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Koizumi S, Iwaizumi M, Baba S, Ushiama M, Hirata M, Kurozumi K. Genomic analysis revealing Lynch syndrome in a case of high-grade glioma: illustrative case. JOURNAL OF NEUROSURGERY. CASE LESSONS 2025; 9:CASE24718. [PMID: 40030159 DOI: 10.3171/case24718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Accepted: 12/18/2024] [Indexed: 03/06/2025]
Abstract
BACKGROUND Advances in cancer genome analysis technology have made individual cancer genome profiling (CGP) possible. CGP can indicate the presence of hereditary tumors, which are caused by germline pathogenic variants in oncogenes or tumor suppressor genes; if a hereditary tumor is suspected, multigene panel testing (MGPT) is performed. Genomic medicine thus plays an important role in diagnosing hereditary tumors. OBSERVATIONS A 41-year-old man presented with headache and depressive symptoms. Close examination revealed a mass lesion with cystic components in the right parietal lobe. The tumor was removed via craniotomy and was pathologically diagnosed as a high-grade glioma. CGP of the tumor area revealed a high tumor mutation burden and multiple presumed germline pathogenic variants. MGPT of peripheral blood detected a germline pathogenic variant in MSH6. The patient was therefore diagnosed with Lynch syndrome. LESSONS Family history and genetic risk assessments, including CGP, are important for diagnosing genetic diseases. Next-generation sequencing technology is essential for genetic analyses, and if many genetic mutations are identified using tumor-only CGP, MGPT of peripheral blood is an efficient option. In addition, MSH6 variant analysis is important for diagnosing Lynch syndrome and determining treatment. In particular, functional analysis of somatic variants is essential for understanding disease associations. https://thejns.org/doi/10.3171/CASE24718.
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Affiliation(s)
- Shinichiro Koizumi
- Department of Neurosurgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Moriya Iwaizumi
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Satoshi Baba
- Department of Pathology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Mineko Ushiama
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Makoto Hirata
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Kazuhiko Kurozumi
- Department of Neurosurgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
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Wang C, Chen J, Wang Y, Luo N, Han T, Yin X, Song Y, Chen D, Gong J. Genetic and clinical characteristics of genetic tumor syndromes in the central nervous system cancers: Implications for clinical practice. iScience 2024; 27:111073. [PMID: 39493880 PMCID: PMC11530818 DOI: 10.1016/j.isci.2024.111073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/02/2024] [Accepted: 09/26/2024] [Indexed: 11/05/2024] Open
Abstract
Recognizing individuals with Genetic tumor syndromes (GTS) in the primary central nervous system (CNS) tumors is crucial for optimizing proper genetic counseling and improving therapeutics and clinical care. We retrospectively analyzed the GTS in a Chinese CNS tumor cohort and examined the molecular characteristics and their clinical significance for diagnostic and therapeutic purposes. Our study identified 34 categories of GTS in 258 patients with CNS tumors. The gene with the highest germline pathogenic or likely pathogenic mutation frequency was TP53, followed by MSH2, NF1, and BRCA2. The top five GTS in CNS tumors showed high genetic heterogeneity GTS analysis reclassifies CNS tumors as "NEC." 53.88% of patients diagnosed with GTS harbor potential precision oncology therapy target mutations. The results of our study deepen our understanding of CNS tumors, provide a reference direction for the future design of clinical trials, and further expect to improve disease entire process management in CNS tumors.
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Affiliation(s)
- Chuanwei Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Health and Function Remodeling, Jinan, Shandong 250012, China
| | - Jian Chen
- Department of Oncology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, China
| | - Yanzhao Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Health and Function Remodeling, Jinan, Shandong 250012, China
| | - Ningning Luo
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, Jiangsu 210000, China
| | - Tiantian Han
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, Jiangsu 210000, China
| | - Xiangyu Yin
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, Jiangsu 210000, China
| | - Yunjie Song
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, Jiangsu 210000, China
| | - Dongsheng Chen
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, Jiangsu 210000, China
- Cancer Center, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121001, China
- Center of Translational Medicine, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121001, China
| | - Jie Gong
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Health and Function Remodeling, Jinan, Shandong 250012, China
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Mangum R, Lin FY, Parsons DW. Recent Advancements and Innovations in Pediatric Precision Oncology. J Pediatr Hematol Oncol 2024; 46:262-271. [PMID: 38857189 DOI: 10.1097/mph.0000000000002871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/29/2024] [Indexed: 06/12/2024]
Abstract
Precision oncology incorporates comprehensive genomic profiling into the individualized clinical care of pediatric cancer patients. In recent years, comprehensive pan-cancer analyses have led to the successful implementation of genomics-based pediatric trials and accelerated approval of novel targeted agents. In addition, disease-specific studies have resulted in molecular subclassification of myriad cancer types with subsequent tailoring of treatment intensity based on the patient's prognostic factors. This review discusses the progress of the field and highlights developments that are leading to more personalized cancer care and improved patient outcomes. Increased understanding of the evolution of precision oncology over recent decades emphasizes the tremendous impact of improved genomic applications. New technologies and improved diagnostic modalities offer further promise for future advancements within the field.
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Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ
| | - Frank Y Lin
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
| | - D Williams Parsons
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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Wimberly CE, Gulrajani NB, Russ JB, Landi D, Wiemels JL, Towry L, Wiencke JK, Walsh KM. Maternal Prenatal Use of Alcohol, Tobacco, and Illicit Drugs and Associations with Childhood Cancer Subtypes. Cancer Epidemiol Biomarkers Prev 2024; 33:347-354. [PMID: 38112788 PMCID: PMC10932842 DOI: 10.1158/1055-9965.epi-23-1027] [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: 08/29/2023] [Revised: 10/17/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND The association between childhood cancer risk and maternal prenatal substance use/abuse remains uncertain due to modest sample sizes and heterogeneous study designs. METHODS We surveyed parents of children with cancer regarding maternal gestational use of tobacco, alcohol, and illicit drugs, using a Likert-type scale, and demographic, perinatal, and clinical variables. Multivariable log-Poisson regression assessed differences in frequency of prenatal substance use across fifteen childhood cancer subtypes, adjusting for birthweight, gestational age, and demographic factors. RESULTS Respondents from 3,145 unique families completed the survey (92% biological mothers). A minority reported gestational use of tobacco products (14%), illicit drugs including marijuana or cocaine (4%), or more than a moderate amount of alcohol (2%). Prenatal illicit drug use was associated with increased prevalence of intracranial embryonal tumors [prevalence ratio (PR) = 1.94; confidence interval [CI], 1.05-3.58], including medulloblastoma (PR = 1.82) and supratentorial primitive neuroectodermal tumors (PNET; PR = 2.66), and was also associated with retinoblastoma (PR = 3.11; CI, 1.20-8.08). Moderate to heavy alcohol consumption was strongly associated with elevated prevalence of non-Hodgkin lymphoma (PR = 5.94; CI, 1.84-19.21). Prenatal smoking was not associated with elevated prevalence of any childhood cancer subtype. CONCLUSIONS We identify novel associations between illicit drug use during pregnancy and increased prevalence of nonglioma central nervous system tumors, including medulloblastoma, supratentorial PNETs, and retinoblastoma. Gestational exposure to alcohol was positively associated with non-Hodgkin lymphoma. IMPACT Although alcohol and tobacco use during pregnancy has declined, gestational cannabis use has risen. Investigating its impact on neurodevelopment and brain tumorigenesis is vital, with important implications for childhood cancer research and public health education.
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Affiliation(s)
- Courtney E. Wimberly
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
- Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, NC, USA
| | - Natalie B. Gulrajani
- Children’s Health and Discovery Institute, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Jeffrey B. Russ
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Daniel Landi
- Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, NC, USA
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Joseph L. Wiemels
- Center for Genetic Epidemiology, Norris Comprehensive Cancer Center, and Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Lisa Towry
- Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA, USA
| | - John K. Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Kyle M. Walsh
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
- Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, NC, USA
- Children’s Health and Discovery Institute, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
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5
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Jovanović A, Tošić N, Marjanović I, Komazec J, Zukić B, Nikitović M, Ilić R, Grujičić D, Janić D, Pavlović S. Germline Variants in Cancer Predisposition Genes in Pediatric Patients with Central Nervous System Tumors. Int J Mol Sci 2023; 24:17387. [PMID: 38139220 PMCID: PMC10744041 DOI: 10.3390/ijms242417387] [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: 11/09/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Central nervous system (CNS) tumors comprise around 20% of childhood malignancies. Germline variants in cancer predisposition genes (CPGs) are found in approximately 10% of pediatric patients with CNS tumors. This study aimed to characterize variants in CPGs in pediatric patients with CNS tumors and correlate these findings with clinically relevant data. Genomic DNA was isolated from the peripheral blood of 51 pediatric patients and further analyzed by the next-generation sequencing approach. Bioinformatic analysis was done using an "in-house" gene list panel, which included 144 genes related to pediatric brain tumors, and the gene list panel Neoplasm (HP:0002664). Our study found that 27% of pediatric patients with CNS tumors have a germline variant in some of the known CPGs, like ALK, APC, CHEK2, ELP1, MLH1, MSH2, NF1, NF2 and TP53. This study represents the first comprehensive evaluation of germline variants in pediatric patients with CNS tumors in the Western Balkans region. Our results indicate the necessity of genomic research to reveal the genetic basis of pediatric CNS tumors, as well as to define targets for the application and development of innovative therapeutics that form the basis of the upcoming era of personalized medicine.
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Affiliation(s)
- Aleksa Jovanović
- Pediatric Oncology Department, National Cancer Research Center, 11000 Belgrade, Serbia; (A.J.); (D.J.)
| | - Nataša Tošić
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (N.T.); (I.M.); (J.K.); (B.Z.)
| | - Irena Marjanović
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (N.T.); (I.M.); (J.K.); (B.Z.)
| | - Jovana Komazec
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (N.T.); (I.M.); (J.K.); (B.Z.)
| | - Branka Zukić
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (N.T.); (I.M.); (J.K.); (B.Z.)
| | - Marina Nikitović
- Pediatric Radiation Oncology Department, National Cancer Research Center, 11000 Belgrade, Serbia;
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (R.I.); (D.G.)
| | - Rosanda Ilić
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (R.I.); (D.G.)
- Neurooncology Department, Neurosurgery Clinic, University Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Danica Grujičić
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (R.I.); (D.G.)
- Neurooncology Department, Neurosurgery Clinic, University Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Dragana Janić
- Pediatric Oncology Department, National Cancer Research Center, 11000 Belgrade, Serbia; (A.J.); (D.J.)
| | - Sonja Pavlović
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (N.T.); (I.M.); (J.K.); (B.Z.)
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Ahmed S, Wedekind MF, Del Rivero J, Raygada M, Lockridge R, Glod JW, Flowers C, Thomas BJ, Bernstein DB, Kapustina OB, Jain A, Miettinen M, Raffeld M, Xi L, Tyagi M, Kim J, Aldape K, Malayeri AA, Kaplan RN, Allen T, Vivelo CA, Sandler AB, Widemann BC, Reilly KM. Longitudinal Natural History Study of Children and Adults with Rare Solid Tumors: Initial Results for First 200 Participants. CANCER RESEARCH COMMUNICATIONS 2023; 3:2468-2482. [PMID: 37966258 PMCID: PMC10699159 DOI: 10.1158/2767-9764.crc-23-0247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/16/2023]
Abstract
Understanding of tumor biology and identification of effective therapies is lacking for many rare tumors. My Pediatric and Adult Rare Tumor (MyPART) network was established to engage patients, advocates, and researchers and conduct a comprehensive longitudinal Natural History Study of Rare Solid Tumors. Through remote or in-person enrollment at the NIH Clinical Center, participants with rare solid tumors ≥4 weeks old complete standardized medical and family history forms, patient reported outcomes, and provide tumor, blood and/or saliva samples. Medical records are extracted for clinical status and treatment history, and tumors undergo genomic analysis. A total of 200 participants (65% female, 35% male, median age at diagnosis 43 years, range = 2-77) enrolled from 46 U.S. states and nine other countries (46% remote, 55% in-person). Frequent diagnoses were neuroendocrine neoplasms (NEN), adrenocortical carcinomas (ACC), medullary thyroid carcinomas (MTC), succinate dehydrogenase (SDH)-deficient gastrointestinal stromal tumors (sdGIST), and chordomas. At enrollment, median years since diagnosis was 3.5 (range = 0-36.6), 63% participants had metastatic disease and 20% had no evidence of disease. Pathogenic germline and tumor mutations included SDHA/B/C (sdGIST), RET (MTC), TP53 and CTNNB1 (ACC), MEN1 (NEN), and SMARCB1 (poorly-differentiated chordoma). Clinically significant anxiety was observed in 20%-35% of adults. Enrollment of participants and comprehensive data collection were feasible. Remote enrollment was critical during the COVID-19 pandemic. Over 30 patients were enrolled with ACC, NEN, and sdGIST, allowing for clinical/genomic analyses across tumors. Longitudinal follow-up and expansion of cohorts are ongoing to advance understanding of disease course and establish external controls for interventional trials. SIGNIFICANCE This study demonstrates that comprehensive, tumor-agnostic data and biospecimen collection is feasible to characterize different rare tumors, and speed progress in research. The findings will be foundational to developing external controls groups for single-arm interventional trials, where randomized control trials cannot be conducted because of small patient populations.
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Affiliation(s)
- Shadin Ahmed
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | | | - Jaydira Del Rivero
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Margarita Raygada
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Robin Lockridge
- Clinical Research Directorate (CRD), Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - John W. Glod
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Crystal Flowers
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - BJ Thomas
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Donna B. Bernstein
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Oxana B. Kapustina
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Ashish Jain
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, Massachusetts
| | - Markku Miettinen
- Laboratory of Pathology, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Mark Raffeld
- Laboratory of Pathology, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Liqiang Xi
- Laboratory of Pathology, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Manoj Tyagi
- Laboratory of Pathology, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Jung Kim
- Laboratory of Pathology, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Ashkan A. Malayeri
- Department of Radiology and Imaging Sciences, Clinical Center, NIH, Bethesda, Maryland
| | - Rosandra N. Kaplan
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Taryn Allen
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
- Clinical Research Directorate (CRD), Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Christina A. Vivelo
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
- Kelly Government Solutions, Bethesda, Maryland
| | - Abby B. Sandler
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | | | - Karlyne M. Reilly
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
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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: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [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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8
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CHEK2 Alterations in Pediatric Malignancy: A Single-Institution Experience. Cancers (Basel) 2023; 15:cancers15061649. [PMID: 36980535 PMCID: PMC10046043 DOI: 10.3390/cancers15061649] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Background: Approximately 10% of pediatric malignancies are secondary to germline alterations in cancer-predisposing genes. Checkpoint kinase 2 (CHEK2) germline loss-of-function variants have been reported in pediatric cancer patients, but clinical phenotypes and outcomes are poorly described. We present our single-institution experience of pediatric oncology patients with CHEK2 germline alterations, including clinical presentations and outcomes. Methods: Pediatric oncology patients with CHEK2 germline alterations were identified among those assessed by clinical or translational research at the Institute for Genomic Medicine at Nationwide Children’s Hospital. A chart review of disease course was conducted on identified patients. Results: We identified 6 patients with germline CHEK2 variants from a cohort of 300 individuals, including 1 patient with concurrent presentation of Burkitt lymphoma and neuroblastoma, 3 patients with brain tumors, 1 patient with Ewing sarcoma, and 1 patient with myelodysplastic syndrome. Three patients had a family history of malignancies. Four patients were in remission; one was undergoing treatment; one patient had developed treatment-related meningiomas. We review prior data regarding CHEK2 variants in this population, challenges associated with variant interpretation, and genetic counseling for individuals with CHEK2 variants. Conclusions: CHEK2 germline loss-of-function alterations occur in patients with a variety of pediatric tumors. Larger multicenter studies will improve our understanding of the incidence, phenotype, and molecular biology of CHEK2 germline variants in pediatric cancers.
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Splicing-Disrupting Mutations in Inherited Predisposition to Solid Pediatric Cancer. Cancers (Basel) 2022; 14:cancers14235967. [PMID: 36497448 PMCID: PMC9739414 DOI: 10.3390/cancers14235967] [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: 10/17/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
The prevalence of hereditary cancer in children was estimated to be very low until recent studies suggested that at least 10% of pediatric cancer patients carry a germline mutation in a cancer predisposition gene. A significant proportion of pathogenic variants associated with an increased risk of hereditary cancer are variants affecting splicing. RNA splicing is an essential process involved in different cellular processes such as proliferation, survival, and differentiation, and alterations in this pathway have been implicated in many human cancers. Hereditary cancer genes are highly susceptible to splicing mutations, and among them there are several genes that may contribute to pediatric solid tumors when mutated in the germline. In this review, we have focused on the analysis of germline splicing-disrupting mutations found in pediatric solid tumors, as the discovery of pathogenic splice variants in pediatric cancer is a growing field for the development of personalized therapies. Therapies developed to correct aberrant splicing in cancer are also discussed as well as the options to improve the diagnostic yield based on the increase in the knowledge in splicing.
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10
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Genetic predisposition to central nervous system tumors in children - what the neurosurgeon should know. Acta Neurochir (Wien) 2022; 164:3025-3034. [PMID: 35660974 DOI: 10.1007/s00701-022-05258-y] [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: 03/29/2022] [Accepted: 05/17/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Historically, few pediatric central nervous system (CNS) tumors were thought to result from genetic predisposition. However, within the last decade, new DNA sequencing methods have led to an increased recognition of high-risk cancer predisposition syndromes in children with CNS tumors. Thus, genetic predisposition is increasingly impacting clinical pediatric neuro-oncology. METHODS In this narrative review, we discuss the current understanding of genetic predisposition to childhood CNS tumors and provide a general overview of involved research methodologies and terminology. Moreover, we consider how germline genetics may influence neurosurgical practice. RESULTS Introduction of next-generation DNA sequencing has greatly increased our understanding of genetic predisposition to pediatric CNS tumors by enabling whole-exome/-genome sequencing of large cohorts. To date, the scientific literature has reported germline sequencing findings for more than 2000 children with CNS tumors. Although varying between tumor types, at least 10% of childhood CNS tumors can currently be explained by rare pathogenic germline variants in known cancer-related genes. Novel methodologies continue to uncover new mechanisms, suggesting that a much higher proportion of children with CNS tumors have underlying genetic causes. Understanding how genetic predisposition influences tumor biology and the clinical course in a given patient may mandate adjustments to neurosurgical treatment. CONCLUSION Germline genetics is becoming increasingly important to clinicians, including neurosurgeons. This review provides an updated overview of genetic predisposition to childhood CNS tumors with focus on aspects relevant to pediatric neurosurgeons.
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11
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Environmental Risk Factors for Childhood Central Nervous System Tumors: an Umbrella Review. CURR EPIDEMIOL REP 2022. [DOI: 10.1007/s40471-022-00309-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Foss-Skiftesvik J, Stoltze UK, van Overeem Hansen T, Ahlborn LB, Sørensen E, Ostrowski SR, Kullegaard SMA, Laspiur AO, Melchior LC, Scheie D, Kristensen BW, Skjøth-Rasmussen J, Schmiegelow K, Wadt K, Mathiasen R. Redefining germline predisposition in children with molecularly characterized ependymoma: a population-based 20-year cohort. Acta Neuropathol Commun 2022; 10:123. [PMID: 36008825 PMCID: PMC9404601 DOI: 10.1186/s40478-022-01429-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/11/2022] [Indexed: 11/10/2022] Open
Abstract
Ependymoma is the second most common malignant brain tumor in children. The etiology is largely unknown and germline DNA sequencing studies focusing on childhood ependymoma are limited. We therefore performed germline whole-genome sequencing on a population-based cohort of children diagnosed with ependymoma in Denmark over the past 20 years (n = 43). Single nucleotide and structural germline variants in 457 cancer related genes and 2986 highly evolutionarily constrained genes were assessed in 37 children with normal tissue available for sequencing. Molecular ependymoma classification was performed using DNA methylation profiling for 39 children with available tumor tissue. Pathogenic germline variants in known cancer predisposition genes were detected in 11% (4/37; NF2, LZTR1, NF1 & TP53). However, DNA methylation profiling resulted in revision of the histopathological ependymoma diagnosis to non-ependymoma tumor types in 8% (3/39). This included the two children with pathogenic germline variants in TP53 and NF1 whose tumors were reclassified to a diffuse midline glioma and a rosette-forming glioneuronal tumor, respectively. Consequently, 50% (2/4) of children with pathogenic germline variants in fact had other tumor types. A meta-analysis combining our findings with pediatric pan-cancer germline sequencing studies showed an overall frequency of pathogenic germline variants of 3.4% (7/207) in children with ependymoma. In summary, less than 4% of childhood ependymoma is explained by genetic predisposition, virtually restricted to pathogenic variants in NF2 and NF1. For children with other cancer predisposition syndromes, diagnostic reconsideration is recommended for ependymomas without molecular classification. Additionally, LZTR1 is suggested as a novel putative ependymoma predisposition gene.
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Affiliation(s)
- Jon Foss-Skiftesvik
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark. .,Department of Neurosurgery, Rigshospitalet University Hospital, Copenhagen, Denmark. .,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Department of Neurosurgery, Section 6031, Rigshospitalet University Hospital, Inge Lehmanns Vej 6, 2100, Copenhagen, Denmark. .,The Pediatric Oncology Research Laboratory, Section 5704, Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Henrik Harpestrengs Vej 6A, 2100, Copenhagen, Denmark.
| | - Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark.,Department of Clinical Genetics, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lise Barlebo Ahlborn
- Department of Genomic Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Immunology, Rigshospitalet University Hospital, Copenhagen, Denmark
| | | | - Adrian Otamendi Laspiur
- Department of Health Technology, Cancer Systems Biology and Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | | | - David Scheie
- Department of Pathology, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Bjarne Winther Kristensen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Pathology, Rigshospitalet University Hospital, Copenhagen, Denmark.,Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Jane Skjøth-Rasmussen
- Department of Neurosurgery, Rigshospitalet University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, University of Copenhagen, Copenhagen, Denmark
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
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13
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Li Y, Xu S, Xu D, Pan T, Guo J, Gu S, Lin Q, Li X, Li K, Xiang W. Pediatric Pan-Central Nervous System Tumor Methylome Analyses Reveal Immune-Related LncRNAs. Front Immunol 2022; 13:853904. [PMID: 35603200 PMCID: PMC9114481 DOI: 10.3389/fimmu.2022.853904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/11/2022] [Indexed: 01/10/2023] Open
Abstract
Pediatric central nervous system (CNS) tumors are the second most common cancer diagnosis among children. Long noncoding RNAs (lncRNAs) emerge as critical regulators of gene expression, and they play fundamental roles in immune regulation. However, knowledge on epigenetic changes in lncRNAs in diverse types of pediatric CNS tumors is lacking. Here, we integrated the DNA methylation profiles of 2,257 pediatric CNS tumors across 61 subtypes with lncRNA annotations and presented the epigenetically regulated landscape of lncRNAs. We revealed the prevalent lncRNA methylation heterogeneity across pediatric pan-CNS tumors. Based on lncRNA methylation profiles, we refined 14 lncRNA methylation clusters with distinct immune microenvironment patterns. Moreover, we found that lncRNA methylations were significantly correlated with immune cell infiltrations in diverse tumor subtypes. Immune-related lncRNAs were further identified by investigating their correlation with immune cell infiltrations and potentially regulated target genes. LncRNA with methylation perturbations potentially regulate the genes in immune-related pathways. We finally identified several candidate immune-related lncRNA biomarkers (i.e., SSTR5-AS1, CNTN4-AS1, and OSTM1-AS1) in pediatric cancer for further functional validation. In summary, our study represents a comprehensive repertoire of epigenetically regulated immune-related lncRNAs in pediatric pan-CNS tumors, and will facilitate the development of immunotherapeutic targets.
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Affiliation(s)
- Yongsheng Li
- College of Biomedical Information and Engineering, NHC Key Laboratory of Control of Tropical Diseases, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China
| | - Sicong Xu
- College of Biomedical Information and Engineering, NHC Key Laboratory of Control of Tropical Diseases, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China
| | - Dahua Xu
- College of Biomedical Information and Engineering, NHC Key Laboratory of Control of Tropical Diseases, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China
| | - Tao Pan
- College of Biomedical Information and Engineering, NHC Key Laboratory of Control of Tropical Diseases, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China
| | - Jing Guo
- College of Biomedical Information and Engineering, NHC Key Laboratory of Control of Tropical Diseases, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China
| | - Shuo Gu
- College of Biomedical Information and Engineering, NHC Key Laboratory of Control of Tropical Diseases, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China
| | - Qiuyu Lin
- College of Biomedical Information and Engineering, NHC Key Laboratory of Control of Tropical Diseases, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China
| | - Xia Li
- College of Biomedical Information and Engineering, NHC Key Laboratory of Control of Tropical Diseases, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China.,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kongning Li
- College of Biomedical Information and Engineering, NHC Key Laboratory of Control of Tropical Diseases, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China
| | - Wei Xiang
- College of Biomedical Information and Engineering, NHC Key Laboratory of Control of Tropical Diseases, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China
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14
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Chen W, Wang S, Tithi SS, Ellison DW, Schaid DJ, Wu G. A rare variant analysis framework using public genotype summary counts to prioritize disease-predisposition genes. Nat Commun 2022; 13:2592. [PMID: 35545612 PMCID: PMC9095601 DOI: 10.1038/s41467-022-30248-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/21/2022] [Indexed: 11/11/2022] Open
Abstract
Sequencing cases without matched healthy controls hinders prioritization of germline disease-predisposition genes. To circumvent this problem, genotype summary counts from public data sets can serve as controls. However, systematic inflation and false positives can arise if confounding factors are not controlled. We propose a framework, consistent summary counts based rare variant burden test (CoCoRV), to address these challenges. CoCoRV implements consistent variant quality control and filtering, ethnicity-stratified rare variant association test, accurate estimation of inflation factors, powerful FDR control, and detection of rare variant pairs in high linkage disequilibrium. When we applied CoCoRV to pediatric cancer cohorts, the top genes identified were cancer-predisposition genes. We also applied CoCoRV to identify disease-predisposition genes in adult brain tumors and amyotrophic lateral sclerosis. Given that potential confounding factors were well controlled after applying the framework, CoCoRV provides a cost-effective solution to prioritizing disease-risk genes enriched with rare pathogenic variants.
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Affiliation(s)
- Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Shuoguo Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- 150 Second Street, Cambridge, MA, USA
| | - Saima Sultana Tithi
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel J Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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15
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Paun L, Lavé A, Patet G, Bartoli A. Supratentorial Pediatric Midline Tumors and Tumor-like Lesions: Clinical Spectrum, Natural History and Treatment Options. CHILDREN (BASEL, SWITZERLAND) 2022; 9:children9040534. [PMID: 35455578 PMCID: PMC9032564 DOI: 10.3390/children9040534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 04/10/2023]
Abstract
Childhood Central Nervous System tumors account for 25% of all pediatric tumors. Large availability and broadening of indications to imaging has made incidental findings more common. Among these, midline lesions have different clinical relevance depending on their intrinsic pattern of behaviour and on their specific location. In this narrative review we describe the natural history and treatment options of midline lesions in children.
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16
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Hahn G, Mentzel HJ. [Tumors of the central nervous system in children and adolescents]. Radiologe 2021; 61:601-610. [PMID: 34191042 DOI: 10.1007/s00117-021-00860-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 11/26/2022]
Abstract
CLINICAL/METHODOLOGICAL ISSUE Brain tumors are the most common solid tumors in childhood and the most frequent cancer after leukemia. The incidence is continuously increasing. The WHO classification of brain tumors, valid since 2016, is now based on the combination of histological and molecular genetic diagnostics. STANDARD RADIOLOGICAL METHODS Diagnostics are mainly performed with magnetic resonance imaging (MRI); only in emergencies with computed tomography (CT). METHODOLOGICAL INNOVATIONS Diffusion and susceptibility weighted and dynamic contrast-enhanced imaging and spectroscopy are used. PERFORMANCE Improved diagnosis regarding dignity, size determination, adjacency assessment, and morphological description of tumor composition. ACHIEVEMENTS Modern MRI with functional techniques is now the gold standard for differential diagnosis and staging of central nervous system (CNS) tumors in pediatrics.
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Affiliation(s)
- G Hahn
- Bereich für Kinderradiologie, Institut und Poliklinik für diagnostische und interventionelle Radiologie, Universitätsklinikum Carl Gustav Carus, Fetscherstr. 74, 01307, Dresden, Deutschland.
| | - H-J Mentzel
- Sektion Kinderradiologie, Institut für Diagnostische und Interventionelle Radiologie, Universitätsklinikum Jena, Jena, Deutschland
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17
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Adel Fahmideh M, Scheurer ME. Pediatric Brain Tumors: Descriptive Epidemiology, Risk Factors, and Future Directions. Cancer Epidemiol Biomarkers Prev 2021; 30:813-821. [PMID: 33653816 DOI: 10.1158/1055-9965.epi-20-1443] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/23/2020] [Accepted: 02/23/2021] [Indexed: 11/16/2022] Open
Abstract
Brain tumors are the most common solid tumors in children and remain a significant contributor to death by disease in this population. Pediatric brain tumors (PBT) are broadly classified into two major categories: glial and neuronal tumors. Various factors, including tumor histology, tumor location, and demographics, influence the incidence and prognosis of this heterogeneous group of neoplasms. Numerous epidemiologic studies have been conducted to identify genetic and environmental risk factors for these malignancies. Thus far, the only established risk factors for PBTs are exposure to ionizing radiation and some rare genetic syndromes. However, relatively consistent evidence of positive associations for birth defects, markers of fetal growth, advanced parental age, maternal dietary N-nitroso compounds, and exposure to pesticides have been reported. The genetic variants associated with susceptibility to PBTs were predominantly identified by a candidate-gene approach. The identified genetic variants belong to four main pathways, including xenobiotic detoxification, inflammation, DNA repair, and cell-cycle regulation. Conducting large and multi-institutional studies is warranted to systematically detect genetic and environmental risk factors for different histologic subtypes of PBTs. This, in turn, might lead to a better understanding of etiology of PBTs and eventually developing risk prediction models to prevent these clinically significate malignancies.
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Affiliation(s)
- Maral Adel Fahmideh
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, Texas. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Center for Epidemiology and Population Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Michael E Scheurer
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Center for Epidemiology and Population Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas
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18
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Foss-Skiftesvik J, Hagen CM, Mathiasen R, Adamsen D, Bækvad-Hansen M, Børglum AD, Nordentoft M, Werge T, Christiansen M, Schmiegelow K, Juhler M, Mortensen PB, Hougaard DM, Bybjerg-Grauholm J. Genome-wide association study across pediatric central nervous system tumors implicates shared predisposition and points to 1q25.2 (PAPPA2) and 11p12 (LRRC4C) as novel candidate susceptibility loci. Childs Nerv Syst 2021; 37:819-830. [PMID: 33226468 DOI: 10.1007/s00381-020-04946-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Central nervous system (CNS) tumors constitute the most common form of solid neoplasms in children, but knowledge on genetic predisposition is sparse. In particular, whether susceptibility attributable to common variants is shared across CNS tumor types in children has not been investigated. The purpose of this study was to explore potential common genetic risk variants exhibiting pleiotropic effects across pediatric CNS tumors. We also investigated whether such susceptibility differs between early and late onset of disease. METHOD A Danish nationwide genome-wide association study (GWAS) of 1,097 consecutive patients (< 15 years of age) with CNS tumors and a cohort of 4,745 population-based controls. RESULTS For both the overall cohort and patients diagnosed after the age of four, the strongest association was rs12064625 which maps to PAPPA2 at 1q25.2 (p = 3.400 × 10-7 and 9.668 × 10-8, respectively). PAPPA2 regulates local bioavailability of insulin-like growth factor I (IGF-I). IGF-I is fundamental to CNS development and is involved in tumorigenesis across a wide range of different cancers. For the younger children, the strongest association was provided by rs11036373 mapping to LRRC4C at 11p12 (p = 7.620 × 10-7), which encoded protein acts as an axon guidance molecule during CNS development and has not formerly been associated with brain tumors. DISCUSSION This GWAS indicates shared susceptibility attributable to common variants across pediatric CNS tumor types. Variations in genetic loci with roles in CNS development appear to be involved, possibly via altered IGF-I related pathways.
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Affiliation(s)
- Jon Foss-Skiftesvik
- Department of Neurosurgery, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark.
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark.
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark.
| | - Christian Munch Hagen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Dea Adamsen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- Department of Biomedicine, Aarhus University and Centre for Integrative Sequencing, iSEQ, Aarhus, Denmark
- Aarhus Genome Center, Aarhus, Denmark
| | - Merete Nordentoft
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Michael Christiansen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Juhler
- Department of Neurosurgery, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neurosurgery, Aarhus University Hospital, Aarhus, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
| | - David Michael Hougaard
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
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Subependymal giant cell astrocytomas are characterized by mTORC1 hyperactivation, a very low somatic mutation rate, and a unique gene expression profile. Mod Pathol 2021; 34:264-279. [PMID: 33051600 PMCID: PMC9361192 DOI: 10.1038/s41379-020-00659-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/22/2022]
Abstract
Subependymal giant-cell astrocytomas (SEGAs) are slow-growing brain tumors that are a hallmark feature seen in 5-10% of patients with Tuberous Sclerosis Complex (TSC). Though histologically benign, they can cause serious neurologic symptoms, leading to death if untreated. SEGAs consistently show biallelic loss of TSC1 or TSC2. Herein, we aimed to define other somatic events beyond TSC1/TSC2 loss and identify potential transcriptional drivers that contribute to SEGA formation. Paired tumor-normal whole-exome sequencing was performed on 21 resected SEGAs from 20 TSC patients. Pathogenic variants in TSC1/TSC2 were identified in 19/21 (90%) SEGAs. Copy neutral loss of heterozygosity (size range: 2.2-46 Mb) was seen in 76% (16/21) of SEGAs (44% chr9q and 56% chr16p). An average of 1.4 other somatic variants (range 0-7) per tumor were identified, unlikely of pathogenic significance. Whole transcriptome RNA-sequencing analyses revealed 190 common differentially expressed genes in SEGA (n = 16, 13 from a prior study) in pairwise comparison to each of: low grade diffuse gliomas (n = 530) and glioblastoma (n = 171) from The Cancer Genome Atlas (TCGA) consortium, ganglioglioma (n = 10), TSC cortical tubers (n = 15), and multiple normal tissues. Among these, homeobox transcription factors (TFs) HMX3, HMX2, VAX1, SIX3; and TFs IRF6 and EOMES were all expressed >12-fold higher in SEGAs (FDR/q-value < 0.05). Immunohistochemistry supported the specificity of IRF6, VAX1, SIX3 for SEGAs in comparison to other tumor entities and normal brain. We conclude that SEGAs have an extremely low somatic mutation rate, suggesting that TSC1/TSC2 loss is sufficient to drive tumor growth. The unique and highly expressed SEGA-specific TFs likely reflect the neuroepithelial cell of origin, and may also contribute to the transcriptional and epigenetic state that enables SEGA growth following two-hit loss of TSC1 or TSC2 and mTORC1 activation.
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Huang W, Sundquist K, Sundquist J, Ji J. Psychiatric disorders in offspring of childhood or adolescent central nervous system tumor survivors: a national cohort study. Cancer Med 2020; 10:675-683. [PMID: 33135321 PMCID: PMC7877351 DOI: 10.1002/cam4.3591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Children experience a higher risk of psychiatric problems when their parents are diagnosed with cancer. However, the psychological effect among offspring who are born after parental cancer diagnosed in childhood or adolescence is unknown. We aimed to investigate the risk of psychiatric disorders in children of survivors with childhood or adolescent central nervous system (CNS) tumors. METHODS By combining several nationwide Swedish registers, we identified all children who had at least one parent previously diagnosed with CNS tumor below the age of 20. Five children without parental CNS tumor were randomly selected for the matching. Cox proportional hazards model was used to calculate hazard ratios (HRs) with 95% confidence interval (CI). RESULTS The incidence rate of psychiatric disorders was 8.46 per 1000 person-years in children of CNS tumor survivors, whereas the rate was 7.47 in the matched comparisons, yielding an adjusted HR of 1.10 (95% CI = 0.94, 1.28). Boys of survivors had a higher risk of psychiatric disorders (adjusted HR = 1.29, 95% CI = 1.04, 1.59). The risk of the specific types of psychiatric disorders in children of tumor survivors was comparable with that in the matched comparisons, except for mental retardation. Children of survivors experienced 2.36 times higher risk of mental retardation (95% CI = 1.21, 4.58), mainly of mild mental retardation (adjusted HR = 2.99, 95% CI = 1.40, 6.38). CONCLUSION Children of survivors with CNS tumor in early life did not experience a significantly increased risk of overall psychiatric disorders, with the exception of an elevated risk of mental retardation that was mainly mild.
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Affiliation(s)
- Wuqing Huang
- Center for Primary Health Care ResearchLund University/Region SkåneLundSweden
| | - Kristina Sundquist
- Center for Primary Health Care ResearchLund University/Region SkåneLundSweden
- Department of Family Medicine and Community HealthDepartment of Population Health Science and PolicyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Center for Community‐based Healthcare Research and Education (CoHRE)Department of Functional PathologySchool of MedicineShimane UniversityMatsueJapan
| | - Jan Sundquist
- Center for Primary Health Care ResearchLund University/Region SkåneLundSweden
- Department of Family Medicine and Community HealthDepartment of Population Health Science and PolicyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
- Center for Community‐based Healthcare Research and Education (CoHRE)Department of Functional PathologySchool of MedicineShimane UniversityMatsueJapan
| | - Jianguang Ji
- Center for Primary Health Care ResearchLund University/Region SkåneLundSweden
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21
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Abstract
Gliomas are a diverse group of primary central nervous system tumors with astrocytic, oligodendroglial, and/or ependymal features and are an important cause of morbidity/mortality in pediatric patients. Glioma classification relies on integrating tumor histology with key molecular alterations. This approach can help establish a diagnosis, guide treatment, and determine prognosis. New categories of pediatric glioma have been recognized in recent years, due to increasing application of molecular profiling in brain tumors. The aim of this review is to alert pediatric pathologists to emerging diagnostic concepts in pediatric glioma neuropathology, emphasizing the incorporation of molecular features into diagnostic practice.
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Affiliation(s)
- Melanie H Hakar
- Department of Pathology, Oregon Health & Science University, 3181 Southwest Sam Jackson Park Road, L-113, Portland, OR 97239, USA
| | - Matthew D Wood
- Department of Pathology, Oregon Health & Science University and Knight Cancer Institute, 3181 Southwest Sam Jackson Park Road, L-113, Portland, OR 97239, USA.
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22
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Muskens IS, Feng Q, Francis SS, Walsh KM, Mckean-Cowdin R, Gauderman WJ, de Smith AJ, Wiemels JL. Pediatric glioma and medulloblastoma risk and population demographics: a Poisson regression analysis. Neurooncol Adv 2020; 2:vdaa089. [PMID: 32864610 PMCID: PMC7447139 DOI: 10.1093/noajnl/vdaa089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background The incidence of pediatric brain tumors varies by race and ethnicity, but these relationships may be confounded by socioeconomic status (SES). In this study, the Surveillance, Epidemiology, and End Results Program (SEER) database was evaluated for associations between race/ethnicity and pediatric glioma and medulloblastoma risk with adjustment for SES. Methods Pediatric glioma and medulloblastoma cases from the SEER database (years: 2000–2016) were included. Differences in incidence rates by ethnicity, sex, age, and SES-related factors were evaluated by calculation of age-adjusted incidence rates (AAIRs) and annual percent change (APC). SES-related factors (percentage without less than high school graduation, median household income, and percentage foreign-born) were derived from the census at the county-level (year: 2000). Multivariable Poisson regression models with adjustment for selected covariates were constructed to evaluate risk factors. Results The highest AAIRs of pediatric glioma were observed among non-Hispanic Whites (AAIR: 2.91 per 100 000, 95%-CI: 2.84–2.99). An increasing incidence of pediatric glioma by calendar time was observed among non-Hispanic Whites and non-Hispanic Blacks (APC: 0.97%, 95%-CI: 0.28–1.68 and APC: 1.59%, 95%-CI: 0.03–3.18, respectively). Hispanic and non-Hispanic Black race/ethnicity was associated with lower risk when compared with non-Hispanic White (incidence rate ratios [IRRs]: 0.66, 95%-CI: 0.63–0.70; and 0.69, 95%-CI: 0.65–0.74, respectively). For medulloblastoma, the highest AAIR was observed for non-Hispanic Whites with a positive APC (1.52%, 95%-CI: 0.15–2.91). Hispanics and non-Hispanic Blacks had statistically significant lower IRRs compared with non-Hispanic Whites (IRRs: 0.83, 95%-CI: 0.73–0.94; and 0.72, 95%-CI: 0.59–0.87, respectively). Conclusion Non-Hispanic White race/ethnicity was associated with higher pediatric glioma and medulloblastoma IRRs in models with adjustments for SES.
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Affiliation(s)
- Ivo S Muskens
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Qianxi Feng
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Stephen S Francis
- Department of Neurosurgery, Division of Neuro and Molecular Epidemiology, University of California, San Francisco, California, USA
| | - Kyle M Walsh
- Department of Neurosurgery, Duke Cancer Institute, and Children's Health and Discovery Institute, Duke University, Durham, North Carolina, USA
| | - Roberta Mckean-Cowdin
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - William J Gauderman
- Division of Biostatistics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Adam J de Smith
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Joseph L Wiemels
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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