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Foss-Skiftesvik J, Li S, Rosenbaum A, Hagen CM, Stoltze UK, Ljungqvist S, Hjalmars U, Schmiegelow K, Morimoto L, de Smith AJ, Mathiasen R, Metayer C, Hougaard D, Melin B, Walsh KM, Bybjerg-Grauholm J, Dahlin AM, Wiemels JL. Multi-ancestry genome-wide association study of 4069 children with glioma identifies 9p21.3 risk locus. Neuro Oncol 2023; 25:1709-1720. [PMID: 36810956 PMCID: PMC10484172 DOI: 10.1093/neuonc/noad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Although recent sequencing studies have revealed that 10% of childhood gliomas are caused by rare germline mutations, the role of common variants is undetermined and no genome-wide significant risk loci for pediatric central nervous system tumors have been identified to date. METHODS Meta-analysis of 3 population-based genome-wide association studies comprising 4069 children with glioma and 8778 controls of multiple genetic ancestries. Replication was performed in a separate case-control cohort. Quantitative trait loci analyses and a transcriptome-wide association study were conducted to assess possible links with brain tissue expression across 18 628 genes. RESULTS Common variants in CDKN2B-AS1 at 9p21.3 were significantly associated with astrocytoma, the most common subtype of glioma in children (rs573687, P-value of 6.974e-10, OR 1.273, 95% CI 1.179-1.374). The association was driven by low-grade astrocytoma (P-value of 3.815e-9) and exhibited unidirectional effects across all 6 genetic ancestries. For glioma overall, the association approached genome-wide significance (rs3731239, P-value of 5.411e-8), while no significant association was observed for high-grade tumors. Predicted decreased brain tissue expression of CDKN2B was significantly associated with astrocytoma (P-value of 8.090e-8). CONCLUSIONS In this population-based genome-wide association study meta-analysis, we identify and replicate 9p21.3 (CDKN2B-AS1) as a risk locus for childhood astrocytoma, thereby establishing the first genome-wide significant evidence of common variant predisposition in pediatric neuro-oncology. We furthermore provide a functional basis for the association by showing a possible link to decreased brain tissue CDKN2B expression and substantiate that genetic susceptibility differs between low- and high-grade astrocytoma.
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Affiliation(s)
- Jon Foss-Skiftesvik
- Department of Neurosurgery, Rigshospitalet University Hospital, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Section for Neonatal Genetics, Statens Serum Institute, Copenhagen, Denmark
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Adam Rosenbaum
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | | | - Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Sally Ljungqvist
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulf Hjalmars
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Libby Morimoto
- Center for Personalized Medicine, Children’s Hospital of Los Angeles, Los Angeles, California, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - David Hougaard
- Section for Neonatal Genetics, Statens Serum Institute, Copenhagen, Denmark
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Kyle M Walsh
- Division of Neuro-Epidemiology, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | | | - Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
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Poll SR, Martin R, Wohler E, Partan ES, Walek E, Salman S, Groepper D, Kratz L, Cernach M, Jesus-Garcia R, Haldeman-Englert C, Choi YJ, Morris CD, Cohen B, Hoover-Fong J, Valle D, Semenza GL, Sobreira NLM. Disruption of the HIF-1 pathway in individuals with Ollier disease and Maffucci syndrome. PLoS Genet 2022; 18:e1010504. [PMID: 36480544 PMCID: PMC9767349 DOI: 10.1371/journal.pgen.1010504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 12/20/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
Ollier disease (OD) and Maffucci Syndrome (MS) are rare disorders characterized by multiple enchondromas, commonly causing bone deformities, limb length discrepancies, and pathological fractures. MS is distinguished from OD by the development of vascular anomalies. Both disorders are cancer predisposition syndromes with malignancies developing in ~50% of the individuals with OD or MS. Somatic gain-of-function variants in IDH1 and IDH2 have been described in the enchondromas, vascular anomalies and chondrosarcomas of approximately 80% of the individuals with OD and MS. To date, however, no investigation of germline causative variants for these diseases has been comprehensively performed. To search for germline causative variants, we performed whole exome sequencing or whole genome sequencing of blood or saliva DNA in 94 unrelated probands (68 trios). We found that 7 had rare germline missense variants in HIF1A, 6 had rare germline missense variants in VHL, and 3 had IDH1 variants including 2 with mosaic IDH1-p.Arg132His variant. A burden analysis using 94 probands assigned as cases and 2,054 unrelated individuals presenting no OD- or MS-related features as controls, found that variants in HIF1A, VHL, and IDH1 were all significantly enriched in cases compared to controls. To further investigate the role of HIF-1 pathway in the pathogenesis of OD and MS, we performed RNA sequencing of fibroblasts from 4 probands with OD or MS at normoxia and at hypoxia. When cultured in hypoxic conditions, both proband and control cells showed altered expression of a subset of HIF-1 regulated genes. However, the set of differentially expressed genes in proband fibroblasts included a significantly reduced number of HIF-1 regulated genes compared to controls. Our findings suggest that germline or early post-zygotic variants identified in HIF1A, VHL, and IDH1 in probands with OD and MS underlie the development of the phenotypic abnormalities in a subset of individuals with OD and MS, but extensive functional studies are needed to further confirm it.
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Affiliation(s)
- Sarah R. Poll
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Renan Martin
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Elizabeth S. Partan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Elizabeth Walek
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Shaima Salman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Daniel Groepper
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
| | - Lisa Kratz
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Mirlene Cernach
- Universidade Metropolitana de Santos, Santos, São Paulo, Brazil
| | - Reynaldo Jesus-Garcia
- Department of Orthopedics-Oncology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Chad Haldeman-Englert
- Mission Fullerton Genetics Center, Asheville, North Carolina, United States of America
| | - Yoon Jae Choi
- Department of Neurology, University of California, Irvine, California, United States of America
| | - Carol D. Morris
- Department of Orthopedic Surgery, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Bernard Cohen
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland, Untied States of America
| | - Julie Hoover-Fong
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gregg L. Semenza
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nara L. M. Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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