1
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Chen WC, Choudhury A, Youngblood MW, Polley MYC, Lucas CHG, Mirchia K, Maas SLN, Suwala AK, Won M, Bayley JC, Harmanci AS, Harmanci AO, Klisch TJ, Nguyen MP, Vasudevan HN, McCortney K, Yu TJ, Bhave V, Lam TC, Pu JKS, Li LF, Leung GKK, Chan JW, Perlow HK, Palmer JD, Haberler C, Berghoff AS, Preusser M, Nicolaides TP, Mawrin C, Agnihotri S, Resnick A, Rood BR, Chew J, Young JS, Boreta L, Braunstein SE, Schulte J, Butowski N, Santagata S, Spetzler D, Bush NAO, Villanueva-Meyer JE, Chandler JP, Solomon DA, Rogers CL, Pugh SL, Mehta MP, Sneed PK, Berger MS, Horbinski CM, McDermott MW, Perry A, Bi WL, Patel AJ, Sahm F, Magill ST, Raleigh DR. Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses. Nat Med 2023; 29:3067-3076. [PMID: 37944590 PMCID: PMC11073469 DOI: 10.1038/s41591-023-02586-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/11/2023] [Indexed: 11/12/2023]
Abstract
Surgery is the mainstay of treatment for meningioma, the most common primary intracranial tumor, but improvements in meningioma risk stratification are needed and indications for postoperative radiotherapy are controversial. Here we develop a targeted gene expression biomarker that predicts meningioma outcomes and radiotherapy responses. Using a discovery cohort of 173 meningiomas, we developed a 34-gene expression risk score and performed clinical and analytical validation of this biomarker on independent meningiomas from 12 institutions across 3 continents (N = 1,856), including 103 meningiomas from a prospective clinical trial. The gene expression biomarker improved discrimination of outcomes compared with all other systems tested (N = 9) in the clinical validation cohort for local recurrence (5-year area under the curve (AUC) 0.81) and overall survival (5-year AUC 0.80). The increase in AUC compared with the standard of care, World Health Organization 2021 grade, was 0.11 for local recurrence (95% confidence interval 0.07 to 0.17, P < 0.001). The gene expression biomarker identified meningiomas benefiting from postoperative radiotherapy (hazard ratio 0.54, 95% confidence interval 0.37 to 0.78, P = 0.0001) and suggested postoperative management could be refined for 29.8% of patients. In sum, our results identify a targeted gene expression biomarker that improves discrimination of meningioma outcomes, including prediction of postoperative radiotherapy responses.
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Affiliation(s)
- William C Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
| | - Abrar Choudhury
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Mark W Youngblood
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Mei-Yin C Polley
- NRG Statistics and Data Management Center, NRG Oncology, Philadelphia, PA, USA
| | | | - Kanish Mirchia
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sybren L N Maas
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Abigail K Suwala
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research, German Cancer Research Center, Heidelberg, Germany
| | - Minhee Won
- NRG Statistics and Data Management Center, NRG Oncology, Philadelphia, PA, USA
| | - James C Bayley
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Akdes S Harmanci
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Arif O Harmanci
- Center for Secure Artificial Intelligence for Healthcare, Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX, USA
| | - Tiemo J Klisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, and Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Minh P Nguyen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen McCortney
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Theresa J Yu
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Varun Bhave
- Department of Neurosurgery, Brigham and Women's Hospital, and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tai-Chung Lam
- Department of Clinical Oncology, The University of Hong Kong, Pokfulam, China
| | - Jenny Kan-Suen Pu
- Division of Neurosurgery, Department of Surgery, The University of Hong Kong, Pokfulam, China
| | - Lai-Fung Li
- Division of Neurosurgery, Department of Surgery, The University of Hong Kong, Pokfulam, China
| | - Gilberto Ka-Kit Leung
- Division of Neurosurgery, Department of Surgery, The University of Hong Kong, Pokfulam, China
| | - Jason W Chan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Haley K Perlow
- Department of Radiation Oncology, Ohio State University, Columbus, OH, USA
| | - Joshua D Palmer
- Department of Radiation Oncology, Ohio State University, Columbus, OH, USA
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Anna S Berghoff
- Division of Oncology, Department of Medicine, Medical University of Vienna, Vienna, Austria
| | - Matthias Preusser
- Division of Oncology, Department of Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Christian Mawrin
- Department of Neuropathology, University of Magdeburg, Magdeburg, Germany
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adam Resnick
- Department of Neurological Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brian R Rood
- Brain Tumor Institute, Children's National Hospital, Washington, DC, USA
| | - Jessica Chew
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Jacob S Young
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Lauren Boreta
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Steve E Braunstein
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Schulte
- Neurosciences Department, University of California San Diego, La Jolla, CA, USA
| | - Nicholas Butowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - James P Chandler
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - David A Solomon
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - C Leland Rogers
- NRG Statistics and Data Management Center, NRG Oncology, Philadelphia, PA, USA
| | - Stephanie L Pugh
- NRG Statistics and Data Management Center, NRG Oncology, Philadelphia, PA, USA
| | - Minesh P Mehta
- NRG Statistics and Data Management Center, NRG Oncology, Philadelphia, PA, USA
- Miami Neuroscience Institute, Baptist Health, Miami, FL, USA
| | - Penny K Sneed
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Craig M Horbinski
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
- Department of Pathology, Northwestern University, Chicago, IL, USA
| | | | - Arie Perry
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Akash J Patel
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research, German Cancer Research Center, Heidelberg, Germany
| | - Stephen T Magill
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA.
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
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2
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Crotty EE, Wilson AL, Davidson T, Tahiri S, Gust J, Griesinger AM, Venkataraman S, Park JR, Mueller S, Rood BR, Hwang EI, Wang LD, Vitanza NA. Cellular Therapy for Children with Central Nervous System Tumors: Mining and Mapping the Correlative Data. Curr Oncol Rep 2023; 25:847-855. [PMID: 37160547 PMCID: PMC10326126 DOI: 10.1007/s11912-023-01423-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2023] [Indexed: 05/11/2023]
Abstract
PURPOSE OF REVIEW Correlative studies should leverage clinical trial frameworks to conduct biospecimen analyses that provide insight into the bioactivity of the intervention and facilitate iteration toward future trials that further improve patient outcomes. In pediatric cellular immunotherapy trials, correlative studies enable deeper understanding of T cell mobilization, durability of immune activation, patterns of toxicity, and early detection of treatment response. Here, we review the correlative science in adoptive cell therapy (ACT) for childhood central nervous system (CNS) tumors, with a focus on existing chimeric antigen receptor (CAR) and T cell receptor (TCR)-expressing T cell therapies. RECENT FINDINGS We highlight long-standing and more recently understood challenges for effective alignment of correlative data and offer practical considerations for current and future approaches to multi-omic analysis of serial tumor, serum, and cerebrospinal fluid (CSF) biospecimens. We highlight the preliminary success in collecting serial cytokine and proteomics from patients with CNS tumors on ACT clinical trials.
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Affiliation(s)
- Erin E Crotty
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, M/S JMB-8, 1900 9thAvenue, Seattle, WA, 98101, USA
- Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | | | - Tom Davidson
- Cancer and Blood Disease Institute, Keck School of Medicine, Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Sophia Tahiri
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, M/S JMB-8, 1900 9thAvenue, Seattle, WA, 98101, USA
| | - Juliane Gust
- Division of Pediatric Neurology, Department of Neurology, University of Washington, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Andrea M Griesinger
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sujatha Venkataraman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Julie R Park
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, M/S JMB-8, 1900 9thAvenue, Seattle, WA, 98101, USA
- Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
- Seattle Children's Therapeutics, Seattle, WA, USA
| | - Sabine Mueller
- Department of Neurology, Neurosurgery, and Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Brian R Rood
- Center for Cancer and Blood Disorders, Children's National Hospital, Washington, DC, USA
| | - Eugene I Hwang
- Center for Cancer and Blood Disorders, Children's National Hospital, Washington, DC, USA
| | - Leo D Wang
- Departments of Pediatrics and ImmunoOncology, City of Hope, Duarte, CA, USA
| | - Nicholas A Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, M/S JMB-8, 1900 9thAvenue, Seattle, WA, 98101, USA.
- Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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3
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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 Genom 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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Lilly JV, Rokita JL, Mason JL, Patton T, Stefankiewiz S, Higgins D, Trooskin G, Larouci CA, Arya K, Appert E, Heath AP, Zhu Y, Brown MA, Zhang B, Farrow BK, Robins S, Morgan AM, Nguyen TQ, Frenkel E, Lehmann K, Drake E, Sullivan C, Plisiewicz A, Coleman N, Patterson L, Koptyra M, Helili Z, Van Kuren N, Young N, Kim MC, Friedman C, Lubneuski A, Blackden C, Williams M, Baubet V, Tauhid L, Galanaugh J, Boucher K, Ijaz H, Cole KA, Choudhari N, Santi M, Moulder RW, Waller J, Rife W, Diskin SJ, Mateos M, Parsons DW, Pollack IF, Goldman S, Leary S, Caporalini C, Buccoliero AM, Scagnet M, Haussler D, Hanson D, Firestein R, Cain J, Phillips JJ, Gupta N, Mueller S, Grant G, Monje-Deisseroth M, Partap S, Greenfield JP, Hashizume R, Smith A, Zhu S, Johnston JM, Fangusaro JR, Miller M, Wood MD, Gardner S, Carter CL, Prolo LM, Pisapia J, Pehlivan K, Franson A, Niazi T, Rubin J, Abdelbaki M, Ziegler DS, Lindsay HB, Stucklin AG, Gerber N, Vaske OM, Quinsey C, Rood BR, Nazarian J, Raabe E, Jackson EM, Stapleton S, Lober RM, Kram DE, Koschmann C, Storm PB, Lulla RR, Prados M, Resnick AC, Waanders AJ. The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science. Neoplasia 2023; 35:100846. [PMID: 36335802 PMCID: PMC9641002 DOI: 10.1016/j.neo.2022.100846] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
Pediatric brain tumors are the leading cause of cancer-related death in children in the United States and contribute a disproportionate number of potential years of life lost compared to adult cancers. Moreover, survivors frequently suffer long-term side effects, including secondary cancers. The Children's Brain Tumor Network (CBTN) is a multi-institutional international clinical research consortium created to advance therapeutic development through the collection and rapid distribution of biospecimens and data via open-science research platforms for real-time access and use by the global research community. The CBTN's 32 member institutions utilize a shared regulatory governance architecture at the Children's Hospital of Philadelphia to accelerate and maximize the use of biospecimens and data. As of August 2022, CBTN has enrolled over 4700 subjects, over 1500 parents, and collected over 65,000 biospecimen aliquots for research. Additionally, over 80 preclinical models have been developed from collected tumors. Multi-omic data for over 1000 tumors and germline material are currently available with data generation for > 5000 samples underway. To our knowledge, CBTN provides the largest open-access pediatric brain tumor multi-omic dataset annotated with longitudinal clinical and outcome data, imaging, associated biospecimens, child-parent genomic pedigrees, and in vivo and in vitro preclinical models. Empowered by NIH-supported platforms such as the Kids First Data Resource and the Childhood Cancer Data Initiative, the CBTN continues to expand the resources needed for scientists to accelerate translational impact for improved outcomes and quality of life for children with brain and spinal cord tumors.
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Affiliation(s)
- Jena V Lilly
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | - Tatiana Patton
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - David Higgins
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gerri Trooskin
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Kamnaa Arya
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | - Yuankun Zhu
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Miguel A Brown
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bo Zhang
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Shannon Robins
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Thinh Q Nguyen
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | - Emily Drake
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | - Noel Coleman
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Luke Patterson
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Zeinab Helili
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Nathan Young
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Meen Chul Kim
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Alex Lubneuski
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Marti Williams
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Valerie Baubet
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lamiya Tauhid
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Katie Boucher
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Heba Ijaz
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | | | | | | | - Whitney Rife
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | | | - Ian F Pollack
- UPMC The Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Stewart Goldman
- Phoenix Children's Hospital, Phoenix AZ, USA; University of Arizona College of Medicine, Phoenix AZ, USA
| | - Sarah Leary
- Seattle Children's Hospital, Seattle, WA, USA
| | | | | | | | - David Haussler
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Derek Hanson
- Joseph M. Sanzari Children's Hospital at Hackensack University Medical Center, Hackensack, NJ, USA
| | - Ron Firestein
- Hudson Institute of Medical Research, Victoria, Australia
| | - Jason Cain
- Hudson Institute of Medical Research, Victoria, Australia
| | - Joanna J Phillips
- University of California San Francisco & Benioff Children's Hospitals, San Francisco, CA, USA
| | - Nalin Gupta
- University of California San Francisco & Benioff Children's Hospitals, San Francisco, CA, USA
| | - Sabine Mueller
- University of California San Francisco & Benioff Children's Hospitals, San Francisco, CA, USA
| | | | | | - Sonia Partap
- Lucille Packard Children's Hospital Stanford, Stanford, CA, USA
| | | | | | - Amy Smith
- Orlando Health Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Shida Zhu
- China National Genebank (Beijing Genomics Institute), China
| | - James M Johnston
- University of Alabama at Birmingham, Children's of Alabama, Birmingham, AL, USA
| | | | - Matthew Miller
- Doernbecher Children's Hospital at Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Matthew D Wood
- Doernbecher Children's Hospital at Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Sharon Gardner
- Hassenfeld Children's Hospital at NYU Langone, New York, NY, USA
| | - Claire L Carter
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Laura M Prolo
- Lucille Packard Children's Hospital Stanford, Stanford, CA, USA
| | - Jared Pisapia
- Maria Fareri Children's Hospital at Westchester Medical Center, Valhalla, NY, USA
| | - Katherine Pehlivan
- Maria Fareri Children's Hospital at Westchester Medical Center, Valhalla, NY, USA
| | - Andrea Franson
- C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI, USA
| | - Toba Niazi
- Nicklaus Children's Hospital, Miami, FL, USA
| | - Josh Rubin
- St. Louis Children's Hospital, St. Louis, MO
| | | | - David S Ziegler
- Kids Cancer Centre, Sydney Children's Hospital, High St, Randwick, NSW, Australia; Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Holly B Lindsay
- Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Olena M Vaske
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Carolyn Quinsey
- UNC Chapel Hill, Chapel Hill, NC, USA; North Carolina Children's Hospital, Chapel Hill, NC, USA
| | - Brian R Rood
- Children's National Hospital, Washington, DC, USA
| | - Javad Nazarian
- University Children's Zürich, Zürich, Switzerland; Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA; The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Eric Raabe
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Eric M Jackson
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | | | | | - David E Kram
- UNC Chapel Hill, Chapel Hill, NC, USA; North Carolina Children's Hospital, Chapel Hill, NC, USA
| | - Carl Koschmann
- C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Michael Prados
- University of California San Francisco Benioff Children's Hospital, San Franscisco, CA, USA
| | - Adam C Resnick
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
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5
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Xu Z, Murad N, Malawsky D, Tao R, Rivero-Hinojosa S, Holdhof D, Schüller U, Zhang P, Lazarski C, Rood BR, Packer R, Gershon T, Pei Y. OLIG2 Is a Determinant for the Relapse of MYC-Amplified Medulloblastoma. Clin Cancer Res 2022; 28:4278-4291. [PMID: 35736214 PMCID: PMC9529814 DOI: 10.1158/1078-0432.ccr-22-0527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/10/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022]
Abstract
PURPOSE Patients with MYC-amplified medulloblastoma (MB) have poor prognosis and frequently develop recurrence, thus new therapeutic approaches to prevent recurrence are needed. EXPERIMENTAL DESIGN We evaluated OLIG2 expression in a panel of mouse Myc-driven MB tumors, patient MB samples, and patient-derived xenograft (PDX) tumors and analyzed radiation sensitivity in OLIG2-high and OLIG2-low tumors in PDX lines. We assessed the effect of inhibition of OLIG2 by OLIG2-CRISPR or the small molecule inhibitor CT-179 combined with radiotherapy on tumor progression in PDX models. RESULTS We found that MYC-associated MB can be stratified into OLIG2-high and OLIG2-low tumors based on OLIG2 protein expression. In MYC-amplified MB PDX models, OLIG2-low tumors were sensitive to radiation and rarely relapsed, whereas OLIG2-high tumors were resistant to radiation and consistently developed recurrence. In OLIG2-high tumors, irradiation eliminated the bulk of tumor cells; however, a small number of tumor cells comprising OLIG2- tumor cells and rare OLIG2+ tumor cells remained in the cerebellar tumor bed when examined immediately post-irradiation. All animals harboring residual-resistant tumor cells developed relapse. The relapsed tumors mirrored the cellular composition of the primary tumors with enriched OLIG2 expression. Further studies demonstrated that OLIG2 was essential for recurrence, as OLIG2 disruption with CRISPR-mediated deletion or with the small molecule inhibitor CT-179 prevented recurrence from the residual radioresistant tumor cells. CONCLUSIONS Our studies reveal that OLIG2 is a biomarker and an effective therapeutic target in a high-risk subset of MYC-amplified MB, and OLIG2 inhibitor combined with radiotherapy represents a novel effective approach for treating this devastating disease.
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Affiliation(s)
- Zhenhua Xu
- Center for Cancer and Immunology, Brain Tumor Institute, Children’s National Health System, Washington, DC 20010, USA
| | - Najiba Murad
- Center for Cancer and Immunology, Brain Tumor Institute, Children’s National Health System, Washington, DC 20010, USA
| | - Daniel Malawsky
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ran Tao
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Samuel Rivero-Hinojosa
- Center for Cancer and Immunology, Brain Tumor Institute, Children’s National Health System, Washington, DC 20010, USA
| | - Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20251, Germany
- Research Institute Children’s Cancer Center, Martinistraße 52, Hamburg 20251, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20251, Germany
- Research Institute Children’s Cancer Center, Martinistraße 52, Hamburg 20251, Germany
- Institute for Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20251, Germany
| | - Peng Zhang
- Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing 100069, China
| | - Christopher Lazarski
- Center for Cancer and Immunology, Brain Tumor Institute, Children’s National Health System, Washington, DC 20010, USA
| | - Brian R. Rood
- Center for Cancer and Immunology, Brain Tumor Institute, Children’s National Health System, Washington, DC 20010, USA
| | - Roger Packer
- Center for Cancer and Immunology, Brain Tumor Institute, Children’s National Health System, Washington, DC 20010, USA
| | - Timothy Gershon
- Department of Neurology, University North Carolina, School of Medicine, Chapel Hill, NC 27516, USA
| | - Yanxin Pei
- Center for Cancer and Immunology, Brain Tumor Institute, Children’s National Health System, Washington, DC 20010, USA
- Lead contact
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6
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Rivero-Hinojosa S, Grant M, Panigrahi A, Zhang H, Caisova V, Bollard CM, Rood BR. Proteogenomic discovery of neoantigens facilitates personalized multi-antigen targeted T cell immunotherapy for brain tumors. Nat Commun 2021; 12:6689. [PMID: 34795224 PMCID: PMC8602676 DOI: 10.1038/s41467-021-26936-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/25/2021] [Indexed: 12/22/2022] Open
Abstract
Neoantigen discovery in pediatric brain tumors is hampered by their low mutational burden and scant tissue availability. Here we develop a proteogenomic approach combining tumor DNA/RNA sequencing and mass spectrometry proteomics to identify tumor-restricted (neoantigen) peptides arising from multiple genomic aberrations to generate a highly target-specific, autologous, personalized T cell immunotherapy. Our data indicate that aberrant splice junctions are the primary source of neoantigens in medulloblastoma, a common pediatric brain tumor. Proteogenomically identified tumor-specific peptides are immunogenic and generate MHC II-based T cell responses. Moreover, polyclonal and polyfunctional T cells specific for tumor-specific peptides effectively eliminate tumor cells in vitro. Targeting tumor-specific antigens obviates the issue of central immune tolerance while potentially providing a safety margin favoring combination with other immune-activating therapies. These findings demonstrate the proteogenomic discovery of immunogenic tumor-specific peptides and lay the groundwork for personalized targeted T cell therapies for children with brain tumors. Targeting tumor-associated antigens in paediatric medulloblastomas (MB) is challenging due to their low mutational burden. Here, the authors develop a sensitive proteogenomic approach to identify tumour specific neoantigens, which may enable personalised T cell immunotherapy in paediatric MB.
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Affiliation(s)
- Samuel Rivero-Hinojosa
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, USA
| | - Melanie Grant
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, USA.,Emory University School of Medicine, Department of Pediatrics, Atlanta, GA, USA
| | - Aswini Panigrahi
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, USA
| | - Huizhen Zhang
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, USA
| | - Veronika Caisova
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, USA
| | - Catherine M Bollard
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, USA.,George Washington University Cancer Center, Washington, DC, USA
| | - Brian R Rood
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, USA. .,George Washington University Cancer Center, Washington, DC, USA.
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7
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Petralia F, Tignor N, Reva B, Koptyra M, Chowdhury S, Rykunov D, Krek A, Ma W, Zhu Y, Ji J, Calinawan A, Whiteaker JR, Colaprico A, Stathias V, Omelchenko T, Song X, Raman P, Guo Y, Brown MA, Ivey RG, Szpyt J, Guha Thakurta S, Gritsenko MA, Weitz KK, Lopez G, Kalayci S, Gümüş ZH, Yoo S, da Veiga Leprevost F, Chang HY, Krug K, Katsnelson L, Wang Y, Kennedy JJ, Voytovich UJ, Zhao L, Gaonkar KS, Ennis BM, Zhang B, Baubet V, Tauhid L, Lilly JV, Mason JL, Farrow B, Young N, Leary S, Moon J, Petyuk VA, Nazarian J, Adappa ND, Palmer JN, Lober RM, Rivero-Hinojosa S, Wang LB, Wang JM, Broberg M, Chu RK, Moore RJ, Monroe ME, Zhao R, Smith RD, Zhu J, Robles AI, Mesri M, Boja E, Hiltke T, Rodriguez H, Zhang B, Schadt EE, Mani DR, Ding L, Iavarone A, Wiznerowicz M, Schürer S, Chen XS, Heath AP, Rokita JL, Nesvizhskii AI, Fenyö D, Rodland KD, Liu T, Gygi SP, Paulovich AG, Resnick AC, Storm PB, Rood BR, Wang P. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. Cell 2020; 183:1962-1985.e31. [PMID: 33242424 PMCID: PMC8143193 DOI: 10.1016/j.cell.2020.10.044] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/19/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.
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Affiliation(s)
- Francesca Petralia
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Tignor
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mateusz Koptyra
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Antonio Colaprico
- Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Vasileios Stathias
- Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Tatiana Omelchenko
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, 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; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yiran Guo
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Miguel A Brown
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Richard G Ivey
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - John Szpyt
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sanjukta Guha Thakurta
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gonzalo Lopez
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Selim Kalayci
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
| | - Lizabeth Katsnelson
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ying Wang
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jacob J Kennedy
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Lei Zhao
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, 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; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Brian M Ennis
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Valerie Baubet
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lamiya Tauhid
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jena V Lilly
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jennifer L Mason
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bailey Farrow
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathan Young
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sarah Leary
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cancer and Blood Disorders Center, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Javad Nazarian
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA; Department of Oncology, Children's Research Center, University Children's Hospital Zürich, Zürich 8032, Switzerland
| | - Nithin D Adappa
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James N Palmer
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert M Lober
- Department of Neurosurgery, Dayton Children's Hospital, Dayton, OH 45404, USA
| | - Samuel Rivero-Hinojosa
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA
| | - Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Joshua M Wang
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Matilda Broberg
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Department of Neurology, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 61-203 Poznań, Poland
| | - Stephan Schürer
- Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Xi S Chen
- Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Allison P Heath
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, 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; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - David Fenyö
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Steven P Gygi
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, 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, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Brian R Rood
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA.
| | - Pei Wang
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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8
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Dubuissez M, Paget S, Abdelfettah S, Spruyt N, Dehennaut V, Boulay G, Loison I, de Schutter C, Rood BR, Duterque-Coquillaud M, Leroy X, Leprince D. HIC1 (Hypermethylated in Cancer 1) modulates the contractile activity of prostate stromal fibroblasts and directly regulates CXCL12 expression. Oncotarget 2020; 11:4138-4154. [PMID: 33227080 PMCID: PMC7665237 DOI: 10.18632/oncotarget.27786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 10/10/2020] [Indexed: 12/17/2022] Open
Abstract
HIC1 (Hypermethylated In Cancer 1) a tumor suppressor gene located at 17p13.3, is frequently deleted or epigenetically silenced in many human tumors. HIC1 encodes a transcriptional repressor involved in various aspects of the DNA damage response and in complex regulatory loops with P53 and SIRT1. HIC1 expression in normal prostate tissues has not yet been investigated in detail. Here, we demonstrated by immunohistochemistry that detectable HIC1 expression is restricted to the stroma of both normal and tumor prostate tissues. By RT-qPCR, we showed that HIC1 is poorly expressed in all tested prostate epithelial lineage cell types: primary (PrEC), immortalized (RWPE1) or transformed androgen-dependent (LnCAP) or androgen-independent (PC3 and DU145) prostate epithelial cells. By contrast, HIC1 is strongly expressed in primary PrSMC and immortalized (WMPY-1) prostate myofibroblastic cells. HIC1 depletion in WPMY-1 cells induced decreases in α-SMA expression and contractile capability. In addition to SLUG, we identified stromal cell-derived factor 1/C-X-C motif chemokine 12 (SDF1/CXCL12) as a new HIC1 direct target-gene. Thus, our results identify HIC1 as a tumor suppressor gene which is poorly expressed in the epithelial cells targeted by the tumorigenic process. HIC1 is expressed in stromal myofibroblasts and regulates CXCL12/SDF1 expression, thereby highlighting a complex interplay mediating the tumor promoting activity of the tumor microenvironment. Our studies provide new insights into the role of HIC1 in normal prostatic epithelial-stromal interactions through direct repression of CXCL12 and new mechanistic clues on how its loss of function through promoter hypermethylation during aging could contribute to prostatic tumors.
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Affiliation(s)
- Marion Dubuissez
- University Lille, CNRS, INSERM, Institut Pasteur de Lille, UMR9020-UMR-S1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France.,Present Address: Maisonneuve-Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital, Montreal, Canada.,These authors contributed equally to this work
| | - Sonia Paget
- University Lille, CNRS, INSERM, Institut Pasteur de Lille, UMR9020-UMR-S1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France.,These authors contributed equally to this work
| | - Souhila Abdelfettah
- University Lille, CNRS, INSERM, Institut Pasteur de Lille, UMR9020-UMR-S1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France.,These authors contributed equally to this work
| | - Nathalie Spruyt
- University Lille, CNRS, INSERM, Institut Pasteur de Lille, UMR9020-UMR-S1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Vanessa Dehennaut
- University Lille, CNRS, INSERM, Institut Pasteur de Lille, UMR9020-UMR-S1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Gaylor Boulay
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ingrid Loison
- University Lille, CNRS, INSERM, Institut Pasteur de Lille, UMR9020-UMR-S1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Clementine de Schutter
- University Lille, CNRS, INSERM, Institut Pasteur de Lille, UMR9020-UMR-S1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Brian R Rood
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC, USA
| | - Martine Duterque-Coquillaud
- University Lille, CNRS, INSERM, Institut Pasteur de Lille, UMR9020-UMR-S1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Xavier Leroy
- University Lille, CNRS, INSERM, Institut Pasteur de Lille, UMR9020-UMR-S1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France.,Department of Pathology, University Lille, Lille, France
| | - Dominique Leprince
- University Lille, CNRS, INSERM, Institut Pasteur de Lille, UMR9020-UMR-S1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
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9
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Rivero-Hinojosa S, Grant M, Panigrahi A, Zhang H, Caisova V, Bollard CM, Rood BR. Abstract 1067: Proteogenomic discovery of novel tumor proteins as neoantigens for personalized T cell immunotherapy in pediatric medulloblastoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Medulloblastoma is a common childhood brain tumor for which current therapies fail to cure high-risk subgroups, including metastatic and recurrent disease. Toxicity limits further intensification of conventional chemo-radiation therapy and most survivors endure significant lifelong sequelae from treatment. There is an urgent need to develop new tools to combat this cancer without increasing the late effects burden. Neoantigens exclusively expressed on tumor cells, are one of the main targets of an effective antitumor T-cell response. The ideal target antigen is abundantly expressed by tumor cells but not by normal tissues, in order to limit off-target effects. Tumors translate a host of unique transcripts that are the result of aberrations in tumor DNA and the unmasking of alternative or novel exons. We used a novel proteogenomic approach to identify tumor-restricted peptides and used them to select and expand T cells capable of mounting a tumor-specific cytotoxic immune response, with no off-target effects for patients with MB. Using RNA-seq and WGS data, we created personalized custom searchable databases containing predicted novel proteins from somatic mutations, novel isoforms and fusion proteins from 46 medulloblastoma tumors. By searching this database with raw mass spectrometry data from the paired medulloblastoma tumor, we have identified tens of peptides arising from the translation of tumor-specific transcripts; these peptides are potential neoantigens. Our data indicates that in cases of tumors with low mutation rates, such as pediatric brain tumors, novel isoforms are the main source of neoantigens. In a pilot study, we tested these peptides for their ability to select and expand polyclonal populations of T cells from a patient whose tumor was the source of the peptides. The immunogenicity of each individual peptide was then determined. Flow cytometry cellular characterization reveals populations of both CD4+ and CD8+ cells with an activation profile marked by IFN-γ and TNF-α production. Inhibitory co-receptor profiles were also characterized for these cells. Using cytotoxicity assays, we demonstrated that tumor specific T cells can eliminate neoantigen bearing tumor cells. These findings demonstrate an initial proof of principle that proteogenomics can be used to identify immunogenic tumor specific peptides and lay the groundwork for a personalized, targeted T cell therapy for children with high risk medulloblastoma.
Citation Format: Samuel Rivero-Hinojosa, Melanie Grant, Aswini Panigrahi, Huizhen Zhang, Veronika Caisova, Catherine M. Bollard, Brian R. Rood. Proteogenomic discovery of novel tumor proteins as neoantigens for personalized T cell immunotherapy in pediatric medulloblastoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1067.
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10
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Kambhampati M, Panditharatna E, Yadavilli S, Saoud K, Lee S, Eze A, Almira-Suarez MI, Hancock L, Bonner ER, Gittens J, Stampar M, Gaonkar K, Resnick AC, Kline C, Ho CY, Waanders AJ, Georgescu MM, Rance NE, Kim Y, Johnson C, Rood BR, Kilburn LB, Hwang EI, Mueller S, Packer RJ, Bornhorst M, Nazarian J. Harmonization of postmortem donations for pediatric brain tumors and molecular characterization of diffuse midline gliomas. Sci Rep 2020; 10:10954. [PMID: 32616776 PMCID: PMC7331588 DOI: 10.1038/s41598-020-67764-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/11/2020] [Indexed: 01/23/2023] Open
Abstract
Children diagnosed with brain tumors have the lowest overall survival of all pediatric cancers. Recent molecular studies have resulted in the discovery of recurrent driver mutations in many pediatric brain tumors. However, despite these molecular advances, the clinical outcomes of high grade tumors, including H3K27M diffuse midline glioma (H3K27M DMG), remain poor. To address the paucity of tissue for biological studies, we have established a comprehensive protocol for the coordination and processing of donated specimens at postmortem. Since 2010, 60 postmortem pediatric brain tumor donations from 26 institutions were coordinated and collected. Patient derived xenograft models and cell cultures were successfully created (76% and 44% of attempts respectively), irrespective of postmortem processing time. Histological analysis of mid-sagittal whole brain sections revealed evidence of treatment response, immune cell infiltration and the migratory path of infiltrating H3K27M DMG cells into other midline structures and cerebral lobes. Sequencing of primary and disseminated tumors confirmed the presence of oncogenic driver mutations and their obligate partners. Our findings highlight the importance of postmortem tissue donations as an invaluable resource to accelerate research, potentially leading to improved outcomes for children with aggressive brain tumors.
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Affiliation(s)
- Madhuri Kambhampati
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.,Brain Tumor Institute, Children's National Hospital, Washington, DC, USA
| | - Eshini Panditharatna
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.,Brain Tumor Institute, Children's National Hospital, Washington, DC, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sridevi Yadavilli
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.,Brain Tumor Institute, Children's National Hospital, Washington, DC, USA
| | - Karim Saoud
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.,Brain Tumor Institute, Children's National Hospital, Washington, DC, USA
| | - Sulgi Lee
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.,Brain Tumor Institute, Children's National Hospital, Washington, DC, USA.,The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Augustine Eze
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.,Brain Tumor Institute, Children's National Hospital, Washington, DC, USA
| | - M I Almira-Suarez
- Department of Pathology, Children's National Hospital, Washington, DC, USA.,The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Lauren Hancock
- Brain Tumor Institute, Children's National Hospital, Washington, DC, USA.,Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA
| | - Erin R Bonner
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.,Brain Tumor Institute, Children's National Hospital, Washington, DC, USA.,The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Jamila Gittens
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.,PTC Therapeutics, South Plainfield, NJ, USA
| | - Mojca Stampar
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Krutika Gaonkar
- Center for Data-Driven Discovery in Biomedicine, 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
| | - Cassie Kline
- Pediatric Hematology-Oncology and Neurology, UCSF Benioff Children's Hospital, San Francisco, CA, USA.,Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Cheng-Ying Ho
- Department of Pathology and Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Angela J Waanders
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Naomi E Rance
- Department of Pathology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Yong Kim
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Courtney Johnson
- Brain Tumor Institute, Children's National Hospital, Washington, DC, USA
| | - Brian R Rood
- Brain Tumor Institute, Children's National Hospital, Washington, DC, USA.,Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA
| | - Lindsay B Kilburn
- Brain Tumor Institute, Children's National Hospital, Washington, DC, USA.,Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA
| | - Eugene I Hwang
- Brain Tumor Institute, Children's National Hospital, Washington, DC, USA.,Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA
| | - Sabine Mueller
- Pediatric Hematology-Oncology and Neurology, UCSF Benioff Children's Hospital, San Francisco, CA, USA.,Department of Oncology, Children's Research Center, University Children's Hospital Zürich, Zurich, Switzerland
| | - Roger J Packer
- Brain Tumor Institute, Children's National Hospital, Washington, DC, USA
| | - Miriam Bornhorst
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA. .,Brain Tumor Institute, Children's National Hospital, Washington, DC, USA. .,The George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
| | - Javad Nazarian
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA. .,Department of Oncology, Children's Research Center, University Children's Hospital Zürich, Zurich, Switzerland. .,The George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
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11
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Abstract
BACKGROUND The germline genetic events underpinning medulloblastoma (MB) initiation, and therefore the ability to determine who is at risk, are still unknown for the majority of cases. Microsatellites are short repeated sequences that make up ~3% of the genome. Repeat lengths vary among individuals and are often nonrandomly associated with disease, including several cancers such as breast, glioma, lung, and ovarian. Due to their effects on gene function, they have been called the "tuning knobs of the genome." METHODS We have developed a novel approach for identifying a microsatellite-based signature to differentiate MB patients from controls using germline DNA. RESULTS Analyzing germline whole exome sequencing data from a training set of 120 MB subjects and 425 controls, we identified 139 individual microsatellite loci whose genotypes differ significantly between the groups. Using a genetic algorithm, we identified a subset of 43 microsatellites that distinguish MB subjects from controls with a sensitivity and specificity of 92% and 88%, respectively. This microsatellite signature was validated in an independent dataset consisting of 102 subjects and 428 controls, with comparable sensitivity and specificity of 95% and 90%, respectively. Analysis of the allele genotypes of those 139 informative loci demonstrates that their association with MB is a consequence of individual microsatellites' genotypes rather than their hypermutability. Finally, an analysis of the genes harboring these microsatellite loci reveals cellular functions important for tumorigenesis. CONCLUSION This study demonstrates that MB-specific germline microsatellite variations mark those at risk for MB development and suggests mechanisms of predisposition.
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Affiliation(s)
- Samuel Rivero-Hinojosa
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center (CNMC), Washington, DC
| | - Nicholas Kinney
- Center for Bioinformatics and Genetics, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia
- Gibbs Cancer Center and Research Institute, Spartanburg, South Carolina
| | - Harold R Garner
- Center for Bioinformatics and Genetics, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia
- Gibbs Cancer Center and Research Institute, Spartanburg, South Carolina
| | - Brian R Rood
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center (CNMC), Washington, DC
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12
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Tao R, Murad N, Xu Z, Zhang P, Okonechnikov K, Kool M, Rivero-Hinojosa S, Lazarski C, Zheng P, Liu Y, Eberhart CG, Rood BR, Packer R, Pei Y. MYC Drives Group 3 Medulloblastoma through Transformation of Sox2 + Astrocyte Progenitor Cells. Cancer Res 2019; 79:1967-1980. [PMID: 30862721 DOI: 10.1158/0008-5472.can-18-1787] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/07/2018] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
A subset of group 3 medulloblastoma frequently harbors amplification or overexpression of MYC lacking additional focal aberrations, yet it remains unclear whether MYC overexpression alone can induce tumorigenesis and which cells give rise to these tumors. Here, we showed that astrocyte progenitors in the early postnatal cerebellum were susceptible to transformation by MYC. The resulting tumors specifically resembled human group 3 medulloblastoma based on histology and gene-expression profiling. Gene-expression analysis of MYC-driven medulloblastoma cells revealed altered glucose metabolic pathways with marked overexpression of lactate dehydrogenase A (LDHA). LDHA abundance correlated positively with MYC expression and was associated with poor prognosis in human group 3 medulloblastoma. Inhibition of LDHA significantly reduced growth of both mouse and human MYC-driven tumors but had little effect on normal cerebellar cells or SHH-associated medulloblastoma. By generating a new mouse model, we demonstrated for the first time that astrocyte progenitors can be transformed by MYC and serve as the cells of origin for group 3 medulloblastoma. Moreover, we identified LDHA as a novel, specific therapeutic target for this devastating disease. SIGNIFICANCE: Insights from a new model identified LDHA as a novel target for group 3 medulloblastoma, paving the way for the development of effective therapies against this disease.
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Affiliation(s)
- Ran Tao
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Najiba Murad
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Zhenhua Xu
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Peng Zhang
- Division of Immunotherapy, Institute of Human Virology, School of Medicine, University of Maryland, College Park, Maryland
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center, NCT, Heidelberg, Germany.,Division of Pediatric Neuro-oncology of the German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center, NCT, Heidelberg, Germany.,Division of Pediatric Neuro-oncology of the German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Samuel Rivero-Hinojosa
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Christopher Lazarski
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Pan Zheng
- Division of Immunotherapy, Institute of Human Virology, School of Medicine, University of Maryland, College Park, Maryland
| | - Yang Liu
- Division of Immunotherapy, Institute of Human Virology, School of Medicine, University of Maryland, College Park, Maryland
| | - Charles G Eberhart
- Division of Neuropathology, Johns Hopkins University, Baltimore, Maryland
| | - Brian R Rood
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Roger Packer
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Yanxin Pei
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC.
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Rivero-Hinojosa S, Lau LS, Stampar M, Staal J, Zhang H, Gordish-Dressman H, Northcott PA, Pfister SM, Taylor MD, Brown KJ, Rood BR. Proteomic analysis of Medulloblastoma reveals functional biology with translational potential. Acta Neuropathol Commun 2018; 6:48. [PMID: 29880060 PMCID: PMC5992829 DOI: 10.1186/s40478-018-0548-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 05/17/2018] [Indexed: 12/14/2022] Open
Abstract
Genomic characterization has begun to redefine diagnostic classifications of cancers. However, it remains a challenge to infer disease phenotypes from genomic alterations alone. To help realize the promise of genomics, we have performed a quantitative proteomics investigation using Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and 41 tissue samples spanning the 4 genomically based subgroups of medulloblastoma and control cerebellum. We have identified and quantitated thousands of proteins across these groups and find that we are able to recapitulate the genomic subgroups based upon subgroup restricted and differentially abundant proteins while also identifying subgroup specific protein isoforms. Integrating our proteomic measurements with genomic data, we calculate a poor correlation between mRNA and protein abundance. Using EPIC 850 k methylation array data on the same tissues, we also investigate the influence of copy number alterations and DNA methylation on the proteome in an attempt to characterize the impact of these genetic features on the proteome. Reciprocally, we are able to use the proteome to identify which genomic alterations result in altered protein abundance and thus are most likely to impact biology. Finally, we are able to assemble protein-based pathways yielding potential avenues for clinical intervention. From these, we validate the EIF4F cap-dependent translation pathway as a novel druggable pathway in medulloblastoma. Thus, quantitative proteomics complements genomic platforms to yield a more complete understanding of functional tumor biology and identify novel therapeutic targets for medulloblastoma.
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Paget S, Dubuissez M, Dehennaut V, Nassour J, Harmon BT, Spruyt N, Loison I, Abbadie C, Rood BR, Leprince D. HIC1 (hypermethylated in cancer 1) SUMOylation is dispensable for DNA repair but is essential for the apoptotic DNA damage response (DDR) to irreparable DNA double-strand breaks (DSBs). Oncotarget 2017; 8:2916-2935. [PMID: 27935866 PMCID: PMC5356852 DOI: 10.18632/oncotarget.13807] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/23/2016] [Indexed: 11/25/2022] Open
Abstract
The tumor suppressor gene HIC1 (Hypermethylated In Cancer 1) encodes a transcriptional repressor mediating the p53-dependent apoptotic response to irreparable DNA double-strand breaks (DSBs) through direct transcriptional repression of SIRT1. HIC1 is also essential for DSB repair as silencing of endogenous HIC1 in BJ-hTERT fibroblasts significantly delays DNA repair in functional Comet assays. HIC1 SUMOylation favours its interaction with MTA1, a component of NuRD complexes. In contrast with irreparable DSBs induced by 16-hours of etoposide treatment, we show that repairable DSBs induced by 1 h etoposide treatment do not increase HIC1 SUMOylation or its interaction with MTA1. Furthermore, HIC1 SUMOylation is dispensable for DNA repair since the non-SUMOylatable E316A mutant is as efficient as wt HIC1 in Comet assays. Upon induction of irreparable DSBs, the ATM-mediated increase of HIC1 SUMOylation is independent of its effector kinase Chk2. Moreover, irreparable DSBs strongly increase both the interaction of HIC1 with MTA1 and MTA3 and their binding to the SIRT1 promoter. To characterize the molecular mechanisms sustained by this increased repression potential, we established global expression profiles of BJ-hTERT fibroblasts transfected with HIC1-siRNA or control siRNA and treated or not with etoposide. We identified 475 genes potentially repressed by HIC1 with cell death and cell cycle as the main cellular functions identified by pathway analysis. Among them, CXCL12, EPHA4, TGFβR3 and TRIB2, also known as MTA1 target-genes, were validated by qRT-PCR analyses. Thus, our data demonstrate that HIC1 SUMOylation is important for the transcriptional response to non-repairable DSBs but dispensable for DNA repair.
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Affiliation(s)
- Sonia Paget
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Marion Dubuissez
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
- Present Address: Maisonneuve-Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital, Boulevard l'Assomption Montreal, Canada
| | - Vanessa Dehennaut
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Joe Nassour
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
- Present Address: The Salk Institute for Biological Studies, Molecular and Cell Biology Department, La Jolla, California, USA
| | - Brennan T. Harmon
- Genomics Core, Children's National Medical Center, Washington DC, USA
| | - Nathalie Spruyt
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Ingrid Loison
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Corinne Abbadie
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Brian R. Rood
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington DC, USA
| | - Dominique Leprince
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
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15
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Staal JA, Pei Y, Rood BR. A Proteogenomic Approach to Understanding MYC Function in Metastatic Medulloblastoma Tumors. Int J Mol Sci 2016; 17:ijms17101744. [PMID: 27775567 PMCID: PMC5085772 DOI: 10.3390/ijms17101744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/23/2016] [Accepted: 10/10/2016] [Indexed: 12/31/2022] Open
Abstract
Brain tumors are the leading cause of cancer-related deaths in children, and medulloblastoma is the most prevalent malignant childhood/pediatric brain tumor. Providing effective treatment for these cancers, with minimal damage to the still-developing brain, remains one of the greatest challenges faced by clinicians. Understanding the diverse events driving tumor formation, maintenance, progression, and recurrence is necessary for identifying novel targeted therapeutics and improving survival of patients with this disease. Genomic copy number alteration data, together with clinical studies, identifies c-MYC amplification as an important risk factor associated with the most aggressive forms of medulloblastoma with marked metastatic potential. Yet despite this, very little is known regarding the impact of such genomic abnormalities upon the functional biology of the tumor cell. We discuss here how recent advances in quantitative proteomic techniques are now providing new insights into the functional biology of these aggressive tumors, as illustrated by the use of proteomics to bridge the gap between the genotype and phenotype in the case of c-MYC-amplified/associated medulloblastoma. These integrated proteogenomic approaches now provide a new platform for understanding cancer biology by providing a functional context to frame genomic abnormalities.
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Affiliation(s)
- Jerome A Staal
- Multiple Sclerosis Department, Florey Institute of Neuroscience and Mental Health, Melbourne, VIC 3052, Australia.
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC 20010, USA.
| | - Yanxin Pei
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC 20010, USA.
| | - Brian R Rood
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC 20010, USA.
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16
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Staal JA, Lau LS, Zhang H, Ingram WJ, Hallahan AR, Northcott PA, Pfister SM, Wechsler-Reya RJ, Rusert JM, Taylor MD, Cho YJ, Packer RJ, Brown KJ, Rood BR. Proteomic profiling of high risk medulloblastoma reveals functional biology. Oncotarget 2016; 6:14584-95. [PMID: 25970789 PMCID: PMC4546489 DOI: 10.18632/oncotarget.3927] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 04/08/2015] [Indexed: 12/11/2022] Open
Abstract
Genomic characterization of medulloblastoma has improved molecular risk classification but struggles to define functional biological processes, particularly for the most aggressive subgroups. We present here a novel proteomic approach to this problem using a reference library of stable isotope labeled medulloblastoma-specific proteins as a spike-in standard for accurate quantification of the tumor proteome. Utilizing high-resolution mass spectrometry, we quantified the tumor proteome of group 3 medulloblastoma cells and demonstrate that high-risk MYC amplified tumors can be segregated based on protein expression patterns. We cross-validated the differentially expressed protein candidates using an independent transcriptomic data set and further confirmed them in a separate cohort of medulloblastoma tissue samples to identify the most robust proteogenomic differences. Interestingly, highly expressed proteins associated with MYC-amplified tumors were significantly related to glycolytic metabolic pathways via alternative splicing of pyruvate kinase (PKM) by heterogeneous ribonucleoproteins (HNRNPs). Furthermore, when maintained under hypoxic conditions, these MYC-amplified tumors demonstrated increased viability compared to non-amplified tumors within the same subgroup. Taken together, these findings highlight the power of proteomics as an integrative platform to help prioritize genetic and molecular drivers of cancer biology and behavior.
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Affiliation(s)
- Jerome A Staal
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington DC, USA
| | - Ling San Lau
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington DC, USA
| | - Huizhen Zhang
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington DC, USA
| | - Wendy J Ingram
- UQ Child Health Research Centre, The University of Queensland and Queensland Children's Medical Research Institute, Children's Health, Queensland, Australia
| | - Andrew R Hallahan
- UQ Child Health Research Centre, The University of Queensland and Queensland Children's Medical Research Institute, Children's Health, Queensland, Australia
| | - Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center, Heidleberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center, Heidleberg, Germany
| | | | - Jessica M Rusert
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Michael D Taylor
- Department of Neurosurgery, Hospital for Sick Children, Toronto, Canada
| | - Yoon-Jae Cho
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Roger J Packer
- Center for Neuroscience and Behavioral Medicine, Children's National Medical Center, Washington DC, USA
| | - Kristy J Brown
- Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Brian R Rood
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington DC, USA
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17
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Karunasena E, McIver LJ, Rood BR, Wu X, Zhu H, Bavarva JH, Garner HR. Somatic intronic microsatellite loci differentiate glioblastoma from lower-grade gliomas. Oncotarget 2015; 5:6003-14. [PMID: 25153720 PMCID: PMC4171608 DOI: 10.18632/oncotarget.2076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Genomic studies of glioma sub-types have amassed new disease specific mutations, yet these only partially explain how mutations are linked to predisposition or progression. We hypothesized that microsatellite variation could expand the understanding of glioma etiology. Furthermore, germline markers for gliomas are typically undetectable; therefore we also hypothesize that the predictability of cancer-associated microsatellite loci in germline DNA may support the current hypothesis of a glioma cell of origin. In this study, “normal” germline exome sequenced DNA from the 1000 Genomes Project (n=390) were compared with exome sequences from germlines of subjects with WHO grade II and III lower-grade glioma (LGG, n=136) and WHO grade IV glioblastoma (GBM, n=252) from The Cancer Genome Atlas to identify microsatellite loci non-randomly associated with glioma. From germline data, we identified 48 GBM-specific loci, 42 Lower-grade glioma specific loci and 29 loci that distinguish GBM from LGG (p≤ 0.01). We then attempted to distinguish WHO grade II glioma (n=67) from GBM resulting in 8 informative loci. Significantly, in all glioma grades, comparisons between tumor and matched germline sequences demonstrated no significant differences in these variants (p≥ 0.01). Therefore, these microsatellite loci are considered to be components of grade-specific signatures for glioma which distinguish germline sequences of individuals with cancer from those of individuals that are “normal”. In order to better understand the significance of these loci, we identified biological processes enriched in genes with these variants. Most strikingly, six helicase genes were enriched in the GBM cohort (p≤ 1.0 ×10−3). The preservation of these glioma-specific loci could therefore serve as valuable diagnostic and therapeutic markers; especially since the heterogeneity of tumor cell populations can obscure the identification of mutations preceding a metastatic phenotype.
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Affiliation(s)
- Enusha Karunasena
- Virginia Bioinformatics Institute, Medical Informatics and Systems Division; Blacksburg, VA; These authors contributed equally to this work
| | - Lauren J McIver
- Virginia Bioinformatics Institute, Medical Informatics and Systems Division; Blacksburg, VA; These authors contributed equally to this work
| | - Brian R Rood
- Center for Cancer and Blood Disorders at Children's National Medical Center; Washington, D.C
| | - Xiaowei Wu
- Department of Statistics at Virginia Tech; Blacksburg, VA
| | - Hongxiao Zhu
- Department of Statistics at Virginia Tech; Blacksburg, VA
| | - Jasmin H Bavarva
- Virginia Bioinformatics Institute, Medical Informatics and Systems Division; Blacksburg, VA
| | - Harold R Garner
- Virginia Bioinformatics Institute, Medical Informatics and Systems Division; Blacksburg, VA
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18
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Avery RA, Hwang EI, Ishikawa H, Acosta MT, Hutcheson KA, Santos D, Zand DJ, Kilburn LB, Rosenbaum KN, Rood BR, Schuman JS, Packer RJ. Handheld optical coherence tomography during sedation in young children with optic pathway gliomas. JAMA Ophthalmol 2014; 132:265-71. [PMID: 24435762 DOI: 10.1001/jamaophthalmol.2013.7649] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
IMPORTANCE Monitoring young children with optic pathway gliomas (OPGs) for visual deterioration can be difficult owing to age-related noncompliance. Optical coherence tomography (OCT) measures of retinal nerve fiber layer (RNFL) thickness have been proposed as a surrogate marker of vision but this technique is also limited by patient cooperation. OBJECTIVE To determine whether measures of circumpapillary RNFL thickness, acquired with handheld OCT (HH-OCT) during sedation, can differentiate between young children with and without vision loss from OPGs. DESIGN, SETTING, AND PARTICIPANTS This cross-sectional analysis of a prospective observational study was conducted at a tertiary-care children's hospital. Children with an OPG (sporadic or secondary to neurofibromatosis type 1) who were cooperative for visual acuity testing, but required sedation to complete magnetic resonance imaging, underwent HH-OCT imaging of the circumpapillary RNFL while sedated. MAIN OUTCOMES AND MEASURES Area under the curve of the receiver operating characteristic, sensitivity, specificity, positive predictive value, and negative predictive value of the average and quadrant-specific RNFL thicknesses. RESULTS Thirty-three children (64 eyes) met inclusion criteria (median age, 4.8 years; range, 1.8-12.6 years). In children with vision loss (abnormal visual acuity and/or visual field), RNFL thickness was decreased in all quadrants compared with the normal-vision group (P < .001 for all comparisons). Using abnormal criteria of less than 5% and less than 1%, the area under the curve was highest for the average RNFL thickness (0.96 and 0.97, respectively) compared with specific anatomic quadrants. The highest discrimination and predictive values were demonstrated for participants with 2 or more quadrants meeting less than 5% (sensitivity = 93.3; specificity = 97.9; positive predictive value = 93.3; and negative predictive value = 97.9) and less than 1% (sensitivity = 93.3; specificity = 100; positive predictive value = 100; and negative predictive value = 98.0) criteria. CONCLUSIONS AND RELEVANCE Measures of RNFL thickness acquired with HH-OCT during sedation can differentiate between young children with and without vision loss from OPGs. For young children who do not cooperate with vision testing, HH-OCT measures may be a surrogate marker of vision. Longitudinal studies are needed to delineate the temporal relationship between RNFL decline and vision loss.
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Affiliation(s)
- Robert A Avery
- The Gilbert Family Neurofibromatosis Institute, Children's National Medical Center, Washington, DC2Department of Neurology, Children's National Medical Center, Washington, DC3Department of Ophthalmology, Children's National Medical Center, Washington, DC7
| | - Eugene I Hwang
- Department of Oncology, Children's National Medical Center, Washington, DC7The Brain Tumor Institute, Children's National Medical Center, Washington, DC
| | - Hiroshi Ishikawa
- University of Pittsburgh Medical Center Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania10Department of Bioengineering
| | - Maria T Acosta
- The Gilbert Family Neurofibromatosis Institute, Children's National Medical Center, Washington, DC2Department of Neurology, Children's National Medical Center, Washington, DC8Center for Neuroscience and Behavior, Children's National Medical Center, Washin
| | - Kelly A Hutcheson
- Department of Ophthalmology, Children's National Medical Center, Washington, DC
| | - Domiciano Santos
- Department of Anesthesiology, Children's National Medical Center, Washington, DC
| | - Dina J Zand
- Department of Genetics, Children's National Medical Center, Washington, DC
| | - Lindsay B Kilburn
- Department of Oncology, Children's National Medical Center, Washington, DC7The Brain Tumor Institute, Children's National Medical Center, Washington, DC
| | | | - Brian R Rood
- Department of Oncology, Children's National Medical Center, Washington, DC7The Brain Tumor Institute, Children's National Medical Center, Washington, DC
| | - Joel S Schuman
- University of Pittsburgh Medical Center Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania10Department of Bioengineering
| | - Roger J Packer
- The Gilbert Family Neurofibromatosis Institute, Children's National Medical Center, Washington, DC2Department of Neurology, Children's National Medical Center, Washington, DC6Department of Oncology, Children's National Medical Center, Washington, DC7The B
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19
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Dubuissez M, Faiderbe P, Pinte S, Dehennaut V, Rood BR, Leprince D. The Reelin receptors ApoER2 and VLDLR are direct target genes of HIC1 (Hypermethylated In Cancer 1). Biochem Biophys Res Commun 2013; 440:424-30. [PMID: 24076391 DOI: 10.1016/j.bbrc.2013.09.091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 09/17/2013] [Indexed: 11/16/2022]
Abstract
The tumor suppressor gene HIC1 (Hypermethylated In Cancer 1) is located in 17p13.3 a region frequently hypermethylated or deleted in tumors and in a contiguous-gene syndrome, the Miller-Dieker syndrome which includes classical lissencephaly (smooth brain) and severe developmental defects. HIC1 encodes a transcriptional repressor involved in the regulation of growth control, DNA damage response and cell migration properties. We previously demonstrated that the membrane-associated G-protein-coupled receptors CXCR7, ADRB2 and the tyrosine kinase receptor EphA2 are direct target genes of HIC1. Here we show that ectopic expression of HIC1 in U2OS and MDA-MB-231 cell lines decreases expression of the ApoER2 and VLDLR genes, encoding two canonical tyrosine kinase receptors for Reelin. Conversely, knock-down of endogenous HIC1 in BJ-Tert normal human fibroblasts through RNA interference results in the up-regulation of these two Reelin receptors. Finally, through chromatin immunoprecipitation (ChIP) in BJ-Tert fibroblasts, we demonstrate that HIC1 is a direct transcriptional repressor of ApoER2 and VLDLR. These data provide evidence that HIC1 is a new regulator of the Reelin pathway which is essential for the proper migration of neuronal precursors during the normal development of the cerebral cortex, of Purkinje cells in the cerebellum and of mammary epithelial cells. Deregulation of this pathway through HIC1 inactivation or deletion may contribute to its role in tumor promotion. Moreover, HIC1, through the direct transcriptional repression of ATOH1 and the Reelin receptors ApoER2 and VLDLR, could play an essential role in normal cerebellar development.
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Affiliation(s)
- Marion Dubuissez
- CNRS-UMR 8161, Institut de Biologie de Lille, Université de Lille Nord de France, Institut Pasteur de Lille, IFR 142, 1 rue Calmette, BP447, 59017 Lille Cedex, France
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20
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Abstract
Cellular hemangioma is a subtype of hemangioma that is associated with cellular immaturity and the potential for recurrence. Intracranial location of these lesions is extremely rare, and definitive treatment often requires radical neurosurgical resection. The authors report a case of a 12-year-old boy with a subtemporal cellular hemangioma. He underwent gross-total resection of the tumor, but within 1.5 months the tumor recurred, necessitating a second resection. Because of its proximity to vascular structures, only subtotal resection was possible. Repeat MRI 1 month after the second surgery showed significant tumor recurrence. Given the tumor's demonstrated capacity for recurrence and its proximity to the vein of Labbé and sigmoid sinus, further resection was not indicated. In an effort to limit radiation therapy for this young patient, treatment with bevacizumab and temozolomide was chosen and achieved a complete response that has proven durable for 36 months after cessation of therapy. This is the first report of the successful use of chemotherapy to treat an intracranial hemangioma, a rare condition with limited therapeutic options.
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Affiliation(s)
- Kee Kiat Yeo
- Department of Pediatrics, Children’s National Medical Center, 111 Michigan Avenue NW, Washington, DC 20010, USA
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21
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Hwang EI, Jakacki RI, Fisher MJ, Kilburn LB, Horn M, Vezina G, Rood BR, Packer RJ. Long-term efficacy and toxicity of bevacizumab-based therapy in children with recurrent low-grade gliomas. Pediatr Blood Cancer 2013; 60:776-82. [PMID: 22976922 DOI: 10.1002/pbc.24297] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 08/02/2012] [Indexed: 01/05/2023]
Abstract
BACKGROUND Because definitive resection or radiotherapy for pediatric low-grade gliomas (LGGs) may be associated with severe and permanent adverse effects, medical management has taken a significant role. Bevacizumab-based therapy has demonstrated encouraging responses; however, longer-term toxicity, response durability and alternative dosing regimens have not been evaluated. PROCEDURE This was a retrospective review of children with multiply recurrent, progressive LGGs treated with bevacizumab-based therapy and followed for at least 12 months after treatment completion. Toxicity was uniformly graded and imaging was centrally reviewed. RESULTS All fourteen patients had failed at least two prior treatment regimens; six had dissemination. Patients received initial bevacizumab-based therapy at a median age of 5.3 years (range, 1-12 years). Median treatment duration was 12 months (range, 1-24 months). 12 patients had an objective response; 2 had stable disease. Median time to maximum response was 9 weeks (range, 7-17 weeks). No patients progressed on therapy, although 13/14 progressed after stopping bevacizumab at a median of 5 months. Four patients were re-treated with bevacizumab and all again responded or stabilized. Alternative dosing strategies were effective, including bevacizumab monotherapy and prolonging the dosing interval to 3 weeks. High-grade bevacizumab-related toxicities consisted of grade 3 proteinuria (n = 2), primary inflammatory arthritis (n = 1), and somnolence (n = 1). Toxicities resolved within 6 months of treatment cessation except one case of hypertension. CONCLUSIONS Bevacizumab-based therapy is successful at inducing rapid LGG response. Patients progressing off-therapy may be successfully re-treated with bevacizumab. Nearly all tumors progress once treatment is discontinued. Toxicities are not insignificant but usually reversible.
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Affiliation(s)
- Eugene I Hwang
- Division of Oncology, Center for Cancer and Blood Disorders, Children's National Medical Center, Washington, District of Columbia, USA.
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22
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Abstract
INTRODUCTION The tumor suppressor gene HIC1 (Hypermethylated in Cancer 1), which encodes a transcriptional repressor with multiple partners and multiple targets, is epigenetically silenced but not mutated in tumors. HIC1 has broad biological roles during normal development and is implicated in many canonical processes of cancer such as control of cell growth, cell survival upon genotoxic stress, cell migration, and motility. AREAS COVERED The HIC1 literature herein discussed includes its discovery as a candidate tumor suppressor gene hypermethylated or deleted in many human tumors, animal models establishing it as tumor suppressor gene, its role as a sequence-specific transcriptional repressor recruiting several chromatin regulatory complexes, its cognate target genes, and its functional roles in normal tissues. Finally, this review discusses how its loss of function contributes to the early steps in tumorigenesis. EXPERT OPINION Given HIC1's ability to direct repressive complexes to sequence-specific binding sites associated with its target genes, its loss results in specific changes in the transcriptional program of the cell. An understanding of this program through identification of HIC1's target genes and their involvement in feedback loops and cell process regulation will yield the ability to leverage this knowledge for therapeutic translation.
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Affiliation(s)
- Brian R Rood
- Center for Cancer and Blood Disorders, Children's National Medical Center, Division of Oncology, 111 Michigan Ave. NW, Washington, DC 20010, USA
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Brown KJ, Formolo CA, Seol H, Marathi RL, Duguez S, An E, Pillai D, Nazarian J, Rood BR, Hathout Y. Advances in the proteomic investigation of the cell secretome. Expert Rev Proteomics 2013; 9:337-45. [PMID: 22809211 DOI: 10.1586/epr.12.21] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Studies of the cell secretome have greatly increased in recent years owing to improvements in proteomic platforms, mass spectrometry instrumentation and to the increased interaction between analytical chemists, biologists and clinicians. Several secretome studies have been implemented in different areas of research, leading to the generation of a valuable secretome catalogs. Secreted proteins continue to be an important source of biomarkers and therapeutic target discovery and are equally valuable in the field of microbiology. Several discoveries have been achieved in vitro using cell culture systems, ex vivo using human tissue specimens and in vivo using animal models. In this review, some of the most recent advances in secretome studies and the fields that have benefited the most from this evolving technology are highlighted.
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Affiliation(s)
- Kristy J Brown
- Children's National Medical Center, Center for Genetic Medicine Research, 111 Michigan Avenue NW, Washington, DC 20010, USA
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Albanese C, Rodriguez OC, VanMeter J, Fricke ST, Rood BR, Lee Y, Wang SS, Madhavan S, Gusev Y, Petricoin EF, Wang Y. Preclinical magnetic resonance imaging and systems biology in cancer research: current applications and challenges. Am J Pathol 2012; 182:312-8. [PMID: 23219428 DOI: 10.1016/j.ajpath.2012.09.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 09/03/2012] [Accepted: 09/18/2012] [Indexed: 01/19/2023]
Abstract
Biologically accurate mouse models of human cancer have become important tools for the study of human disease. The anatomical location of various target organs, such as brain, pancreas, and prostate, makes determination of disease status difficult. Imaging modalities, such as magnetic resonance imaging, can greatly enhance diagnosis, and longitudinal imaging of tumor progression is an important source of experimental data. Even in models where the tumors arise in areas that permit visual determination of tumorigenesis, longitudinal anatomical and functional imaging can enhance the scope of studies by facilitating the assessment of biological alterations, (such as changes in angiogenesis, metabolism, cellular invasion) as well as tissue perfusion and diffusion. One of the challenges in preclinical imaging is the development of infrastructural platforms required for integrating in vivo imaging and therapeutic response data with ex vivo pathological and molecular data using a more systems-based multiscale modeling approach. Further challenges exist in integrating these data for computational modeling to better understand the pathobiology of cancer and to better affect its cure. We review the current applications of preclinical imaging and discuss the implications of applying functional imaging to visualize cancer progression and treatment. Finally, we provide new data from an ongoing preclinical drug study demonstrating how multiscale modeling can lead to a more comprehensive understanding of cancer biology and therapy.
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Affiliation(s)
- Chris Albanese
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Washington, District of Columbia 20057, USA.
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Saratsis AM, Yadavilli S, Magge S, Rood BR, Perez J, Hill DA, Hwang E, Kilburn L, Packer RJ, Nazarian J. Insights into pediatric diffuse intrinsic pontine glioma through proteomic analysis of cerebrospinal fluid. Neuro Oncol 2012; 14:547-60. [PMID: 22492959 DOI: 10.1093/neuonc/nos067] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a leading cause of brain tumor-related death in children. DIPG is not surgically resectable, resulting in a paucity of tissue available for molecular studies. As such, tumor biology is poorly understood, and, currently, there are no effective treatments. In the absence of frozen tumor specimens, body fluids--such as cerebrospinal fluid (CSF), serum, and urine--can serve as more readily accessible vehicles for detecting tumor-secreted proteins. We analyzed a total of 76 specimens, including CSF, serum, urine, and normal and tumor brainstem tissue. Protein profiling of CSF from patients with DIPG was generated by mass spectrometry using an LTQ-Orbitrap-XL and database search using the Sequest algorithm. Quantitative and statistical analyses were performed with ProteoIQ and Partek Genomics Suite. A total of 528 unique proteins were identified, 71% of which are known secreted proteins. CSF proteomic analysis revealed selective upregulation of Cyclophillin A (CypA) and dimethylarginase 1 (DDAH1) in DIPG (n = 10), compared with controls (n = 4). Protein expression was further validated with Western blot analysis and immunohistochemical assays using CSF, brain tissue, serum, and urine from DIPG and control specimens. Immunohistochemical staining showed selective upregulation of secreted but not cytosolic CypA and DDAH1 in patients with DIPG. In this study, we present the first comprehensive protein profile of CSF specimens from patients with DIPG to demonstrate selective expression of tumor proteins potentially involved in brainstem gliomagenesis. Detection of secreted CypA and DDAH1 in serum and urine has potential clinical application, with implications for assessing treatment response and detecting tumor recurrence in patients with DIPG.
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Affiliation(s)
- Amanda M Saratsis
- Department of Neurosurgery, Georgetown University Hospital, Research Center for Genetic Medicine, Children's National Medical Center NW, Washington, DC 20010, USA.
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Foveau B, Boulay G, Pinte S, Van Rechem C, Rood BR, Leprince D. The receptor tyrosine kinase EphA2 is a direct target gene of hypermethylated in cancer 1 (HIC1). J Biol Chem 2012; 287:5366-78. [PMID: 22184117 PMCID: PMC3285316 DOI: 10.1074/jbc.m111.329466] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Indexed: 11/06/2022] Open
Abstract
The tumor suppressor gene hypermethylated in cancer 1 (HIC1), which encodes a transcriptional repressor, is epigenetically silenced in many human tumors. Here, we show that ectopic expression of HIC1 in the highly malignant MDA-MB-231 breast cancer cell line severely impairs cell proliferation, migration, and invasion in vitro. In parallel, infection of breast cancer cell lines with a retrovirus expressing HIC1 also induces decreased mRNA and protein expression of the tyrosine kinase receptor EphA2. Moreover, chromatin immunoprecipitation (ChIP) and sequential ChIP experiments demonstrate that endogenous HIC1 proteins are bound, together with the MTA1 corepressor, to the EphA2 promoter in WI38 cells. Taken together, our results identify EphA2 as a new direct target gene of HIC1. Finally, we observe that inactivation of endogenous HIC1 through RNA interference in normal breast epithelial cells results in the up-regulation of EphA2 and is correlated with increased cellular migration. To conclude, our results involve the tumor suppressor HIC1 in the transcriptional regulation of the tyrosine kinase receptor EphA2, whose ligand ephrin-A1 is also a HIC1 target gene. Thus, loss of the regulation of this Eph pathway through HIC1 epigenetic silencing could be an important mechanism in the pathogenesis of epithelial cancers.
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Affiliation(s)
- Bénédicte Foveau
- From the CNRS UMR 8161, Institut de Biologie de Lille, CNRS-Institut Pasteur de Lille-Université de Lille 1-Université de Lille 2, 59021 Lille Cedex, France and
| | - Gaylor Boulay
- From the CNRS UMR 8161, Institut de Biologie de Lille, CNRS-Institut Pasteur de Lille-Université de Lille 1-Université de Lille 2, 59021 Lille Cedex, France and
| | - Sébastien Pinte
- From the CNRS UMR 8161, Institut de Biologie de Lille, CNRS-Institut Pasteur de Lille-Université de Lille 1-Université de Lille 2, 59021 Lille Cedex, France and
| | - Capucine Van Rechem
- From the CNRS UMR 8161, Institut de Biologie de Lille, CNRS-Institut Pasteur de Lille-Université de Lille 1-Université de Lille 2, 59021 Lille Cedex, France and
| | - Brian R. Rood
- the Children's National Medical Center, The George Washington University School of Medicine, Washington, D. C. 20010-2970
| | - Dominique Leprince
- From the CNRS UMR 8161, Institut de Biologie de Lille, CNRS-Institut Pasteur de Lille-Université de Lille 1-Université de Lille 2, 59021 Lille Cedex, France and
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Boulay G, Malaquin N, Loison I, Foveau B, Van Rechem C, Rood BR, Pourtier A, Leprince D. Loss of Hypermethylated in Cancer 1 (HIC1) in breast cancer cells contributes to stress-induced migration and invasion through β-2 adrenergic receptor (ADRB2) misregulation. J Biol Chem 2011; 287:5379-89. [PMID: 22194601 DOI: 10.1074/jbc.m111.304287] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The transcriptional repressor HIC1 (Hypermethylated in Cancer 1) is a tumor suppressor gene inactivated in many human cancers including breast carcinomas. In this study, we show that HIC1 is a direct transcriptional repressor of β-2 adrenergic receptor (ADRB2). Through promoter luciferase activity, chromatin immunoprecipitation (ChIP) and sequential ChIP experiments, we demonstrate that ADRB2 is a direct target gene of HIC1, endogenously in WI-38 cells and following HIC1 re-expression in breast cancer cells. Agonist-mediated stimulation of ADRB2 increases the migration and invasion of highly malignant MDA-MB-231 breast cancer cells but these effects are abolished following HIC1 re-expression or specific down-regulation of ADRB2 by siRNA treatment. Our results suggest that early inactivation of HIC1 in breast carcinomas could predispose to stress-induced metastasis through up-regulation of the β-2 adrenergic receptor.
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Affiliation(s)
- Gaylor Boulay
- CNRS UMR 8161, CNRS-Université de Lille 1-Institut Pasteur de Lille, Lille 59021, France
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Rajagopal MU, Hathout Y, MacDonald TJ, Kieran MW, Gururangan S, Blaney SM, Phillips P, Packer R, Gordish-Dressman H, Rood BR. Proteomic profiling of cerebrospinal fluid identifies prostaglandin D2 synthase as a putative biomarker for pediatric medulloblastoma: A pediatric brain tumor consortium study. Proteomics Clin Appl 2011. [DOI: 10.1002/prca.201190065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Rajagopal MU, Hathout Y, MacDonald TJ, Kieran MW, Gururangan S, Blaney SM, Phillips P, Packer R, Gordish-Dressman H, Rood BR. Proteomic profiling of cerebrospinal fluid identifies prostaglandin D2 synthase as a putative biomarker for pediatric medulloblastoma: A pediatric brain tumor consortium study. Proteomics 2011; 11:935-43. [PMID: 21271676 PMCID: PMC3088509 DOI: 10.1002/pmic.201000198] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 09/24/2010] [Accepted: 12/05/2010] [Indexed: 01/25/2023]
Abstract
The aims of this study were to demonstrate the feasibility of centrally collecting and processing high-quality cerebrospinal fluid (CSF) samples for proteomic studies within a multi-center consortium and to identify putative biomarkers for medulloblastoma in CSF. We used 2-DE to investigate the CSF proteome from 33 children with medulloblastoma and compared it against the CSF proteome from 25 age-matched controls. Protein spots were subsequently identified by a combination of in-gel tryptic digestion and MALDI-TOF TOF MS analysis. On average, 160 protein spots were detected by 2-DE and 76 protein spots corresponding to 25 unique proteins were identified using MALDI-TOF. Levels of prostaglandin D2 synthase (PGD2S) were found to be six-fold decreased in the tumor samples versus control samples (p<0.00001). These data were further validated using ELISA. Close examination of PGD2S spots revealed the presence of complex sialylated carbohydrates at residues Asn(78) and Asn(87) . Total PGD2S levels are reduced six-fold in the CSF of children with medulloblastoma most likely representing a host response to the presence of the tumor. In addition, our results demonstrate the feasibility of performing proteomic studies on CSF samples collected from patients at multiple institutions within the consortium setting.
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Affiliation(s)
- Meena U. Rajagopal
- Center for Genetic Medicine, Children’s National Medical Center, Washington DC USA
| | - Yetrib Hathout
- Center for Genetic Medicine, Children’s National Medical Center, Washington DC USA
| | - Tobey J. MacDonald
- Center for Cancer and Immunology, Children’s National Medical Center, Washington DC USA
- Pediatric Brain Tumor Consortium (PBTC)
| | - Mark W. Kieran
- Pediatric Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA USA
| | | | - Susan M. Blaney
- Pediatric Brain Tumor Consortium (PBTC)
- Texas Children’s Cancer Center/Baylor College of Medicine, Houston, TX USA
| | | | | | | | - Brian R. Rood
- Center for Cancer and Immunology, Children’s National Medical Center, Washington DC USA
- Pediatric Brain Tumor Consortium (PBTC)
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Dubrovsky L, Wong EC, Perez-Albuerne E, Loechelt B, Kamani N, Sande J, Mintz K, Paul W, Luban NL, Rood BR, Fry T. CD34+ collection efficiency as a function of blood volumes processed in pediatric autologous peripheral blood stem cell collection. J Clin Apher 2011; 26:131-7. [DOI: 10.1002/jca.20281] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 12/02/2010] [Indexed: 11/08/2022]
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Abstract
Anaplastic ependymoma is a malignant glial tumor thought to arise from radial glial cells of the ventricular zone. Because ependymoma is frequently encountered within ventricular spaces, they are prone to leptomeningeal dissemination. Metastatic extracranial ependymoma has been reported, but in the context of progressive intracranial disease. We report on a boy who developed isolated extracranial recurrence of his anaplastic ependymoma, initially at the scalp and later metastases to cervical lymph nodes. The location of tumor recurrence proximate to the surgical site suggested surgical seeding. This case demonstrates an unusual site of recurrence of anaplastic ependymoma and highlights a previously underappreciated surgical complication.
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Affiliation(s)
- Mwe Mwe Chao
- Children's National Medical Center, Division of Pediatric Oncology, Washington, District of Columbia 20010, USA.
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Smith C, Santi M, Rajan B, Rushing EJ, Choi MR, Rood BR, Cornelison R, MacDonald TJ, Vukmanovic S. A novel role of HLA class I in the pathology of medulloblastoma. J Transl Med 2009; 7:59. [PMID: 19594892 PMCID: PMC2714836 DOI: 10.1186/1479-5876-7-59] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Accepted: 07/12/2009] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND MHC class I expression by cancer cells enables specific antigen recognition by the immune system and protection of the host. However, in some cancer types MHC class I expression is associated with an unfavorable outcome. We explored the basis of MHC class I association with unfavorable prognostic marker expression in the case of medulloblastoma. METHODS We investigated expression of four essential components of MHC class I (heavy chain, beta2m, TAP1 and TAP2) in 10 medulloblastoma mRNA samples, a tissue microarray containing 139 medulloblastoma tissues and 3 medulloblastoma cell lines. Further, in medulloblastoma cell lines we evaluated the effects of HLA class I engagement on activation of ERK1/2 and migration in vitro. RESULTS The majority of specimens displayed undetectable or low levels of the heavy chains. Medulloblastomas expressing high levels of HLA class I displayed significantly higher levels of anaplasia and c-myc expression, markers of poor prognosis. Binding of beta2m or a specific antibody to open forms of HLA class I promoted phosphorylation of ERK1/2 in medulloblastoma cell line with high levels, but not in the cell line with low levels of HLA heavy chain. This treatment also promoted ERK1/2 activation dependent migration of medulloblastoma cells. CONCLUSION MHC class I expression in medulloblastoma is associated with anaplasia and c-myc expression, markers of poor prognosis. Peptide- and/or beta2m-free forms of MHC class I may contribute to a more malignant phenotype of medulloblastoma by modulating activation of signaling molecules such as ERK1/2 that stimulates cell mobility.
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Affiliation(s)
- Courtney Smith
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, DC, USA.
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Crawford JR, Rood BR, Rossi CT, Vezina G. Medulloblastoma associated with novel PTCH mutation as primary manifestation of Gorlin syndrome. Neurology 2009; 72:1618. [PMID: 19414732 DOI: 10.1212/wnl.0b013e3181a413d6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- John R Crawford
- Department of Neurology, Children's National Medical Center, The George Washington University, Washington, DC 20010, USA.
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Pistollato F, Chen HL, Rood BR, Zhang HZ, D'Avella D, Denaro L, Gardiman M, te Kronnie G, Schwartz PH, Favaro E, Indraccolo S, Basso G, Panchision DM. Hypoxia and HIF1alpha repress the differentiative effects of BMPs in high-grade glioma. Stem Cells 2009; 27:7-17. [PMID: 18832593 DOI: 10.1634/stemcells.2008-0402] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hypoxia commonly occurs in solid tumors of the central nervous system (CNS) and often interferes with therapies designed to stop their growth. We found that pediatric high-grade glioma (HGG)-derived precursors showed greater expansion under lower oxygen tension, typical of solid tumors, than normal CNS precursors. Hypoxia inhibited p53 activation and subsequent astroglial differentiation of HGG precursors. Surprisingly, although HGG precursors generated endogenous bone morphogenetic protein (BMP) signaling that promoted mitotic arrest under high oxygen tension, this signaling was actively repressed by hypoxia. An acute increase in oxygen tension led to Smad activation within 30 minutes, even in the absence of exogenous BMP treatment. Treatment with BMPs further promoted astroglial differentiation or death of HGG precursors under high oxygen tension, but this effect was inhibited under hypoxic conditions. Silencing of hypoxia-inducible factor 1alpha (HIF1alpha) led to Smad activation even under hypoxic conditions, indicating that HIF1alpha is required for BMP repression. Conversely, BMP activation at high oxygen tension led to reciprocal degradation of HIF1alpha; this BMP-induced degradation was inhibited in low oxygen. These results show a novel, mutually antagonistic interaction of hypoxia-response and neural differentiation signals in HGG proliferation, and suggest differences between normal and HGG precursors that may be exploited for pediatric brain cancer therapy.
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Van Rechem C, Rood BR, Touka M, Pinte S, Jenal M, Guérardel C, Ramsey K, Monté D, Bégue A, Tschan MP, Stephan DA, Leprince D. Scavenger chemokine (CXC motif) receptor 7 (CXCR7) is a direct target gene of HIC1 (hypermethylated in cancer 1). J Biol Chem 2009; 284:20927-35. [PMID: 19525223 DOI: 10.1074/jbc.m109.022350] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The tumor suppressor gene HIC1 (Hypermethylated in Cancer 1) that is epigenetically silenced in many human tumors and is essential for mammalian development encodes a sequence-specific transcriptional repressor. The few genes that have been reported to be directly regulated by HIC1 include ATOH1, FGFBP1, SIRT1, and E2F1. HIC1 is thus involved in the complex regulatory loops modulating p53-dependent and E2F1-dependent cell survival and stress responses. We performed genome-wide expression profiling analyses to identify new HIC1 target genes, using HIC1-deficient U2OS human osteosarcoma cells infected with adenoviruses expressing either HIC1 or GFP as a negative control. These studies identified several putative direct target genes, including CXCR7, a G-protein-coupled receptor recently identified as a scavenger receptor for the chemokine SDF-1/CXCL12. CXCR7 is highly expressed in human breast, lung, and prostate cancers. Using quantitative reverse transcription-PCR analyses, we demonstrated that CXCR7 was repressed in U2OS cells overexpressing HIC1. Inversely, inactivation of endogenous HIC1 by RNA interference in normal human WI38 fibroblasts results in up-regulation of CXCR7 and SIRT1. In silico analyses followed by deletion studies and luciferase reporter assays identified a functional and phylogenetically conserved HIC1-responsive element in the human CXCR7 promoter. Moreover, chromatin immunoprecipitation (ChIP) and ChIP upon ChIP experiments demonstrated that endogenous HIC1 proteins are bound together with the C-terminal binding protein corepressor to the CXCR7 and SIRT1 promoters in WI38 cells. Taken together, our results implicate the tumor suppressor HIC1 in the transcriptional regulation of the chemokine receptor CXCR7, a key player in the promotion of tumorigenesis in a wide variety of cell types.
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Affiliation(s)
- Capucine Van Rechem
- CNRS UMR 8161 Institut de Biologie de Lille, Université de Lille NORD de France, Institut Pasteur de Lille, 59017 Lille, France
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Fleuriel C, Touka M, Boulay G, Guérardel C, Rood BR, Leprince D. HIC1 (Hypermethylated in Cancer 1) epigenetic silencing in tumors. Int J Biochem Cell Biol 2008; 41:26-33. [PMID: 18723112 DOI: 10.1016/j.biocel.2008.05.028] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 05/19/2008] [Accepted: 05/19/2008] [Indexed: 12/27/2022]
Abstract
HIC1 (Hypermethylated in Cancer 1), as it name implied, was originally isolated as a new candidate tumor suppressor gene located at 17p13.3 because it resides in a CpG island that is hypermethylated in many types of human cancers. HIC1 encodes a transcription factor associating an N-terminal BTB/POZ domain to five C-terminal Krüppel-like C(2)H(2) zinc finger motifs. In this review, we will begin by providing an overview of the current knowledge on HIC1 function, mainly gained from in vitro studies, as a sequence-specific transcriptional repressor interacting with a still growing range of HDAC-dependent and HDAC-independent corepressor complexes. We will then summarize the studies that have demonstrated frequent hypermethylation changes or losses of heterozygosity of the HIC1 locus in human cancers. Next, we will review animal models which have firmly established HIC1 as a bona fide tumor suppressor gene epigenetically silenced and functionally cooperating notably with p53 within a complex HIC1-p53-SIRT1 regulatory loop. Finally, we will discuss how this epigenetic inactivation of HIC1 might "addict" cancer cells to altered survival and signaling pathways or to lineage-specific transcription factors during the early stages of tumorigenesis.
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Affiliation(s)
- Capucine Fleuriel
- Université de Lille 1 et de Lille 2, Institut PASTEUR de LILLE, 59017 Lille Cedex, France
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Crawford JR, Santi MR, Vezina G, Myseros JS, Keating RF, LaFond DA, Rood BR, MacDonald TJ, Packer RJ. CNS germ cell tumor (CNSGCT) of childhood: presentation and delayed diagnosis. Neurology 2007; 68:1668-73. [PMID: 17502547 DOI: 10.1212/01.wnl.0000261908.36803.ac] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To describe the relationship between symptomatology and time to diagnosis of an institutional series of patients with CNS germ cell tumor (CNSGCT) over a 16-year period. METHODS Thirty consecutive patients newly diagnosed with CNSGCT (mean age 10.9 years; range 6 to 17 years; 70% boys) were evaluated at our institution between 1990 and 2006. RESULTS Duration of symptoms prior to diagnosis ranged from 5 days to 3 years (mean 8.4 months). Tumor location included pineal (14), suprasellar (8), pineal/suprasellar (3), pineal/thalamic (4), and basal ganglionic/thalamic (3). Five patients had disseminated disease at the time of diagnosis. Features including headache, nausea, vomiting, and visual changes led to earlier diagnosis. Symptoms including movement disorders, enuresis, anorexia, and psychiatric complaints delayed diagnosis in 9 of 30 patients, diagnosed 7 months to 3 years (mean 22.3 months) from symptom onset. In 7 of 9 patients with delayed diagnosis, enuresis was present. Seventeen of 30 patients had signs of endocrine dysfunction at presentation that included diabetes insipidus (4), hypothyroidism (8), and growth hormone deficiency (4). Ophthalmologic findings of decreased visual acuity, visual field deficits, or ocular abnormalities were present in 13 patients. Duration of symptoms did not correlate with tumor subtype or event-free survival. In three patients with basal ganglionic/temporal lobe, thalamic, or pineal/suprasellar signal abnormalities on MRI, neuroradiographic diagnosis was difficult. CONCLUSIONS Diagnosis of CNS germ cell tumor is often delayed, and presentation may include movement disorders or mimic psychiatric disease. MRI interpretation can be challenging and may require serum/CSF markers and biopsy for diagnosis.
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Affiliation(s)
- J R Crawford
- Comprehensive Pediatric Brain Tumor Program, Children's National Medical Center, The George Washington University, Washington, DC 20010, USA.
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Abstract
High grade glioma remains the most intractable childhood tumor of the central nervous system. The molecular genetics of childhood high grade glioma remain largely unknown in comparison to that of their adult counterparts. In an era of molecularly targeted therapies, this dearth of knowledge will present particular challenges to those who must design and implement the next generation of therapeutic trials with these new agents. In this review, we discuss the current understanding of the molecular genetics of childhood high grade glioma and compare/contrast it to that of the adult tumors bearing the same classification for the purpose of beginning to identify the most promising therapeutic targets.
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Affiliation(s)
- Brian R Rood
- Division of Hematology/Oncology, Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC 20010, USA.
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Abstract
Medulloblastoma (MB) is the most common malignant brain tumor of childhood, yet it makes up only 1% of adult brain tumors. MB is uniquely sensitive to chemotherapy and radiation, but successful surgical resection continues to be an important component of therapeutic success. Progress in the treatment of MB has occurred in multiple areas from improved neurosurgical techniques, refined dosing and delivery of radiation, and optimized chemotherapy. Tumors are currently risk-stratified as average risk or high risk depending on clinical factors such as age, extent of resection, and presence of metastases. Molecular biology is beginning to improve upon clinical prognostication and may soon provide the means to accurately predict response to therapy. Treatment for average-risk MB has achieved a level of success that allows efforts to be focused on the limitation of adverse treatment effects. Therapy for high-risk and relapsed MB has been positively affected by the advent of high-dose chemotherapy with stem cell rescue. In addition, molecular targets are being elucidated and new therapeutic agents are being tested for safety and efficacy. Treatment for this disease has evolved a great deal over the preceding decades, but a great deal of work remains to be done to effect reliable cures while reducing long-term sequelae of therapy.
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Affiliation(s)
- Brian R Rood
- Division of Hematology/Oncology, Center for Cancer Research, Children's National Medical Center, Washington, DC 20010, USA.
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40
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Abstract
DNA methylation and epigenetic inactivation of the O6-methylguanine methyltransferase (MGMT) gene induces MGMT deficiency, reducing the tumor cell's DNA repair capacity and increasing its susceptibility to alkylating chemotherapeutic agents. Consequently, adult patients whose tumors are deficient in MGMT have better outcomes with alkylator chemotherapy, and MGMT methylation has been proposed as a screening marker of deficient tumors. In order to test the feasibility of this approach for medulloblastoma, a common brain tumor in children, we determined the methylation status, mRNA expression pattern, and protein expression of MGMT in a panel of clinical specimens. Methylation-specific polymerase chain reaction analysis revealed methylation of MGMT in 28 of 37 tumor samples. Quantitative real-time reverse transcriptase-polymerase chain reaction showed a range of expression of MGMT mRNA varying more than 20-fold. However, there was no correlation found between MGMT methylation and mRNA expression. Immunohistochemistry demonstrated that all tumors were immunoreactive for MGMT in the nucleus of the medulloblastoma cells in a heterogeneous pattern. The intercell variability of MGMT complement explained the discordance between methylation and expression. Therefore, MGMT methylation as determined by methylation-specific polymerase chain reaction cannot be used as a marker for MGMT deficiency in medulloblastoma. Further, these findings support the use of pharmacological MGMT depletion as a rational approach for intensification of alkylator chemotherapy in the treatment of medulloblastoma.
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Affiliation(s)
- Brian R Rood
- Children's Research Institute, Children's National Medical Center, Washington, DC 20010, USA.
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Pinte S, Stankovic-Valentin N, Deltour S, Rood BR, Guérardel C, Leprince D. The tumor suppressor gene HIC1 (hypermethylated in cancer 1) is a sequence-specific transcriptional repressor: definition of its consensus binding sequence and analysis of its DNA binding and repressive properties. J Biol Chem 2004; 279:38313-24. [PMID: 15231840 DOI: 10.1074/jbc.m401610200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
HIC1 (hypermethylated in cancer 1) is a tumor suppressor gene located at chromosome 17p13.3, a region frequently hypermethylated or deleted in human tumors and in a contiguous-gene syndrome, the Miller-Dieker syndrome. HIC1 is a transcriptional repressor containing five Krüppel-like C(2)H(2) zinc fingers and an N-terminal dimerization and autonomous repression domain called BTB/POZ. Although some of the HIC1 transcriptional repression mechanisms have been recently deciphered, target genes are still to be discovered. In this study, we determined the consensus binding sequence for HIC1 and investigated its DNA binding properties. Using a selection and amplification of binding sites technique, we identified the sequence 5'-(C)/(G)NG(C)/(G)GGGCA(C)/(A) CC-3' as an optimal binding site. In silico and functional analyses fully validated this consensus and highlighted a GGCA core motif bound by zinc fingers 3 and 4. The BTB/POZ domain inhibits the binding of HIC1 to a single site but mediates cooperative binding to a probe containing five concatemerized binding sites, a property shared by other BTB/POZ proteins. Finally, full-length HIC1 proteins transiently expressed in RK13 cells and more importantly, endogenous HIC1 proteins from the DAOY medulloblastoma cell line, repress the transcription of a reporter gene through their direct binding to these sites, as confirmed by chromatin immunoprecipitation experiments. The definition of the HIC1-specific DNA binding sequence as well as the requirement for multiple sites for optimal binding of the full-length protein are mandatory prerequisites for the identification and analyses of bona fide HIC1 target genes.
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Affiliation(s)
- Sébastien Pinte
- CNRS UMR 8526, Institut de Biologie de Lille, Institut Pasteur de Lille, 1 Rue Calmette, Lille Cedex 59017, France
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MacDonald TJ, Rood BR, Santi MR, Vezina G, Bingaman K, Cogen PH, Packer RJ. Advances in the diagnosis, molecular genetics, and treatment of pediatric embryonal CNS tumors. Oncologist 2003; 8:174-86. [PMID: 12697942 DOI: 10.1634/theoncologist.8-2-174] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Embryonal central nervous system (CNS) tumors are the most common group of malignant brain tumors in children. The diagnosis and classification of tumors belonging to this family have been controversial; however, utilization of molecular genetics is helping to refine traditional histopathologic and clinical classification schemes. Currently, this group of tumors includes medulloblastomas, supratentorial primitive neuroectodermal tumors, atypical teratoid/rhabdoid tumors, ependymoblastomas, and medulloepitheliomas. While the survival of older children with nonmetastatic medulloblastomas has improved considerably within the past two decades, the outcomes for infants and for those with metastatic medulloblastomas or other high-risk embryonal CNS tumors remain poor. It is anticipated that the emerging field of molecular biology will greatly aid in the future stratification and therapy for pediatric patients with malignant embryonal tumors. In this review, recent advances in the diagnosis, molecular genetics, and treatment of the most common pediatric embryonal CNS tumors are discussed.
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Affiliation(s)
- Tobey J MacDonald
- Departments of Hematology/Oncology, Children's Hospital National Medical Center, Washington, DC 20010, USA.
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Chopra A, Brown KM, Rood BR, Packer RJ, MacDonald TJ. The use of gene expression analysis to gain insights into signaling mechanisms of metastatic medulloblastoma. Pediatr Neurosurg 2003; 39:68-74. [PMID: 12845196 DOI: 10.1159/000071317] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2003] [Accepted: 03/06/2003] [Indexed: 11/19/2022]
Abstract
Metastasis is the leading cause of treatment failure in medulloblastoma. Understanding the genetic regulation of metastasis may aid in the development of novel treatments. We therefore performed in silico analysis of the mRNA expression of 83 medulloblastomas compiled from two independent microarray studies by focusing on 135 genes most frequently linked to metastasis in other tumors. We then asked whether expression of these genes correlated with metastasis in the medulloblastoma array data sets. We found the platelet-derived growth factor receptor alpha, early growth response protein 1 and insulin-like growth factor 2 genes as well as several genes associated with MYCC and ERBB2 overexpressed by at least 2-fold in metastatic tumors in both array data sets. We conclude that these genes may interact to promote prometastatic signaling in medulloblastoma.
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Affiliation(s)
- Arun Chopra
- Department of Pediatrics, Children's National Medical Center, Washington, DC 20010, USA
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Abstract
For the past two decades, staging studies have been used to stratify children with medulloblastoma into risk groups. Therapeutic approaches have been based on separation of patients into 'average-risk' and 'poor-risk' categories. The extent of disease at diagnosis has been most reproducibly shown to be of prognostic significance, but age at diagnosis and amount of residual disease after surgery or extent of resection have also been commonly incorporated into stratification schemata. Tumor histology has been variably related to outcome. Biologic markers, especially molecular genetic findings, have not yet been incorporated into risk classifications, but will likely add to the understanding of medulloblastoma and may significantly alter concepts of staging and treatment.
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Affiliation(s)
- Roger J Packer
- Department of Neurology, Center for Neuroscience and Behavioral Medicine, Children's National Medical Center, Washington, DC 20010, USA.
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Rood BR, Zhang H, Weitman DM, Cogen PH. Hypermethylation of HIC-1 and 17p allelic loss in medulloblastoma. Cancer Res 2002; 62:3794-7. [PMID: 12097291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Medulloblastoma is the most common malignant brain tumor in children. Chromosome arm 17p13.3 is reduced to homozygosity in 35-50% of medulloblastomas,making it the most frequent genetic alteration in these tumors. HIC-1 (hypermethylated in cancer) is a putative tumor suppressor gene located in the area of common deletion. HIC-1 resides in a CpG island and is hypermethylated in many different tumor types. Therefore, we studied a series of tumor specimens for hypermethylation and deletion of the region containing the HIC-1 gene to determine whether these two mechanisms of gene inactivation play a complimentary role in medulloblastoma. Southern blotting was performed using the methylation-sensitive restriction endonuclease NotI. Methylation of NotI restriction sites located in HIC-1 was demonstrated in 26 (72%) of 36 tumors and 11 (92%) of 12 specimens of normal brain. Of these 26 tumors, 23 differed significantly from normal brain. A greater proportion of the cells from the tumors showed methylated alleles of the HIC-1 gene. A group of 15 (42%) of 36 tumors exhibited loss of heterozygosity (LOH) for DNA sequences located on chromosome arm 17p. There was no significant correlation between LOH and methylation status (P = 0.19). Methylation in tumors beyond that seen in normal brain predicted poor overall survival independent of clinical risk category (P = 0.014). The results of our study show that methylation of the CpG island that contains the HIC-1 gene is common in medulloblastoma and, together with LOH of 17p, may be a critical event in the formation and aggressiveness of this tumor.
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Affiliation(s)
- Brian R Rood
- Department of Pediatric Hematology/Oncology, Children's Research Institute, Children's National Medical Center, Washington, DC. 20010, USA
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