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Faisal M, Stark H, Büsche G, Schlue J, Teiken K, Kreipe HH, Lehmann U, Bartels S. Comprehensive mutation profiling and mRNA expression analysis in atypical chronic myeloid leukemia in comparison with chronic myelomonocytic leukemia. Cancer Med 2019; 8:742-750. [PMID: 30635983 PMCID: PMC6382710 DOI: 10.1002/cam4.1946] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/30/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023] Open
Abstract
Atypical chronic myeloid leukemia (aCML) and chronic myelomonocytic leukemia (CMML) represent two histologically and clinically overlapping myelodysplastic/myeloproliferative neoplasms. Also the mutational landscapes of both entities show congruencies. We analyzed and compared an aCML cohort (n = 26) and a CMML cohort (n = 59) by next‐generation sequencing of 25 genes and by an nCounter approach for differential expression in 107 genes. Significant differences were found with regard to the mutation frequency of TET2, SETBP1, and CSF3R. Blast content of the bone marrow revealed an inverse correlation with the mutation status of SETBP1 in aCML and TET2 in CMML, respectively. By linear discriminant analysis, a mutation‐based machine learning algorithm was generated which placed 19/26 aCML cases (73%) and 54/59 (92%) CMML cases into the correct category. After multiple correction, differential mRNA expression could be detected between both cohorts in a subset of genes (FLT3, CSF3R, and SETBP1 showed the strongest correlation). However, due to high variances in the mRNA expression, the potential utility for the clinic is limited. We conclude that a medium‐sized NGS panel provides a valuable assistance for the correct classification of aCML and CMML.
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Affiliation(s)
- Muhammad Faisal
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Helge Stark
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Guntram Büsche
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Jerome Schlue
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Kristin Teiken
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Hans H Kreipe
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Stephan Bartels
- Institute of Pathology, Hannover Medical School, Hannover, Germany
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Acuna-Hidalgo R, Deriziotis P, Steehouwer M, Gilissen C, Graham SA, van Dam S, Hoover-Fong J, Telegrafi AB, Destree A, Smigiel R, Lambie LA, Kayserili H, Altunoglu U, Lapi E, Uzielli ML, Aracena M, Nur BG, Mihci E, Moreira LMA, Borges Ferreira V, Horovitz DDG, da Rocha KM, Jezela-Stanek A, Brooks AS, Reutter H, Cohen JS, Fatemi A, Smitka M, Grebe TA, Di Donato N, Deshpande C, Vandersteen A, Marques Lourenço C, Dufke A, Rossier E, Andre G, Baumer A, Spencer C, McGaughran J, Franke L, Veltman JA, De Vries BBA, Schinzel A, Fisher SE, Hoischen A, van Bon BW. Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies. PLoS Genet 2017; 13:e1006683. [PMID: 28346496 PMCID: PMC5386295 DOI: 10.1371/journal.pgen.1006683] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 04/10/2017] [Accepted: 03/10/2017] [Indexed: 11/18/2022] Open
Abstract
Schinzel-Giedion syndrome (SGS) is a rare developmental disorder characterized by multiple malformations, severe neurological alterations and increased risk of malignancy. SGS is caused by de novo germline mutations clustering to a 12bp hotspot in exon 4 of SETBP1. Mutations in this hotspot disrupt a degron, a signal for the regulation of protein degradation, and lead to the accumulation of SETBP1 protein. Overlapping SETBP1 hotspot mutations have been observed recurrently as somatic events in leukemia. We collected clinical information of 47 SGS patients (including 26 novel cases) with germline SETBP1 mutations and of four individuals with a milder phenotype caused by de novo germline mutations adjacent to the SETBP1 hotspot. Different mutations within and around the SETBP1 hotspot have varying effects on SETBP1 stability and protein levels in vitro and in in silico modeling. Substitutions in SETBP1 residue I871 result in a weak increase in protein levels and mutations affecting this residue are significantly more frequent in SGS than in leukemia. On the other hand, substitutions in residue D868 lead to the largest increase in protein levels. Individuals with germline mutations affecting D868 have enhanced cell proliferation in vitro and higher incidence of cancer compared to patients with other germline SETBP1 mutations. Our findings substantiate that, despite their overlap, somatic SETBP1 mutations driving malignancy are more disruptive to the degron than germline SETBP1 mutations causing SGS. Additionally, this suggests that the functional threshold for the development of cancer driven by the disruption of the SETBP1 degron is higher than for the alteration in prenatal development in SGS. Drawing on previous studies of somatic SETBP1 mutations in leukemia, our results reveal a genotype-phenotype correlation in germline SETBP1 mutations spanning a molecular, cellular and clinical phenotype.
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MESH Headings
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Abnormalities, Multiple/pathology
- Blotting, Western
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Line
- Cell Proliferation/genetics
- Cell Transformation, Neoplastic/genetics
- Child
- Child, Preschool
- Craniofacial Abnormalities/genetics
- Craniofacial Abnormalities/metabolism
- Craniofacial Abnormalities/pathology
- Female
- Gene Expression Profiling
- Genetic Association Studies
- Genetic Predisposition to Disease/genetics
- Germ-Line Mutation
- HEK293 Cells
- Hand Deformities, Congenital/genetics
- Hand Deformities, Congenital/metabolism
- Hand Deformities, Congenital/pathology
- Hematologic Neoplasms/genetics
- Hematologic Neoplasms/metabolism
- Hematologic Neoplasms/pathology
- Humans
- Infant
- Infant, Newborn
- Intellectual Disability/genetics
- Intellectual Disability/metabolism
- Intellectual Disability/pathology
- Male
- Mutation
- Nails, Malformed/genetics
- Nails, Malformed/metabolism
- Nails, Malformed/pathology
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phenotype
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Affiliation(s)
- Rocio Acuna-Hidalgo
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pelagia Deriziotis
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah A. Graham
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Sipko van Dam
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Julie Hoover-Fong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | | | - Anne Destree
- Institute of Pathology and Genetics (IPG), Gosselies, Belgium
| | - Robert Smigiel
- Department of Pediatrics and Rare Disorders, Medical University, Wroclaw, Poland
| | - Lindsday A. Lambie
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Hülya Kayserili
- Medical Genetics Department, Koç University School of Medicine (KUSOM), İstanbul, Turkey
| | - Umut Altunoglu
- Medical Genetics Department, İstanbul Medical Faculty, İstanbul University, İstanbul, Turkey
| | - Elisabetta Lapi
- Medical Genetics Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | | | - Mariana Aracena
- División de Pediatría, Pontificia Universidad Católica de Chile and Unidad de Genética, Hospital Dr. Luis Calvo Mackenna, Santiago Chile
| | - Banu G. Nur
- Department of Pediatric Genetics, Akdeniz University Medical School, Antalya, Turkey
| | - Ercan Mihci
- Department of Pediatric Genetics, Akdeniz University Medical School, Antalya, Turkey
| | - Lilia M. A. Moreira
- Laboratory of Human Genetics, Biology Institute, Federal University of Bahia (UFBA), Bahia, Brazil
| | | | - Dafne D. G. Horovitz
- CERES-Genetica Reference Center and Studies in Medical Genetics and Instituto Fernandes Figueira / Fiocruz, Rio de Janeiro, Brazil
| | - Katia M. da Rocha
- Center for Human Genome Studies, Institute of Biosciences, USP, Sao Paulo, Brazil
| | | | - Alice S. Brooks
- Department of Clinical Genetics, Sophia Children's Hospital, Erasmus MC, Rotterdam, The Netherlands
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany and Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Julie S. Cohen
- Division of Neurogenetics, Kennedy Krieger Institute, Departments of Neurology and Pediatrics, The Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Ali Fatemi
- Division of Neurogenetics, Kennedy Krieger Institute, Departments of Neurology and Pediatrics, The Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Martin Smitka
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Theresa A. Grebe
- Division of Genetics & Metabolism, Phoenix Children’s Hospital, Phoenix, Arizona, United States of America
| | | | - Charu Deshpande
- Department of Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Anthony Vandersteen
- North West Thames Regional Genetics Unit, Kennedy Galton Centre, North West London Hospitals NHS Trust, Northwick Park & St Marks Hospital, Harrow, Middlesex, United Kingdom
| | - Charles Marques Lourenço
- Neurogenetics Unit, Department of Medical Genetics School of Medicine of Ribeirao Preto, University of Sao Paulo, Sao Paulo, Brazil
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Eva Rossier
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Gwenaelle Andre
- Unité de foetopathologie, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Careni Spencer
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland and School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bert B. A. De Vries
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Albert Schinzel
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Simon E. Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail: (BWvB); (AH)
| | - Bregje W. van Bon
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail: (BWvB); (AH)
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