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Sung PJ, Selvam M, Riedel SS, Xie HM, Bryant K, Manning B, Wertheim GB, Kulej K, Pham L, Bowman RL, Peresie J, Nemeth MJ, Levine RL, Garcia BA, Meyer SE, Sidoli S, Bernt KM, Carroll M. FLT3 tyrosine kinase inhibition modulates PRC2 and promotes differentiation in acute myeloid leukemia. Leukemia 2024; 38:291-301. [PMID: 38182819 DOI: 10.1038/s41375-023-02131-4] [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: 04/10/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024]
Abstract
Internal tandem duplication mutations in fms-like tyrosine kinase 3 (FLT3-ITD) are recurrent in acute myeloid leukemia (AML) and increase the risk of relapse. Clinical responses to FLT3 inhibitors (FLT3i) include myeloid differentiation of the FLT3-ITD clone in nearly half of patients through an unknown mechanism. We identified enhancer of zeste homolog 2 (EZH2), a component of polycomb repressive complex 2 (PRC2), as a mediator of this effect using a proteomic-based screen. FLT3i downregulated EZH2 protein expression and PRC2 activity on H3K27me3. FLT3-ITD and loss-of-function mutations in EZH2 are mutually exclusive in human AML. We demonstrated that FLT3i increase myeloid maturation with reduced stem/progenitor cell populations in murine Flt3-ITD AML. Combining EZH1/2 inhibitors with FLT3i increased terminal maturation of leukemic cells and reduced leukemic burden. Our data suggest that reduced EZH2 activity following FLT3 inhibition promotes myeloid differentiation of FLT3-ITD leukemic cells, providing a mechanistic explanation for the clinical observations. These results demonstrate that in addition to its known cell survival and proliferation signaling, FLT3-ITD has a second, previously undefined function to maintain a myeloid stem/progenitor cell state through modulation of PRC2 activity. Our findings support exploring EZH1/2 inhibitors as therapy for FLT3-ITD AML.
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Affiliation(s)
- Pamela J Sung
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
- Department of Medicine, Division of Hematology/Oncology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
| | - Murugan Selvam
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Simone S Riedel
- Department of Pediatrics, Children's Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania, Perelman School of Medicine and Abramson Cancer Center, Philadelphia, PA, USA
| | - Hongbo M Xie
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katie Bryant
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Bryan Manning
- Department of Medicine, Division of Hematology/Oncology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Gerald B Wertheim
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katarzyna Kulej
- Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Lucie Pham
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Robert L Bowman
- Department of Cancer Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Jennifer Peresie
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Michael J Nemeth
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
| | - Sara E Meyer
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Kathrin M Bernt
- Department of Pediatrics, Children's Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania, Perelman School of Medicine and Abramson Cancer Center, Philadelphia, PA, USA
| | - Martin Carroll
- Department of Medicine, Division of Hematology/Oncology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
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2
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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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3
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Karakasheva TA, Zhou Y, Xie HM, Soto GE, Johnson TD, Stoltz MA, Roach DM, Nema N, Umeweni CN, Naughton K, Dolinsky L, Pippin JA, Wells AD, Grant SFA, Ghanem L, Terry N, Muir AB, Hamilton KE. Patient-derived Colonoids From Disease-spared Tissue Retain Inflammatory Bowel Disease-specific Transcriptomic Signatures. Gastro Hep Adv 2023; 2:830-842. [PMID: 37736163 PMCID: PMC10512767 DOI: 10.1016/j.gastha.2023.05.003] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
BACKGROUND AND AIMS A key histopathological feature of inflammatory bowel disease is damage to the mucosa, including breakdown of the epithelial barrier. Human enteroids and colonoids are a critical bench-to-bedside tool for studying the epithelium in inflammatory bowel disease. The goal of the current study was to define transcriptional differences in healthy versus diseased subjects that are sustained in enteroids and colonoids, including from disease-spared tissue. METHODS Biopsies and matching enteroid or colonoid cultures from pediatric patients with ileal Crohn disease (N = 6) and control subjects (N = 17) were subjected to RNA sequencing followed by bioinformatic and machine learning analyses. Late passage enteroids were exposed to cytokines to assess durable transcriptional differences. RESULTS We observed substantial overlap of pathways upregulated in Crohn disease in enteroids and ileal biopsies, as well as colonoids and rectal biopsies. KEGG pathways for cytokine-cytokine receptor interaction, chemokine signaling, protein export, and Toll-like receptor signaling were upregulated in both ileal and rectal biopsies, as well as enteroids and colonoids. In vitro cytokine exposure reactivated genes previously increased in biopsies. Machine learning predicted biopsy location (100% accuracy) and donor disease status (83% accuracy). A random forest classifier generated using ileal enteroids identified rectal colonoids from ileal Crohn disease subjects with 80% accuracy. CONCLUSION We confirmed transcriptional profiles of Crohn disease biopsies are expressed in enteroids and colonoids. Furthermore, transcriptomic data from disease-spared rectal tissue can identify patients with ileal Crohn disease. Our data support the use of patient enteroids and colonoids as critical translational tools for the study of inflammatory bowel disease.
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Affiliation(s)
- Tatiana A. Karakasheva
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Yusen Zhou
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Hongbo M. Xie
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Gloria E. Soto
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Tiana D. Johnson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Madison A. Stoltz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Daana M. Roach
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Noor Nema
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Chizoba N. Umeweni
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kaitlyn Naughton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lauren Dolinsky
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - James A. Pippin
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Struan F. A. Grant
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Division of Diabetes and Endocrinology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Louis Ghanem
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Immunology, Translational Sciences and Medicine, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Natalie Terry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Immunology, Clinical Development, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Amanda B. Muir
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kathryn E. Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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4
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Parthasarathy S, Ruggiero SM, Gelot A, Soardi FC, Ribeiro BFR, Pires DEV, Ascher DB, Schmitt A, Rambaud C, Represa A, Xie HM, Lusk L, Wilmarth O, McDonnell PP, Juarez OA, Grace AN, Buratti J, Mignot C, Gras D, Nava C, Pierce SR, Keren B, Kennedy BC, Pena SDJ, Helbig I, Cuddapah VA. A recurrent de novo splice site variant involving DNM1 exon 10a causes developmental and epileptic encephalopathy through a dominant-negative mechanism. Am J Hum Genet 2022; 109:2253-2269. [PMID: 36413998 PMCID: PMC9748255 DOI: 10.1016/j.ajhg.2022.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 05/31/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
Abstract
Heterozygous pathogenic variants in DNM1 cause developmental and epileptic encephalopathy (DEE) as a result of a dominant-negative mechanism impeding vesicular fission. Thus far, pathogenic variants in DNM1 have been studied with a canonical transcript that includes the alternatively spliced exon 10b. However, after performing RNA sequencing in 39 pediatric brain samples, we find the primary transcript expressed in the brain includes the downstream exon 10a instead. Using this information, we evaluated genotype-phenotype correlations of variants affecting exon 10a and identified a cohort of eleven previously unreported individuals. Eight individuals harbor a recurrent de novo splice site variant, c.1197-8G>A (GenBank: NM_001288739.1), which affects exon 10a and leads to DEE consistent with the classical DNM1 phenotype. We find this splice site variant leads to disease through an unexpected dominant-negative mechanism. Functional testing reveals an in-frame upstream splice acceptor causing insertion of two amino acids predicted to impair oligomerization-dependent activity. This is supported by neuropathological samples showing accumulation of enlarged synaptic vesicles adherent to the plasma membrane consistent with impaired vesicular fission. Two additional individuals with missense variants affecting exon 10a, p.Arg399Trp and p.Gly401Asp, had a similar DEE phenotype. In contrast, one individual with a missense variant affecting exon 10b, p.Pro405Leu, which is less expressed in the brain, had a correspondingly less severe presentation. Thus, we implicate variants affecting exon 10a as causing the severe DEE typically associated with DNM1-related disorders. We highlight the importance of considering relevant isoforms for disease-causing variants as well as the possibility of splice site variants acting through a dominant-negative mechanism.
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Affiliation(s)
- Shridhar Parthasarathy
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Sarah McKeown Ruggiero
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Antoinette Gelot
- AP-HP, Hôpital Armand-Trousseau, Service d'Anatomie Pathologique, 75012 Paris, France; INMED INSERM U 901 Parc Scientifique de Luminy, 13273 Marseille, France; Centre de Recherche Clinique ConCer-LD, Paris, France
| | - Fernanda C Soardi
- GENE - Núcleo de Genética Médica, Belo Horizonte, MG, Brazil; Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC 3052, Australia; School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3053, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC 3052, Australia; School of Chemistry and Molecular Biology, University of Queensland, St Lucia, QLD 4072, Australia
| | - Alain Schmitt
- INSERM U 1016, Institut Cochin, Paris, France; CNRS UMR 8104, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Caroline Rambaud
- AP-HP, Hôpital Raymond-Poincaré, Laboratoire Anatomie Pathologique, Garches, France
| | - Alfonso Represa
- INMED, INSERM, Aix-Marseille Université, Campus de Luminy, 13009 Marseille, France
| | - Hongbo M Xie
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Laina Lusk
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Olivia Wilmarth
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pamela Pojomovsky McDonnell
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Olivia A Juarez
- Baylor College of Medicine Genetics Clinic, Children's Hospital of San Antonio, San Antonio, TX, USA
| | - Alexandra N Grace
- Baylor College of Medicine Genetics Clinic, Children's Hospital of San Antonio, San Antonio, TX, USA
| | - Julien Buratti
- AP-HP, Hôpital de la Pitié Salpêtrière, Département de Génétique, 75013 Paris, France
| | - Cyril Mignot
- AP-HP, Hôpital de la Pitié Salpêtrière, Département de Génétique, 75013 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, INSERM U 1127, CNRS UMR 7225, ICM, 75013 Paris, France; AP-HP, Hôpital Robert Debré, Service de Neurologie Pediatrique et de Maladies Métaboliques, 75019 Paris, France
| | - Domitille Gras
- AP-HP, Hôpital Robert Debré, Service de Neurologie Pediatrique et de Maladies Métaboliques, 75019 Paris, France
| | - Caroline Nava
- AP-HP, Hôpital de la Pitié Salpêtrière, Département de Génétique, 75013 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, INSERM U 1127, CNRS UMR 7225, ICM, 75013 Paris, France; AP-HP, Hôpital Robert Debré, Service de Neurologie Pediatrique et de Maladies Métaboliques, 75019 Paris, France
| | - Samuel R Pierce
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Physical Therapy, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Boris Keren
- AP-HP, Hôpital de la Pitié Salpêtrière, Département de Génétique, 75013 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, INSERM U 1127, CNRS UMR 7225, ICM, 75013 Paris, France; AP-HP, Hôpital Robert Debré, Service de Neurologie Pediatrique et de Maladies Métaboliques, 75019 Paris, France
| | - Benjamin C Kennedy
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA; Department of Neurosurgery, The University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sergio D J Pena
- GENE - Núcleo de Genética Médica, Belo Horizonte, MG, Brazil; Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA; Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Vishnu Anand Cuddapah
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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5
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Olson TS, Frost BF, Duke JL, Dribus M, Xie HM, Prudowsky ZD, Furutani E, Gudera J, Shah YB, Ferriola D, Dinou A, Pagkrati I, Kim S, Xu Y, He M, Zheng S, Nijim S, Lin P, Xu C, Nakano TA, Oved JH, Carreno BM, Bolon YT, Gadalla SM, Marsh SG, Paczesny S, Lee SJ, Monos DS, Shimamura A, Bertuch AA, Gragert L, Spellman SR, Babushok DV. Pathogenicity and impact of HLA class I alleles in aplastic anemia patients of different ethnicities. JCI Insight 2022; 7:163040. [PMID: 36219480 PMCID: PMC9746824 DOI: 10.1172/jci.insight.163040] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/05/2022] [Indexed: 12/15/2022] Open
Abstract
Acquired aplastic anemia (AA) is caused by autoreactive T cell-mediated destruction of early hematopoietic cells. Somatic loss of human leukocyte antigen (HLA) class I alleles was identified as a mechanism of immune escape in surviving hematopoietic cells of some patients with AA. However, pathogenicity, structural characteristics, and clinical impact of specific HLA alleles in AA remain poorly understood. Here, we evaluated somatic HLA loss in 505 patients with AA from 2 multi-institutional cohorts. Using a combination of HLA mutation frequencies, peptide-binding structures, and association with AA in an independent cohort of 6,323 patients from the National Marrow Donor Program, we identified 19 AA risk alleles and 12 non-risk alleles and established a potentially novel AA HLA pathogenicity stratification. Our results define pathogenicity for the majority of common HLA-A/B alleles across diverse populations. Our study demonstrates that HLA alleles confer different risks of developing AA, but once AA develops, specific alleles are not associated with response to immunosuppression or transplant outcomes. However, higher pathogenicity alleles, particularly HLA-B*14:02, are associated with higher rates of clonal evolution in adult patients with AA. Our study provides insights into the immune pathogenesis of AA, opening the door to future autoantigen identification and improved understanding of clonal evolution in AA.
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Affiliation(s)
- Timothy S Olson
- Comprehensive Bone Marrow Failure Center and.,Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Benjamin F Frost
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jamie L Duke
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marian Dribus
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Hongbo M Xie
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zachary D Prudowsky
- Department of Pediatrics, Division of Hematology/Oncology, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Cancer and Hematology Center, Houston, Texas, USA
| | - Elissa Furutani
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonas Gudera
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU Klinikum Munich, Munich, Germany
| | - Yash B Shah
- Comprehensive Bone Marrow Failure Center and.,Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Deborah Ferriola
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Amalia Dinou
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ioanna Pagkrati
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Soyoung Kim
- Center for International Blood and Marrow Transplant Research and.,Division of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Yixi Xu
- Center for International Blood and Marrow Transplant Research and
| | - Meilun He
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minneapolis, USA
| | - Shannon Zheng
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sally Nijim
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ping Lin
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Chong Xu
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Parker Institute for Cancer Immunotherapy and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Taizo A Nakano
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Joseph H Oved
- Comprehensive Bone Marrow Failure Center and.,Department of Pediatric Transplant and Cell Therapy, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Beatriz M Carreno
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Parker Institute for Cancer Immunotherapy and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yung-Tsi Bolon
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minneapolis, USA
| | - Shahinaz M Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, Maryland, USA
| | - Steven Ge Marsh
- Anthony Nolan Research Institute and University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research and.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Dimitrios S Monos
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Akiko Shimamura
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Alison A Bertuch
- Department of Pediatrics, Division of Hematology/Oncology, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Cancer and Hematology Center, Houston, Texas, USA
| | - Loren Gragert
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minneapolis, USA
| | - Daria V Babushok
- Comprehensive Bone Marrow Failure Center and.,Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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6
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Xie HM, Bernt KM. HOXA Amplification Defines a Genetically Distinct Subset of Angiosarcomas. Biomolecules 2022; 12:biom12081124. [PMID: 36009018 PMCID: PMC9406048 DOI: 10.3390/biom12081124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 12/12/2022] Open
Abstract
Angiosarcoma is a rare, devastating malignancy with few curative options for disseminated disease. We analyzed a recently published genomic data set of 48 angiosarcomas and noticed recurrent amplifications of HOXA-cluster genes in 33% of patients. HOXA genes are master regulators of embryonic vascular development and adult neovascularization, which provides a molecular rationale to suspect that amplified HOXA genes act as oncogenes in angiosarcoma. HOXA amplifications typically affected multiple pro-angiogenic HOXA genes and co-occurred with amplifications of CD36 and KDR, whereas the overall mutation rate in these tumors was relatively low. HOXA amplifications were found most commonly in angiosarcomas located in the breast and were rare in angiosarcomas arising in sun-exposed areas on the head, neck, face and scalp. Our data suggest that HOXA-amplified angiosarcoma is a distinct molecular subgroup. Efforts to develop therapies targeting oncogenic HOX gene expression in AML and other sarcomas may have relevance for HOXA-amplified angiosarcoma.
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Affiliation(s)
- Hongbo M. Xie
- Division of Pediatric Oncology, Department of Pediatrics, Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, 3501 Civic Center Boulevard, CTRB 3064, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics (DBHI), Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kathrin M. Bernt
- Division of Pediatric Oncology, Department of Pediatrics, Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, 3501 Civic Center Boulevard, CTRB 3064, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Philadelphia, PA 19106, USA
- Correspondence: ; Tel.: +1-215-370-3171
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7
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Oluwafemi OO, Musfee FI, Mitchell LE, Goldmuntz E, Xie HM, Hakonarson H, Morrow BE, Guo T, Taylor DM, McDonald-McGinn DM, Emanuel BS, Agopian AJ. Genome-Wide Association Studies of Conotruncal Heart Defects with Normally Related Great Vessels in the United States. Genes (Basel) 2021; 12:genes12071030. [PMID: 34356046 PMCID: PMC8306129 DOI: 10.3390/genes12071030] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/22/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022] Open
Abstract
Conotruncal defects with normally related great vessels (CTD-NRGVs) occur in both patients with and without 22q11.2 deletion syndrome (22q11.2DS), but it is unclear to what extent the genetically complex etiologies of these heart defects may overlap across these two groups, potentially involving variation within and/or outside of the 22q11.2 region. To explore this potential overlap, we conducted genome-wide SNP-level, gene-level, and gene set analyses using common variants, separately in each of five cohorts, including two with 22q11.2DS (N = 1472 total cases) and three without 22q11.2DS (N = 935 total cases). Results from the SNP-level analyses were combined in meta-analyses, and summary statistics from these analyses were also used in gene and gene set analyses. Across all these analyses, no association was significant after correction for multiple comparisons. However, several SNPs, genes, and gene sets with suggestive evidence of association were identified. For common inherited variants, we did not identify strong evidence for shared genomic mechanisms for CTD-NRGVs across individuals with and without 22q11.2 deletions. Nevertheless, several of our top gene-level and gene set results have been linked to cardiogenesis and may represent candidates for future work.
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Affiliation(s)
- Omobola O. Oluwafemi
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, TX 77030, USA; (O.O.O.); (F.I.M.); (L.E.M.)
| | - Fadi I. Musfee
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, TX 77030, USA; (O.O.O.); (F.I.M.); (L.E.M.)
| | - Laura E. Mitchell
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, TX 77030, USA; (O.O.O.); (F.I.M.); (L.E.M.)
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; (H.H.); (D.M.T.); (B.S.E.)
| | - Hongbo M. Xie
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Hakon Hakonarson
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; (H.H.); (D.M.T.); (B.S.E.)
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bernice E. Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (B.E.M.); (T.G.); (D.M.M.-M.)
| | - Tingwei Guo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (B.E.M.); (T.G.); (D.M.M.-M.)
| | - Deanne M. Taylor
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; (H.H.); (D.M.T.); (B.S.E.)
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Donna M. McDonald-McGinn
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (B.E.M.); (T.G.); (D.M.M.-M.)
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Beverly S. Emanuel
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; (H.H.); (D.M.T.); (B.S.E.)
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - A. J. Agopian
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, TX 77030, USA; (O.O.O.); (F.I.M.); (L.E.M.)
- Correspondence:
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8
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Libbrecht C, Xie HM, Kingsley MC, Haladyna JN, Riedel SS, Alikarami F, Lenard A, McGeehan GM, Ernst P, Bernt KM. Menin is necessary for long term maintenance of meningioma-1 driven leukemia. Leukemia 2021; 35:1405-1417. [PMID: 33542482 PMCID: PMC8102197 DOI: 10.1038/s41375-021-01146-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/06/2020] [Revised: 12/04/2020] [Accepted: 01/21/2021] [Indexed: 01/30/2023]
Abstract
Translocations of Meningioma-1 (MN1) occur in a subset of acute myeloid leukemias (AML) and result in high expression of MN1, either as a full-length protein, or as a fusion protein that includes most of the N-terminus of MN1. High levels of MN1 correlate with poor prognosis. When overexpressed in murine hematopoietic progenitors, MN1 causes an aggressive AML characterized by an aberrant myeloid precursor-like gene expression program that shares features of KMT2A-rearranged (KMT2A-r) leukemia, including high levels of Hoxa and Meis1 gene expression. Compounds that target a critical KMT2A-Menin interaction have proven effective in KMT2A-r leukemia. Here, we demonstrate that Menin (Men1) is also critical for the self-renewal of MN1-driven AML through the maintenance of a distinct gene expression program. Genetic inactivation of Men1 led to a decrease in the number of functional leukemia-initiating cells. Pharmacologic inhibition of the KMT2A-Menin interaction decreased colony-forming activity, induced differentiation programs in MN1-driven murine leukemia and decreased leukemic burden in a human AML xenograft carrying an MN1-ETV6 translocation. Collectively, these results nominate Menin inhibition as a promising therapeutic strategy in MN1-driven leukemia.
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Affiliation(s)
- Clara Libbrecht
- grid.239552.a0000 0001 0680 8770Division of Pediatric Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.452431.50000 0004 0442 349XInstitut d’Hématologie et d’Oncologie Pédiatrique, Lyon, France
| | - Hongbo M. Xie
- grid.239552.a0000 0001 0680 8770Department of Bioinformatics and Health Informatics (DBHI), Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Molly C. Kingsley
- grid.239552.a0000 0001 0680 8770Division of Pediatric Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Jessica N. Haladyna
- grid.430503.10000 0001 0703 675XDepartment of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO USA
| | - Simone S. Riedel
- grid.239552.a0000 0001 0680 8770Division of Pediatric Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Fatemeh Alikarami
- grid.239552.a0000 0001 0680 8770Division of Pediatric Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Alexandra Lenard
- grid.239552.a0000 0001 0680 8770Division of Pediatric Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | | | - Patricia Ernst
- grid.430503.10000 0001 0703 675XDepartment of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO USA ,grid.430503.10000 0001 0703 675XDepartment of Pharmacology, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO USA
| | - Kathrin M. Bernt
- grid.239552.a0000 0001 0680 8770Division of Pediatric Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania and Abramson Cancer Center, Philadelphia, PA USA ,grid.239552.a0000 0001 0680 8770Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, 3501 Civic Center Boulevard, CTRB 3064, Philadelphia, PA 19104 USA
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9
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Mai JJ, Zhang H, Peng YY, Yang X, Mao L, Luo L, Xie HM, Zhang YJ, Li XJ, Ding YH. [Evaluation of drug-drug interactions between yimitasvir phosphate capsules with sofosbuvir tablets, omeprazole magnesium enteric-coated tablets, and rosuvastatin calcium tablets]. Zhonghua Gan Zang Bing Za Zhi 2020; 28:838-843. [PMID: 33105928 DOI: 10.3760/cma.j.cn501113-20200907-00503] [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] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To evaluate the drug-drug interactions and the tolerability of combined medication between yimitasvir phosphate capsules with sofosbuvir tablets, omeprazole magnesium enteric-coated tablets, and rosuvastatin calcium tablets in healthy volunteers. Methods: A randomized, open, and continuous administration design was used in trial 1 (yimitasvir phosphate capsules with sofosbuvir tablets). 28 subjects were randomly divided into two groups. A non-randomized, open design was used in trial 2 (yimitasvir phosphate capsules with omeprazole magnesium enteric-coated tablets), and included 42 subjects divided into three groups. The open design method was used in trial 3 (yimitasvir phosphate capsules with rosuvastatin calcium tablets), and included 14 subjects. The plasma concentrations of yimitasvir phosphate, sofosbuvir and their main metabolites GS-331007, omeprazole and rosuvastatin were validated by a liquid chromatography/tandem mass spectrometry (LC-MS/MS). The pharmacokinetic parameters were calculated by Phoenix winNonlin software. Results: (1) in trial 1, after single and co-administration, the 90% CI of sofosbuvir C(max) and AUC(0-tau) geometric mean ratio (GMR) were 152.0% (118.0% ~ 197.0%) and 230.0% (184.0% ~ 287.0%), with an increase of 52.0% and 130.0% compared to single dose of sofosbuvir, respectively. The 90% CI of GS-331007 C(max) GMR was 74.0% (67.5% ~ 81.2%) and reduced by 26% compared to single dose of sofosbuvir. (2) in trial 2, the 90% CI of C(max) GMR after yimitasvir single or co-administration at the same time, with a 4-hours interval, or with a 12- hours interval were 68.9% (44.5% ~ 106.7%) , 64.0% (43.8% ~ 93.6%) and 56.4%(38.9% ~ 81.9%), and the 90% CI of AUC(0-t) GMR were 68.6% (46.5% ~ 101.2%), 68.3% (47.6% ~ 98.0%) and 60.5% (41.8% ~ 87.5%), respectively. Compared with single dose of yimitasvir, the C(max) and AUC(0-t) were decreased by 31.1% and 31.4%, 36.0% and 31.7%, 43.6% and 39.5%, respectively. (3) In trial 3, after single and co-administration, the 90% CI of rosuvastatin C(max) and AUC(0-72) GMR were 172.4% (153.6% ~ 193.5%) and 158.0% (144.3% ~ 172.9%), respectively, with an increase of 74.9% and 60.5% compared to single dose of rosuvastatin. There were no serious adverse events and adverse events leading to withdrawal from the trial. Conclusion: Yimitasvir phosphate capsules have drug-drug interactions with sofosbuvir tablets, omeprazole magnesium enteric-coated tablets, and rosuvastatin calcium tablets.
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Affiliation(s)
- J J Mai
- Phase I Clinical Trials Unit of the First Hospital of Jilin University, Changchun 130021, China
| | - H Zhang
- Phase I Clinical Trials Unit of the First Hospital of Jilin University, Changchun 130021, China
| | - Y Y Peng
- Guangdong Hec Technology Holding CO.,Ltd., State Key Laboratory of Anti-infective Drug Development No.2015DQ780357, Guangzhou 510000, China
| | - X Yang
- Guangdong Hec Technology Holding CO.,Ltd., State Key Laboratory of Anti-infective Drug Development No.2015DQ780357, Guangzhou 510000, China
| | - L Mao
- Guangdong Hec Technology Holding CO.,Ltd., State Key Laboratory of Anti-infective Drug Development No.2015DQ780357, Guangzhou 510000, China
| | - L Luo
- Guangdong Hec Technology Holding CO.,Ltd., State Key Laboratory of Anti-infective Drug Development No.2015DQ780357, Guangzhou 510000, China
| | - H M Xie
- Guangdong Hec Technology Holding CO.,Ltd., State Key Laboratory of Anti-infective Drug Development No.2015DQ780357, Guangzhou 510000, China
| | - Y J Zhang
- Guangdong Hec Technology Holding CO.,Ltd., State Key Laboratory of Anti-infective Drug Development No.2015DQ780357, Guangzhou 510000, China
| | - X J Li
- Phase I Clinical Trials Unit of the First Hospital of Jilin University, Changchun 130021, China
| | - Y H Ding
- Phase I Clinical Trials Unit of the First Hospital of Jilin University, Changchun 130021, China
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10
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Xie HM, Taylor DM, Zhang Z, McDonald-McGinn DM, Zackai EH, Stambolian D, Hakonarson H, Morrow BE, Emanuel BS, Goldmuntz E. Copy number variations in individuals with conotruncal heart defects reveal some shared developmental pathways irrespective of 22q11.2 deletion status. Birth Defects Res 2019; 111:888-905. [PMID: 31222980 DOI: 10.1002/bdr2.1534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 02/18/2019] [Revised: 03/28/2019] [Accepted: 05/23/2019] [Indexed: 12/26/2022]
Abstract
Over 50% of patients with 22q11.2 deletion syndrome (DS) have a conotruncal or related cardiac defect (CTRD). We hypothesized that similar genetic variants, developmental pathways and biological functions, contribute to disease risk for CTRD in patients without a 22q11.2 deletion (ND-CTRD) and with a 22q11.2 deletion (DS-CTRD). To test this hypothesis, we performed rare CNV (rCNV)-based analyses on 630 ND-CTRD cases and 602 DS-CTRD cases with comparable cardiac lesions separately and jointly. First, we detected a collection of heart development related pathways from Gene Ontology and Mammalian Phenotype Ontology analysis. We then constructed gene regulation networks using unique genes collected from the rCNVs found in the ND-CTRD and DS-CTRD cohorts. These gene networks were clustered and their predicted functions were examined. We further investigated expression patterns of those unique genes using publicly available mouse embryo microarray expression data from single-cell embryos to fully developed hearts. By these bioinformatics approaches, we identified a commonly shared gene expression pattern in both the ND-CTRD and DS-CTRD cohorts. Computational analysis of gene functions characterized with this expression pattern revealed a collection of significantly enriched terms related to cardiovascular development. By our combined analysis of rCNVs in the ND-CTRD and DS-CTRD cohorts, a group of statistically significant shared pathways, biological functions, and gene expression patterns were identified that can be tested in future studies for their biological relevance.
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Affiliation(s)
- Hongbo M Xie
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Deanne M Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Donna M McDonald-McGinn
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elaine H Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dwight Stambolian
- Department of Ophthalmology and Human Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Hakon Hakonarson
- The Center for Applied Genomics, Department of Pediatrics, The Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bernice E Morrow
- Department of Genetics, Yeshiva University, Albert Einstein College of Medicine, Bronx, New York
| | - Beverly S Emanuel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elizabeth Goldmuntz
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Cardiology, The Children's Hospital of Philadelphia, Department of Pediatrics, Philadelphia, Pennsylvania
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11
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Bujakowska KM, Fernandez-Godino R, Place E, Consugar M, Navarro-Gomez D, White J, Bedoukian EC, Zhu X, Xie HM, Gai X, Leroy BP, Pierce EA. Copy-number variation is an important contributor to the genetic causality of inherited retinal degenerations. Genet Med 2017; 19:643-651. [PMID: 27735924 PMCID: PMC6377944 DOI: 10.1038/gim.2016.158] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 05/12/2016] [Accepted: 08/30/2016] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Despite substantial progress in sequencing, current strategies can genetically solve only approximately 55-60% of inherited retinal degeneration (IRD) cases. This can be partially attributed to elusive mutations in the known IRD genes, which are not easily identified by the targeted next-generation sequencing (NGS) or Sanger sequencing approaches. We hypothesized that copy-number variations (CNVs) are a major contributor to the elusive genetic causality of IRDs. METHODS Twenty-eight cases previously unsolved with a targeted NGS were investigated with whole-genome single-nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) arrays. RESULTS Deletions in the IRD genes were detected in 5 of 28 families, including a de novo deletion. We suggest that the de novo deletion occurred through nonallelic homologous recombination (NAHR) and we constructed a genomic map of NAHR-prone regions with overlapping IRD genes. In this article, we also report an unusual case of recessive retinitis pigmentosa due to compound heterozygous mutations in SNRNP200, a gene that is typically associated with the dominant form of this disease. CONCLUSIONS CNV mapping substantially increased the genetic diagnostic rate of IRDs, detecting genetic causality in 18% of previously unsolved cases. Extending the search to other structural variations will probably demonstrate an even higher contribution to genetic causality of IRDs.Genet Med advance online publication 13 October 2016.
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Affiliation(s)
- Kinga M Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rosario Fernandez-Godino
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily Place
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark Consugar
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Navarro-Gomez
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph White
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Emma C Bedoukian
- Ophthalmic Genetics &Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Xiaosong Zhu
- Ophthalmic Genetics &Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hongbo M Xie
- Department of BioMedical Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Bart P Leroy
- Ophthalmic Genetics &Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Ophthalmology &Center for Medical Genetics, Ghent University Hospital &Ghent University, Ghent, Belgium
| | - Eric A Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
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12
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Xie HM, Werner P, Stambolian D, Bailey-Wilson JE, Hakonarson H, White PS, Taylor DM, Goldmuntz E. Rare copy number variants in patients with congenital conotruncal heart defects. Birth Defects Res 2017; 109:271-295. [PMID: 28398664 DOI: 10.1002/bdra.23609] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 06/06/2016] [Revised: 09/22/2016] [Accepted: 11/30/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND Previous studies using different cardiac phenotypes, technologies and designs suggest a burden of large, rare or de novo copy number variants (CNVs) in subjects with congenital heart defects. We sought to identify disease-related CNVs, candidate genes, and functional pathways in a large number of cases with conotruncal and related defects that carried no known genetic syndrome. METHODS Cases and control samples were divided into two cohorts and genotyped to assess each subject's CNV content. Analyses were performed to ascertain differences in overall CNV prevalence and to identify enrichment of specific genes and functional pathways in conotruncal cases relative to healthy controls. RESULTS Only findings present in both cohorts are presented. From 973 total conotruncal cases, a burden of rare CNVs was detected in both cohorts. Candidate genes from rare CNVs found in both cohorts were identified based on their association with cardiac development or disease, and/or their reported disruption in published studies. Functional and pathway analyses revealed significant enrichment of terms involved in either heart or early embryonic development. CONCLUSION Our study tested one of the largest cohorts specifically with cardiac conotruncal and related defects. These results confirm and extend previous findings that CNVs contribute to disease risk for congenital heart defects in general and conotruncal defects in particular. As disease heterogeneity renders identification of single recurrent genes or loci difficult, functional pathway and gene regulation network analyses appear to be more informative. Birth Defects Research 109:271-295, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Hongbo M Xie
- The Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Petra Werner
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Dwight Stambolian
- Department of Ophthalmology and Human Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joan E Bailey-Wilson
- Statistical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - Hakon Hakonarson
- The Center for Applied Genomics, Department of Pediatrics, The Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peter S White
- Division of Biomedical Informatics, Cincinnati Children's Hospital, Department of Biomedical Informatics, University of Cincinnati, Cincinnati, Ohio
| | - Deanne M Taylor
- The Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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13
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Babushok DV, Stanley N, Xie HM, Huang H, Bagg A, Olson TS, Bessler M. Clonal Replacement Underlies Spontaneous Remission in Paroxysmal Nocturnal Haemoglobinuria. Br J Haematol 2016; 176:487-490. [PMID: 26913981 DOI: 10.1111/bjh.13963] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Daria V Babushok
- Division of Hematology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA.,Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Natasha Stanley
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hongbo M Xie
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hugh Huang
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy S Olson
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Blood and Marrow Transplant Program, Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA, USA
| | - Monica Bessler
- Division of Hematology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA.,Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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14
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Babushok DV, Grignon A, Li Y, Atienza J, Xie HM, Lam H, Hartung H, Bessler M, Olson TS. Disrupted lymphocyte homeostasis in hepatitis-associated acquired aplastic anemia is associated with short telomeres. Am J Hematol 2016; 91:243-7. [PMID: 26615915 PMCID: PMC4724330 DOI: 10.1002/ajh.24256] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 11/19/2015] [Accepted: 11/24/2015] [Indexed: 12/13/2022]
Abstract
Hepatitis‐associated aplastic anemia (HAA) is a variant of acquired aplastic anemia (AA) in which immune‐mediated bone marrow failure (BMF) develops following an acute episode of seronegative hepatitis. Dyskeratosis congenita (DC) is an inherited BMF syndrome characterized by the presence of short telomeres, mucocutaneous abnormalities, and cancer predisposition. While both conditions may cause BMF and hepatic impairment, therapeutic approaches are distinct, making it imperative to establish the correct diagnosis. In clinical practice, lymphocyte telomere lengths (TL) are used as a first‐line screen to rule out inherited telomeropathies before initiating treatment for AA. To evaluate the reliability of TL in the HAA population, we performed a retrospective analysis of TL in 10 consecutively enrolled HAA patients compared to 19 patients with idiopathic AA (IAA). HAA patients had significantly shorter telomeres than IAA patients (P = 0.009), including four patients with TL at or below the 1st percentile for age‐matched controls. HAA patients had no clinical features of DC and did not carry disease‐causing mutations in known genes associated with inherited telomere disorders. Instead, short TLs were significantly correlated with severe lymphopenia and skewed lymphocyte subsets, features characteristic of HAA. Our results indicate the importance of caution in the interpretation of TL measurements in HAA, because, in this patient population, short telomeres have limited specificity. Am. J. Hematol. 91:243–247, 2016. © 2015 The Authors. American Journal of Hematology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Daria V. Babushok
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of PediatricsChildren's Hospital of PhiladelphiaPhiladelphia Pennsylvania
- Division of Hematology–Oncology, Department of MedicineHospital of the University of PennsylvaniaPhiladelphia Pennsylvania
| | - Anne‐Laure Grignon
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of PediatricsChildren's Hospital of PhiladelphiaPhiladelphia Pennsylvania
| | - Yimei Li
- Department of Biostatistics and EpidemiologyPerelman School of Medicine at the University of PennsylvaniaPhiladelphia Pennsylvania
| | - Jamie Atienza
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of PediatricsChildren's Hospital of PhiladelphiaPhiladelphia Pennsylvania
| | - Hongbo M. Xie
- Division of Health and Biomedical InformaticsChildren's Hospital of PhiladelphiaPhiladelphia Pennsylvania
| | - Ho‐Sun Lam
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of PediatricsChildren's Hospital of PhiladelphiaPhiladelphia Pennsylvania
| | - Helge Hartung
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of PediatricsChildren's Hospital of PhiladelphiaPhiladelphia Pennsylvania
| | - Monica Bessler
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of PediatricsChildren's Hospital of PhiladelphiaPhiladelphia Pennsylvania
| | - Timothy S. Olson
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of PediatricsChildren's Hospital of PhiladelphiaPhiladelphia Pennsylvania
- Division of Oncology, Department of PediatricsChildren's Hospital of Philadelphia and University of PennsylvaniaPhiladelphia Pennsylvania
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15
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Babushok DV, Perdigones N, Perin JC, Olson TS, Ye W, Roth JJ, Lind C, Cattier C, Li Y, Hartung H, Paessler ME, Frank DM, Xie HM, Busse TM, Cross S, Podsakoff GM, Monos D, Biegel JA, Mason PJ, Bessler M. Abstract 2977: Most patients with acquired aplastic anemia develop clonal hematopoiesis early in disease. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2977] [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
Clonal hematopoiesis is an expansion of hematopoietic stem cells, caused by somatic mutations or epigenetic changes that confer a growth advantage to the host cell. Although recently recognized as a phenomenon of aging, clonal hematopoiesis has been traditionally associated with pre-cancerous states and malignant transformation. Acquired aplastic anemia (AA), a non-neoplastic autoimmune blood disorder occurring in children and adults, has been associated with clonal hematopoietic disorders; transformation to myelodysplastic syndrome (MDS) or acute leukemia is a late complication in 10-15% of AA patients. Based on the association of AA with clonal disorders, we hypothesized that clonal hematopoiesis is a general phenomenon in AA, and can be seen in the majority of AA patients, including children. To evaluate somatic genetic changes in AA, we used a combination of single nucleotide polymorphism array (SNP-A) genotyping and comparative whole exome sequencing of paired bone marrow aspirates and skin in twenty nine patients with AA. All somatic mutations were validated by bi-directional Sanger sequencing. The median age of diagnosis was 14 years (range 1.5-65). Patients were analyzed at a median of 1.1 years from diagnosis. None of the patients had histopathological evidence of MDS at the time of analysis. Somatic mutations were identified in the majority of patients, including patients with pediatric-onset AA. Three patients (10%) had somatic loss-of-function mutations in HLA class I alleles. Although MDS-associated mutations were identified in 2 of 29 patients, the majority of mutations were not in genes associated with MDS and hematologic malignancies. Pathway analysis of mutated genes revealed an enrichment of genes in pathways of immunity and transcriptional regulation. Comparison of somatic mutations in AA to a patient with a 30-year history of AA who progressed to MDS revealed that, unlike in AA, which was characterized by diverse and frequently oligoclonal hematopoiesis, progression to MDS was associated with an expansion of a dominant clone carrying multiple classical mutations linked to malignancy: pathogenic mutations in SUZ12 (homozygous for the mutated region due to copy number-neutral loss of heterozygosity (CN-LOH) at the chromosomal region 17q11.2qter), ASXL1, RUNX1, and PHF6. In conclusion, our data show that clonal hematopoiesis emerges in the majority of patients with AA, including children and young adults, can be detected early in disease, and has a mutational spectrum largely distinct from MDS. Our results highlight that in the absence of morphologic features of myelodysplasia, the presence of clonal hematopoiesis with somatic mutations cannot be used to distinguish MDS from AA. Future longitudinal studies of clonal hematopoiesis in AA will help to explain differences in patients’ disease course, and will enable personalized treatment approaches in AA.
Citation Format: Daria V. Babushok, Nieves Perdigones, Juan C. Perin, Timothy S. Olson, Wenda Ye, Jacquelyn J. Roth, Curt Lind, Carine Cattier, Yimei Li, Helge Hartung, Michele E. Paessler, Dale M. Frank, Hongbo M. Xie, Tracy M. Busse, Shanna Cross, Gregory M. Podsakoff, Dimitrios Monos, Jaclyn A. Biegel, Philip J. Mason, Monica Bessler. Most patients with acquired aplastic anemia develop clonal hematopoiesis early in disease. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2977. doi:10.1158/1538-7445.AM2015-2977
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Affiliation(s)
- Daria V. Babushok
- 1Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Nieves Perdigones
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Juan C. Perin
- 3Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Timothy S. Olson
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Wenda Ye
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jacquelyn J. Roth
- 4Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Curt Lind
- 5Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Carine Cattier
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Yimei Li
- 6Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Helge Hartung
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Michele E. Paessler
- 5Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Dale M. Frank
- 4Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Hongbo M. Xie
- 3Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Tracy M. Busse
- 5Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Shanna Cross
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Gregory M. Podsakoff
- 7Center for Cellular and Molecular Therapeutics, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Dimitrios Monos
- 5Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jaclyn A. Biegel
- 5Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Philip J. Mason
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Monica Bessler
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
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16
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Babushok DV, Perdigones N, Perin JC, Olson TS, Ye W, Roth JJ, Lind C, Cattier C, Li Y, Hartung H, Paessler ME, Frank DM, Xie HM, Cross S, Cockroft JD, Podsakoff GM, Monos D, Biegel JA, Mason PJ, Bessler M. Emergence of clonal hematopoiesis in the majority of patients with acquired aplastic anemia. Cancer Genet 2015; 208:115-28. [PMID: 25800665 DOI: 10.1016/j.cancergen.2015.01.007] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 11/28/2022]
Abstract
Acquired aplastic anemia (aAA) is a nonmalignant disease caused by autoimmune destruction of early hematopoietic cells. Clonal hematopoiesis is a late complication, seen in 20-25% of older patients. We hypothesized that clonal hematopoiesis in aAA is a more general phenomenon, which can arise early in disease, even in younger patients. To evaluate clonal hematopoiesis in aAA, we used comparative whole exome sequencing of paired bone marrow and skin samples in 22 patients. We found somatic mutations in 16 patients (72.7%) with a median disease duration of 1 year; of these, 12 (66.7%) were patients with pediatric-onset aAA. Fifty-eight mutations in 51 unique genes were found primarily in pathways of immunity and transcriptional regulation. Most frequently mutated was PIGA, with seven mutations. Only two mutations were in genes recurrently mutated in myelodysplastic syndrome. Two patients had oligoclonal loss of the HLA alleles, linking immune escape to clone emergence. Two patients had activating mutations in key signaling pathways (STAT5B (p.N642H) and CAMK2G (p.T306M)). Our results suggest that clonal hematopoiesis in aAA is common, with two mechanisms emerging-immune escape and increased proliferation. Our findings expand conceptual understanding of this nonneoplastic blood disorder. Future prospective studies of clonal hematopoiesis in aAA will be critical for understanding outcomes and for designing personalized treatment strategies.
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Affiliation(s)
- Daria V Babushok
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
| | - Nieves Perdigones
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Juan C Perin
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Timothy S Olson
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wenda Ye
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jacquelyn J Roth
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Curt Lind
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carine Cattier
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Yimei Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Helge Hartung
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Michele E Paessler
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dale M Frank
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hongbo M Xie
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Shanna Cross
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joshua D Cockroft
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Gregory M Podsakoff
- Center for Cellular and Molecular Therapeutics, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dimitrios Monos
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Philip J Mason
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Monica Bessler
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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White PS, Xie HM, Werner P, Glessner J, Latney B, Hakonarson H, Goldmuntz E. Analysis of chromosomal structural variation in patients with congenital left-sided cardiac lesions. ACTA ACUST UNITED AC 2014; 100:951-64. [DOI: 10.1002/bdra.23279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Peter S. White
- The Center for Biomedical Informatics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
- Department of Pediatrics; Perelman School of Medicine, University of Pennsylvania; Philadelphia Pennsylvania
| | - Hongbo M. Xie
- The Center for Biomedical Informatics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Petra Werner
- The Division of Cardiology; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Joseph Glessner
- The Center for Applied Genomics, Department of Pediatrics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Brande Latney
- The Division of Cardiology; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Hakon Hakonarson
- Department of Pediatrics; Perelman School of Medicine, University of Pennsylvania; Philadelphia Pennsylvania
- The Center for Applied Genomics, Department of Pediatrics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Elizabeth Goldmuntz
- Department of Pediatrics; Perelman School of Medicine, University of Pennsylvania; Philadelphia Pennsylvania
- The Division of Cardiology; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
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18
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Zhang Z, Leipzig J, Sasson A, Yu AM, Perin JC, Xie HM, Sarmady M, Warren PV, White PS. Efficient digest of high-throughput sequencing data in a reproducible report. BMC Bioinformatics 2014; 14 Suppl 11:S3. [PMID: 24564231 PMCID: PMC3846741 DOI: 10.1186/1471-2105-14-s11-s3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background High-throughput sequencing (HTS) technologies are spearheading the accelerated development of biomedical research. Processing and summarizing the large amount of data generated by HTS presents a non-trivial challenge to bioinformatics. A commonly adopted standard is to store sequencing reads aligned to a reference genome in SAM (Sequence Alignment/Map) or BAM (Binary Alignment/Map) files. Quality control of SAM/BAM files is a critical checkpoint before downstream analysis. The goal of the current project is to facilitate and standardize this process. Results We developed bamchop, a robust program to efficiently summarize key statistical metrics of HTS data stored in BAM files, and to visually present the results in a formatted report. The report documents information about various aspects of HTS data, such as sequencing quality, mapping to a reference genome, sequencing coverage, and base frequency. Bamchop uses the R language and Bioconductor packages to calculate statistical matrices and the Sweave utility and associated LaTeX markup for documentation. Bamchop's efficiency and robustness were tested on BAM files generated by local sequencing facilities and the 1000 Genomes Project. Source code, instruction and example reports of bamchop are freely available from https://github.com/CBMi-BiG/bamchop. Conclusions Bamchop enables biomedical researchers to quickly and rigorously evaluate HTS data by providing a convenient synopsis and user-friendly reports.
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Babushok DV, Xie HM, Roth JJ, Perdigones N, Olson TS, Cockroft JD, Gai X, Perin JC, Li Y, Paessler ME, Hakonarson H, Podsakoff GM, Mason PJ, Biegel JA, Bessler M. Single nucleotide polymorphism array analysis of bone marrow failure patients reveals characteristic patterns of genetic changes. Br J Haematol 2013; 164:73-82. [PMID: 24116929 DOI: 10.1111/bjh.12603] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [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: 07/05/2013] [Accepted: 08/28/2013] [Indexed: 11/29/2022]
Abstract
The bone marrow failure syndromes (BMFS) are a heterogeneous group of rare blood disorders characterized by inadequate haematopoiesis, clonal evolution, and increased risk of leukaemia. Single nucleotide polymorphism arrays (SNP-A) have been proposed as a tool for surveillance of clonal evolution in BMFS. To better understand the natural history of BMFS and to assess the clinical utility of SNP-A in these disorders, we analysed 124 SNP-A from a comprehensively characterized cohort of 91 patients at our BMFS centre. SNP-A were correlated with medical histories, haematopathology, cytogenetic and molecular data. To assess clonal evolution, longitudinal analysis of SNP-A was performed in 25 patients. We found that acquired copy number-neutral loss of heterozygosity (CN-LOH) was significantly more frequent in acquired aplastic anaemia (aAA) than in other BMFS (odds ratio 12·2, P < 0·01). Homozygosity by descent was most common in congenital BMFS, frequently unmasking autosomal recessive mutations. Copy number variants (CNVs) were frequently polymorphic, and we identified CNVs enriched in neutropenia and aAA. Our results suggest that acquired CN-LOH is a general phenomenon in aAA that is probably mechanistically and prognostically distinct from typical CN-LOH of myeloid malignancies. Our analysis of clinical utility of SNP-A shows the highest yield of detecting new clonal haematopoiesis at diagnosis and at relapse.
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Affiliation(s)
- Daria V Babushok
- Division of Hematology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA; Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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20
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Bannwarth S, Procaccio V, Lebre AS, Jardel C, Chaussenot A, Hoarau C, Maoulida H, Charrier N, Gai X, Xie HM, Ferre M, Fragaki K, Hardy G, Mousson de Camaret B, Marlin S, Dhaenens CM, Slama A, Rocher C, Paul Bonnefont J, Rötig A, Aoutil N, Gilleron M, Desquiret-Dumas V, Reynier P, Ceresuela J, Jonard L, Devos A, Espil-Taris C, Martinez D, Gaignard P, Le Quan Sang KH, Amati-Bonneau P, Falk MJ, Florentz C, Chabrol B, Durand-Zaleski I, Paquis-Flucklinger V. Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders. J Med Genet 2013; 50:704-14. [PMID: 23847141 PMCID: PMC3786640 DOI: 10.1136/jmedgenet-2013-101604] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [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] [Indexed: 12/02/2022]
Abstract
Background Mitochondrial DNA (mtDNA) diseases are rare disorders whose prevalence is estimated around 1 in 5000. Patients are usually tested only for deletions and for common mutations of mtDNA which account for 5–40% of cases, depending on the study. However, the prevalence of rare mtDNA mutations is not known. Methods We analysed the whole mtDNA in a cohort of 743 patients suspected of manifesting a mitochondrial disease, after excluding deletions and common mutations. Both heteroplasmic and homoplasmic variants were identified using two complementary strategies (Surveyor and MitoChip). Multiple correspondence analyses followed by hierarchical ascendant cluster process were used to explore relationships between clinical spectrum, age at onset and localisation of mutations. Results 7.4% of deleterious mutations and 22.4% of novel putative mutations were identified. Pathogenic heteroplasmic mutations were more frequent than homoplasmic mutations (4.6% vs 2.8%). Patients carrying deleterious mutations showed symptoms before 16 years of age in 67% of cases. Early onset disease (<1 year) was significantly associated with mutations in protein coding genes (mainly in complex I) while late onset disorders (>16 years) were associated with mutations in tRNA genes. MTND5 and MTND6 genes were identified as ‘hotspots’ of mutations, with Leigh syndrome accounting for the large majority of associated phenotypes. Conclusions Rare mitochondrial DNA mutations probably account for more than 7.4% of patients with respiratory chain deficiency. This study shows that a comprehensive analysis of mtDNA is essential, and should include young children, for an accurate diagnosis that is now accessible with the development of next generation sequencing technology.
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Affiliation(s)
- Sylvie Bannwarth
- IRCAN, CNRS UMR 7284/Inserm U1081/UNS, Faculté de Médecine, Nice, France
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21
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D'Alessandro LCA, Werner P, Xie HM, Hakonarson H, White PS, Goldmuntz E. The prevalence of 16p12.1 microdeletion in patients with left-sided cardiac lesions. CONGENIT HEART DIS 2013; 9:83-6. [PMID: 23682798 DOI: 10.1111/chd.12097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/11/2013] [Indexed: 11/28/2022]
Abstract
SETTING Left-sided cardiac lesions have a birth prevalence of approximately 1 in 1000 and have been shown to be heritable in pedigree studies. A large microdeletion at 16p12.1 is associated with childhood developmental delay, and initial studies describing this deletion identified left-sided lesions as an enriched phenotype compared with a control population. OBJECTIVE The aim of this study is to determine whether patients with left-sided cardiac lesions have an increased frequency of 16p12.1 microdeletions as compared with control populations. DESIGN A cohort of 262 probands with left-sided lesions, including 53 with isolated aortic stenosis/bicuspid aortic valve, 83 with coarctation of the aorta with or without aortic stenosis/bicuspid aortic valve, and 126 with hypoplastic left heart syndrome were assessed for copy number variation at 16p12.1. The control cohort included 595 patients with conotruncal defects as a cardiac control and 971 healthy children. RESULTS We detected one patient in the left-sided lesion cohort with a large duplication partially overlapping the reported 16p12.1 microdeletion, along with one patient each in the conotruncal and control cohorts with a deletion in the same region. None of these patients had dysmorphic features, extracardiac malformations, or developmental delay. CONCLUSION In our cohort, structural variation at 16p12.1 was not identified with increased frequency in patients with left-sided lesions as compared with controls.
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Affiliation(s)
- Lisa C A D'Alessandro
- The Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, Pa, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa, USA
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22
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Gai X, Xie HM, Perin JC, Takahashi N, Murphy K, Wenocur AS, D'arcy M, O'Hara RJ, Goldmuntz E, Grice DE, Shaikh TH, Hakonarson H, Buxbaum JD, Elia J, White PS. Rare structural variation of synapse and neurotransmission genes in autism. Mol Psychiatry 2012; 17:402-11. [PMID: 21358714 PMCID: PMC3314176 DOI: 10.1038/mp.2011.10] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Autism spectrum disorders (ASDs) comprise a constellation of highly heritable neuropsychiatric disorders. Genome-wide studies of autistic individuals have implicated numerous minor risk alleles but few common variants, suggesting a complex genetic model with many contributing loci. To assess commonality of biological function among rare risk alleles, we compared functional knowledge of genes overlapping inherited structural variants in idiopathic ASD subjects relative to healthy controls. In this study we show that biological processes associated with synapse function and neurotransmission are significantly enriched, with replication, in ASD subjects versus controls. Analysis of phenotypes observed for mouse models of copy-variant genes established significant and replicated enrichment of observable phenotypes consistent with ASD behaviors. Most functional terms retained significance after excluding previously reported ASD loci. These results implicate several new variants that involve synaptic function and glutamatergic signaling processes as important contributors of ASD pathophysiology and suggest a sizable pool of additional potential ASD risk loci.
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Affiliation(s)
- X Gai
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - H M Xie
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - J C Perin
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - N Takahashi
- Seaver Autism Center and Department of Psychiatry, Mt Sinai School of Medicine, New York, NY, USA
| | - K Murphy
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - A S Wenocur
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - M D'arcy
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - R J O'Hara
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - E Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA,Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - D E Grice
- Department of Child and Adolescent Psychiatry, Columbia University, New York, NY, USA
| | - T H Shaikh
- Department of Pediatrics, University of Colorado School of Medicine, Denver, CO, USA
| | - H Hakonarson
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA,Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA,Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - J D Buxbaum
- Seaver Autism Center and Department of Psychiatry, Mt Sinai School of Medicine, New York, NY, USA
| | - J Elia
- Department of Child and Adolescent Psychiatry, Children's Hospital of Philadelphia, Philadelphia, PA, USA,Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - P S White
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA,Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA,Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA,Children's Hospital of Philadelphia, 34th Street and Civic Center Boulevard, Room 1407 CHOP North, Philadelphia, PA 19104-4318, USA. E-mail:
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23
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Elia J, Gai X, Xie HM, Perin JC, Geiger E, Glessner JT, D'arcy M, deBerardinis R, Frackelton E, Kim C, Lantieri F, Muganga BM, Wang L, Takeda T, Rappaport EF, Grant SFA, Berrettini W, Devoto M, Shaikh TH, Hakonarson H, White PS. Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes. Mol Psychiatry 2010; 15:637-46. [PMID: 19546859 PMCID: PMC2877197 DOI: 10.1038/mp.2009.57] [Citation(s) in RCA: 414] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a common and highly heritable disorder, but specific genetic factors underlying risk remain elusive. To assess the role of structural variation in ADHD, we identified 222 inherited copy number variations (CNVs) within 335 ADHD patients and their parents that were not detected in 2026 unrelated healthy individuals. Although no excess CNVs, either deletions or duplications, were found in the ADHD cohort relative to controls, the inherited rare CNV-associated gene set was significantly enriched for genes reported as candidates in studies of autism, schizophrenia and Tourette syndrome, including A2BP1, AUTS2, CNTNAP2 and IMMP2L. The ADHD CNV gene set was also significantly enriched for genes known to be important for psychological and neurological functions, including learning, behavior, synaptic transmission and central nervous system development. Four independent deletions were located within the protein tyrosine phosphatase gene, PTPRD, recently implicated as a candidate gene for restless legs syndrome, which frequently presents with ADHD. A deletion within the glutamate receptor gene, GRM5, was found in an affected parent and all three affected offspring whose ADHD phenotypes closely resembled those of the GRM5 null mouse. Together, these results suggest that rare inherited structural variations play an important role in ADHD development and indicate a set of putative candidate genes for further study in the etiology of ADHD.
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Affiliation(s)
- J Elia
- Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia Philadelphia, PA, USA,Department of Psychiatry, University of Pennsylvania School of Medicine Philadelphia, PA, USA
| | - X Gai
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - H M Xie
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - J C Perin
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - E Geiger
- Division of Genetics, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - J T Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - M D'arcy
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - R deBerardinis
- Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - E Frackelton
- Center for Applied Genomics, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - C Kim
- Center for Applied Genomics, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - F Lantieri
- Division of Genetics, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - B M Muganga
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - L Wang
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - T Takeda
- Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - E F Rappaport
- Joseph Stokes Jr Research Institute, The Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - S F A Grant
- Division of Genetics, The Children's Hospital of Philadelphia Philadelphia, PA, USA,Center for Applied Genomics, The Children's Hospital of Philadelphia Philadelphia, PA, USA,Department of Pediatrics, University of Pennsylvania School of Medicine Philadelphia, PA, USA
| | - W Berrettini
- Department of Psychiatry, University of Pennsylvania School of Medicine Philadelphia, PA, USA
| | - M Devoto
- Division of Genetics, The Children's Hospital of Philadelphia Philadelphia, PA, USA,Department of Pediatrics, University of Pennsylvania School of Medicine Philadelphia, PA, USA,Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine Philadelphia, PA, USA,Dipartimento di Medicina Sperimentale, University La Sapienza Rome, Italy
| | - T H Shaikh
- Division of Genetics, The Children's Hospital of Philadelphia Philadelphia, PA, USA,Department of Pediatrics, University of Pennsylvania School of Medicine Philadelphia, PA, USA
| | - H Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia Philadelphia, PA, USA,Department of Pediatrics, University of Pennsylvania School of Medicine Philadelphia, PA, USA,Division of Pulmonary Medicine, The Children's Hospital of Philadelphia Philadelphia, PA, USA,Author for correspondence:
| | - P S White
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia Philadelphia, PA, USA,Department of Pediatrics, University of Pennsylvania School of Medicine Philadelphia, PA, USA,Division of Oncology, The Children's Hospital of Philadelphia Philadelphia, PA, USA,Author for correspondence:
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24
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Fan ZF, Du LM, Ji X, Xie HM. [A study on the effect of rare earth metal ions on fluorescence spectra of the tryptophan using fluorescence spectroscopy]. Guang Pu Xue Yu Guang Pu Fen Xi 2001; 21:682-684. [PMID: 12945331] [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] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Rare earth metal ions and tryptophan form ion-association complex in basic medium. The complex causes fluorescence quenching of tryptophan. Fluorescence emission of tryptophan and quenching caused by rare earth metal ions both reach a climax in H3BO4-HAc-H3PO4-NaOH at pH 10 to 11, and all rare earth metal ions have the approximate effects on fluorescence quenching of tryptophan. The molecular mode of complex of rare earth metal ions and tryptophan has been founded and mechanism of fluorescence quenching has been studied in this paper.
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Affiliation(s)
- Z F Fan
- Center of Analysis and Testing, Shanxi Teacher's University, LinFen 041004, China
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25
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Zhang H, Zhang X, Zheng RL, Gao QX, Wei ZQ, Li WJ, Chen WQ, Liang JP, Han GW, Huang T, Xie HM. Alleviation of pre-exposure to low-dose 16O8+ ion on mouse testicular histological damage induced by subsequent high-dose irradiation. Shi Yan Sheng Wu Xue Bao 2000; 33:97-100. [PMID: 12548972] [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] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
The testes of the B6C3F1 hybrid strain mice were irradiated with 0.05 Gy of 16O8+ ion as the pre-exposure dose (D1), and were then irradiated with 2 Gy of 16O8+ ion as challenging radiation dose (D2) at 4 h after per-exposure. Testicular morphology was observed by light microscope at 35th day after radiation. The results showed that irradiation of mouse testes with 2 Gy of 16O8+ ion significantly impaired, mainly reduction of tubule diameter and decrease or loss of germ cells in various developing stages, especially spermatogenic elements. Pre-exposure to a low-dose (0.05 Gy) of 16O8+ ion significantly alleviated above mentioned damage on testicular morphology induced by subsequent a high-dose (2 Gy) radiation.
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Affiliation(s)
- H Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000
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26
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Zhang H, Wei ZQ, Li WJ, Li Q, Dang BR, Chen WQ, Xie HM, Zhang SM, He J, Huang T, Zheng RL. Effects of 16O+6 ion irradiation on human sperm spontaneous chemiluminescence, motility, acrosome reaction and viability in vitro. Shi Yan Sheng Wu Xue Bao 1999; 32:1-6. [PMID: 12548788] [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] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
Effects of 16O+6 ion irradiation with different doses on human sperm spontaneous chemiluminescence (SCL), motility, acrosome reaction (AR) and viability were examined. Spermatozoa were irradiated with 0, 0.25, 0.5, 1, 2, 4, 8, 16, 32, or 64 Gy 16O+6 ion beam at the energy of 3.17 MeV/u. After irradiation, samples were analyzed by SCL measurement at 1, 2 and 3 h of incubation; motility was determined by the transmembrane migration method within 2 h of incubation; the percentage of AR and viability was evaluated by the triple-stain technique at 3.5 h of incubation. The results showed: sperm SCL was significantly increased with irradiation doses and the lowest effective dose was 0.5 Gy; compared with controls, the transmembrane migration ratio of spermatozoa progressively elevated with irradiation doses at 0.5, 1, and 2 Gy; the percentage of sperm AR markedly increased in 0.5-4 Gy irradiation and the optimal dose was 2 Gy, and then significant decreased with further increase of irradiation doses; the viability had no significant change within 0.25-8 Gy, but was progressively decreased at 16, 32 and 64 Gy. These data suggested that heavy ion at low doses increased motility and AR, whereas had deleterious effects at higher doses, which are associated with free radical reactions induced by heavy ion irradiation.
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Affiliation(s)
- H Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000
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Zhang H, Zheng RL, Wei ZQ, Li WJ, Gao QX, Chen WQ, Wang ZH, He J, Liang JP, Han GW, Huang T, Li Q, Xie HM, Zhang SM, Cai XC. Effects of pre-exposure of mouse testis with low-dose (16)O8+ ions or 60Co gamma-rays on sperm shape abnormalities, lipid peroxidation and superoxide dismutase (SOD) activity induced by subsequent high-dose irradiation. Int J Radiat Biol 1998; 73:163-7. [PMID: 9489563 DOI: 10.1080/095530098142545] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [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: 02/06/2023]
Abstract
PURPOSE To investigate the effects of pre-exposure of mouse testis with low-doses of (16)O8+ ions or 60Co gamma-rays on sperm shape abnormalities, lipid peroxidation and superoxide dismutase (SOD) activity induced by subsequent high-dose irradiation. MATERIALS AND METHODS Testes of the B6C3F1 hybrid strain mice were pre-irradiated with 0.05 Gy of (16)O8+ ions or 60Co gamma-rays and then after 4 h given a test irradiation with 2 Gy of the same radiation type. SOD activity and thiobarbituric acid reactive substances (TBARS) in the testes were determined by spectrophotometric and TBA methods respectively at 4 h after irradiation. Testis weight, sperm count and sperm morphology were analysed at day 35 after irradiation. RESULTS Compared with controls, there was a significant increase in SOD activity and a significant decrease in TBARS level of pretreated testes. Testis weight loss, sperm count reduction and sperm abnormalities were significantly lower in the pretreated testes. The bioeffects of a 2 Gy dose of (16)O8+ ions relative to 60Co gamma-rays were 1.84 +/- 0.28 for testis weight, 1.22 +/- 0.25 for sperm count and 1.29 +/- 0.10 for sperm abnormalities. CONCLUSIONS These data suggest that pre-exposure of testes with a low dose of heavy ions or gamma-rays renders the organ more resistant to subsequent high-dose irradiation. The increase of SOD activity and the decrease of lipid peroxidation levels induced by low-dose ionizing irradiation may be involved in this resistance. The effects with heavy ion irradiation were greater than with gamma-rays.
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Affiliation(s)
- H Zhang
- Department of Application of Heavy Ions, Institute of Modern Physics, The Chinese Academy of Sciences, Lanzhou
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Ma XX, Xu JW, Xie HM. An in vitro study on roughening of the metal surface with lost crystal salts to increase the metal-resin bond strength. Quintessence Int 1991; 22:911-4. [PMID: 1812515] [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] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Good mechanical retention between metal and resin or luting agent can be obtained by roughening the metal surface with lost crystal salts. The relationship of metal-resin bond strength to the shape and size of the crystals was studied. The results indicated that cuboid crystal salts provided the best roughening among the tested crystal shapes (cube, irregular, spherical, and cuboid). There was no relationship between the tensile bond strength and the size of the crystals. Furthermore, the bending strength of metal coated with resin was improved by the roughening of the metal surface.
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Affiliation(s)
- X X Ma
- Department of Prosthodontics, Fourth Military Medical University, Dental College, Qin Du Dental Hospital, China
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Xie HM. [A PM visible light-cured dental bonding agent]. Zhonghua Kou Qiang Yi Xue Za Zhi 1989; 24:283-5, 319. [PMID: 2517931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In order to get a better adhesion, less tooth abrasion and a good marginal sealing, bonding agent was used in the composites restorations. PM visible light cured bonding agent containing coupling agent 4-META was made. Polyfunctional monomer was used as the resin matrix. CQ and PA were used as the initiator. The tensile bonding strength of this bondx286p4ent to enamel was 84.5 kg/cm2. The shear bonding strength of this bonding agent to enamel when used with visible light cured composites together was 317.3 kg/cm2, which was higher then the report in the recent literatures. PM visible light cured bonding agent got a satisfied clinical result.
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Xie HM, Liu JL. [A simple method of producing tungsten microelectrodes]. Sheng Li Ke Xue Jin Zhan 1982; 13:182-183. [PMID: 7123193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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