a KIF5B-NTRK2 fusion in extraventricular neurocytoma. J Neuropathol Exp Neurol 2023; 82:272-275. [PMID: 36655517 PMCID: PMC10167923 DOI: 10.1093/jnen/nlad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Maria A Gubbiotti
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Philip B Storm
- Department of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Marilyn Li
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Feng Xu
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zied Abdullaev
- Laboratory of Pathology and Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Kenneth Aldape
- Laboratory of Pathology and Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Angela N Viaene
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
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16
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Crainic N, Furtner J, Pallud J, Bielle F, Lombardi G, Rudà R, Idbaih A. Rare Neuronal, Glial and Glioneuronal Tumours in Adults. Cancers (Basel) 2023; 15:cancers15041120. [PMID: 36831464 PMCID: PMC9954092 DOI: 10.3390/cancers15041120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Rare glial, neuronal and glioneuronal tumours in adults form a heterogeneous group of rare, primary central nervous system tumours. These tumours, with a glial and/or neuronal component, are challenging in terms of diagnosis and therapeutic management. The novel classification of primary brain tumours published by the WHO in 2021 has significantly improved the diagnostic criteria of these entities. Indeed, diagnostic criteria are nowadays multimodal, including histological, immunohistochemical and molecular (i.e., genetic and methylomic). These integrated parameters have allowed the specification of already known tumours but also the identification of novel tumours for a better diagnosis.
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Affiliation(s)
- Nicolas Crainic
- Sorbonne Université, Institut du Cerveau—Paris Brain Institute—ICM, Inserm, CNRS, AP-HP, Hôpital Universitaire La Pitié Salpêtrière, DMU Neurosciences, Service de Neurologie 2, 75013 Paris, France
- Department of Neurology, University Hospital of Brest, 29200 Brest, France
- Correspondence: (N.C.); (A.I.)
| | - Julia Furtner
- Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
- Research Center of Medical Image Analysis and Artificial Intelligence (MIAAI), Danube Private University, 3500 Krems, Austria
| | - Johan Pallud
- Service de Neurochirurgie, GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte-Anne, 75014 Paris, France
- Institute of Psychiatry and Neuroscience of Paris, IMABRAIN, INSERM U1266, Université de Paris, 75014 Paris, France
| | - Franck Bielle
- Sorbonne Université, Institut du Cerveau—Paris Brain Institute—ICM, Inserm, CNRS, AP-HP, Hôpital Universitaire La Pitié Salpêtrière, DMU Neurosciences, Service de Neuropathologie, 75013 Paris, France
| | - Giuseppe Lombardi
- Department of Oncology, Oncology 1, Veneto Institute of Oncology-IRCCS, 35128 Padua, Italy
| | - Roberta Rudà
- Division of Neurology, Castelfranco Veneto and Treviso Hospitals, 31033 Treviso, Italy
- Department of Neuro-Oncology, University of Turin, 10126 Turin, Italy
| | - Ahmed Idbaih
- Sorbonne Université, Institut du Cerveau—Paris Brain Institute—ICM, Inserm, CNRS, AP-HP, Hôpital Universitaire La Pitié Salpêtrière, DMU Neurosciences, Service de Neurologie 2, 75013 Paris, France
- Correspondence: (N.C.); (A.I.)
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17
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Chadda KR, Solano-Páez P, Khan S, Llempén-López M, Phyu P, Horan G, Trotman J, Tarpey P, Erker C, Lindsay H, Addy D, Jacques TS, Allinson K, Pizer B, Huang A, Murray MJ. Embryonal tumor with multilayered rosettes: Overview of diagnosis and therapy. Neurooncol Adv 2023; 5:vdad052. [PMID: 37727849 PMCID: PMC10506690 DOI: 10.1093/noajnl/vdad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Affiliation(s)
- Karan R Chadda
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Palma Solano-Páez
- Department of Pediatric Hematology and Oncology, Hospital Infantil Virgen del Rocio, Seville, Spain
| | - Sara Khan
- Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
- Monash Children’s Cancer Centre, Monash Children’s Hospital, Monash Health, Melbourne, Victoria, Australia
- Center for Cancer Research, Hudson Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Molecular and Translational Science, School of Medicine, Nursing and Health Science, Monash University, Melbourne, Victoria, Australia
| | - Mercedes Llempén-López
- Department of Pediatric Hematology and Oncology, Hospital Infantil Virgen del Rocio, Seville, Spain
| | - Poe Phyu
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gail Horan
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jamie Trotman
- East Genomics Laboratory Hub (GLH) Genetics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Patrick Tarpey
- East Genomics Laboratory Hub (GLH) Genetics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Craig Erker
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Dalhousie University and IWK Health Centre, Halifax, Nova Scotia, Canada
| | - Holly Lindsay
- Department of Pediatrics, Division of Hematology and Oncology, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas, USA
| | - Dilys Addy
- SIHMDS-Acquired Genomics Laboratory, NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer Department, University College London Great Ormond Street Institute of Child Health, London, UK
- Department of Histopathology, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Kieren Allinson
- Department of Neuropathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Barry Pizer
- Department of Paediatric Oncology, Alder Hey Children’s NHS Foundation Trust, Liverpool, UK
| | - Annie Huang
- Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Haematology/Oncology, Department of Pediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Matthew J Murray
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Paediatric Haematology and Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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18
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Choi JY. Medulloblastoma: Current Perspectives and Recent Advances. Brain Tumor Res Treat 2023; 11:28-38. [PMID: 36762806 PMCID: PMC9911713 DOI: 10.14791/btrt.2022.0046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 02/05/2023] Open
Abstract
Medulloblastoma is the most common embryonal tumor of the central nervous system in childhood. Combined multimodality approaches, including surgery, radiation, and chemotherapy, have improved the outcome of medulloblastoma. Advances in genomic research have shown that medulloblastoma is not a biologically or clinically discrete entity. Previously, the risk was divided according to histology, presence of metastasis, degree of resection, and age at diagnosis. Through the development of integrated genomics, new biology-based risk stratification methods have recently been proposed. It is also important to understand the genetic predisposition of patients with medulloblastoma. Therefore, treatment goal aimed to improve the survival rate with minimal additional adverse effects and reduced long-term sequelae. It is necessary to incorporate genetic findings into the standard of care, and clinical trials that reflect this need to be conducted.
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Affiliation(s)
- Jung Yoon Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Cancer Research Institute, Seoul, Korea.
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19
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DNA methylation profiling of meningiomas highlights clinically distinct molecular subgroups. J Neurooncol 2023; 161:339-356. [PMID: 36564673 DOI: 10.1007/s11060-022-04220-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND Introduction of the classification of brain tumours based on DNA methylation profile has significantly changed the diagnostic approach. Due to the paucity of data on the molecular profiling of meningiomas and their clinical implications, no effective therapies and new treatments have been implemented. METHODS DNA methylation profiling, copy number analysis, targeted sequencing and H3K27me3 expression was performed on 35 meningiomas and 5 controls. RESULTS Unsupervised hierarchical clustering (UHC) analysis revealed four distinct molecular subgroups: Malignant; Intermediate; Benign A, and Benign B. Molecular heterogeneity was observed within the same grade as the Intermediate, Benign A, and Benign B subgroups were composed of WHO grade 1 as well as grade 2 cases. There was association of mutations with distinct methylation subgroups (NF2, AKT1, SMO, TRAF7 and pTERT). Loss of chromosome 22q was observed across all subgroups. 1p/14q co-deletion was seen in 50% of malignant and intermediate while CDKN2A loss was predominantly observed in malignant subgroup (50%). Majority of malignant (75%) and a small proportion of other subgroups (Intermediate: 25%, Benign A: 38.5%, and Benign B: 20%) harboured H3K27me3 loss. 38,734 genes were dysregulated amongst the four subgroups. DKFZ classified 71% cases with acceptable score. On survival analysis, methylation profiling had significant impact on progression-free-survival in WHO grade1 and 2 meningiomas (p = 0.0051). CONCLUSION Genome-wide DNA methylation profiling highlights clinically distinct molecular subgroups and heterogeneity within the same grade of meningiomas. Molecular profiling can usher in a paradigm shift in meningioma classification, prognostic prediction, and treatment strategy.
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20
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Chen CG, Aldape K, Dhillon KS, Laske DW, Abdullaev Z, Marotta DA, Miettinen M, Curtis MT. DNA methylation profiling and histologic analysis of sellar TTF-1-positive papillary epithelial tumor supports a novel CNS entity. J Neuropathol Exp Neurol 2022; 82:96-98. [PMID: 36367825 PMCID: PMC9764077 DOI: 10.1093/jnen/nlac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Carolyn G Chen
- Department of Pathology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
| | - Kenneth Aldape
- Laboratory of Pathology and Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Kiratpreet S Dhillon
- Department of Pathology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
| | - Douglas W Laske
- Department of Neurosurgery, Abington Hospital Jefferson Health, Abington, Pennsylvania, USA
| | - Zied Abdullaev
- Laboratory of Pathology and Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Dario A Marotta
- Department of Neurosurgery, Alabama College of Osteopathic Medicine, Dothan, Alabama, USA
| | - Markku Miettinen
- Laboratory of Pathology and Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Mark T Curtis
- Department of Pathology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
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21
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Tran S, Bielle F. WHO 2021 and beyond: new types, molecular markers and tools for brain tumor classification. Curr Opin Oncol 2022; 34:670-675. [PMID: 36093875 DOI: 10.1097/cco.0000000000000903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW The fifth edition of the WHO classification of central nervous system tumors was published in 2021. It implemented major advances in the current diagnostic practice such as DNA methylation profiling. The review addresses how our understanding of the diversity of brain tumors has recently much improved through omics analysis and derived molecular biomarkers. RECENT FINDINGS Latest impactful studies identifying new diagnostic or prognostic biomarkers in frequent tumors and describing new rare tumor types are summarized about adult and pediatric gliomas, rare neuroepithelial tumors, ependymomas, medulloblastomas and meningiomas. Some controversies are debated. The role of methylation classes and surrogate immunohistochemical markers is highlighted. SUMMARY New diagnostic criteria and better definitions of tumor types aim at improving the management of brain tumor patients and at better evaluating new treatments in clinical trials. The rapidly evolving field of brain tumor classification opens exciting perspectives and many challenges to integrate clinical, radiological, histological and molecular information into a framework relevant for care and research.
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Affiliation(s)
- Suzanne Tran
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital Universitaire La Pitié Salpêtrière, DMU Neurosciences, Department of Neuropathology
| | - Franck Bielle
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital Universitaire La Pitié Salpêtrière, DMU Neurosciences, Department of Neuropathology
- Sorbonne Université, AP-HP, SIRIC CURAMUS, Paris, France
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22
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Smith HL, Wadhwani N, Horbinski C. Major Features of the 2021 WHO Classification of CNS Tumors. Neurotherapeutics 2022; 19:1691-1704. [PMID: 35578106 PMCID: PMC9723092 DOI: 10.1007/s13311-022-01249-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2022] [Indexed: 12/13/2022] Open
Abstract
Advances in the understanding of the molecular biology of central nervous system (CNS) tumors prompted a new World Health Organization (WHO) classification scheme in 2021, only 5 years after the prior iteration. The 2016 version was the first to include specific molecular alterations in the diagnoses of a few tumors, but the 2021 system greatly expanded this approach, with over 40 tumor types and subtypes now being defined by their key molecular features. Many tumors have also been reconceptualized into new "supercategories," including adult-type diffuse gliomas, pediatric-type diffuse low- and high-grade gliomas, and circumscribed astrocytic gliomas. Some entirely new tumors are in this scheme, particularly pediatric tumors. Naturally, these changes will impact how CNS tumor patients are diagnosed and treated, including clinical trial enrollment. This review addresses the most clinically relevant changes in the 2021 WHO book, including diffuse and circumscribed gliomas, ependymomas, embryonal tumors, and meningiomas.
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Affiliation(s)
- Heather L Smith
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Nitin Wadhwani
- Department of Pathology, Lurie Children's Hospital, Chicago, IL, USA
| | - Craig Horbinski
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Feinberg School of Medicine, Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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23
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Kalawi AZ, Malicki DM, Abdullaev Z, Pratt DW, Quezado M, Aldape K, Elster JD, Paul MR, Khanna PC, Levy ML, Crawford JR. The role of methylation profiling in histologically diagnosed neurocytoma: a case series. J Neurooncol 2022; 159:725-733. [PMID: 35994156 PMCID: PMC9477906 DOI: 10.1007/s11060-022-04117-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/16/2022] [Indexed: 11/28/2022]
Abstract
Purpose To highlight the clinical, neuroradiographic, neuropathologic, and molecular features of histologically identified neurocytoma in a pediatric cohort and highlight the evolving use methylation profiling in providing diagnostic clarity in difficult to diagnosis pediatric brain tumors. Methods Five consecutive children (ages 9–13, 2 girls 3 boys) were histologically diagnosed with neurocytoma at Rady Children’s Hospital San Diego from 2012 to 2018. Clinical and molecular features were analyzed with regards to treatment course and outcome. Results Presenting symptoms included seizures (n = 2), syncope (n = 1), headache (n = 2), visual disturbances (n = 2) and emesis (n = 2). Tumor location included intraventricular (n = 2), intraventricular with parenchymal spread (n = 1), and extraventricular (n = 2). Magnetic resonance imaging demonstrated reduced diffusivity (2/5), signal abnormality on susceptibility-weighted sequences (3/5), and varying degrees of contrast enhancement (4/5). All patients underwent surgical resection alone. Recurrence occurred in four children that were treated with surgery (4/4), adjuvant radiation (2/4), and chemoradiation (1/4). Neuropathologic features included positivity for GFAP (4/5), synaptophysin (4/5), NSE (2/2), NeuN (4/4), and variable Ki-67 (< 1% to 15%). Next generation sequencing (3/5) and microarray (3/5) collectively were abnormal in four of five tumors. Methylation profiling was successfully performed on four of five samples which led to modification of diagnosis in two patients and the others were either unclassifiable or confirmatory with the histologic diagnosis. Mean time to follow up was 77 months (range 44–112 months). Mean progression free survival and overall survival were 24 months (range 6 to 52 months) and 100% respectively. Conclusion Neurocytomas are a rare clinical entity that warrants further investigation into molecular and pathologic prognosticating features. Methylation profiling may aid in differentiation of neurocytoma from other difficult to diagnose tumors who share similar histologic features.
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Affiliation(s)
- Adam Z Kalawi
- Division of Child Neurology, Department of Neurosciences, University of California, San Diego, CA, USA.
- Rady Children's Hospital, San Diego, CA, USA.
| | - Denise M Malicki
- Rady Children's Hospital, San Diego, CA, USA
- Department of Pathology, University of California, San Diego, CA, USA
| | - Zied Abdullaev
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Drew W Pratt
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Martha Quezado
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Jennifer D Elster
- Rady Children's Hospital, San Diego, CA, USA
- Division of Hematology Oncology, Department of Pediatrics, University of California, San Diego, CA, USA
| | - Megan R Paul
- Rady Children's Hospital, San Diego, CA, USA
- Division of Hematology Oncology, Department of Pediatrics, University of California, San Diego, CA, USA
| | - Paritosh C Khanna
- Rady Children's Hospital, San Diego, CA, USA
- Department of Radiology, University of California, San Diego, CA, USA
| | - Michael L Levy
- Rady Children's Hospital, San Diego, CA, USA
- Division of Pediatric Neurosurgery, Department of Neurosurgery, University of California, San Diego, CA, USA
| | - John R Crawford
- Division of Child Neurology, Department of Neurosciences, University of California, San Diego, CA, USA
- Rady Children's Hospital, San Diego, CA, USA
- Division of Hematology Oncology, Department of Pediatrics, University of California, San Diego, CA, USA
- Division of Child Neurology, Children's Hospital of Orange County, Orange, CA, USA
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24
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Richardson TE, Walker JM, Abdullah KG, McBrayer SK, Viapiano MS, Mussa ZM, Tsankova NM, Snuderl M, Hatanpaa KJ. Chromosomal instability in adult-type diffuse gliomas. Acta Neuropathol Commun 2022; 10:115. [PMID: 35978439 PMCID: PMC9386991 DOI: 10.1186/s40478-022-01420-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/04/2022] [Indexed: 11/14/2022] Open
Abstract
Chromosomal instability (CIN) is a fundamental property of cancer and a key underlying mechanism of tumorigenesis and malignant progression, and has been documented in a wide variety of cancers, including colorectal carcinoma with mutations in genes such as APC. Recent reports have demonstrated that CIN, driven in part by mutations in genes maintaining overall genomic stability, is found in subsets of adult-type diffusely infiltrating gliomas of all histologic and molecular grades, with resulting elevated overall copy number burden, chromothripsis, and poor clinical outcome. Still, relatively few studies have examined the effect of this process, due in part to the difficulty of routinely measuring CIN clinically. Herein, we review the underlying mechanisms of CIN, the relationship between chromosomal instability and malignancy, the prognostic significance and treatment potential in various cancers, systemic disease, and more specifically, in diffusely infiltrating glioma subtypes. While still in the early stages of discovery compared to other solid tumor types in which CIN is a known driver of malignancy, the presence of CIN as an early factor in gliomas may in part explain the ability of these tumors to develop resistance to standard therapy, while also providing a potential molecular target for future therapies.
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Affiliation(s)
- Timothy E. Richardson
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
| | - Jamie M. Walker
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Kalil G. Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA 15213 USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA 15232 USA
| | - Samuel K. McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Mariano S. Viapiano
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY 13210 USA
- Department of Neurosurgery, State University of New York, Upstate Medical University, Syracuse, NY 13210 USA
| | - Zarmeen M. Mussa
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
| | - Nadejda M. Tsankova
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, Annenberg Building, 15th Floor, 1468 Madison Avenue, New York, NY 10029 USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York City, NY 10016 USA
| | - Kimmo J. Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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25
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Marquardt A, Kollmannsberger P, Krebs M, Argentiero A, Knott M, Solimando AG, Kerscher AG. Visual Clustering of Transcriptomic Data from Primary and Metastatic Tumors-Dependencies and Novel Pitfalls. Genes (Basel) 2022; 13:genes13081335. [PMID: 35893071 PMCID: PMC9394300 DOI: 10.3390/genes13081335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/20/2022] [Accepted: 07/23/2022] [Indexed: 02/06/2023] Open
Abstract
Personalized oncology is a rapidly evolving area and offers cancer patients therapy options that are more specific than ever. However, there is still a lack of understanding regarding transcriptomic similarities or differences of metastases and corresponding primary sites. Applying two unsupervised dimension reduction methods (t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP)) on three datasets of metastases (n = 682 samples) with three different data transformations (unprocessed, log10 as well as log10 + 1 transformed values), we visualized potential underlying clusters. Additionally, we analyzed two datasets (n = 616 samples) containing metastases and primary tumors of one entity, to point out potential familiarities. Using these methods, no tight link between the site of resection and cluster formation outcome could be demonstrated, or for datasets consisting of solely metastasis or mixed datasets. Instead, dimension reduction methods and data transformation significantly impacted visual clustering results. Our findings strongly suggest data transformation to be considered as another key element in the interpretation of visual clustering approaches along with initialization and different parameters. Furthermore, the results highlight the need for a more thorough examination of parameters used in the analysis of clusters.
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Affiliation(s)
- André Marquardt
- Institute of Pathology, Klinikum Stuttgart, 70174 Stuttgart, Germany
- Institute of Pathology, University of Würzburg, 97080 Würzburg, Germany
- Bavarian Center for Cancer Research (BZKF), 97080 Würzburg, Germany
- Correspondence: (A.M.); (A.G.K.)
| | - Philip Kollmannsberger
- Center for Computational and Theoretical Biology, University of Würzburg, 97074 Würzburg, Germany;
| | - Markus Krebs
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany;
- Department of Urology and Pediatric Urology, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Antonella Argentiero
- IRCCS Istituto Tumori “Giovanni Paolo II” of Bari, 70124 Bari, Italy; (A.A.); (A.G.S.)
| | - Markus Knott
- Department of Hematology, Oncology, Stem Cell Transplantation and Palliative Care, Klinikum Stuttgart, 70174 Stuttgart, Germany;
- Stuttgart Cancer Center–Tumor Unit Eva Mayr-Stihl, Klinikum Stuttgart, 70174 Stuttgart, Germany
| | - Antonio Giovanni Solimando
- IRCCS Istituto Tumori “Giovanni Paolo II” of Bari, 70124 Bari, Italy; (A.A.); (A.G.S.)
- Guido Baccelli Unit of Internal Medicine, Department of Biomedical Sciences and Human Oncology, School of Medicine, Aldo Moro University of Bari, 70124 Bari, Italy
| | - Alexander Georg Kerscher
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany;
- Correspondence: (A.M.); (A.G.K.)
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26
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Next generation sequencing in adult patients with glioblastoma in Switzerland: a multi-centre decision analysis. J Neurooncol 2022; 158:359-367. [PMID: 35486306 DOI: 10.1007/s11060-022-04022-7] [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: 03/07/2022] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Glioblastoma is the most common malignant primary brain tumour in adults and driven by various genomic alterations. Next generation sequencing (NGS) provides timely information about the genetic landscape of tumours and might detect targetable mutations. To date, differences exist in the application and NGS assays used as it remains unclear to what extent these variants may affect clinical decision making. In this survey-based study, we investigated the use of NGS in adult patients with glioblastoma in Switzerland. METHODS All eight primary care centres for Neuro-Oncology in Switzerland participated in this survey. The NGS assays used as well as the criteria for the application of NGS in newly diagnosed glioblastoma were investigated. Decision trees were analysed for consensus and discrepancies using the objective consensus methodology. RESULTS Seven out of eight centres perform NGS in patients with newly diagnosed glioblastoma using custom made or commercially available assays. The criteria most relevant to decision making were age, suitability of standard treatment and fitness. NGS is most often used in fitter patients under the age of 60 years who are not suitable for standard therapy, while it is rarely performed in patients in poor general health. CONCLUSION NGS is frequently applied in glioblastomas in adults in Neuro-Oncology centres in Switzerland despite seldom changing the course of treatment to date.
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27
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Liu Y, Sathe AA, Abdullah KG, McBrayer SK, Adams SH, Brenner AJ, Hatanpaa KJ, Viapiano MS, Xing C, Walker JM, Richardson TE. Global DNA methylation profiling reveals chromosomal instability in IDH-mutant astrocytomas. Acta Neuropathol Commun 2022; 10:32. [PMID: 35264242 PMCID: PMC8908645 DOI: 10.1186/s40478-022-01339-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/24/2022] [Indexed: 12/21/2022] Open
Abstract
Diffusely infiltrating gliomas are among the most common central nervous system tumors in adults. Over the past decade, the subcategorization of these tumors has changed to include both traditional histologic features and more recently identified molecular factors. However, one molecular feature that has yet to be integrated is the presence/absence of chromosomal instability (CIN). Herein, we use global methylation profiling to evaluate a reference cohort of IDH-mutant astrocytomas with and without prior evidence of CIN (n = 42), and apply the resulting methylation-based characteristics to a larger test cohort of publicly-available IDH-mutant astrocytomas (n = 245). We demonstrate that IDH-mutant astrocytomas with evidence of CIN cluster separately from their chromosomally-stable counterparts. CIN cases were associated with higher initial histologic grade, altered expression patterns of genes related to CIN in other cancers, elevated initial total copy number burden, and significantly worse progression-free and overall survival. In addition, in a grade-for-grade analysis, patients with CIN-positive WHO grade 2 and 3 tumors had significantly worse survival. These results suggest that global methylation profiling can be used to discriminate between chromosomally stable and unstable IDH-mutant astrocytomas, and may therefore provide a reliable and cost-effective method for identifying gliomas with chromosomal instability and resultant poor clinical outcome.
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Affiliation(s)
- Yan Liu
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Adwait Amod Sathe
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Kalil G. Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA 15213 USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA 15232 USA
| | - Samuel K. McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Steven H. Adams
- Department of Pathology, Stony Brook University Hospital, Stony Brook, NY 11794 USA
| | - Andrew J. Brenner
- Department of Internal Medicine, Division of Hematology & Oncology, University of Texas Health San Antonio, San Antonio, TX 78229 USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX 78229 USA
| | - Kimmo J. Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Mariano S. Viapiano
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY 13210 USA
- Department of Neurosurgery, State University of New York, Upstate Medical University, Syracuse, NY 13210 USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Jamie M. Walker
- Department of Pathology and Laboratory Medicine, Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Disease, University of Texas Health San Antonio, 7703 Floyd Curl Dr., MC 8070, San Antonio, TX 78229 USA
| | - Timothy E. Richardson
- Department of Pathology and Laboratory Medicine, Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Disease, University of Texas Health San Antonio, 7703 Floyd Curl Dr., MC 8070, San Antonio, TX 78229 USA
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28
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Di Ruscio V, Carai A, Del Baldo G, Vinci M, Cacchione A, Miele E, Rossi S, Antonelli M, Barresi S, Caulo M, Colafati GS, Mastronuzzi A. Molecular Landscape in Infant High-Grade Gliomas: A Single Center Experience. Diagnostics (Basel) 2022; 12:diagnostics12020372. [PMID: 35204463 PMCID: PMC8871476 DOI: 10.3390/diagnostics12020372] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
High-grade gliomas (HGG) represent about 15% of all pediatric brain tumors, with a dismal prognosis and survival rates ranging from 15 to 35%. Approximately 10–12% of pediatric HGGs (pHGG) occur in children younger than five years of age at diagnosis, specifically infants (iHGG), with an unexpected overall survival rate (OS) in 60–70% of cases. In the literature, iHGGs include a large variety of heterogeneous lesions with different molecular profiles that likely explain their different outcomes. We report our single-institution experience of iHGG including 11 children under five years of age with newly diagnosed HGG between 2011 and 2021. All patients received surgery and adjuvant chemotherapy; only two patients received radiotherapy because their age at diagnosis was more than four years-old. Molecular investigations, including next generation sequencing (NGS) and DNA methylation, detected three NTRK-fusions, one ROS1-fusions, one MN1-rearrangement, and two PATZ1-fusions. According to the molecular results, when chemotherapy failed to control the disease, two patients benefited from target therapy with a NTRK-Inhibitor larotrectinib, achieving a complete remission and a very good partial response, respectively, and no severe side-effects. In conclusion, molecular investigations play a fundamental role in the diagnostic work-up and also in the therapeutic decision. Their routine use in clinical practice could help to replace highly toxic chemotherapy regimens with a target therapy that has moderate adverse effects, even in long-term follow-up.
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Affiliation(s)
- Valentina Di Ruscio
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Scientific Institute for Reasearch, Hospitalization and Healthcare (IRCCS), 00165 Rome, Italy; (V.D.R.); (G.D.B.); (M.V.); (A.C.); (E.M.); (A.M.)
| | - Andrea Carai
- Neurosurgery Unit, Department of Neurosciences, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
- Correspondence:
| | - Giada Del Baldo
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Scientific Institute for Reasearch, Hospitalization and Healthcare (IRCCS), 00165 Rome, Italy; (V.D.R.); (G.D.B.); (M.V.); (A.C.); (E.M.); (A.M.)
| | - Maria Vinci
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Scientific Institute for Reasearch, Hospitalization and Healthcare (IRCCS), 00165 Rome, Italy; (V.D.R.); (G.D.B.); (M.V.); (A.C.); (E.M.); (A.M.)
| | - Antonella Cacchione
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Scientific Institute for Reasearch, Hospitalization and Healthcare (IRCCS), 00165 Rome, Italy; (V.D.R.); (G.D.B.); (M.V.); (A.C.); (E.M.); (A.M.)
| | - Evelina Miele
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Scientific Institute for Reasearch, Hospitalization and Healthcare (IRCCS), 00165 Rome, Italy; (V.D.R.); (G.D.B.); (M.V.); (A.C.); (E.M.); (A.M.)
| | - Sabrina Rossi
- Department of Pathology, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (S.R.); (S.B.)
| | - Manila Antonelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, University Sapienza of Rome, 00185 Rome, Italy;
| | - Sabina Barresi
- Department of Pathology, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (S.R.); (S.B.)
| | - Massimo Caulo
- Department of Neuroscience, Imaging and Clinical Sciences, G. D’Annunzio University of Chieti, 66100 Chieti, Italy;
| | - Giovanna Stefania Colafati
- Department of Diagnostic Imaging Oncological Neuroradiology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Angela Mastronuzzi
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Scientific Institute for Reasearch, Hospitalization and Healthcare (IRCCS), 00165 Rome, Italy; (V.D.R.); (G.D.B.); (M.V.); (A.C.); (E.M.); (A.M.)
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