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Shapiro JA, Gaonkar KS, Spielman SJ, Savonen CL, Bethell CJ, Jin R, Rathi KS, Zhu Y, Egolf LE, Farrow BK, Miller DP, Yang Y, Koganti T, Noureen N, Koptyra MP, Duong N, Santi M, Kim J, Robins S, Storm PB, Mack SC, Lilly JV, Xie HM, Jain P, Raman P, Rood BR, Lulla RR, Nazarian J, Kraya AA, Vaksman Z, Heath AP, Kline C, Scolaro L, Viaene AN, Huang X, Way GP, Foltz SM, Zhang B, Poetsch AR, Mueller S, Ennis BM, Prados M, Diskin SJ, Zheng S, Guo Y, Kannan S, Waanders AJ, Margol AS, Kim MC, Hanson D, Van Kuren N, Wong J, Kaufman RS, Coleman N, Blackden C, Cole KA, Mason JL, Madsen PJ, Koschmann CJ, Stewart DR, Wafula E, Brown MA, Resnick AC, Greene CS, Rokita JL, Taroni JN. OpenPBTA: The Open Pediatric Brain Tumor Atlas. CELL GENOMICS 2023; 3:100340. [PMID: 37492101 PMCID: PMC10363844 DOI: 10.1016/j.xgen.2023.100340] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/28/2023] [Accepted: 05/04/2023] [Indexed: 07/27/2023]
Abstract
Pediatric brain and spinal cancers are collectively the leading disease-related cause of death in children; thus, we urgently need curative therapeutic strategies for these tumors. To accelerate such discoveries, the Children's Brain Tumor Network (CBTN) and Pacific Pediatric Neuro-Oncology Consortium (PNOC) created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to establish OpenPBTA, an open collaborative project with over 40 scalable analysis modules that genomically characterize 1,074 pediatric brain tumors. Transcriptomic classification reveals universal TP53 dysregulation in mismatch repair-deficient hypermutant high-grade gliomas and TP53 loss as a significant marker for poor overall survival in ependymomas and H3 K28-mutant diffuse midline gliomas. Already being actively applied to other pediatric cancers and PNOC molecular tumor board decision-making, OpenPBTA is an invaluable resource to the pediatric oncology community.
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Affiliation(s)
- Joshua A. Shapiro
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
| | - Krutika S. Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stephanie J. Spielman
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- Rowan University, Glassboro, NJ 08028, USA
| | - Candace L. Savonen
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
| | - Chante J. Bethell
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
| | - Run Jin
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Komal S. Rathi
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Laura E. Egolf
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bailey K. Farrow
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Daniel P. Miller
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yang Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Tejaswi Koganti
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nighat Noureen
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Mateusz P. Koptyra
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nhat Duong
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Shannon Robins
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Phillip B. Storm
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stephen C. Mack
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jena V. Lilly
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hongbo M. Xie
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Payal Jain
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Brian R. Rood
- Children’s National Research Institute, Washington, DC 20012, USA
- George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Rishi R. Lulla
- Division of Hematology/Oncology, Hasbro Children’s Hospital, Providence, RI 02903, USA
- Department of Pediatrics, The Warren Alpert School of Brown University, Providence, RI 02912, USA
| | - Javad Nazarian
- Children’s National Research Institute, Washington, DC 20012, USA
- George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
- Department of Pediatrics, University of Zurich, Zurich, Switzerland
| | - Adam A. Kraya
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zalman Vaksman
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Allison P. Heath
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Cassie Kline
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Laura Scolaro
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Angela N. Viaene
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Xiaoyan Huang
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gregory P. Way
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Steven M. Foltz
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anna R. Poetsch
- Biotechnology Center, Technical University Dresden, Dresden, Germany
- National Center for Tumor Diseases, Dresden, Germany
| | - Sabine Mueller
- Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Brian M. Ennis
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael Prados
- University of California, San Francisco, San Francisco, CA 94115, USA
| | - Sharon J. Diskin
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Siyuan Zheng
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Yiran Guo
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shrivats Kannan
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Angela J. Waanders
- Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ashley S. Margol
- Division of Hematology and Oncology, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA
- Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA
| | - Meen Chul Kim
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Derek Hanson
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
- Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - Nicholas Van Kuren
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jessica Wong
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Rebecca S. Kaufman
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Noel Coleman
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher Blackden
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kristina A. Cole
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer L. Mason
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peter J. Madsen
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carl J. Koschmann
- Department of Pediatrics, University of Michigan Health, Ann Arbor, MI 48105, USA
- Pediatric Hematology Oncology, Mott Children’s Hospital, Ann Arbor, MI 48109, USA
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Eric Wafula
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Miguel A. Brown
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Adam C. Resnick
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Casey S. Greene
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jaclyn N. Taroni
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
| | - Children’s Brain Tumor Network
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Rowan University, Glassboro, NJ 08028, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Children’s National Research Institute, Washington, DC 20012, USA
- George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
- Division of Hematology/Oncology, Hasbro Children’s Hospital, Providence, RI 02903, USA
- Department of Pediatrics, The Warren Alpert School of Brown University, Providence, RI 02912, USA
- Department of Pediatrics, University of Zurich, Zurich, Switzerland
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Biotechnology Center, Technical University Dresden, Dresden, Germany
- National Center for Tumor Diseases, Dresden, Germany
- Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, CA 94115, USA
- University of California, San Francisco, San Francisco, CA 94115, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Division of Hematology and Oncology, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA
- Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
- Hackensack University Medical Center, Hackensack, NJ 07601, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Michigan Health, Ann Arbor, MI 48105, USA
- Pediatric Hematology Oncology, Mott Children’s Hospital, Ann Arbor, MI 48109, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pacific Pediatric Neuro-Oncology Consortium
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Rowan University, Glassboro, NJ 08028, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Children’s National Research Institute, Washington, DC 20012, USA
- George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
- Division of Hematology/Oncology, Hasbro Children’s Hospital, Providence, RI 02903, USA
- Department of Pediatrics, The Warren Alpert School of Brown University, Providence, RI 02912, USA
- Department of Pediatrics, University of Zurich, Zurich, Switzerland
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Biotechnology Center, Technical University Dresden, Dresden, Germany
- National Center for Tumor Diseases, Dresden, Germany
- Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, CA 94115, USA
- University of California, San Francisco, San Francisco, CA 94115, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Division of Hematology and Oncology, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA
- Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
- Hackensack University Medical Center, Hackensack, NJ 07601, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Michigan Health, Ann Arbor, MI 48105, USA
- Pediatric Hematology Oncology, Mott Children’s Hospital, Ann Arbor, MI 48109, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Gundem G, Levine MF, Roberts SS, Cheung IY, Medina-Martínez JS, Feng Y, Arango-Ossa JE, Chadoutaud L, Rita M, Asimomitis G, Zhou J, You D, Bouvier N, Spitzer B, Solit DB, Dela Cruz F, LaQuaglia MP, Kushner BH, Modak S, Shukla N, Iacobuzio-Donahue CA, Kung AL, Cheung NKV, Papaemmanuil E. Clonal evolution during metastatic spread in high-risk neuroblastoma. Nat Genet 2023:10.1038/s41588-023-01395-x. [PMID: 37169874 DOI: 10.1038/s41588-023-01395-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/12/2023] [Indexed: 05/13/2023]
Abstract
Patients with high-risk neuroblastoma generally present with widely metastatic disease and often relapse despite intensive therapy. As most studies to date focused on diagnosis-relapse pairs, our understanding of the genetic and clonal dynamics of metastatic spread and disease progression remain limited. Here, using genomic profiling of 470 sequential and spatially separated samples from 283 patients, we characterize subtype-specific genetic evolutionary trajectories from diagnosis through progression and end-stage metastatic disease. Clonal tracing timed disease initiation to embryogenesis. Continuous acquisition of structural variants at disease-defining loci (MYCN, TERT, MDM2-CDK4) followed by convergent evolution of mutations targeting shared pathways emerged as the predominant feature of progression. At diagnosis metastatic clones were already established at distant sites where they could stay dormant, only to cause relapses years later and spread via metastasis-to-metastasis and polyclonal seeding after therapy.
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Affiliation(s)
- Gunes Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Max F Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephen S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irene Y Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan S Medina-Martínez
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yi Feng
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan E Arango-Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Loic Chadoutaud
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mathieu Rita
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Georgios Asimomitis
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joe Zhou
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, New York, NY, USA
| | - Filemon Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael P LaQuaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian H Kushner
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shakeel Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- The David M. Rubenstein Center for Pancreatic Cancer Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nai-Kong V Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elli Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Wieczorek A, Stefanowicz J, Hennig M, Adamkiewicz-Drozynska E, Stypinska M, Dembowska-Baginska B, Gamrot Z, Woszczyk M, Geisler J, Szczepanski T, Skoczen S, Ussowicz M, Pogorzala M, Janczar S, Balwierz W. Isolated central nervous system relapses in patients with high-risk neuroblastoma -clinical presentation and prognosis: experience of the Polish Paediatric Solid Tumours Study Group. BMC Cancer 2022; 22:701. [PMID: 35752779 PMCID: PMC9233790 DOI: 10.1186/s12885-022-09776-x] [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: 10/23/2021] [Accepted: 06/08/2022] [Indexed: 11/26/2022] Open
Abstract
Although isolated central nervous system (CNS) relapses are rare, they may become a serious clinical problem in intensively treated patients with high-risk neuroblastoma (NBL). The aim of this study is the presentation and assessment of the incidence and clinical course of isolated CNS relapses. Retrospective analysis involved 848 NBL patients treated from 2001 to 2019 at 8 centres of the Polish Paediatric Solid Tumours Study Group (PPSTSG). Group characteristics at diagnosis, treatment and patterns of relapse were analysed. Observation was completed in December 2020. We analysed 286 high risk patients, including 16 infants. Isolated CNS relapse, defined as the presence of a tumour in brain parenchyma or leptomeningeal involvement, was found in 13 patients (4.5%; 8.4% of all relapses), all of whom were stage 4 at diagnosis. Isolated CNS relapses seem to be more common in young patients with stage 4 MYCN amplified NBL, and in this group they may occur early during first line therapy. The only or the first symptom may be bleeding into the CNS, especially in younger children, even without a clear relapse picture on imaging, or the relapse may be clinically asymptomatic and found during routine screening. Although the incidence of isolated CNS relapses is not statistically significantly higher in patients after immunotherapy, their occurrence should be carefully monitored, especially in intensively treated infants, with potential disruption of the brain-blood barrier.
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Affiliation(s)
- Aleksandra Wieczorek
- Department of Paediatric Oncology and Haematology, Faculty of Medicine, Jagiellonian University, Medical College, Krakow, Poland.
| | - Joanna Stefanowicz
- Department of Paediatrics, Haematology and Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Marcin Hennig
- Department of Paediatrics, Haematology and Oncology, Medical University of Gdansk, Gdansk, Poland
| | | | - Marzena Stypinska
- Department of Oncology, The Children Memorial Health Institute in Warsaw, Warsaw, Poland
| | | | - Zuzanna Gamrot
- Unit of Paediatric Haematology and Oncology, City Hospital, Chorzow, Poland
| | - Mariola Woszczyk
- Unit of Paediatric Haematology and Oncology, City Hospital, Chorzow, Poland
| | - Julia Geisler
- Department of Paediatric Haematology and Oncology, Medical University of Silesia, Zabrze, Poland
| | - Tomasz Szczepanski
- Department of Paediatric Haematology and Oncology, Medical University of Silesia, Zabrze, Poland
| | - Szymon Skoczen
- Department of Paediatric Oncology and Haematology, Faculty of Medicine, Jagiellonian University, Medical College, Krakow, Poland
| | - Marek Ussowicz
- Department and Clinic of Paediatric Oncology, Haematology and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland
| | - Monika Pogorzala
- Paediatric Haematology and Oncology, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Szymon Janczar
- Department of Paediatrics, Oncology and Haematology, Medical University of Lodz, Lodz, Poland
| | - Walentyna Balwierz
- Department of Paediatric Oncology and Haematology, Faculty of Medicine, Jagiellonian University, Medical College, Krakow, Poland
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4
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Luo S, Lin R, Liao X, Li D, Qin Y. Identification and verification of the molecular mechanisms and prognostic values of the cadherin gene family in gastric cancer. Sci Rep 2021; 11:23674. [PMID: 34880371 PMCID: PMC8655011 DOI: 10.1038/s41598-021-03086-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022] Open
Abstract
While cadherin (CDH) genes are aberrantly expressed in cancers, the functions of CDH genes in gastric cancer (GC) remain poorly understood. The clinical significance and molecular mechanisms of CDH genes in GC were assessed in this study. Data from a total of 1226 GC patients included in The Cancer Genome Atlas (TCGA) and Kaplan–Meier plotter database were used to independently explore the value of CDH genes in clinical application. The TCGA RNA sequencing dataset was used to explore the molecular mechanisms of CDH genes in GC. Using enrichment analysis tools, CDH genes were found to be related to cell adhesion and calcium ion binding in function. In TCGA cohort, 12 genes were found to be differentially expressed between GC para-carcinoma and tumor tissue. By analyzing GC patients in two independent cohorts, we identified and verified that CDH2, CDH6, CDH7 and CDH10 were significantly associated with a poor GC prognosis. In addition, CDH2 and CDH6 were used to construct a GC risk score signature that can significantly improve the accuracy of predicting the 5-year survival of GC patients. The GSEA approach was used to explore the functional mechanisms of the four prognostic CDH genes and their associated risk scores. It was found that these genes may be involved in multiple classic cancer-related signaling pathways, such as the Wnt and phosphoinositide 3-kinase signaling pathways in GC. In the subsequent CMap analysis, three small molecule compounds (anisomycin, nystatin and bumetanide) that may be the target molecules that determine the risk score in GC, were initially screened. In conclusion, our current study suggests that four CDH genes can be used as potential biomarkers for GC prognosis. In addition, a prognostic signature based on the CDH2 and CDH6 genes was constructed, and their potential functional mechanisms and drug interactions explored.
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Affiliation(s)
- Shanshan Luo
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Guangxi Clinical Research Center for Colorectal Cancer, He Di Road 71, Nanning, 530021, Guangxi Autonomous Region, People's Republic of China.
| | - Rujing Lin
- Department of General Surgery, The People's Hospital of Binyang County, Nanning, 530405, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Daimou Li
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Guangxi Clinical Research Center for Colorectal Cancer, He Di Road 71, Nanning, 530021, Guangxi Autonomous Region, People's Republic of China
| | - Yuzhou Qin
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Guangxi Clinical Research Center for Colorectal Cancer, He Di Road 71, Nanning, 530021, Guangxi Autonomous Region, People's Republic of China.
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5
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High Grade of Amplification of Six Regions on Chromosome 2p in a Neuroblastoma Patient with Very Poor Outcome: The Putative New Oncogene TSSC1. Cancers (Basel) 2021; 13:cancers13225792. [PMID: 34830942 PMCID: PMC8616235 DOI: 10.3390/cancers13225792] [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: 09/28/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Here, a case of neuroblastoma (NB) carrying a high-grade amplification of six loci besides MYCN is described. Since the patient had a very poor outcome, we postulated that these DNA co-amplifications might have a synergistic effect in increasing NB cell proliferation. In order to verify this hypothesis, we analyzed in silico the impact of high expression of the genes located within the amplifications on the NB patients’ outcome using a large dataset integrating three different platforms. These analyses disclosed that high expression of the TSSC1 gene was the most significantly associated with reduced overall survival of NB patients, suggesting that it may have a potential prognostic role in NB in both MYCN amplified and MYCN not amplified tumors. Further studies on TSSC1 interactions and functioning could lead to possible focused therapies for high-risk NB patients. Abstract We observed a case of high-risk neuroblastoma (NB) carried by a 28-month-old girl, displaying metastatic disease and a rapid decline of clinical conditions. By array-CGH analysis of the tumor tissue and of the metastatic bone marrow aspirate cells, we found a high-grade amplification of six regions besides MYCN on bands 2p25.3–p24.3. The genes involved in these amplifications were MYT1L, TSSC1, CMPK2, RSAD2, RNF144A, GREB1, NTSR2, LPIN1, NBAS, and the two intergenic non-protein coding RNAs LOC730811 and LOC339788. We investigated if these DNA co-amplifications may have an effect on enhancing tumor aggressiveness. We evaluated the association between the high expression of the amplified genes and NB patient’s outcome using the integration of gene expression data of 786 NB samples profiled with different public platforms from patients with at least five-year follow-up. NB patients with high expression of the TSSC1 gene were associated with a reduced survival rate. Immunofluorescence staining on primary tumor tissues confirmed that the TSSC1 protein expression was high in the relapsed or dead stage 4 cases, but it was generally low in NB patients in complete remission. TSSC1 appears as a putative new oncogene in NB.
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6
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Gaonkar KS, Marini F, Rathi KS, Jain P, Zhu Y, Chimicles NA, Brown MA, Naqvi AS, Zhang B, Storm PB, Maris JM, Raman P, Resnick AC, Strauch K, Taroni JN, Rokita JL. annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions. BMC Bioinformatics 2020; 21:577. [PMID: 33317447 PMCID: PMC7737294 DOI: 10.1186/s12859-020-03922-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 12/03/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Gene fusion events are significant sources of somatic variation across adult and pediatric cancers and are some of the most clinically-effective therapeutic targets, yet low consensus of RNA-Seq fusion prediction algorithms makes therapeutic prioritization difficult. In addition, events such as polymerase read-throughs, mis-mapping due to gene homology, and fusions occurring in healthy normal tissue require informed filtering, making it difficult for researchers and clinicians to rapidly discern gene fusions that might be true underlying oncogenic drivers of a tumor and in some cases, appropriate targets for therapy. RESULTS We developed annoFuse, an R package, and shinyFuse, a companion web application, to annotate, prioritize, and explore biologically-relevant expressed gene fusions, downstream of fusion calling. We validated annoFuse using a random cohort of TCGA RNA-Seq samples (N = 160) and achieved a 96% sensitivity for retention of high-confidence fusions (N = 603). annoFuse uses FusionAnnotator annotations to filter non-oncogenic and/or artifactual fusions. Then, fusions are prioritized if previously reported in TCGA and/or fusions containing gene partners that are known oncogenes, tumor suppressor genes, COSMIC genes, and/or transcription factors. We applied annoFuse to fusion calls from pediatric brain tumor RNA-Seq samples (N = 1028) provided as part of the Open Pediatric Brain Tumor Atlas (OpenPBTA) Project to determine recurrent fusions and recurrently-fused genes within different brain tumor histologies. annoFuse annotates protein domains using the PFAM database, assesses reciprocality, and annotates gene partners for kinase domain retention. As a standard function, reportFuse enables generation of a reproducible R Markdown report to summarize filtered fusions, visualize breakpoints and protein domains by transcript, and plot recurrent fusions within cohorts. Finally, we created shinyFuse for algorithm-agnostic interactive exploration and plotting of gene fusions. CONCLUSIONS annoFuse provides standardized filtering and annotation for gene fusion calls from STAR-Fusion and Arriba by merging, filtering, and prioritizing putative oncogenic fusions across large cancer datasets, as demonstrated here with data from the OpenPBTA project. We are expanding the package to be widely-applicable to other fusion algorithms and expect annoFuse to provide researchers a method for rapidly evaluating, prioritizing, and translating fusion findings in patient tumors.
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Affiliation(s)
- Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Center for Thrombosis and Hemostasis, Mainz, Germany
| | - Komal S Rathi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Payal Jain
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nicholas A Chimicles
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Miguel A Brown
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ammar S Naqvi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Maris
- Division of Oncology, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Konstantin Strauch
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jaclyn N Taroni
- Alex's Lemonade Stand Foundation Childhood Cancer Data Lab, Philadelphia, PA, USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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7
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Cimmino F, Avitabile M, Lasorsa VA, Pezone L, Cardinale A, Montella A, Cantalupo S, Iolascon A, Capasso M. Functional characterization of full-length BARD1 strengthens its role as a tumor suppressor in neuroblastoma. J Cancer 2020; 11:1495-1504. [PMID: 32047556 PMCID: PMC6995383 DOI: 10.7150/jca.36164] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/12/2019] [Indexed: 01/10/2023] Open
Abstract
BARD1 is associated with the development of high-risk neuroblastoma patients. Particularly, the expression of full length (FL) isoform, FL BARD1, correlates to high-risk neuroblastoma development and its inhibition is sufficient to induce neuroblastoma cells towards a worst phenotype. Here we have investigated the mechanisms of FL BARD1 in neuroblastoma cell lines depleted for FL BARD1 expression. We have shown that FL BARD1 expression protects the cells from spontaneous DNA damage and from damage accumulated after irradiation. We demonstrated a role for FL BARD1 as tumor suppressor to prevent unscheduled mitotic entry of DNA damaged cells and to lead to death cells that have bypassed cell cycle checkpoints. FL BARD1-depleted cells that have survived to checkpoints acquire features of aggressiveness. Overall, our results show that FL BARD1 may defend cells against cancer and prevent malignant transformation of cells.
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Affiliation(s)
- Flora Cimmino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Marianna Avitabile
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Vito Alessandro Lasorsa
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Lucia Pezone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | - Antonella Cardinale
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Naples, Italy
| | | | | | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
- IRCCS SDN, Naples, Italy
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8
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Abstract
Neuroblastomas (NB) are one of the most common extracranial solid tumors in children, and they frequently display high heterogeneity in the disease course. With ongoing research, more information regarding the genetic etiology and molecular mechanisms underlying these contrasting phenotypes is being uncovered. The proto-oncogene MYCN is amplified in approximately 20% of NB cases and is considered a indicator of poor prognosis and an indicator of high-risk NB. The poor prognosis of high risk NB is incompletely explained by MYCN amplification. Recently, massive parallel sequencing studies reported several relatively common gene alterations, such as ATRX mutation and TERT rearrangement that are involved in telomere maintenance through telomerase activity and alternative lengthening of telomeres. Thus, these are important for understanding the etiology and molecular pathogenesis of NB, and hence, for identifying diagnostic and treatment markers. Development of telomerase inhibitors and identification of alternative lengthening of telomeres related targets will contribute to the individualized treatment for high-risk NB. In this mini-review, we will discuss the research progress of TERT-mediated and ATRX-mediated telomere maintenance and NB, especially high-risk tumors.
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9
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Lee S, Borah S, Bahrami A. Detection of Aberrant TERT Promoter Methylation by Combined Bisulfite Restriction Enzyme Analysis for Cancer Diagnosis. J Mol Diagn 2017; 19:378-386. [PMID: 28284778 DOI: 10.1016/j.jmoldx.2017.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/13/2016] [Accepted: 01/05/2017] [Indexed: 12/12/2022] Open
Abstract
Aberrant CpG dinucleotide methylation in a specific region of the telomerase reverse transcriptase (TERT) promoter is associated with increased TERT mRNA levels and malignancy in several cancer types. However, routine screening of this region to aid cancer diagnosis can be challenging because i) several established methylation assays may inaccurately report on hypermethylation of this particular region, ii) interpreting the results of methylation assays can sometimes be difficult for clinical laboratories, and iii) use of high-throughput methylation assays for a few patient samples can be cost prohibitive. Herein, we describe the use of combined bisulfite restriction enzyme analysis (COBRA) as a diagnostic tool for detecting the hypermethylated TERT promoter using in vitro methylated and unmethylated genomic DNA as well as genomic DNA from four melanomas and two benign melanocytic lesions. We compare COBRA with MassARRAY, a more commonly used high-throughput approach, in screening for promoter hypermethylation in 28 formalin-fixed, paraffin-embedded neuroblastoma samples. COBRA sensitively and specifically detected samples with hypermethylated TERT promoter and was as effective as MassARRAY at differentiating high-risk from benign or low-risk tumors. This study demonstrates the utility of this low-cost, technically straightforward, and easily interpretable assay for cancer diagnosis in tumors of an ambiguous nature.
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Affiliation(s)
- Seungjae Lee
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sumit Borah
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Armita Bahrami
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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10
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Abbasi MR, Rifatbegovic F, Brunner C, Mann G, Ziegler A, Pötschger U, Crazzolara R, Ussowicz M, Benesch M, Ebetsberger-Dachs G, Chan GCF, Jones N, Ladenstein R, Ambros IM, Ambros PF. Impact of Disseminated Neuroblastoma Cells on the Identification of the Relapse-Seeding Clone. Clin Cancer Res 2017; 23:4224-4232. [PMID: 28228384 DOI: 10.1158/1078-0432.ccr-16-2082] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/20/2016] [Accepted: 02/12/2017] [Indexed: 02/07/2023]
Abstract
Purpose: Tumor relapse is the most frequent cause of death in stage 4 neuroblastomas. Since genomic information on the relapse precursor cells could guide targeted therapy, our aim was to find the most appropriate tissue for identifying relapse-seeding clones.Experimental design: We analyzed 10 geographically and temporally separated samples of a single patient by SNP array and validated the data in 154 stage 4 patients.Results: In the case study, aberrations unique to certain tissues and time points were evident besides concordant aberrations shared by all samples. Diagnostic bone marrow-derived disseminated tumor cells (DTCs) as well as the metastatic tumor and DTCs at relapse displayed a 1q deletion, not detected in any of the seven primary tumor samples. In the validation cohort, the frequency of 1q deletion was 17.8%, 10%, and 27.5% in the diagnostic DTCs, diagnostic tumors, and DTCs at relapse, respectively. This aberration was significantly associated with 19q and ATRX deletions. We observed a significant increased likelihood of an adverse event in the presence of 19q deletion in the diagnostic DTCs.Conclusions: Different frequencies of 1q and 19q deletions in the primary tumors as compared with DTCs, their relatively high frequency at relapse, and their effect on event-free survival (19q deletion) indicate the relevance of analyzing diagnostic DTCs. Our data support the hypothesis of a branched clonal evolution and a parallel progression of primary and metastatic tumor cells. Therefore, searching for biomarkers to identify the relapse-seeding clone should involve diagnostic DTCs alongside the tumor tissue. Clin Cancer Res; 23(15); 4224-32. ©2017 AACR.
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Affiliation(s)
- M Reza Abbasi
- CCRI, Children's Cancer Research Institute, Vienna, Austria.
| | | | | | - Georg Mann
- St. Anna Children's Hospital, Vienna, Austria
| | - Andrea Ziegler
- CCRI, Children's Cancer Research Institute, Vienna, Austria
| | | | - Roman Crazzolara
- Department of Pediatrics, Medical University of Innsbruck, Innsbruck, Austria
| | - Marek Ussowicz
- Department of Pediatric Hematology and Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Martin Benesch
- Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | | | - Godfrey C F Chan
- Department of Pediatrics and Adolescent Medicine, University of Hong Kong, Hong Kong
| | - Neil Jones
- Department of Pediatrics and Adolescent Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Ruth Ladenstein
- CCRI, Children's Cancer Research Institute, Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Inge M Ambros
- CCRI, Children's Cancer Research Institute, Vienna, Austria
| | - Peter F Ambros
- CCRI, Children's Cancer Research Institute, Vienna, Austria. .,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
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11
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Cheng D, Zhao Y, Wang S, Zhang F, Russo M, McMahon SB, Zhu J. Repression of telomerase gene promoter requires human-specific genomic context and is mediated by multiple HDAC1-containing corepressor complexes. FASEB J 2016; 31:1165-1178. [PMID: 27940549 DOI: 10.1096/fj.201601111r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/28/2016] [Indexed: 12/16/2022]
Abstract
The human telomerase reverse transcriptase (hTERT) gene is repressed in most somatic cells, whereas the expression of the mouse mTert gene is widely detected. To understand the mechanisms of this human-specific repression, we constructed bacterial artificial chromosome (BAC) reporters using human and mouse genomic DNAs encompassing the TERT genes and neighboring loci. Upon chromosomal integration, the hTERT, but not the mTert, reporter was stringently repressed in telomerase-negative human cells in a histone deacetylase (HDAC)-dependent manner, replicating the expression of their respective endogenous genes. In chimeric BACs, the mTert promoter became strongly repressed in the human genomic context, but the hTERT promoter was highly active in the mouse genomic context. Furthermore, an unrelated herpes simplex virus-thymidine kinase (HSV-TK) promoter was strongly repressed in the human, but not in the mouse, genomic context. These results demonstrated that the repression of hTERT gene was dictated by distal elements and its chromatin environment. This repression depended on class I HDACs and involved multiple corepressor complexes, including HDAC1/2-containing Sin3B, nucleosome remodeling and histone deacetylase (NuRD), and corepressor of RE1 silencing transcription factor (CoREST) complexes. Together, our data indicate that the lack of telomerase expression in most human somatic cells results from its repressive genomic environment, providing new insight into the mechanism of long-recognized differential telomerase regulation in mammalian species.-Cheng, D., Zhao, Y., Wang, S., Zhang, F., Russo, M., McMahon, S. B., Zhu, J. Repression of telomerase gene promoter requires human-specific genomic context and is mediated by multiple HDAC1-containing corepressor complexes.
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Affiliation(s)
- De Cheng
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, Washington, USA
| | - Yuanjun Zhao
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA; and
| | - Shuwen Wang
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, Washington, USA
| | - Fan Zhang
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, Washington, USA
| | - Mariano Russo
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA; and
| | - Steven B McMahon
- Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Jiyue Zhu
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, Washington, USA;
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12
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Qi DL, Cobrinik D. MDM2 but not MDM4 promotes retinoblastoma cell proliferation through p53-independent regulation of MYCN translation. Oncogene 2016; 36:1760-1769. [PMID: 27748758 PMCID: PMC5374018 DOI: 10.1038/onc.2016.350] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 08/12/2016] [Accepted: 08/15/2016] [Indexed: 12/13/2022]
Abstract
Retinoblastomas can arise from cone photoreceptor precursors in response to the loss of pRB function. Cone precursor-specific circuitry cooperates with pRB loss to initiate this process and subsequently contributes to the malignancy. Intrinsic high-level MDM2 expression is a key component of the cone precursor circuitry and is thought to inactivate p53-mediated tumor surveillance, which could otherwise be induced in response to pRB loss. However, the MDM2-related MDM4 has also been proposed to abrogate p53-mediated tumor surveillance in the absence of detectable MDM2 in retinoblastoma cells, bringing into question the importance of high-level MDM2 versus MDM4 expression. Here we report that high-level MDM2 but not MDM4 has a consistent critical role in retinoblastoma cell proliferation in vitro, as well as in orthotopic xenografts. Reduction of either MDM2 or MDM4 weakly induced p53, yet reduction of MDM2 but not MDM4 severely impaired proliferation and survival through a p53-independent mechanism. Specifically, MDM2 upregulated the mRNA expression and translation of another component of the cone circuitry, MYCN, in retinoblastoma cells. Moreover, MYCN was essential to retinoblastoma cell growth and tumor formation, and ectopic MYCN partially reversed the effects of MDM2 depletion, indicating that MYCN is an important MDM2 target. These findings indicate that high-level MDM2 expression is needed in order to perform a critical p53-independent function and may obviate the need for genomic alterations to the p53 pathway during retinoblastoma tumorigenesis.
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Affiliation(s)
- D-L Qi
- The Vision Center, Division of Ophthalmology, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - D Cobrinik
- The Vision Center, Division of Ophthalmology, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.,Department of Ophthalmology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.,Department of Biochemistry and Molecular Biology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
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13
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Galli S, Naranjo A, Van Ryn C, Tilan JU, Trinh E, Yang C, Tsuei J, Hong SH, Wang H, Izycka-Swieszewska E, Lee YC, Rodriguez OC, Albanese C, Kitlinska J. Neuropeptide Y as a Biomarker and Therapeutic Target for Neuroblastoma. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:3040-3053. [PMID: 27743558 DOI: 10.1016/j.ajpath.2016.07.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 12/17/2022]
Abstract
Neuroblastoma (NB) is a pediatric malignant neoplasm of sympathoadrenal origin. Challenges in its management include stratification of this heterogeneous disease and a lack of both adequate treatments for high-risk patients and noninvasive biomarkers of disease progression. Our previous studies have identified neuropeptide Y (NPY), a sympathetic neurotransmitter expressed in NB, as a potential therapeutic target for these tumors by virtue of its Y5 receptor (Y5R)-mediated chemoresistance and Y2 receptor (Y2R)-mediated proliferative and angiogenic activities. The goal of this study was to determine the clinical relevance and utility of these findings. Expression of NPY and its receptors was evaluated in corresponding samples of tumor RNA, tissues, and sera from 87 patients with neuroblastic tumors and in tumor tissues from the TH-MYCN NB mouse model. Elevated serum NPY levels correlated with an adverse clinical presentation, poor survival, metastasis, and relapse, whereas strong Y5R immunoreactivity was a marker of angioinvasive tumor cells. In NB tissues from TH-MYCN mice, high immunoreactivity of both NPY and Y5R marked angioinvasive NB cells. Y2R was uniformly expressed in undifferentiated tumor cells, which supports its previously reported role in NB cell proliferation. Our findings validate NPY as a therapeutic target for advanced NB and implicate the NPY/Y5R axis in disease dissemination. The correlation between elevated systemic NPY and NB progression identifies serum NPY as a novel NB biomarker.
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Affiliation(s)
- Susana Galli
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Arlene Naranjo
- Department of Biostatistics, Children's Oncology Group Statistics & Data Center, University of Florida, Gainesville, Florida
| | - Collin Van Ryn
- Department of Biostatistics, Children's Oncology Group Statistics & Data Center, University of Florida, Gainesville, Florida
| | - Jason U Tilan
- Department of Nursing, School of Nursing and Health Studies, Georgetown University, Washington, District of Columbia; Department of Human Science, School of Nursing and Health Studies, Georgetown University, Washington, District of Columbia
| | - Emily Trinh
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Chao Yang
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Jessica Tsuei
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Sung-Hyeok Hong
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Hongkun Wang
- Department of Biostatistics and Bioinformatics, Georgetown University Medical Center, Washington, District of Columbia
| | - Ewa Izycka-Swieszewska
- Department of Pathology and Neuropathology, Medical University of Gdańsk, Gdańsk, Poland
| | - Yi-Chien Lee
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Olga C Rodriguez
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Chris Albanese
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia; Department of Pathology, Georgetown University Medical Center, Washington, District of Columbia
| | - Joanna Kitlinska
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia.
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14
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Zhang F, Cheng D, Wang S, Zhu J. Human Specific Regulation of the Telomerase Reverse Transcriptase Gene. Genes (Basel) 2016; 7:genes7070030. [PMID: 27367732 PMCID: PMC4962000 DOI: 10.3390/genes7070030] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/15/2016] [Accepted: 06/17/2016] [Indexed: 12/19/2022] Open
Abstract
Telomerase, regulated primarily by the transcription of its catalytic subunit telomerase reverse transcriptase (TERT), is critical for controlling cell proliferation and tissue homeostasis by maintaining telomere length. Although there is a high conservation between human and mouse TERT genes, the regulation of their transcription is significantly different in these two species. Whereas mTERT expression is widely detected in adult mice, hTERT is expressed at extremely low levels in most adult human tissues and cells. As a result, mice do not exhibit telomere-mediated replicative aging, but telomere shortening is a critical factor of human aging and its stabilization is essential for cancer development in humans. The chromatin environment and epigenetic modifications of the hTERT locus, the binding of transcriptional factors to its promoter, and recruitment of nucleosome modifying complexes all play essential roles in restricting its transcription in different cell types. In this review, we will discuss recent progress in understanding the molecular mechanisms of TERT regulation in human and mouse tissues and cells, and during cancer development.
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Affiliation(s)
- Fan Zhang
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, PO Box 1495, Spokane, WA 99210, USA.
| | - De Cheng
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, PO Box 1495, Spokane, WA 99210, USA.
| | - Shuwen Wang
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, PO Box 1495, Spokane, WA 99210, USA.
| | - Jiyue Zhu
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, PO Box 1495, Spokane, WA 99210, USA.
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15
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Telomerase activation by genomic rearrangements in high-risk neuroblastoma. Nature 2015; 526:700-4. [PMID: 26466568 DOI: 10.1038/nature14980] [Citation(s) in RCA: 405] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/22/2015] [Indexed: 12/14/2022]
Abstract
Neuroblastoma is a malignant paediatric tumour of the sympathetic nervous system. Roughly half of these tumours regress spontaneously or are cured by limited therapy. By contrast, high-risk neuroblastomas have an unfavourable clinical course despite intensive multimodal treatment, and their molecular basis has remained largely elusive. Here we have performed whole-genome sequencing of 56 neuroblastomas (high-risk, n = 39; low-risk, n = 17) and discovered recurrent genomic rearrangements affecting a chromosomal region at 5p15.33 proximal of the telomerase reverse transcriptase gene (TERT). These rearrangements occurred only in high-risk neuroblastomas (12/39, 31%) in a mutually exclusive fashion with MYCN amplifications and ATRX mutations, which are known genetic events in this tumour type. In an extended case series (n = 217), TERT rearrangements defined a subgroup of high-risk tumours with particularly poor outcome. Despite a large structural diversity of these rearrangements, they all induced massive transcriptional upregulation of TERT. In the remaining high-risk tumours, TERT expression was also elevated in MYCN-amplified tumours, whereas alternative lengthening of telomeres was present in neuroblastomas without TERT or MYCN alterations, suggesting that telomere lengthening represents a central mechanism defining this subtype. The 5p15.33 rearrangements juxtapose the TERT coding sequence to strong enhancer elements, resulting in massive chromatin remodelling and DNA methylation of the affected region. Supporting a functional role of TERT, neuroblastoma cell lines bearing rearrangements or amplified MYCN exhibited both upregulated TERT expression and enzymatic telomerase activity. In summary, our findings show that remodelling of the genomic context abrogates transcriptional silencing of TERT in high-risk neuroblastoma and places telomerase activation in the centre of transformation in a large fraction of these tumours.
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16
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Schramm A, Köster J, Assenov Y, Althoff K, Peifer M, Mahlow E, Odersky A, Beisser D, Ernst C, Henssen AG, Stephan H, Schröder C, Heukamp L, Engesser A, Kahlert Y, Theissen J, Hero B, Roels F, Altmüller J, Nürnberg P, Astrahantseff K, Gloeckner C, De Preter K, Plass C, Lee S, Lode HN, Henrich KO, Gartlgruber M, Speleman F, Schmezer P, Westermann F, Rahmann S, Fischer M, Eggert A, Schulte JH. Mutational dynamics between primary and relapse neuroblastomas. Nat Genet 2015; 47:872-7. [PMID: 26121086 DOI: 10.1038/ng.3349] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/08/2015] [Indexed: 12/11/2022]
Abstract
Neuroblastoma is a malignancy of the developing sympathetic nervous system that is often lethal when relapse occurs. We here used whole-exome sequencing, mRNA expression profiling, array CGH and DNA methylation analysis to characterize 16 paired samples at diagnosis and relapse from individuals with neuroblastoma. The mutational burden significantly increased in relapsing tumors, accompanied by altered mutational signatures and reduced subclonal heterogeneity. Global allele frequencies at relapse indicated clonal mutation selection during disease progression. Promoter methylation patterns were consistent over disease course and were patient specific. Recurrent alterations at relapse included mutations in the putative CHD5 neuroblastoma tumor suppressor, chromosome 9p losses, DOCK8 mutations, inactivating mutations in PTPN14 and a relapse-specific activity pattern for the PTPN14 target YAP. Recurrent new mutations in HRAS, KRAS and genes mediating cell-cell interaction in 13 of 16 relapse tumors indicate disturbances in signaling pathways mediating mesenchymal transition. Our data shed light on genetic alteration frequency, identity and evolution in neuroblastoma.
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Affiliation(s)
- Alexander Schramm
- Pediatric Oncology and Hematology, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Johannes Köster
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Yassen Assenov
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristina Althoff
- Pediatric Oncology and Hematology, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Martin Peifer
- 1] Department of Translational Genomics, University of Cologne, Cologne, Germany. [2] Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Ellen Mahlow
- Pediatric Oncology and Hematology, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Andrea Odersky
- Pediatric Oncology and Hematology, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Daniela Beisser
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Corinna Ernst
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anton G Henssen
- Pediatric Oncology and Hematology, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Harald Stephan
- Pediatric Oncology and Hematology, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christopher Schröder
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | | - Anne Engesser
- Pediatric Oncology and Hematology, University Children's Hospital, Cologne, Germany
| | - Yvonne Kahlert
- Pediatric Oncology and Hematology, University Children's Hospital, Cologne, Germany
| | - Jessica Theissen
- Pediatric Oncology and Hematology, University Children's Hospital, Cologne, Germany
| | - Barbara Hero
- Pediatric Oncology and Hematology, University Children's Hospital, Cologne, Germany
| | - Frederik Roels
- Pediatric Oncology and Hematology, University Children's Hospital, Cologne, Germany
| | - Janine Altmüller
- 1] Cologne Center for Genomics, University of Cologne, Cologne, Germany. [2] Human Genetics, University Hospital Cologne, Cologne, Germany
| | - Peter Nürnberg
- 1] Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany. [2] Cologne Center for Genomics, University of Cologne, Cologne, Germany. [3] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Kathy Astrahantseff
- Pediatric Oncology and Hematology, Charité University Medicine, Berlin, Germany
| | | | - Katleen De Preter
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Christoph Plass
- 1] Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Sangkyun Lee
- Computer Science, TU Dortmund, Dortmund, Germany
| | - Holger N Lode
- Pediatric Oncology and Hematology, University Medicine Greifswald, Greifswald, Germany
| | - Kai-Oliver Henrich
- Neuroblastoma Genomics, B087, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Moritz Gartlgruber
- Neuroblastoma Genomics, B087, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Speleman
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Peter Schmezer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Westermann
- Neuroblastoma Genomics, B087, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sven Rahmann
- 1] Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany. [2] Computer Science, TU Dortmund, Dortmund, Germany
| | - Matthias Fischer
- 1] Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany. [2] Pediatric Oncology and Hematology, University Children's Hospital, Cologne, Germany
| | - Angelika Eggert
- 1] Pediatric Oncology and Hematology, Charité University Medicine, Berlin, Germany. [2] German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Johannes H Schulte
- 1] Pediatric Oncology and Hematology, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany. [2] Pediatric Oncology and Hematology, Charité University Medicine, Berlin, Germany. [3] German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
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17
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Lindner S, Bachmann HS, Odersky A, Schaefers S, Klein-Hitpass L, Hero B, Fischer M, Eggert A, Schramm A, Schulte JH. Absence of telomerase reverse transcriptase promoter mutations in neuroblastoma. Biomed Rep 2015; 3:443-446. [PMID: 26171145 DOI: 10.3892/br.2015.463] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/22/2015] [Indexed: 11/06/2022] Open
Abstract
Maintenance of telomere length is a critical hallmark of malignant transformation. While silenced in somatic cells, telomerase reverse transcriptase (TERT), the catalytic subunit of telomerase, is frequently overexpressed in malignant cells thereby maintaining their telomere length. Specific point mutations in the TERT promoter region have recently been identified in melanoma and other tumor entities resulting in high TERT expression. Neuroblastoma is the most common extracranial tumor of childhood, arising from neural-crest progenitor cells. TERT overexpression has been observed in the majority of neuroblastoma. Taking into consideration that TERT promoter mutations are frequently described in neural-crest-derived tumors such as melanoma, as well as a variety of other neuronal tumors, the present study analyzed the frequency of TERT promoter mutations in primary neuroblastoma and neuroblastoma cell lines. In 131 neuroblastoma primary tumors representing the whole spectrum of neuroblastoma, no TERT promoter mutations were detected. However, in 3 out of 19 neuroblastoma cell lines the previously described C228T TERT promoter mutation was present. In conclusion, the TERT promoter mutations are not a frequent mechanism of TERT overexpression in neuroblastoma.
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Affiliation(s)
- Sven Lindner
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, D-45122 Essen, Germany ; German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Duesseldorf, D-45122 Essen, Germany ; German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Hagen S Bachmann
- Institute of Pharmacogenetics, University Hospital Essen, D-45147 Essen, Germany
| | - Andrea Odersky
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, D-45122 Essen, Germany
| | - Simon Schaefers
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, D-45122 Essen, Germany ; German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Duesseldorf, D-45122 Essen, Germany ; German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Ludger Klein-Hitpass
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, D-45122 Essen, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, D-50924 Cologne, Germany
| | - Matthias Fischer
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, D-50924 Cologne, Germany ; Center for Molecular Medicine Cologne (CMMC), University of Cologne, D-50931 Cologne, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, D-10117 Berlin, Germany
| | - Alexander Schramm
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, D-45122 Essen, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, D-45122 Essen, Germany ; German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Duesseldorf, D-45122 Essen, Germany ; German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany ; Translational Neuro-Oncology, West German Cancer Center (WTZ), University Hospital Essen, D-45147 Essen, Germany ; Centre for Medical Biotechnology, University Duisburg-Essen, D-45147 Essen, Germany
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18
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Juhlin CC, Goh G, Healy JM, Fonseca AL, Scholl UI, Stenman A, Kunstman JW, Brown TC, Overton JD, Mane SM, Nelson-Williams C, Bäckdahl M, Suttorp AC, Haase M, Choi M, Schlessinger J, Rimm DL, Höög A, Prasad ML, Korah R, Larsson C, Lifton RP, Carling T. Whole-exome sequencing characterizes the landscape of somatic mutations and copy number alterations in adrenocortical carcinoma. J Clin Endocrinol Metab 2015; 100:E493-502. [PMID: 25490274 PMCID: PMC5393505 DOI: 10.1210/jc.2014-3282] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
CONTEXT Adrenocortical carcinoma (ACC) is a rare and lethal malignancy with a poorly defined etiology, and the molecular genetics of ACC are incompletely understood. OBJECTIVE To utilize whole-exome sequencing for genetic characterization of the underlying somatic mutations and copy number alterations present in ACC. DESIGN Screening for somatic mutation events and copy number alterations (CNAs) was performed by comparative analysis of tumors and matched normal samples from 41 patients with ACC. RESULTS In total, 966 nonsynonymous somatic mutations were detected, including 40 tumors with a mean of 16 mutations per sample and one tumor with 314 mutations. Somatic mutations in ACC-associated genes included TP53 (8/41 tumors, 19.5%) and CTNNB1 (4/41, 9.8%). Genes with potential disease-causing mutations included GNAS, NF2, and RB1, and recurrently mutated genes with unknown roles in tumorigenesis comprised CDC27, SCN7A, and SDK1. Recurrent CNAs included amplification at 5p15.33 including TERT (6/41, 14.6%) and homozygous deletion at 22q12.1 including the Wnt repressors ZNRF3 and KREMEN1 (4/41 9.8% and 3/41, 7.3%, respectively). Somatic mutations in ACC-established genes and recurrent ZNRF3 and TERT loci CNAs were mutually exclusive in the majority of cases. Moreover, gene ontology identified Wnt signaling as the most frequently mutated pathway in ACCs. CONCLUSIONS These findings highlight the importance of Wnt pathway dysregulation in ACC and corroborate the finding of homozygous deletion of Wnt repressors ZNRF3 and KREMEN1. Overall, mutations in either TP53 or CTNNB1 as well as focal CNAs at the ZNRF3 or TERT loci denote mutually exclusive events, suggesting separate mechanisms underlying the development of these tumors.
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Affiliation(s)
- C Christofer Juhlin
- Yale Endocrine Neoplasia Laboratory (C.C.J., J.M.H., A.L.F., J.W.K., T.C.B., R.K., T.C.), Yale School of Medicine, New Haven, Connecticut 06520; Department of Surgery (C.C.J., J.M.H., A.L.F., J.W.K., T.C.B., R.K., T.C.), Yale School of Medicine, New Haven, Connecticut, 06520; Department of Genetics (G.G., C.N.W., M.C., R.P.L.), Yale School of Medicine and Howard Hughes Medical Institute, New Haven, Connecticut, 06520; Department of Oncology-Pathology (C.C.J., A.S., A.H., C.L.), Karolinska Institutet, Karolinska University Hospital, CCK, SE-171 76 Stockholm, Sweden; Yale Center for Genome Analysis (JDO, SMM), Orange, Connecticut, 06477; Department of Pathology (D.L.R., M.L.P.), Yale School of Medicine, New Haven, Connecticut, 06520; Department of Pharmacology (J.S.), Yale School of Medicine, New Haven, Connecticut 06520; Department of Molecular Medicine and Surgery (M.B.), Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden; Division of Nephrology (U.I.S.), University Hospital Düsseldorf, 40225 Düsseldorf, Germany; Department of Pathology (A.C.S.), University Hospital Düsseldorf, 40225 Düsseldorf, Germany; and Division of Endocrinology and Diabetology (M.H.), University Hospital Düsseldorf, 40225 Düsseldorf, Germany
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19
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Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays. PLoS One 2014; 9:e106780. [PMID: 25198154 PMCID: PMC4157799 DOI: 10.1371/journal.pone.0106780] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/07/2014] [Indexed: 12/28/2022] Open
Abstract
Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.
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20
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Schleiermacher G, Janoueix-Lerosey I, Delattre O. Recent insights into the biology of neuroblastoma. Int J Cancer 2014; 135:2249-61. [PMID: 25124476 DOI: 10.1002/ijc.29077] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/08/2014] [Indexed: 01/24/2023]
Abstract
Neuroblastoma (NB) is an embryonal tumor of the sympathetic nervous system which accounts for 8-10% of pediatric cancers. It is characterized by a broad spectrum of clinical behaviors from spontaneous regression to fatal outcome despite aggressive therapies. Considerable progress has been made recently in the germline and somatic genetic characterization of patients and tumors. Indeed, predisposition genes that account for a significant proportion of familial and syndromic cases have been identified and genome-wide association studies have retrieved a number of susceptibility loci. In addition, genome-wide sequencing, copy-number and expression studies have been conducted on tumors and have detected important gene modifications, profiles and signatures that have strong implications for the therapeutic stratification of patients. The identification of major players in NB oncogenesis, including MYCN, ALK, PHOX2B and LIN28B, has enabled the development of new animal models. Our review focuses on these recent advances, on the insights they provide on the mechanisms involved in NB development and their applications for the clinical management of patients.
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Affiliation(s)
- Gudrun Schleiermacher
- Equipe SIRIC Recherche Translationnelle en Oncologie Pédiatrique, Département de Recherche Translationnelle et Inserm U830, Centre de Recherche, Paris Cedex, 05, France; Département de pédiatrie, Institut Curie, Paris Cedex, 05, France; Unité Génétique et Biologie des Cancers, Inserm U830, Centre de Recherche, Institut Curie, Paris Cedex, 05, France
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21
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Cheung IY, Farazi TA, Ostrovnaya I, Xu H, Tran H, Mihailovic A, Tuschl T, Cheung NKV. Deep MicroRNA sequencing reveals downregulation of miR-29a in neuroblastoma central nervous system metastasis. Genes Chromosomes Cancer 2014; 53:803-14. [PMID: 24898736 DOI: 10.1002/gcc.22189] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/24/2014] [Indexed: 12/27/2022] Open
Abstract
Central nervous system (CNS) is an increasingly common site of isolated metastasis for patients with Stage 4 neuroblastoma. To explore the microRNA (miRNA) profile of this metastatic process, miRNA sequencing was performed to identify miRNA sequence families with differential expression between tumor pairs (pre-CNS primary and CNS metastasis) from 13 patients with Stage 4 neuroblastoma. Seven miRNA sequence families had distinct expression in CNS metastases when compared with their corresponding pre-CNS primaries. MiR-7 was upregulated (3.75-fold), and miR-21, miR-22, miR-29a, miR-143, miR-199a-1-3p, and miR-199a-1-5p were downregulated (3.5-6.1-fold), all confirmed by quantitative reverse transcription-PCR. MiR-29a, previously shown to be downregulated in a broad spectrum of solid tumors including neuroblastoma, had the most significant decrease in all 13 CNS metastases (P = 0.001). Its known onco-targets CDC6, CDK6, and DNMT3A, as well as B7-H3, an inhibitory ligand for T cells, and natural killer cells, were found to have higher differential expression in these 13 CNS metastases when compared with their paired primaries. Additionally, miR-29a expression in primary tumors was significantly lower among patients who eventually relapsed in the CNS. Irrespective of the amplification status of MYCN, which is known to be associated with metastasis, pre-CNS primaries, and CNS metastases had significantly lower miR-29a expression than non-CNS primary tumors. Among MYCN amplified cell lines, those from CNS relapse also had lower miR-29a expression than non-CNS relapse. These findings raised the hypothesis that miR-29a could be a biomarker for neuroblastoma CNS metastasis, and its downregulation may play a pivotal role in CNS progression.
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Affiliation(s)
- Irene Y Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
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