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Alharbi M, Mobark N, Bashawri Y, Abu Safieh L, Alowayn A, Aljelaify R, AlSaeed M, Almutairi A, Alqubaishi F, AlSolme E, Ahmad M, Al-Banyan A, Alotabi FE, Serrano J, Snuderl M, Al-Rashed M, Abedalthagafi M. Methylation Profiling of Medulloblastoma in a Clinical Setting Permits Sub-classification and Reveals New Outcome Predictions. Front Neurol 2020; 11:167. [PMID: 32265819 PMCID: PMC7100767 DOI: 10.3389/fneur.2020.00167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/21/2020] [Indexed: 12/11/2022] Open
Abstract
Medulloblastoma (MB) is the most common childhood malignant brain tumor and is a leading cause of cancer-related death in children. DNA methylation profiling has rapidly advanced our understanding of MB pathogenesis at the molecular level, but assessments in Saudi Arabian (SA)-MB cases are sparse. MBs can be sub-grouped according to methylation patterns from FPPE samples into Wingless (WNT-MB), Sonic Hedgehog (SHH-MB), Group 3 (G3), and Group 4 (G4) tumors. The WNT-MB and SHH-MB subgroups are characterized by gain-of function mutations that activate oncogenic cell signaling, whilst G3/G4 tumors show recurrent chromosomal alterations. Given that each subgroup has distinct clinical outcomes, the ability to subgroup SA-FPPE samples holds significant prognostic and therapeutic value. Here, we performed the first assessment of MB-DNA methylation patterns in an SA cohort using archival biopsy material (FPPE n = 49). Of the 41 materials available for methylation assessments, 39 could be classified into the major DNA methylation subgroups (SHH, WNT, G3, and G4). Furthermore, methylation analysis was able to reclassify tumors that could not be sub-grouped through next-generation sequencing, highlighting its superior accuracy for MB molecular classifications. Independent assessments demonstrated known clinical relationships of the subgroups, exemplified by the high survival rates observed for WNT tumors. Surprisingly, the G4 subgroup did not conform to previously identified phenotypes, with a high prevalence in females, high metastatic rates, and a large number of tumor-associated deaths. Taking our results together, we demonstrate that DNA methylation profiling enables the robust sub-classification of four disease sub-groups in archival FFPE biopsy material from SA-MB patients. Moreover, we show that the incorporation of DNA methylation biomarkers can significantly improve current disease-risk stratification schemes, particularly concerning the identification of aggressive G4 tumors. These findings have important implications for future clinical disease management in MB cases across the Arab world.
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Affiliation(s)
- Musa Alharbi
- Department of Paediatric Oncology Comprehensive Cancer Centre, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Nahla Mobark
- Department of Paediatric Oncology Comprehensive Cancer Centre, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Yara Bashawri
- Department of Biostatistics, Research Centre, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Leen Abu Safieh
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Albandary Alowayn
- Department of Biostatistics, Research Centre, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Rasha Aljelaify
- Department of Biostatistics, Research Centre, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Mariam AlSaeed
- Department of Biostatistics, Research Centre, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Amal Almutairi
- Department of Biostatistics, Research Centre, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fatimah Alqubaishi
- Department of Biostatistics, Research Centre, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ebtehal AlSolme
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Maqsood Ahmad
- Department of Neuroscience, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ayman Al-Banyan
- Department of Neuroscience, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fahad E Alotabi
- Department of Neuroscience, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Jonathan Serrano
- Department of Pathology, NYU Langone Medical Center, New York, NY, United States
| | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center, New York, NY, United States
| | - May Al-Rashed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Malak Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
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Ostrom QT, Fahmideh MA, Cote DJ, Muskens IS, Schraw JM, Scheurer ME, Bondy ML. Risk factors for childhood and adult primary brain tumors. Neuro Oncol 2019; 21:1357-1375. [PMID: 31301133 PMCID: PMC6827837 DOI: 10.1093/neuonc/noz123] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Primary brain tumors account for ~1% of new cancer cases and ~2% of cancer deaths in the United States; however, they are the most commonly occurring solid tumors in children. These tumors are very heterogeneous and can be broadly classified into malignant and benign (or non-malignant), and specific histologies vary in frequency by age, sex, and race/ethnicity. Epidemiological studies have explored numerous potential risk factors, and thus far the only validated associations for brain tumors are ionizing radiation (which increases risk in both adults and children) and history of allergies (which decreases risk in adults). Studies of genetic risk factors have identified 32 germline variants associated with increased risk for these tumors in adults (25 in glioma, 2 in meningioma, 3 in pituitary adenoma, and 2 in primary CNS lymphoma), and further studies are currently under way for other histologic subtypes, as well as for various childhood brain tumors. While identifying risk factors for these tumors is difficult due to their rarity, many existing datasets can be leveraged for future discoveries in multi-institutional collaborations. Many institutions are continuing to develop large clinical databases including pre-diagnostic risk factor data, and developments in molecular characterization of tumor subtypes continue to allow for investigation of more refined phenotypes. Key Point 1. Brain tumors are a heterogeneous group of tumors that vary significantly in incidence by age, sex, and race/ethnicity.2. The only well-validated risk factors for brain tumors are ionizing radiation (which increases risk in adults and children) and history of allergies (which decreases risk).3. Genome-wide association studies have identified 32 histology-specific inherited genetic variants associated with increased risk of these tumors.
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Affiliation(s)
- Quinn T Ostrom
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Maral Adel Fahmideh
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Solna, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - David J Cote
- Channing Division of Network Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Computational Neuroscience Outcomes Center, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Ivo S Muskens
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jeremy M Schraw
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Michael E Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Melissa L Bondy
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
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