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Wagener R, Brandes D, Jung M, Huetzen MA, Bergmann AK, Panier S, Picard D, Fischer U, Jachimowicz RD, Borkhardt A, Brozou T. Optical genome mapping identifies structural variants in potentially new cancer predisposition candidate genes in pediatric cancer patients. Int J Cancer 2024; 154:607-614. [PMID: 37776287 DOI: 10.1002/ijc.34721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 08/01/2023] [Accepted: 08/11/2023] [Indexed: 10/02/2023]
Abstract
Genetic predisposition is one of the major risk factors for pediatric cancer, with ~10% of children being carriers of a predisposing germline alteration. It is likely that this is the tip of the iceberg and many children are underdiagnosed, as most of the analysis focuses on single or short nucleotide variants, not considering the full spectrum of DNA alterations. Hence, we applied optical genome mapping (OGM) to our cohort of 34 pediatric cancer patients to perform an unbiased germline screening and analyze the frequency of structural variants (SVs) and their impact on cancer predisposition. All children were clinically highly suspicious for germline alterations (concomitant conditions or congenital anomalies, positive family cancer history, particular cancer type, synchronous or metachronous tumors), but whole exome sequencing (WES) had failed to detect pathogenic variants in cancer predisposing genes. OGM detected a median of 49 rare SVs (range 27-149) per patient. By analysis of 18 patient-parent trios, we identified three de novo SVs. Moreover, we discovered a likely pathogenic deletion of exon 3 in the known cancer predisposition gene BRCA2, and identified a duplication in RPA1, which might represent a new cancer predisposition gene. We conclude that optical genome mapping is a suitable tool for detecting potentially predisposing SVs in addition to WES in pediatric cancer patients.
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Affiliation(s)
- Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Danielle Brandes
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marie Jung
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Maxim A Huetzen
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Anke K Bergmann
- Institute of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Stephanie Panier
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Cologne, Germany
| | - Daniel Picard
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Ron D Jachimowicz
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne and Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Zipper L, Wagener R, Fischer U, Hoffmann A, Yasin L, Brandes D, Soura S, Anwar A, Walter C, Varghese J, Hauer J, Auer F, Bhatia S, Dugas M, Junk SV, Stanulla M, Haas OA, Borkhardt A, Reiff T, Brozou T. Hyperdiploid acute lymphoblastic leukemia in children with LZTR1 germline variants. Hemasphere 2024; 8:e26. [PMID: 38434521 PMCID: PMC10878188 DOI: 10.1002/hem3.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 03/05/2024] Open
Affiliation(s)
- Lisa Zipper
- Department of Biology, Institute of Genetics, The Faculty of Mathematics and Natural SciencesHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
- German Cancer Consortium (DKTK)partner site Essen/DüsseldorfDüsseldorfGermany
| | - Anna Hoffmann
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Layal Yasin
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Danielle Brandes
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Stavrieta Soura
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Ammarah Anwar
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Carolin Walter
- Institute of Medical InformaticsUniversity of MünsterMünsterGermany
| | - Julian Varghese
- Institute of Medical InformaticsUniversity of MünsterMünsterGermany
| | - Julia Hauer
- Department of PediatricsSchool of Medicine, Technical University of MunichMunichGermany
| | - Franziska Auer
- Department of PediatricsSchool of Medicine, Technical University of MunichMunichGermany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Martin Dugas
- Institute of Medical InformaticsHeidelberg University HospitalHeidelbergGermany
| | - Stefanie V. Junk
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
- Department of Pediatric Hematology and OncologyHannover Medical SchoolHannoverGermany
| | - Martin Stanulla
- Department of Pediatric Hematology and OncologyHannover Medical SchoolHannoverGermany
| | - Oskar A. Haas
- St. Anna Children's Hospital, Pediatric ClinicMedical UniversityViennaAustria
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
- German Cancer Consortium (DKTK)partner site Essen/DüsseldorfDüsseldorfGermany
| | - Tobias Reiff
- Department of Biology, Institute of Genetics, The Faculty of Mathematics and Natural SciencesHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
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Vogt M, Dienstbier N, Schliehe-Diecks J, Scharov K, Tu JW, Gebing P, Hogenkamp J, Bilen BS, Furlan S, Picard D, Remke M, Yasin L, Bickel D, Kalia M, Iacoangeli A, Lenz T, Stühler K, Pandyra AA, Hauer J, Fischer U, Wagener R, Borkhardt A, Bhatia S. Co-targeting HSP90 alpha and CDK7 overcomes resistance against HSP90 inhibitors in BCR-ABL1+ leukemia cells. Cell Death Dis 2023; 14:799. [PMID: 38057328 PMCID: PMC10700369 DOI: 10.1038/s41419-023-06337-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/08/2023]
Abstract
HSP90 has emerged as an appealing anti-cancer target. However, HSP90 inhibitors (HSP90i) are characterized by limited clinical utility, primarily due to the resistance acquisition via heat shock response (HSR) induction. Understanding the roles of abundantly expressed cytosolic HSP90 isoforms (α and β) in sustaining malignant cells' growth and the mechanisms of resistance to HSP90i is crucial for exploiting their clinical potential. Utilizing multi-omics approaches, we identified that ablation of the HSP90β isoform induces the overexpression of HSP90α and extracellular-secreted HSP90α (eHSP90α). Notably, we found that the absence of HSP90α causes downregulation of PTPRC (or CD45) expression and restricts in vivo growth of BCR-ABL1+ leukemia cells. Subsequently, chronic long-term exposure to the clinically advanced HSP90i PU-H71 (Zelavespib) led to copy number gain and mutation (p.S164F) of the HSP90AA1 gene, and HSP90α overexpression. In contrast, acquired resistance toward other tested HSP90i (Tanespimycin and Coumermycin A1) was attained by MDR1 efflux pump overexpression. Remarkably, combined CDK7 and HSP90 inhibition display synergistic activity against therapy-resistant BCR-ABL1+ patient leukemia cells via blocking pro-survival HSR and HSP90α overexpression, providing a novel strategy to avoid the emergence of resistance against treatment with HSP90i alone.
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Affiliation(s)
- Melina Vogt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Niklas Dienstbier
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Julian Schliehe-Diecks
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Katerina Scharov
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jia-Wey Tu
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Philip Gebing
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Julian Hogenkamp
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Berna-Selin Bilen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Silke Furlan
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Picard
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Marc Remke
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Layal Yasin
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - David Bickel
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Munishikha Kalia
- Department of Biostatistics and Health Informatics, King's College London, London, UK
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, King's College London, London, UK
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
- National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - Thomas Lenz
- Molecular Proteomics Laboratory, Biological Medical Research Center, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Kai Stühler
- Institute for Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Aleksandra A Pandyra
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Julia Hauer
- Department of Pediatrics and Children's Cancer Research Center, Children's Hospital Munich Schwabing, Technical University of Munich, School of Medicine, Munich, Germany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.
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Brandes D, Yasin L, Nebral K, Ebler J, Schinnerl D, Picard D, Bergmann AK, Alam J, Köhrer S, Haas OA, Attarbaschi A, Marschall T, Stanulla M, Borkhardt A, Brozou T, Fischer U, Wagener R. Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia. Hemasphere 2023; 7:e925. [PMID: 37469802 PMCID: PMC10353714 DOI: 10.1097/hs9.0000000000000925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/01/2023] [Indexed: 07/21/2023] Open
Abstract
The mutational landscape of B-cell precursor acute lymphoblastic leukemia (BCP-ALL), the most common pediatric cancer, is not fully described partially because commonly applied short-read next generation sequencing has a limited ability to identify structural variations. By combining comprehensive analysis of structural variants (SVs), single-nucleotide variants (SNVs), and small insertions-deletions, new subtype-defining and therapeutic targets may be detected. We analyzed the landscape of somatic alterations in 60 pediatric patients diagnosed with the most common BCP-ALL subtypes, ETV6::RUNX1+ and classical hyperdiploid (HD), using conventional cytogenetics, single nucleotide polymorphism (SNP) array, whole exome sequencing (WES), and the novel optical genome mapping (OGM) technique. Ninety-five percent of SVs detected by cytogenetics and SNP-array were verified by OGM. OGM detected an additional 677 SVs not identified using the conventional methods, including (subclonal) IKZF1 deletions. Based on OGM, ETV6::RUNX1+ BCP-ALL harbored 2.7 times more SVs than HD BCP-ALL, mainly focal deletions. Besides SVs in known leukemia development genes (ETV6, PAX5, BTG1, CDKN2A), we identified 19 novel recurrently altered regions (in n ≥ 3) including 9p21.3 (FOCAD/HACD4), 8p11.21 (IKBKB), 1p34.3 (ZMYM1), 4q24 (MANBA), 8p23.1 (MSRA), and 10p14 (SFMBT2), as well as ETV6::RUNX1+ subtype-specific SVs (12p13.1 (GPRC5A), 12q24.21 (MED13L), 18q11.2 (MIB1), 20q11.22 (NCOA6)). We detected 3 novel fusion genes (SFMBT2::DGKD, PDS5B::STAG2, and TDRD5::LPCAT2), for which the sequence and expression were validated by long-read and whole transcriptome sequencing, respectively. OGM and WES identified double hits of SVs and SNVs (ETV6, BTG1, STAG2, MANBA, TBL1XR1, NSD2) in the same patient demonstrating the power of the combined approach to define the landscape of genomic alterations in BCP-ALL.
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Affiliation(s)
- Danielle Brandes
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
- Dusseldorf School of Oncology (DSO), Medical Faculty, Heinrich-Heine University, Dusseldorf, Germany
| | - Layal Yasin
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
| | - Karin Nebral
- Labdia Labordiagnostik, Clinical Genetics, Vienna, Austria
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich-Heine University, Dusseldorf, Germany
- Center for Digital Medicine, Heinrich-Heine University, Dusseldorf, Germany
| | - Dagmar Schinnerl
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Daniel Picard
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
| | - Anke K. Bergmann
- Institute of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Jubayer Alam
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
| | - Stefan Köhrer
- Labdia Labordiagnostik, Clinical Genetics, Vienna, Austria
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Oskar A. Haas
- St. Anna Children’s Hospital, Department of Pediatric Hematology/Oncology, Pediatric Clinic, Medical University, Vienna, Austria
| | - Andishe Attarbaschi
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
- St. Anna Children’s Hospital, Department of Pediatric Hematology/Oncology, Pediatric Clinic, Medical University, Vienna, Austria
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich-Heine University, Dusseldorf, Germany
- Center for Digital Medicine, Heinrich-Heine University, Dusseldorf, Germany
| | - Martin Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School (MHH), Hannover, Germany
| | - Arndt Borkhardt
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Dusseldorf, Germany
| | - Triantafyllia Brozou
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Dusseldorf, Germany
| | - Ute Fischer
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Dusseldorf, Germany
| | - Rabea Wagener
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Dusseldorf, Germany
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Friedrich UA, Bienias M, Zinke C, Prazenicova M, Lohse J, Jahn A, Menzel M, Langanke J, Walter C, Wagener R, Brozou T, Varghese J, Dugas M, Erlacher M, Schröck E, Suttorp M, Borkhardt A, Hauer J, Auer F. A clinical screening tool to detect genetic cancer predisposition in pediatric oncology shows high sensitivity but can miss a substantial percentage of affected children. Genet Med 2023:100875. [PMID: 37149759 DOI: 10.1016/j.gim.2023.100875] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/08/2023] Open
Abstract
PURPOSE Clinical checklists are the standard of care to determine whether a child with cancer shows indications for genetic testing. Nevertheless, the efficacy of these tests to reliably detect genetic cancer predisposition in children with cancer is still insufficiently investigated. METHODS We assessed the validity of clinically recognizable signs to identify cancer predisposition by correlating a state-of-the-art clinical checklist to the corresponding exome sequencing analysis in an unselected single-center cohort of 139 child-parent datasets. RESULTS In total, 1/3rd of patients had a clinical indication for genetic testing according to current recommendations and 10.1% (n=14/139) of children harbored a cancer predisposition. Out of these, 71.4% (n=10/14) were identified through the clinical checklist. In addition, >2 clinical findings in the checklist increased the likelihood to identifying genetic predisposition from 12.5% to 50%. While our data revealed a high rate of genetic predisposition (40%, n=4/10) in Myelodysplastic Syndrome cases, no (likely) pathogenic variants were identified in the sarcoma and lymphoma group. CONCLUSION In summary, our data shows high checklist sensitivity, particular to identify childhood cancer predisposition syndromes. Nevertheless, the here employed checklist also missed 29% of children with a cancer predisposition, highlighting the drawbacks of sole clinical evaluation and underlining the need for routine germline sequencing in pediatric oncology.
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Affiliation(s)
- Ulrike Anne Friedrich
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital "Carl Gustav Carus", TU Dresden, 01307 Dresden, Germany; DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Marc Bienias
- Technical University of Munich, Germany; School of Medicine; Department of Pediatrics, 80804 Munich, Germany
| | - Claudia Zinke
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital "Carl Gustav Carus", TU Dresden, 01307 Dresden, Germany
| | - Maria Prazenicova
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital "Carl Gustav Carus", TU Dresden, 01307 Dresden, Germany
| | - Judith Lohse
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital "Carl Gustav Carus", TU Dresden, 01307 Dresden, Germany
| | - Arne Jahn
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany, ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Germany; National Center for Tumor Diseases Dresden (NCT/UCC), Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria Menzel
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital "Carl Gustav Carus", TU Dresden, 01307 Dresden, Germany
| | - Jonas Langanke
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital "Carl Gustav Carus", TU Dresden, 01307 Dresden, Germany
| | - Carolin Walter
- Institute of Medical Informatics, University of Muenster, 48149 Muenster, Germany
| | - Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Muenster, 48149 Muenster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Muenster, 48149 Muenster, Germany; Institute of Medical Informatics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Miriam Erlacher
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Evelin Schröck
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany, ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Germany; National Center for Tumor Diseases Dresden (NCT/UCC), Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden; Germany
| | - Meinolf Suttorp
- Pediatric Hematology and Oncology, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Julia Hauer
- Technical University of Munich, Germany; School of Medicine; Department of Pediatrics, 80804 Munich, Germany.
| | - Franziska Auer
- Technical University of Munich, Germany; School of Medicine; Department of Pediatrics, 80804 Munich, Germany.
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6
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Borkhardt A, Wagener R, Brozou T. Reply to: Comments on "The CHK2 kinase is recurrently mutated and functionally impaired in the germline of pediatric cancer patients". Int J Cancer 2023; 152:2013. [PMID: 36647327 DOI: 10.1002/ijc.34431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 01/18/2023]
Affiliation(s)
- Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Düsseldorf, Germany
| | - Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Düsseldorf, Germany
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Wagener R, Walter C, Auer F, Alzoubi D, Hauer J, Fischer U, Varghese J, Dugas M, Borkhardt A, Brozou T. The CHK2 kinase is recurrently mutated and functionally impaired in the germline of pediatric cancer patients. Int J Cancer 2023; 152:1388-1398. [PMID: 36468172 DOI: 10.1002/ijc.34390] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 05/09/2022] [Revised: 10/25/2022] [Accepted: 11/16/2022] [Indexed: 12/11/2022]
Abstract
Predisposing CHEK2 germline variants are associated with various adult-type malignancies, whereas their impact on cancer susceptibility in childhood cancer is unclear. To understand the frequency of germline variants in the CHEK2 gene and their impact on pediatric malignancies, we used whole-exome sequencing to search for CHEK2 variants in the germlines of 418 children diagnosed with cancer in our clinics. Moreover, we performed functional analysis of the pathogenic CHEK2 variants to analyze the effect of the alterations on CHK2 protein function. We detected a CHEK2 germline variant in 32/418 (7.7%) pediatric cancer patients and 46.8% of them had leukemia. Functional analysis of the pathogenic variants revealed that 5 pathogenic variants impaired CHK2 protein function. 6/32 patients carried one of these clearly damaging CHEK2 variants and two of them harbored a matching family history of cancer. In conclusion, we detected germline CHEK2 variants in 7.7% of all pediatric cancer patients, of which a minority but still relevant fraction of approximately 20% had a profound impact on protein expression or its phosphorylation after irradiation-induced DNA damage. Accordingly, we conclude that CHEK2 variants increase the risk for not only adult-onset but also pediatric cancer.
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Affiliation(s)
- Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Carolin Walter
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Franziska Auer
- TUM School of Medicine, Department of Pediatrics, Technical University of Munich, Munchen, Germany
| | - Deya Alzoubi
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Julia Hauer
- TUM School of Medicine, Department of Pediatrics, Technical University of Munich, Munchen, Germany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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8
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Wagener R, Walter C, Surowy HM, Brandes D, Soura S, Alzoubi D, Yasin L, Fischer U, Dugas M, Borkhardt A, Brozou T. Noncancer-related Secondary Findings in a Cohort of 231 Children With Cancer and Their Parents. J Pediatr Hematol Oncol 2023; 45:e244-e248. [PMID: 35537032 DOI: 10.1097/mph.0000000000002475] [Citation(s) in RCA: 1] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Application of next-generation sequencing may lead to the detection of secondary findings (SF) not related to the initially analyzed disease but to other severe medically actionable diseases. However, the analysis of SFs is not yet routinely performed. We mined whole-exome sequencing data of 231 pediatric cancer patients and their parents who had been treated in our center for the presence of SFs. By this approach, we identified in 6 children (2.6%) pathogenic germline variants in 5 of the noncancer-related genes on the American College of Medical Genetics and Genomics (ACMG) SF v3.0 list, of which the majority were related to cardiovascular diseases ( RYR2 , MYBPC3 , KCNQ1 ). Interestingly, only the patient harboring the KCNQ1 variant showed at the time point of the analysis signs of the related Long QT syndrome. Moreover, we report 3 variants of unknown significance which, although not classified as pathogenic, have been reported in the literature to occur in individuals with the respective disease. While the frequency of patients with SFs is low, the impact of such findings on the patients' life is enormous, with regard to the potential prevention of life-threatening diseases. Hence, we are convinced that such actionable SF should be routinely analyzed.
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Affiliation(s)
- Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Carolin Walter
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf
| | - Harald M Surowy
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf
| | - Danielle Brandes
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Stavrieta Soura
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Deya Alzoubi
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Layal Yasin
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
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9
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Bosch JVDWT, Hlaváčková E, Derpoorter C, Fischer U, Saettini F, Ghosh S, Farah R, Bogaert D, Wagener R, Loeffen J, Bacon CM, Bomken S. How to recognize inborn errors of immunity in a child presenting with a malignancy: guidelines for the pediatric hemato-oncologist. Pediatr Hematol Oncol 2023; 40:131-146. [PMID: 35913104 DOI: 10.1080/08880018.2022.2085830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/16/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023]
Abstract
Inborn errors of immunity (IEI) are a group of disorders caused by genetically determined defects in the immune system, leading to infections, autoimmunity, autoinflammation and an increased risk of malignancy. In some cases, a malignancy might be the first sign of an underlying IEI. As therapeutic strategies might be different in these patients, recognition of the underlying IEI by the pediatric hemato-oncologist is important. This article, written by a group of experts in pediatric immunology, hemato-oncology, pathology and genetics, aims to provide guidelines for pediatric hemato-oncologists on how to recognize a possible underlying IEI and what diagnostic tests can be performed, and gives some consideration to treatment possibilities.
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Affiliation(s)
| | - Eva Hlaváčková
- Department of Clinical Immunology and Allergology, St. Anne s University Hospital in Brno, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Department of Pediatric Oncology, Brno University Hospital, Brno, Czech Republic
| | - Charlotte Derpoorter
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Ute Fischer
- Department for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Francesco Saettini
- Department of Pediatric Hematology, Fondazione MBBM, University of Milano-Bicocca, Monza, Italy
| | - Sujal Ghosh
- Department for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Roula Farah
- Department of pediatrics, University-Medical-Center-Rizk-Hospital, Beirut, Lebanon
| | - Delfien Bogaert
- Department of Pediatrics, Division of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Rabea Wagener
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jan Loeffen
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Chris M Bacon
- Translational & Clinical Research Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Newcastle upon Tyne, UK
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Simon Bomken
- Translational & Clinical Research Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Newcastle upon Tyne, UK
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, 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S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, 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Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, 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Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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12
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Hoffmann DC, Hai L, Wagener R, Mandelbaum H, Xie R, Hausmann D, Dominguez Azorín D, Weil S, Sievers P, Cebulla G, Ito J, Warnken U, Venkataramani V, Ernst K, Reibold D, Will R, Suvà ML, Herold-Mende C, Sahm F, Winkler F, Schlesner M, Wick W, Kessler T. JS08.6.A A connectivity signature for glioblastoma. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac174.025] [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: 11/13/2022] Open
Abstract
Abstract
Background
Tumor cell extensions called tumor microtubes (TMs) in glioma resemble neurites during neurodevelopment and connect glioma cells to a network that has considerable relevance for tumor progression and therapy resistance. The determination of interconnectivity in individual tumors has been challenging and the impact of tumor cell connectivity on patient survival remained unresolved so far.
Material and Methods
A connectivity signature was derived by single-cell RNA-sequencing (scRNA-Seq) of highly and lowly connected cells obtained from an SR101 dye transfer xenograft model of primary glioblastoma (GB). The signature was validated in different in vitro models of cell-to-cell connectivity and could be translated to GB clinical specimens.
Results
34 of 40 connectivity genes were related to neurogenesis, neural tube development or glioma progression, including the TM-network-relevant GAP43 gene. Astrocytic-like and mesenchymal-like GB cells had the highest connectivity signature scores in scRNA-Seq data of patient-derived xenografts and patient samples. In 230 human GBs, high connectivity correlated with the mesenchymal expression subtype, TP53 wildtype, and with dismal patient survival. CHI3L1 was identified and validated as a robust molecular marker of connectivity with a functional relevance.
Conclusion
The connectivity signature gives novel insights into brain tumor biology, provides a proof-of-principle that tumor cell connectivity is relevant for patients’ prognosis, and serves as a robust biomarker that can be used for future clinical trials
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Affiliation(s)
- D C Hoffmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital , Heidelberg , Germany
- Faculty of Biosciences, Heidelberg University , Heidelberg , Germany
| | - L Hai
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital , Heidelberg , Germany
- Bioinformatics and Omics Data Analytics, DKFZ , Heidelberg , Germany
| | - R Wagener
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital , Heidelberg , Germany
| | - H Mandelbaum
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - R Xie
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - D Hausmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - D Dominguez Azorín
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - S Weil
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital , Heidelberg , Germany
| | - P Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg , Heidelberg , Germany
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ , Heidelberg , Germany
| | - G Cebulla
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - J Ito
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - U Warnken
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - V Venkataramani
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital , Heidelberg , Germany
- Department of Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University , Heidelberg , Germany
| | - K Ernst
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ) , Heidelberg , Germany
- Division of Pediatric Neurooncology, DKTK, DKFZ , Heidelberg , Germany
| | - D Reibold
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - R Will
- Genomics and Proteomics Core Facility, DKTK, DKFZ , Heidelberg , Germany
| | - M L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, United States; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School , Boston, MA , United States
| | - C Herold-Mende
- Department of Neurosurgery, Heidelberg University Hospital , Heidelberg , Germany
| | - F Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg , Heidelberg , Germany
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ , Heidelberg , Germany
| | - F Winkler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital , Heidelberg , Germany
| | - M Schlesner
- Bioinformatics and Omics Data Analytics, DKFZ , Heidelberg , Germany
- Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg , Augsburg , Germany
| | - W Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital , Heidelberg , Germany
| | - T Kessler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital , Heidelberg , Germany
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13
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Bock T, Bewarder M, Cetin O, Fadle N, Regitz E, Schwarz EC, Held J, Roth S, Lohse S, Pfuhl T, Wagener R, Smola S, Becker SL, Bohle RM, Trümper L, Siebert R, Hansmann M, Pfreundschuh M, Drexler HG, Hoth M, Kubuschok B, Roemer K, Preuss K, Hartmann S, Thurner L. B‐cell receptors of EBV‐negative Burkitt lymphoma bind modified isoforms of autoantigens. eJHaem 2022; 3:739-747. [PMID: 36051037 PMCID: PMC9421956 DOI: 10.1002/jha2.475] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/29/2022] [Accepted: 05/01/2022] [Indexed: 11/08/2022]
Abstract
Burkitt lymphoma (BL) represents the most aggressive B‐cell‐lymphoma. Beside the hallmark of IG‐MYC‐translocation, surface B‐cell receptor (BCR) is expressed, and mutations in the BCR pathway are frequent. Coincidental infections in endemic BL, and specific extra‐nodal sites suggest antigenic triggers. To explore this hypothesis, BCRs of BL cell lines and cases were screened for reactivities against a panel of bacterial lysates, lysates of Plasmodium falciparum, a custom‐made virome array and against self‐antigens, including post‐translationally modified antigens. An atypically modified, SUMOylated isoform of Bystin, that is, SUMO1‐BYSL was identified as the antigen of the BCR of cell line CA46. SUMO1‐BYSL was exclusively expressed in CA46 cells with K139 as site of the SUMOylation. Secondly, an atypically acetylated isoform of HSP40 was identified as the antigen of the BCR of cell line BL41. K104 and K179 were the sites of immunogenic acetylation, and the acetylated HSP40 isoform was solely present in BL41 cells. Functionally, addition of SUMO1‐BYSL and acetylated HSP40 induced BCR pathway activation in CA46 and BL41 cells, respectively. Accordingly, SUMO1‐BYSL‐ETA’ immunotoxin, produced by a two‐step intein‐based conjugation, led to the specific killing of CA46 cells. Autoantibodies directed against SUMO1‐BYSL were found in 3 of 14 (21.4%), and autoantibodies against acetylated HSP40 in 1/14(7.1%) patients with sporadic Burkitt‐lymphoma. No reactivities against antigens of the infectious agent spectrum could be observed. These results indicate a pathogenic role of autoreactivity evoked by immunogenic post‐translational modifications in a subgroup of sporadic BL including two EBV‐negative BL cell lines.
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Affiliation(s)
- Theresa Bock
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Moritz Bewarder
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Onur Cetin
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Natalie Fadle
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Evi Regitz
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Eva C. Schwarz
- Center for Integrative Physiology and Molecular Medicine (CIPMM) School of Medicine Homburg Germany
| | - Jana Held
- Institute of Tropical Medicine Eberhard Karls Universität Tübingen Tübingen Germany
| | - Sophie Roth
- Institute of Medical Microbiology and Hygiene Saarland University Homburg/Saar Germany
| | - Stefan Lohse
- Institute of Virology University of Saarland Homburg Germany
| | - Thorsten Pfuhl
- Institute of Virology University of Saarland Homburg Germany
| | - Rabea Wagener
- Institute of Human Genetics Ulm University and Ulm University Medical Center Ulm Germany
| | - Sigrun Smola
- Institute of Virology University of Saarland Homburg Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Saarbrücken Germany
| | - Sören L. Becker
- Institute of Medical Microbiology and Hygiene Saarland University Homburg/Saar Germany
| | - Rainer Maria Bohle
- Institute of Pathology Saarland University Medical School Homburg/Saar Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology Georg August University Göttingen Göttingen Germany
| | - Reiner Siebert
- Institute of Human Genetics Ulm University and Ulm University Medical Center Ulm Germany
| | - Martin‐Leo Hansmann
- Dr. Senckenberg Institute of Pathology Goethe University Hospital of Frankfurt a. Main Frankfurt a. Main Germany
| | - Michael Pfreundschuh
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Hans G. Drexler
- Faculty of Life sciences Technical University of Braunschweig Braunschweig Germany
| | - Markus Hoth
- Center for Integrative Physiology and Molecular Medicine (CIPMM) School of Medicine Homburg Germany
| | - Boris Kubuschok
- Department of Internal Medicine II Augsburg University Medical Center Augsburg Germany
| | - Klaus Roemer
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Klaus‐Dieter Preuss
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology Goethe University Hospital of Frankfurt a. Main Frankfurt a. Main Germany
| | - Lorenz Thurner
- Department of Internal Medicine I and José Carreras Center for Immuno‐ and Gene Therapy Saarland University Medical School Homburg/Saar Germany
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14
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Schedel A, Friedrich UA, Morcos MNF, Wagener R, Mehtonen J, Watrin T, Saitta C, Brozou T, Michler P, Walter C, Försti A, Baksi A, Menzel M, Horak P, Paramasivam N, Fazio G, Autry RJ, Fröhling S, Suttorp M, Gertzen C, Gohlke H, Bhatia S, Wadt K, Schmiegelow K, Dugas M, Richter D, Glimm H, Heinäniemi M, Jessberger R, Cazzaniga G, Borkhardt A, Hauer J, Auer F. Recurrent Germline Variant in RAD21 Predisposes Children to Lymphoblastic Leukemia or Lymphoma. Int J Mol Sci 2022; 23:ijms23095174. [PMID: 35563565 PMCID: PMC9106003 DOI: 10.3390/ijms23095174] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/02/2022] [Indexed: 12/04/2022] Open
Abstract
Somatic loss of function mutations in cohesin genes are frequently associated with various cancer types, while cohesin disruption in the germline causes cohesinopathies such as Cornelia-de-Lange syndrome (CdLS). Here, we present the discovery of a recurrent heterozygous RAD21 germline aberration at amino acid position 298 (p.P298S/A) identified in three children with lymphoblastic leukemia or lymphoma in a total dataset of 482 pediatric cancer patients. While RAD21 p.P298S/A did not disrupt the formation of the cohesin complex, it altered RAD21 gene expression, DNA damage response and primary patient fibroblasts showed increased G2/M arrest after irradiation and Mitomycin-C treatment. Subsequent single-cell RNA-sequencing analysis of healthy human bone marrow confirmed the upregulation of distinct cohesin gene patterns during hematopoiesis, highlighting the importance of RAD21 expression within proliferating B- and T-cells. Our clinical and functional data therefore suggest that RAD21 germline variants can predispose to childhood lymphoblastic leukemia or lymphoma without displaying a CdLS phenotype.
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Affiliation(s)
- Anne Schedel
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.S.); (U.A.F.); (P.M.); (M.M.); (M.S.)
| | - Ulrike Anne Friedrich
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.S.); (U.A.F.); (P.M.); (M.M.); (M.S.)
| | - Mina N. F. Morcos
- Department of Pediatrics, School of Medicine, Technical University of Munich; 80804 Munich, Germany; (M.N.F.M.); (F.A.)
| | - Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, 40225 Duesseldorf, Germany; (R.W.); (T.W.); (T.B.); (S.B.); (A.B.)
| | - Juha Mehtonen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211 Kuopio, Finland; (J.M.); (M.H.)
| | - Titus Watrin
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, 40225 Duesseldorf, Germany; (R.W.); (T.W.); (T.B.); (S.B.); (A.B.)
| | - Claudia Saitta
- Tettamanti Research Center, Pediatrics, University of Milan Bicocca, Fondazione MBBM/San Gerardo Hospital, 20900 Monza, Italy; (C.S.); (G.F.); (G.C.)
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, 40225 Duesseldorf, Germany; (R.W.); (T.W.); (T.B.); (S.B.); (A.B.)
| | - Pia Michler
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.S.); (U.A.F.); (P.M.); (M.M.); (M.S.)
| | - Carolin Walter
- Institute of Medical Informatics, University of Muenster, 48149 Muenster, Germany; (C.W.); (M.D.)
| | - Asta Försti
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.F.); (R.J.A.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
| | - Arka Baksi
- Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.B.); (R.J.)
| | - Maria Menzel
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.S.); (U.A.F.); (P.M.); (M.M.); (M.S.)
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (P.H.); (S.F.)
| | - Nagarajan Paramasivam
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
| | - Grazia Fazio
- Tettamanti Research Center, Pediatrics, University of Milan Bicocca, Fondazione MBBM/San Gerardo Hospital, 20900 Monza, Italy; (C.S.); (G.F.); (G.C.)
| | - Robert J Autry
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.F.); (R.J.A.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (P.H.); (S.F.)
| | - Meinolf Suttorp
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.S.); (U.A.F.); (P.M.); (M.M.); (M.S.)
| | - Christoph Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (C.G.); (H.G.)
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (C.G.); (H.G.)
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, 40225 Duesseldorf, Germany; (R.W.); (T.W.); (T.B.); (S.B.); (A.B.)
| | - Karin Wadt
- Department of Clinical Genetics, University Hospital of Copenhagen, Faculty of health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Martin Dugas
- Institute of Medical Informatics, University of Muenster, 48149 Muenster, Germany; (C.W.); (M.D.)
- Institute of Medical Informatics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Daniela Richter
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden, 01307 Dresden, Germany; (D.R.); (H.G.)
- German Cancer Consortium (DKTK), 01307 Dresden, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden, 01307 Dresden, Germany; (D.R.); (H.G.)
- German Cancer Consortium (DKTK), 01307 Dresden, Germany
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211 Kuopio, Finland; (J.M.); (M.H.)
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (A.B.); (R.J.)
| | - Gianni Cazzaniga
- Tettamanti Research Center, Pediatrics, University of Milan Bicocca, Fondazione MBBM/San Gerardo Hospital, 20900 Monza, Italy; (C.S.); (G.F.); (G.C.)
- Medical Genetics, Department of Medicine and Surgery, University of Milan Bicocca, 20900 Monza, Italy
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, 40225 Duesseldorf, Germany; (R.W.); (T.W.); (T.B.); (S.B.); (A.B.)
| | - Julia Hauer
- Department of Pediatrics, School of Medicine, Technical University of Munich; 80804 Munich, Germany; (M.N.F.M.); (F.A.)
- German Cancer Consortium (DKTK), 81675 Munich, Germany
- Correspondence: ; Tel.: +49-(89)-3068-3940
| | - Franziska Auer
- Department of Pediatrics, School of Medicine, Technical University of Munich; 80804 Munich, Germany; (M.N.F.M.); (F.A.)
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15
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López C, Schleussner N, Bernhart SH, Kleinheinz K, Sungalee S, Sczakiel HL, Kretzmer H, Toprak UH, Glaser S, Wagener R, Ammerpohl O, Bens S, Giefing M, González Sánchez JC, Apic G, Hübschmann D, Janz M, Kreuz M, Mottok A, Müller JM, Seufert J, Hoffmann S, Korbel JO, Russell RB, Schüle R, Trümper L, Klapper W, Radlwimmer B, Lichter P, Küppers R, Schlesner M, Mathas S, Siebert R. Focal structural variants revealed by whole genome sequencing disrupt the histone demethylase KDM4C in B-cell lymphomas. Haematologica 2022; 108:543-554. [PMID: 35522148 PMCID: PMC9890021 DOI: 10.3324/haematol.2021.280005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 09/13/2021] [Indexed: 02/03/2023] Open
Abstract
Histone methylation-modifiers, such as EZH2 and KMT2D, are recurrently altered in B-cell lymphomas. To comprehensively describe the landscape of alterations affecting genes encoding histone methylation-modifiers in lymphomagenesis we investigated whole genome and transcriptome data of 186 mature B-cell lymphomas sequenced in the ICGC MMML-Seq project. Besides confirming common alterations of KMT2D (47% of cases), EZH2 (17%), SETD1B (5%), PRDM9 (4%), KMT2C (4%), and SETD2 (4%), also identified by prior exome or RNA-sequencing studies, we here found recurrent alterations to KDM4C in chromosome 9p24, encoding a histone demethylase. Focal structural variation was the main mechanism of KDM4C alterations, and was independent from 9p24 amplification. We also identified KDM4C alterations in lymphoma cell lines including a focal homozygous deletion in a classical Hodgkin lymphoma cell line. By integrating RNA-sequencing and genome sequencing data we predict that KDM4C structural variants result in loss-offunction. By functional reconstitution studies in cell lines, we provide evidence that KDM4C can act as a tumor suppressor. Thus, we show that identification of structural variants in whole genome sequencing data adds to the comprehensive description of the mutational landscape of lymphomas and, moreover, establish KDM4C as a putative tumor suppressive gene recurrently altered in subsets of B-cell derived lymphomas.
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Affiliation(s)
- Cristina López
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,*CL and NS contributed equally as co-first authors
| | - Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany,*CL and NS contributed equally as co-first authors
| | - Stephan H. Bernhart
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Kortine Kleinheinz
- Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany
| | | | - Henrike L. Sczakiel
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany
| | - Helene Kretzmer
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Umut H. Toprak
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany,Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Division of Neuroblastoma Genomics (B087), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Maciej Giefing
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Gordana Apic
- BioQuant and Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Heidelberg, Germany
| | - Daniel Hübschmann
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany,Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany
| | - Markus Kreuz
- Institute for Medical Informatics Statistics and Epidemiology, Leipzig, Germany
| | - Anja Mottok
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Judith M. Müller
- Klinik fur Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Julian Seufert
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steve Hoffmann
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany,Leibniz Institute on Ageing-Fritz Lipmann Institute (FLI), Computational Biology, Jena, Germany
| | - Jan O. Korbel
- EMBL Heidelberg, Genome Biology Unit, Heidelberg,, Germany
| | - Robert B. Russell
- BioQuant and Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Heidelberg, Germany
| | - Roland Schüle
- Klinik fur Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany,BIOSS Centre of Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August-University of Göttingen, Göttingen, Germany
| | - Wolfram Klapper
- Hematopathology Section, Christian-Albrechts-University, Kiel, Germany
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany, and German Cancer Consortium (DKTK)
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany,Biomedical Informatics, Data Mining and Data Analytics, Augsburg University, Augsburg, Germany
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany,SM and RS contributed equally as co-senior authors
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,SM and RS contributed equally as co-senior authors
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16
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Geron I, Savino AM, Fishman H, Tal N, Brown J, Turati VA, James C, Sarno J, Hameiri-Grossman M, Lee YN, Rein A, Maniriho H, Birger Y, Zemlyansky A, Muler I, Davis KL, Marcu-Malina V, Mattson N, Parnas O, Wagener R, Fischer U, Barata JT, Jamieson CHM, Müschen M, Chen CW, Borkhardt A, Kirsch IR, Nagler A, Enver T, Izraeli S. An instructive role for Interleukin-7 receptor α in the development of human B-cell precursor leukemia. Nat Commun 2022; 13:659. [PMID: 35115489 PMCID: PMC8814001 DOI: 10.1038/s41467-022-28218-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 04/22/2020] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
Kinase signaling fuels growth of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Yet its role in leukemia initiation is unclear and has not been shown in primary human hematopoietic cells. We previously described activating mutations in interleukin-7 receptor alpha (IL7RA) in poor-prognosis "ph-like" BCP-ALL. Here we show that expression of activated mutant IL7RA in human CD34+ hematopoietic stem and progenitor cells induces a preleukemic state in transplanted immunodeficient NOD/LtSz-scid IL2Rγnull mice, characterized by persistence of self-renewing Pro-B cells with non-productive V(D)J gene rearrangements. Preleukemic CD34+CD10highCD19+ cells evolve into BCP-ALL with spontaneously acquired Cyclin Dependent Kinase Inhibitor 2 A (CDKN2A) deletions, as commonly observed in primary human BCP-ALL. CRISPR mediated gene silencing of CDKN2A in primary human CD34+ cells transduced with activated IL7RA results in robust development of BCP-ALLs in-vivo. Thus, we demonstrate that constitutive activation of IL7RA can initiate preleukemia in primary human hematopoietic progenitors and cooperates with CDKN2A silencing in progression into BCP-ALL.
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MESH Headings
- Animals
- Antigens, CD34/genetics
- Antigens, CD34/immunology
- Antigens, CD34/metabolism
- Base Sequence
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Cyclin-Dependent Kinase Inhibitor p16/genetics
- Cyclin-Dependent Kinase Inhibitor p16/immunology
- Cyclin-Dependent Kinase Inhibitor p16/metabolism
- Gene Expression/immunology
- Humans
- Interleukin-7 Receptor alpha Subunit/genetics
- Interleukin-7 Receptor alpha Subunit/immunology
- Interleukin-7 Receptor alpha Subunit/metabolism
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Precursor Cells, B-Lymphoid/immunology
- Precursor Cells, B-Lymphoid/metabolism
- RNA-Seq/methods
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- Receptors, Cytokine/metabolism
- Signal Transduction/genetics
- Signal Transduction/immunology
- Single-Cell Analysis/methods
- Transplantation, Heterologous
- Mice
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Affiliation(s)
- Ifat Geron
- Felsenstein Medical Research Center and The Molecular Genetics and Biochemistry Department, Sackler Faculty of Medicine, Tel Aviv University, Petach Tikva, Israel
- Institute of Pediatric Research, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Israel
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Angela Maria Savino
- Felsenstein Medical Research Center and The Molecular Genetics and Biochemistry Department, Sackler Faculty of Medicine, Tel Aviv University, Petach Tikva, Israel
- Institute of Pediatric Research, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Israel
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Hila Fishman
- Felsenstein Medical Research Center and The Molecular Genetics and Biochemistry Department, Sackler Faculty of Medicine, Tel Aviv University, Petach Tikva, Israel
- Institute of Pediatric Research, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Israel
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Noa Tal
- Felsenstein Medical Research Center and The Molecular Genetics and Biochemistry Department, Sackler Faculty of Medicine, Tel Aviv University, Petach Tikva, Israel
- Institute of Pediatric Research, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - John Brown
- Department of Cancer Biology, UCL Cancer Institute, UCL, London, UK
| | | | - Chela James
- Department of Cancer Biology, UCL Cancer Institute, UCL, London, UK
| | - Jolanda Sarno
- Department of Pediatrics, Bass Center for Childhood Cancer and Blood Disorders, Stanford University, Stanford, CA, USA
| | - Michal Hameiri-Grossman
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Yu Nee Lee
- Felsenstein Medical Research Center and The Molecular Genetics and Biochemistry Department, Sackler Faculty of Medicine, Tel Aviv University, Petach Tikva, Israel
- Pediatric Department and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital Sheba Medical Center, Tel-Hashomer, Israel
| | - Avigail Rein
- Felsenstein Medical Research Center and The Molecular Genetics and Biochemistry Department, Sackler Faculty of Medicine, Tel Aviv University, Petach Tikva, Israel
- Institute of Pediatric Research, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Israel
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Hillary Maniriho
- Felsenstein Medical Research Center and The Molecular Genetics and Biochemistry Department, Sackler Faculty of Medicine, Tel Aviv University, Petach Tikva, Israel
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Yehudit Birger
- Felsenstein Medical Research Center and The Molecular Genetics and Biochemistry Department, Sackler Faculty of Medicine, Tel Aviv University, Petach Tikva, Israel
- Institute of Pediatric Research, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Israel
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Anna Zemlyansky
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Inna Muler
- Institute of Pediatric Research, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Kara L Davis
- Department of Pediatrics, Bass Center for Childhood Cancer and Blood Disorders, Stanford University, Stanford, CA, USA
| | - Victoria Marcu-Malina
- Cytogenetic Unit laboratory of Hematology, Chaim Sheba Medical Center Tel Hashomer, Tel Hashomer, Israel
| | - Nicole Mattson
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, CA, USA
| | - Oren Parnas
- The Concern Foundation Laboratories at the Lautenberg Center for immunology and Cancer Research, IMRIC, Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - João T Barata
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Catriona H M Jamieson
- UC San Diego, Moores Cancer Center, Division of Regenerative Medicine, Department of Medicine and Sanford Stem Cell Clinical Center, Ja Jolla, CA, USA
| | - Markus Müschen
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, CA, USA
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | | | - Arnon Nagler
- Felsenstein Medical Research Center and The Molecular Genetics and Biochemistry Department, Sackler Faculty of Medicine, Tel Aviv University, Petach Tikva, Israel
- Hematology Division BMT and Cord Blood Bank Chaim Sheba Medical Center Tel-Hashomer, Tel-Hashomer, Israel
| | - Tariq Enver
- Department of Cancer Biology, UCL Cancer Institute, UCL, London, UK
| | - Shai Izraeli
- Felsenstein Medical Research Center and The Molecular Genetics and Biochemistry Department, Sackler Faculty of Medicine, Tel Aviv University, Petach Tikva, Israel.
- Institute of Pediatric Research, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Israel.
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel.
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, CA, USA.
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17
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Michler P, Schedel A, Witschas M, Friedrich UA, Wagener R, Mehtonen J, Brozou T, Menzel M, Walter C, Nabi D, Pearce G, Erlacher M, Göhring G, Dugas M, Heinäniemi M, Borkhardt A, Stölzel F, Hauer J, Auer F. Germline POT1 Deregulation Can Predispose to Myeloid Malignancies in Childhood. Int J Mol Sci 2021; 22:ijms222111572. [PMID: 34769003 PMCID: PMC8583981 DOI: 10.3390/ijms222111572] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 12/11/2022] Open
Abstract
While the shelterin complex guards and coordinates the mechanism of telomere regulation, deregulation of this process is tightly linked to malignant transformation and cancer. Here, we present the novel finding of a germline stop-gain variant (p.Q199*) in the shelterin complex gene POT1, which was identified in a child with acute myeloid leukemia. We show that the cells overexpressing the mutated POT1 display increased DNA damage and chromosomal instabilities compared to the wildtype counterpart. Protein and mRNA expression analyses in the primary patient cells further confirm that, physiologically, the variant leads to a nonfunctional POT1 allele in the patient. Subsequent telomere length measurements in the primary cells carrying heterozygous POT1 p.Q199* as well as POT1 knockdown AML cells revealed telomeric elongation as the main functional effect. These results show a connection between POT1 p.Q199* and telomeric dysregulation and highlight POT1 germline deficiency as a predisposition to myeloid malignancies in childhood.
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Affiliation(s)
- Pia Michler
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital “Carl Gustav Carus”, TU Dresden, 01307 Dresden, Germany; (P.M.); (A.S.); (M.W.); (U.A.F.); (M.M.)
| | - Anne Schedel
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital “Carl Gustav Carus”, TU Dresden, 01307 Dresden, Germany; (P.M.); (A.S.); (M.W.); (U.A.F.); (M.M.)
| | - Martha Witschas
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital “Carl Gustav Carus”, TU Dresden, 01307 Dresden, Germany; (P.M.); (A.S.); (M.W.); (U.A.F.); (M.M.)
| | - Ulrike Anne Friedrich
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital “Carl Gustav Carus”, TU Dresden, 01307 Dresden, Germany; (P.M.); (A.S.); (M.W.); (U.A.F.); (M.M.)
| | - Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany; (R.W.); (T.B.); (A.B.)
| | - Juha Mehtonen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211 Kuopio, Finland; (J.M.); (M.H.)
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany; (R.W.); (T.B.); (A.B.)
| | - Maria Menzel
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital “Carl Gustav Carus”, TU Dresden, 01307 Dresden, Germany; (P.M.); (A.S.); (M.W.); (U.A.F.); (M.M.)
| | - Carolin Walter
- Institute of Medical Informatics, University of Muenster, 48149 Muenster, Germany;
| | - Dalileh Nabi
- Department of Neuropediatrics Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany;
| | - Glen Pearce
- Institute of Physiological Chemistry, Medical Faculty “Carl Gustav Carus”, TU Dresden, 01307 Dresden, Germany;
| | - Miriam Erlacher
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Faculty of Medicine, University Medical Center Freiburg, 79106 Freiburg, Germany;
- German Cancer Consortium (DKTK), 79106 Freiburg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany;
| | - Martin Dugas
- Institute of Medical Informatics, Heidelberg University Hospital, 69120 Heidelberg, Germany;
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211 Kuopio, Finland; (J.M.); (M.H.)
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany; (R.W.); (T.B.); (A.B.)
| | - Friedrich Stölzel
- Hematology and Oncology, University Hospital “Carl Gustav Carus”, TU Dresden, 01307 Dresden, Germany;
| | - Julia Hauer
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital “Carl Gustav Carus”, TU Dresden, 01307 Dresden, Germany; (P.M.); (A.S.); (M.W.); (U.A.F.); (M.M.)
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany;
- Correspondence: ; Tel.: +49-351-458-3522
| | - Franziska Auer
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany;
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18
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Elgaafary S, López C, Nagel I, Vater I, Bens S, Szczepanowski M, Aukema SM, Wagener R, Hopp L, Binder H, de Leval L, Klapper W, Siebert R. Molecular characterization of Burkitt lymphoma in the breast or ovary. Leuk Lymphoma 2021; 62:2120-2129. [PMID: 34165048 DOI: 10.1080/10428194.2021.1907374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Breast and ovary have been described as rare but typical sites of presentation of Burkitt lymphoma (BL) in females, particularly after puberty. We revised a historic series of 44 lymphomas of the breast or the ovary in women diagnosed between 1973 and 2014 as BL. Fluorescence in situ hybridization (FISH) was applied to all, and array-based copy number analysis as well as expression profiling to a subset of those cases. Of the 42 cases evaluable for FISH, 19 cases showed an IG-MYC translocation but only 9 of those fulfilled the criteria of the current WHO classification for the diagnosis of BL. Those nine cases resembled BL of other sites with regard to molecular features. Our findings along with literature data suggest that breast and ovarian BL (1) seem to be rarer than hitherto assumed, (2) share typical molecular features with other BL, and (3) predominantly affect women in the fertile age.
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Affiliation(s)
- Shaymaa Elgaafary
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Department of Human Cytogenetics, National Research centre, Division of Human Genetics and Genome Research, Cairo, Egypt
| | - Cristina López
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Inga Nagel
- Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Experimental and Clinical Pharmacology, Christian-Albrechts University Kiel and University, Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Inga Vater
- Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Monika Szczepanowski
- Hematopathology Section and Lymph Node Registry, Christian-Albrechts University Kiel and University Hospital, Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Clinic of Internal Medicine II, Laboratory of Hematology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Sietse M Aukema
- Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Hematopathology Section and Lymph Node Registry, Christian-Albrechts University Kiel and University Hospital, Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Lydia Hopp
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Hans Binder
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Laurence de Leval
- Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
| | - Wolfram Klapper
- Hematopathology Section and Lymph Node Registry, Christian-Albrechts University Kiel and University Hospital, Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
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19
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Horn H, Kalmbach S, Wagener R, Staiger AM, Hüttl K, Mottok A, Bens S, Traverse-Glehen A, Fontaine J, Siebert R, Rosenwald A, Ott G. A Diagnostic Approach to the Identification of Burkitt-like Lymphoma With 11q Aberration in Aggressive B-Cell Lymphomas. Am J Surg Pathol 2021; 45:356-364. [PMID: 33136583 DOI: 10.1097/pas.0000000000001613] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 12/29/2022]
Abstract
Rare cases of aggressive B-cell lymphomas with a morphology similar to Burkitt lymphoma (BL) present with the BL-typical immunophenotype, but lacked MYC translocation (MYC-negative Burkitt-like lymphoma: mnBLL). A proportion of those with an imbalance pattern in chromosome 11q has been designated Burkitt-like lymphoma with 11q aberration in the recent update of the World Health Organization (WHO) classification. Because of the problems in the identification of Burkitt-like lymphoma with 11q aberration, our goal was to retrospectively analyze their frequency in a cohort of "candidate" aggressive lymphomas (cohort 1, n=35) such as mnBLL (n=16), diffuse large B-cell lymphoma with similarities to Burkitt lymphoma (DLBCL-BL; n=3), high-grade B-cell lymphomas, not otherwise specified (NOS) (n=16), as well as in a cohort of MYC-negative diffuse large B-cell lymphoma NOS (cohort 2, n=62). In total, 17/33 cohort 1 cases (52%) harbored the typical 11q aberration pattern, predominantly those that had been classified as mnBLL (12/16, 75%), but also as DLBCL-BL (2/3, 67%) and high-grade B-cell lymphomas, NOS (3/14; 21%). The specimens with this typical 11q aberration pattern were usually negative for the BCL2 protein. Of interest and as a new finding, samples harboring the 11q aberration pattern were often characterized by strikingly coarse apoptotic debris within starry sky macrophages facilitating their recognition. In contrast, only 1 of 62 garden variety DLBCL, NOS was positive for the 11q aberration pattern. In 2 DLBCL-BL, a dual MYC translocation/11q aberration pattern was detected. As a diagnostic algorithm, we, therefore, propose analysis of 11q status in MYC-negative high-grade lymphomas with features of BL, especially showing BCL2 negativity and a conspicuous coarse apoptotic debris in starry sky macrophages.
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Affiliation(s)
- Heike Horn
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart
- University of Tübingen, Tübingen
| | - Sabrina Kalmbach
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology
- University of Tübingen, Tübingen
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf
| | - Annette M Staiger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart
- University of Tübingen, Tübingen
| | - Katrin Hüttl
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart
| | - Anja Mottok
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm
| | - Alexandra Traverse-Glehen
- Service d'Anatomie Pathologie, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Juliette Fontaine
- Service d'Anatomie Pathologie, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm
| | - Andreas Rosenwald
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Center Mainfranken (CCCMF), Würzburg, Germany
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart
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20
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Dugge R, Wagener R, Mӧller P, Barth TFE. Genome-wide DNA methylation analysis along the progression of gastric marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue (MALT) type. Br J Haematol 2021; 193:369-374. [PMID: 33590882 DOI: 10.1111/bjh.17193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/17/2020] [Accepted: 09/23/2020] [Indexed: 01/16/2023]
Abstract
Extra-nodal marginal zone B-cell lymphoma (MZBL) of mucosa-associated lymphoid tissue is an indolent lymphoma mostly affecting the gastrointestinal tract. The lymphoma initially has small-cell morphology (SC-MZBL) and often arises in the background of Helicobacter pylori-induced gastritis. In some cases, a clonal malignant progression to large-cell morphology (LC-MZBL) is observed. Here, we studied the DNA methylation profile of 30 gastric MZBLs along their progression. Genome-wide DNA methylation profiling, identified 7698 significantly differentially methylated loci during gastric MZBL progression (σ/σmax ≥0·4, q ≤ 0·001). LC-MZBL showed hypermethylation in comparison to SC-MZBL with an enrichment of regions involved in transcriptional regulation. In conclusion, our present data show that the morphological distinction between SC- and LC-MZBL is reflected by characteristic DNA methylation profiles.
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Affiliation(s)
- Rucha Dugge
- Institute of Pathology, Ulm University, Ulm, Germany
| | - Rabea Wagener
- Ulm University Medical Center, Institute of Human Genetics, Ulm University, Ulm, Germany
| | - Peter Mӧller
- Institute of Pathology, Ulm University, Ulm, Germany
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21
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Seifer P, Hay E, Fleischhauer L, Heilig J, Bloch W, Sonntag S, Shmerling D, Clausen-Schaumann H, Aszodi A, Niehoff A, Cohen-Solal M, Paulsson M, Wagener R, Zaucke F. The Matrilin-3 T298M mutation predisposes for post-traumatic osteoarthritis in a knock-in mouse model. Osteoarthritis Cartilage 2021; 29:78-88. [PMID: 33227438 DOI: 10.1016/j.joca.2020.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/04/2020] [Accepted: 09/29/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The human matrilin-3 T303M (in mouse T298M) mutation has been proposed to predispose for osteoarthritis, but due to the lack of an appropriate animal model this hypothesis could not be tested. This study was carried out to identify pathogenic mechanisms in a transgenic mouse line by which the mutation might contribute to disease development. METHODS A mouse line carrying the T298M point mutation in the Matn3 locus was generated and features of skeletal development in ageing animals were characterized by immunohistology, micro computed tomography, transmission electron microscopy and atomic force microscopy. The effect of transgenic matrilin-3 was also studied after surgically induced osteoarthritis. RESULTS The matrilin-3 T298M mutation influences endochondral ossification and leads to larger cartilage collagen fibril diameters. This in turn leads to an increased compressive stiffness of the articular cartilage, which, upon challenge, aggravates osteoarthritis development. CONCLUSIONS The mouse matrilin-3 T298M mutation causes a predisposition for post-traumatic osteoarthritis and the corresponding knock-in mouse line therefore represents a valid model for investigating the pathogenic mechanisms involved in osteoarthritis development.
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Affiliation(s)
- P Seifer
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - E Hay
- Inserm UMR1132 and Paris Diderot University, Paris, France
| | - L Fleischhauer
- Center for Applied Tissue Engineering and Regenerative Medicine, Munich University of Applied Sciences, Munich, Germany; Experimental Surgery and Regenerative Medicine (ExperiMed), Department of General, Trauma and Reconstructive Surgery, Munich University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - J Heilig
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany; Cologne Center for Musculoskeletal Biomechanics (CCMB), Medical Faculty, University of Cologne, Cologne, Germany
| | - W Bloch
- Department of Molecular and Cellular Sports Medicine, Institute of Cardiology and Sports Medicine, German Sport University Cologne, Cologne, Germany
| | - S Sonntag
- ETH Phenomics Center (EPIC), Zurich, Switzerland
| | | | - H Clausen-Schaumann
- Center for Applied Tissue Engineering and Regenerative Medicine, Munich University of Applied Sciences, Munich, Germany
| | - A Aszodi
- Center for Applied Tissue Engineering and Regenerative Medicine, Munich University of Applied Sciences, Munich, Germany; Experimental Surgery and Regenerative Medicine (ExperiMed), Department of General, Trauma and Reconstructive Surgery, Munich University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - A Niehoff
- Cologne Center for Musculoskeletal Biomechanics (CCMB), Medical Faculty, University of Cologne, Cologne, Germany; Institute of Biomechanics and Orthopaedics, German Sport University Cologne, Cologne, Germany
| | - M Cohen-Solal
- Inserm UMR1132 and Paris Diderot University, Paris, France
| | - M Paulsson
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - R Wagener
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - F Zaucke
- Dr. Rolf M. Schwiete Research Unit for Osteoarthritis, Orthopedic University Hospital Friedrichsheim GGmbH, Frankfurt Am Main, Germany.
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22
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Elgaafary S, Nagel I, López C, Bens S, Szczepanowski M, Wagener R, Klapper W, Siebert R. Double-hit lymphoma of the male breast: a case report. J Med Case Rep 2020; 14:245. [PMID: 33339535 PMCID: PMC7747391 DOI: 10.1186/s13256-020-02526-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 06/18/2020] [Accepted: 09/08/2020] [Indexed: 12/04/2022] Open
Abstract
Background Whereas lymphoma of the female breast is already rare, lymphoma of the male breast has only anecdotally been reported. Within a study of 32 lymphoma of the breast reported between 1973 and 2014 as Burkitt lymphoma, we observed a single male case, which we report here. Case presentation A 72-years-old Caucasian man presented with a mass in his left breast. Clinical history included prior basal cell carcinoma, leiomyosarcoma, and administration of spironolactone. The reference pathology diagnosis at presentation was Burkitt lymphoma according to the Kiel Classification. The present re-investigation using fluorescence in situ hybridization revealed an IGH-MYC translocation and a break in the BCL2 locus in the tumor cells. Thus, in light of the current WHO classification, the diagnosis was revised to high-grade B-cell lymphoma with MYC and BCL2 rearrangement, Burkitt morphology (so-called “double-hit” lymphoma). Genome-wide chromosomal imbalance mapping revealed a complex pattern of aberrations in line with this diagnosis. The aberrations, including copy-number gains in chromosomes 3q and 18 and focal homozygous loss in 9p21.3, resembled typical changes of lymphomas affecting “immune-privileged” sites. Conclusion The present case adds to the understanding of the pathogenesis of male breast lymphomas, about which hardly any molecular characterization has been published yet.
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Affiliation(s)
- Shaymaa Elgaafary
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, D-89081, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, D-24105, Kiel, Germany.,Division of Human Genetics and Genome Research, Department of Human Cytogenetic, Cairo, 12622, Egypt
| | - Inga Nagel
- Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, D-24105, Kiel, Germany.,Institute of Experimental and Clinical Pharmacology, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein Campus Kiel, D-24105, Kiel, Germany
| | - Cristina López
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, D-89081, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, D-24105, Kiel, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, D-89081, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, D-24105, Kiel, Germany
| | - Monika Szczepanowski
- Department of Internal Medicine II (Hematology), Laboratory of Hematology, University Hospital, Schleswig-Holstein Campus Kiel, D-24105, Kiel, Germany.,Hematopathology Section and Lymph Node Registry, Institute of Pathology Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, D-24105, Kiel, Germany
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, D-89081, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, D-24105, Kiel, Germany
| | - Wolfram Klapper
- Hematopathology Section and Lymph Node Registry, Institute of Pathology Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, D-24105, Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, D-89081, Ulm, Germany. .,Institute of Human Genetics, Christian-Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, D-24105, Kiel, Germany.
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23
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Chong AS, Nadaf J, Grau E, Apellaniz-Ruiz M, Fahiminiya S, Saskin A, Han H, Turcotte R, Muchantef K, Thomas C, Wagener R, Bassenden A, Mete O, Pusztaszeri M, Paulus W, Berghuis A, Siebert R, Albrecht S, Hasselblatt M, Lazaro C, Teule A, Fabian M, Brunet J, Foulkes W, Rivera B. RARE-22. GERMLINE PATHOGENIC VARIANT c.1552G>A;p.E518K IN DGCR8 CONFERS SUSCEPTIBILITY FOR SCHWANNOMATOSIS AND THYROID TUMORS. Neuro Oncol 2020. [PMCID: PMC7715759 DOI: 10.1093/neuonc/noaa222.733] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Germline mutations in DICER1 cause a pleiotropic susceptibility syndrome characterized by the development of pediatric or early-onset tumors including pleuropulmonary blastoma, Wilms tumors, pineoblastomas, multinodular goiter (MNG) and thyroid cancers. Somatic mutations in the other two microprocessors DROSHA and DGCR8 have been found in Wilms Tumors and pineoblastomas. We present here two families with peripheral schwannomatosis and thyroid tumors carrying a germline variant c.1552G>A;p.E518K in DGCR8. Family one had six affected members with early-onset MNG and five of them developed schwannomatosis. All five members were heterozygous for the variant. One of the carriers had also been diagnosed with a choroid plexus papilloma at 7 years old. The common second event in all tumors tested was the loss of chromosome 22 at the somatic level. In family two, a 35-year-old male was diagnosed with a peripheral schwannoma at the age of 12. Since then, he has developed seven extra peripheral schwannomas (one of which was an ancient schwannoma) and papillary thyroid cancer. DGCR8 lies on chromosome 22q, adjacent to the three schwannoma genes: LZTR1, SMARCB1 and NF2. The variant, c.1552G>A;p.E518K localizes to the first RNA-binding domain of DGCR8 and structural modelling predicts that it abolishes proper binding of RNA. It is also a hotspot somatic mutation in Wilms tumors. Using miRNA profiling, we show that this variant disrupts global microRNA production and DGCR8 mutated tumors show a specific miRNA profile different from DGCR8 wild type tumors. These findings reinforce DGCR8 as a novel susceptibility gene for schwannomatosis and thyroid tumors.
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Affiliation(s)
| | - Javad Nadaf
- Jewish General Hospital, Montreal, QC, Canada
| | - Elia Grau
- Catalan Institute of Oncology, Barcelona, Spain
| | - Maria Apellaniz-Ruiz
- McGill University, Montreal, QC, Canada
- Jewish General Hospital, Montreal, QC, Canada
| | | | - Avi Saskin
- McGill University, Montreal, QC, Canada
- McGill University Health Centre, Montreal, QC, Canada
| | - HyeRim Han
- Bellvitge Biomedical Research Institute, IDIBELL, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Robert Turcotte
- McGill University, Montreal, QC, Canada
- McGill University Health Centre, Montreal, QC, Canada
| | - Karl Muchantef
- McGill University, Montreal, QC, Canada
- McGill University Health Centre, Montreal, QC, Canada
| | | | - Rabea Wagener
- University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | | | - Ozgur Mete
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | | | | | - Reiner Siebert
- University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | | | | | | | | | - Marc Fabian
- Jewish General Hospital, Montreal, QC, Canada
- McGill University, Montreal, QC, Canada
| | - Joan Brunet
- Catalan Institute of Oncology, Barcelona, Spain
| | - William Foulkes
- McGill University, Montreal, QC, Canada
- Jewish General Hospital, Montreal, QC, Canada
| | - Barbara Rivera
- Bellvitge Biomedical Research Institute, IDIBELL, Barcelona, Spain
- McGill University, Montreal, QC, Canada
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Rivera B, Nadaf J, Fahiminiya S, Apellaniz-Ruiz M, Saskin A, Chong AS, Sharma S, Wagener R, Revil T, Condello V, Harra Z, Hamel N, Sabbaghian N, Muchantef K, Thomas C, de Kock L, Hébert-Blouin MN, Bassenden AV, Rabenstein H, Mete O, Paschke R, Pusztaszeri MP, Paulus W, Berghuis A, Ragoussis J, Nikiforov YE, Siebert R, Albrecht S, Turcotte R, Hasselblatt M, Fabian MR, Foulkes WD. DGCR8 microprocessor defect characterizes familial multinodular goiter with schwannomatosis. J Clin Invest 2020; 130:1479-1490. [PMID: 31805011 DOI: 10.1172/jci130206] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 05/10/2019] [Accepted: 11/26/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUNDDICER1 is the only miRNA biogenesis component associated with an inherited tumor syndrome, featuring multinodular goiter (MNG) and rare pediatric-onset lesions. Other susceptibility genes for familial forms of MNG likely exist.METHODSWhole-exome sequencing of a kindred with early-onset MNG and schwannomatosis was followed by investigation of germline pathogenic variants that fully segregated with the disease. Genome-wide analyses were performed on 13 tissue samples from familial and nonfamilial DGCR8-E518K-positive tumors, including MNG, schwannomas, papillary thyroid cancers (PTCs), and Wilms tumors. miRNA profiles of 4 tissue types were compared, and sequencing of miRNA, pre-miRNA, and mRNA was performed in a subset of 9 schwannomas, 4 of which harbor DGCR8-E518K.RESULTSWe identified c.1552G>A;p.E518K in DGCR8, a microprocessor component located in 22q, in the kindred. The variant identified is a somatic hotspot in Wilms tumors and has been identified in 2 PTCs. Copy number loss of chromosome 22q, leading to loss of heterozygosity at the DGCR8 locus, was found in all 13 samples harboring c.1552G>A;p.E518K. miRNA profiling of PTCs, MNG, schwannomas, and Wilms tumors revealed a common profile among E518K hemizygous tumors. In vitro cleavage demonstrated improper processing of pre-miRNA by DGCR8-E518K. MicroRNA and RNA profiling show that this variant disrupts precursor microRNA production, impacting populations of canonical microRNAs and mirtrons.CONCLUSIONWe identified DGCR8 as the cause of an unreported autosomal dominant mendelian tumor susceptibility syndrome: familial multinodular goiter with schwannomatosis.FUNDINGCanadian Institutes of Health Research, Compute Canada, Alex's Lemonade Stand Foundation, the Mia Neri Foundation for Childhood Cancer, Cassa di Sovvenzioni e Risparmio fra il Personale della Banca d'Italia, and the KinderKrebsInitiative Buchholz/Holm-Seppensen.
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Affiliation(s)
- Barbara Rivera
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Javad Nadaf
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Somayyeh Fahiminiya
- Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada
| | - Maria Apellaniz-Ruiz
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Avi Saskin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Division of Medical Genetics, Department of Medicine, McGill University Health Centre and Jewish General Hospital, Montreal, Quebec, Canada
| | - Anne-Sophie Chong
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Sahil Sharma
- Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Rabea Wagener
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Génome Québec Innovation Centre, McGill University, Montreal, Quebec, Canada
| | - Vincenzo Condello
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Zineb Harra
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Nancy Hamel
- Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada
| | - Nelly Sabbaghian
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Karl Muchantef
- Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada.,Pediatric Radiology, Montreal Children's Hospital, Montreal, Quebec, Canada
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Muenster, Muenster, Germany
| | - Leanne de Kock
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | | | - Hannah Rabenstein
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Ozgur Mete
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Ralf Paschke
- Department of Medicine.,Department of Oncology.,Department of Pathology.,Biochemistry and Molecular Biology Institute, and.,Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Marc P Pusztaszeri
- Department of Pathology, Jewish General Hospital, Montreal, Quebec, Canada
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Muenster, Muenster, Germany
| | - Albert Berghuis
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jiannis Ragoussis
- Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada.,Génome Québec Innovation Centre, McGill University, Montreal, Quebec, Canada
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Reiner Siebert
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Steffen Albrecht
- Department of Pathology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Robert Turcotte
- Division of Orthopedic Surgery (Experimental Surgery), McGill University, Montreal, Quebec, Canada.,Department of Surgical Oncology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Muenster, Muenster, Germany
| | - Marc R Fabian
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - William D Foulkes
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Division of Medical Genetics, Department of Medicine, McGill University Health Centre and Jewish General Hospital, Montreal, Quebec, Canada
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Tonelli F, Cotti S, Leoni L, Besio R, Gioia R, Marchese L, Giorgetti S, Villani S, Gistelinck C, Wagener R, Kobbe B, Fiedler I, Larionova D, Busse B, Eyre D, Rossi A, Witten P, Forlino A. Crtap and p3h1 knock out zebrafish support defective collagen chaperoning as the cause of their osteogenesis imperfecta phenotype. Matrix Biol 2020; 90:40-60. [DOI: 10.1016/j.matbio.2020.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/05/2020] [Accepted: 03/05/2020] [Indexed: 12/15/2022]
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Akpa CA, Kleo K, Oker E, Tomaszewski N, Messerschmidt C, López C, Wagener R, Oehl-Huber K, Dettmer K, Schoeler A, Lenze D, Oefner PJ, Beule D, Siebert R, Capper D, Dimitrova L, Hummel M. Acquired resistance to DZNep-mediated apoptosis is associated with copy number gains of AHCY in a B-cell lymphoma model. BMC Cancer 2020; 20:427. [PMID: 32408898 PMCID: PMC7227222 DOI: 10.1186/s12885-020-06937-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 05/07/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Enhancer of zeste homolog 2 (EZH2) is considered an important driver of tumor development and progression by its histone modifying capabilities. Inhibition of EZH2 activity is thought to be a potent treatment option for eligible cancer patients with an aberrant EZH2 expression profile, thus the indirect EZH2 inhibitor 3-Deazaneplanocin A (DZNep) is currently under evaluation for its clinical utility. Although DZNep blocks proliferation and induces apoptosis in different tumor types including lymphomas, acquired resistance to DZNep may limit its clinical application. METHODS To investigate possible mechanisms of acquired DZNep resistance in B-cell lymphomas, we generated a DZNep-resistant clone from a previously DZNep-sensitive B-cell lymphoma cell line by long-term treatment with increasing concentrations of DZNep (ranging from 200 to 2000 nM) and compared the molecular profiles of resistant and wild-type clones. This comparison was done using molecular techniques such as flow cytometry, copy number variation assay (OncoScan and TaqMan assays), fluorescence in situ hybridization, Western blot, immunohistochemistry and metabolomics analysis. RESULTS Whole exome sequencing did not indicate the acquisition of biologically meaningful single nucleotide variants. Analysis of copy number alterations, however, demonstrated among other acquired imbalances an amplification (about 30 times) of the S-adenosyl-L-homocysteine hydrolase (AHCY) gene in the resistant clone. AHCY is a direct target of DZNep and is critically involved in the biological methylation process, where it catalyzes the reversible hydrolysis of S-adenosyl-L-homocysteine to L-homocysteine and adenosine. The amplification of the AHCY gene is paralleled by strong overexpression of AHCY at both the transcriptional and protein level, and persists upon culturing the resistant clone in a DZNep-free medium. CONCLUSIONS This study reveals one possible molecular mechanism how B-cell lymphomas can acquire resistance to DZNep, and proposes AHCY as a potential biomarker for investigation during the administration of EZH2-targeted therapy with DZNep.
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Affiliation(s)
- Chidimma Agatha Akpa
- Department of Experimental Hematopathology, Institute of Pathology, Charité Medical University, Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- Berlin School of Integrative Oncology, Charité - Medical University of Berlin, Berlin, Germany.
| | - Karsten Kleo
- Department of Experimental Hematopathology, Institute of Pathology, Charité Medical University, Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Elisabeth Oker
- Department of Experimental Hematopathology, Institute of Pathology, Charité Medical University, Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Nancy Tomaszewski
- Department of Experimental Hematopathology, Institute of Pathology, Charité Medical University, Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | | | - Cristina López
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Kathrin Oehl-Huber
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Katja Dettmer
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Anne Schoeler
- Department of Neuropathology, Charité, Medical University of Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK); Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dido Lenze
- Department of Experimental Hematopathology, Institute of Pathology, Charité Medical University, Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Peter J Oefner
- Berlin School of Integrative Oncology, Charité - Medical University of Berlin, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health, Charité Core Unit Bioinformatics, Berlin, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - David Capper
- Berlin School of Integrative Oncology, Charité - Medical University of Berlin, Berlin, Germany
- Department of Neuropathology, Charité, Medical University of Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK); Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lora Dimitrova
- Department of Experimental Hematopathology, Institute of Pathology, Charité Medical University, Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Michael Hummel
- Department of Experimental Hematopathology, Institute of Pathology, Charité Medical University, Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Berlin School of Integrative Oncology, Charité - Medical University of Berlin, Berlin, Germany
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Patil P, Cieslak A, Bernhart SH, Toprak UH, Wagener R, López C, Wiehle L, Bens S, Altmüller J, Franitza M, Scholz I, Jayne S, Ahearne MJ, Scheffold A, Jebaraj BMC, Schneider C, Costa D, Braun T, Schrader A, Campo E, Dyer MJS, Nürnberg P, Dürig J, Johansson P, Böttcher S, Schlesner M, Herling M, Stilgenbauer S, Macintyre E, Siebert R. Reconstruction of rearranged T-cell receptor loci by whole genome and transcriptome sequencing gives insights into the initial steps of T-cell prolymphocytic leukemia. Genes Chromosomes Cancer 2019; 59:261-267. [PMID: 31677197 DOI: 10.1002/gcc.22821] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 12/20/2022] Open
Abstract
T-cell prolymphocytic leukemia (T-PLL) is an aggressive tumor with leukemic presentation of mature T-lymphocytes. Here, we aimed at characterizing the initial events in the molecular pathogenesis of T-PLL and particularly, at determining the point in T-cell differentiation when the hallmark oncogenic events, that is, inv(14)(q11q32)/t(14;14)(q11;q32) and t(X;14)(q28;q11) occur. To this end, we mined whole genome and transcriptome sequencing data of 17 and 11 T-PLL cases, respectively. Mapping of the 14q32.1 locus breakpoints identified only TCL1A, which was moreover significantly overexpressed in T-PLL as compared to benign CD4+ and CD8+ T-cells, as the only common oncogenic target of aberrations. In cases with t(14;14), the breakpoints mapped telomeric and in cases with inv(14) centromeric or in the 3'-untranslated region of TCL1A. Regarding the T-cell receptor alpha (TRA) locus-TCL1A breakpoint junctions, all 17 breakpoints involved recombination signal sequences and 15 junctions contained nontemplated (N-) nucleotides. All T-PLL cases studied carried in-frame TRA rearrangements on the intact allele, which skewed significantly toward usage of distal/central TRAV/TRAJ gene segments as compared to the illegitimate TRA rearrangements. Our findings suggest that the oncogenic TRA-TCL1A/MTCP1 rearrangements in T-PLL occur during opening of the TRA locus, that is, during the progression from CD4+ immature single positive to early double positive thymocyte stage, just before physiologic TCL1A expression is silenced. The cell carrying such an oncogenic event continues maturation and rearranges the second TRA allele to achieve a functional T-cell receptor. Thereafter, it switches off RAG and DNTT expression in line with the mature T-cell phenotype at presentation of T-PLL.
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Affiliation(s)
- Paurnima Patil
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Agata Cieslak
- Diagnostic Haematology, Necker-Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris, Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM), Paris, France
| | - Stephan H Bernhart
- Interdisciplinary Center for Bioinformatics, Transcriptome Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Umut H Toprak
- Bioinformatics and Omics Data Analytics, German Cancer Research Center, Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Division Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Rabea Wagener
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany.,Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Cristina López
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany.,Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Laura Wiehle
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Susanne Bens
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany.,Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Marek Franitza
- Cologne Center for Genomics, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Ingrid Scholz
- Omics IT and Data Management Core Facility, German Cancer Research Center, Heidelberg, Germany
| | - Sandrine Jayne
- Ernest and Helen Scott Haematological Research Institute, Department of Cancer Studies, University of Leicester, Leicester, UK
| | - Matthew J Ahearne
- Ernest and Helen Scott Haematological Research Institute, Department of Cancer Studies, University of Leicester, Leicester, UK
| | - Annika Scheffold
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Billy M C Jebaraj
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | | | - Dolors Costa
- Haematopathology Section, Hospital Clínic, Institut d'Investigaciones Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Till Braun
- Department I of Internal Medicine, Center for Integrated Oncology Köln Bonn, Deutsche CLL Studiengruppe (DCLLSG), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Alexandra Schrader
- Department I of Internal Medicine, Center for Integrated Oncology Köln Bonn, Deutsche CLL Studiengruppe (DCLLSG), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Elias Campo
- Haematopathology Section, Hospital Clínic, Institut d'Investigaciones Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Martin J S Dyer
- Ernest and Helen Scott Haematological Research Institute, Department of Cancer Studies, University of Leicester, Leicester, UK
| | - Peter Nürnberg
- Cologne Center for Genomics, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Jan Dürig
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Patricia Johansson
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sebastian Böttcher
- Department III of Internal Medicine, University Hospital Rostock, Rostock, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center, Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Marco Herling
- Department I of Internal Medicine, Center for Integrated Oncology Köln Bonn, Deutsche CLL Studiengruppe (DCLLSG), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | - Elizabeth Macintyre
- Diagnostic Haematology, Necker-Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris, Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM), Paris, France
| | - Reiner Siebert
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany.,Institute for Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
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Bolduc V, Foley A, Solomon Degefa H, Sarathy A, Donkervoort S, Hu Y, Zhou H, Cummings B, Lek M, Regev O, Jimenez-Mallebrera C, Allamand V, Ferlini A, Wilton S, Hanssen E, Lamandé S, MacArthur D, Wagener R, Muntoni F, Bönnemann C. O.10A novel target for splice-modulating therapies: a common pseudoexon-inducing mutation that causes a severe collagen VI-related muscular dystrophy. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Elezagic D, Mörgelin M, Hermes G, Hamprecht A, Sengle G, Lau D, Höllriegl S, Wagener R, Paulsson M, Streichert T, Klatt AR. Antimicrobial peptides derived from the cartilage.-specific C-type Lectin Domain Family 3 Member A (CLEC3A) - potential in the prevention and treatment of septic arthritis. Osteoarthritis Cartilage 2019; 27:1564-1573. [PMID: 31279936 DOI: 10.1016/j.joca.2019.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/20/2019] [Accepted: 06/11/2019] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To investigate the antimicrobial activity of peptides derived from C-type Lectin Domain Family 3 Member A (CLEC3A), shed light on the mechanism of antimicrobial activity and assess their potential application in prevention and treatment of septic arthritis. DESIGN We performed immunoblot to detect CLEC3A peptides in human cartilage extracts. To investigate their antimicrobial activity, we designed peptides and recombinantly expressed CLEC3A domains and used them to perform viable count assays using E.coli, P.aeruginosa and S.aureus. We investigated the mechanism of their antimicrobial activity by fluorescence and scanning electron microscopy, performed ELISA-style immunoassays and transmission electron microscopy to test for lipopolysaccharide binding and surface plasmon resonance to test for lipoteichoic acid (LTA) binding. We coated CLEC3A peptides on titanium, a commonly used prosthetic material, and performed fluorescence microscopy to quantify bacterial adhesion. Moreover, we assessed the peptides' cytotoxicity against primary human chondrocytes using MTT cell viability assays. RESULTS CLEC3A fragments were detected in human cartilage extracts. Moreover, bacterial supernatants lead to fragmentation of recombinant and cartilage-derived CLEC3A. CLEC3A-derived peptides killed E.coli, P.aeruginosa and S.aureus, permeabilized bacterial membranes and bound lipopolysaccharide and LTA. Coating CLEC3A antimicrobial peptides (AMPs) on titanium lead to significantly reduced bacterial adhesion to the material. In addition, microbicidal concentrations of CLEC3A peptides in vitro displayed no direct cytotoxicity against primary human chondrocytes. CONCLUSIONS We identify cartilage-specific AMPs originating from CLEC3A, resolve the mechanism of their antimicrobial activity and point to a novel approach in the prevention and treatment of septic arthritis using potent, non-toxic, AMPs.
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Affiliation(s)
- D Elezagic
- Institute for Clinical Chemistry, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany
| | - M Mörgelin
- Department of Clinical Sciences, Division of Infection Medicine, Biomedical Center, Lund University, 22184 Lund, Sweden
| | - G Hermes
- Institute for Clinical Chemistry, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany
| | - A Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine, University of Cologne, 50935 Cologne, Germany
| | - G Sengle
- Center for Biochemistry, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany; Department of Pediatrics and Adolescent Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - D Lau
- Institute for Clinical Chemistry, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany
| | - S Höllriegl
- Cologne Braunsfeld Trinity Hospital, 50933 Cologne, Germany
| | - R Wagener
- Center for Biochemistry, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany
| | - M Paulsson
- Center for Biochemistry, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Ageing-associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - T Streichert
- Institute for Clinical Chemistry, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany
| | - A R Klatt
- Institute for Clinical Chemistry, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany.
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Doose G, Bernhart SH, Wagener R, Hoffmann S. DIEGO: detection of differential alternative splicing using Aitchison's geometry. Bioinformatics 2019; 34:1066-1068. [PMID: 29088309 PMCID: PMC5860559 DOI: 10.1093/bioinformatics/btx690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/26/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Alternative splicing is a biological process of fundamental importance in most eukaryotes. It plays a pivotal role in cell differentiation and gene regulation and has been associated with a number of different diseases. The widespread availability of RNA-Sequencing capacities allows an ever closer investigation of differentially expressed isoforms. However, most tools for differential alternative splicing (DAS) analysis do not take split reads, i.e. the most direct evidence for a splice event, into account. Here, we present DIEGO, a compositional data analysis method able to detect DAS between two sets of RNA-Seq samples based on split reads. Results The python tool DIEGO works without isoform annotations and is fast enough to analyze large experiments while being robust and accurate. We provide python and perl parsers for common formats. Availability and implementation The software is available at: www.bioinf.uni-leipzig.de/Software/DIEGO. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gero Doose
- Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig.,Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, 04107 Leipzig, Germany.,ecSeq Bioinformatics, 04103 Leipzig, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig.,Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, 04107 Leipzig, Germany
| | - Rabea Wagener
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, 89081 Ulm, Germany
| | - Steve Hoffmann
- Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig.,Chair of Bioinformatics, Faculty of Mathematics and Computer Science, Leipzig University, 04107 Leipzig, Germany.,Computational Biology Group, Leibniz Institute on Ageing - Fritz Lipmann Institute (FLI) and Friedrich-Schiller-University Jena, 07745 Jena, Germany
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32
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Wagener R, Bens S, Toprak UH, Seufert J, López C, Scholz I, Herbrueggen H, Oschlies I, Stilgenbauer S, Schlesner M, Klapper W, Burkhardt B, Siebert R. Cryptic insertion of MYC exons 2 and 3 into the immunoglobulin heavy chain locus detected by whole genome sequencing in a case of " MYC-negative" Burkitt lymphoma. Haematologica 2019; 105:e202-e205. [PMID: 31073073 DOI: 10.3324/haematol.2018.208140] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm
| | - Umut H Toprak
- German Cancer Research Center (DKFZ), Bioinformatics and Omics Data Analytics, Heidelberg.,German Caner Research Center (DKFZ), Division of Neuroblastoma Genomics Heidelberg.,Faculty of Biosciences, Heidelberg University, Heidelberg
| | - Julian Seufert
- German Cancer Research Center (DKFZ), Bioinformatics and Omics Data Analytics, Heidelberg.,Faculty of Biosciences, Heidelberg University, Heidelberg
| | - Cristina López
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm
| | - Ingrid Scholz
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg
| | - Heidi Herbrueggen
- Department of Pediatric Hematology and Oncology, NHL-BFM Study Center, University Children's Hospital, Münster
| | - Ilske Oschlies
- Hematopathology Section, Christian-Albrechts University, Kiel
| | | | - Matthias Schlesner
- German Cancer Research Center (DKFZ), Bioinformatics and Omics Data Analytics, Heidelberg
| | - Wolfram Klapper
- Hematopathology Section, Christian-Albrechts University, Kiel
| | - Birgit Burkhardt
- Department of Pediatric Hematology and Oncology, NHL-BFM Study Center, University Children's Hospital, Münster
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm
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Apellaniz-Ruiz M, Segni M, Kettwig M, Glüer S, Pelletier D, Nguyen VH, Wagener R, López C, Muchantef K, Bouron-Dal Soglio D, Sabbaghian N, Wu MK, Zannella S, Fabian MR, Siebert R, Menke J, Priest JR, Foulkes WD. Mesenchymal Hamartoma of the Liver and DICER1 Syndrome. N Engl J Med 2019; 380:1834-1842. [PMID: 31067372 DOI: 10.1056/nejmoa1812169] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mesenchymal hamartoma of the liver (MHL) is a benign tumor affecting children that is characterized by a primitive myxoid stroma with cystically dilated bile ducts. Alterations involving chromosome 19q13 are a recurrent underlying cause of MHL; these alterations activate the chromosome 19 microRNA cluster (C19MC). Other cases remain unexplained. We describe two children with MHLs that harbored germline DICER1 pathogenic variants. Analysis of tumor tissue from one of the children revealed two DICER1 "hits." Mutations in DICER1 dysregulate microRNAs, mimicking the effect of the activation of C19MC. Our data suggest that MHL is a new phenotype of DICER1 syndrome. (Funded by the Canadian Institutes of Health Research and others.).
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Affiliation(s)
- Maria Apellaniz-Ruiz
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Maria Segni
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Matthias Kettwig
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Sylvia Glüer
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Dylan Pelletier
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Van-Hung Nguyen
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Rabea Wagener
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Cristina López
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Karl Muchantef
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Dorothée Bouron-Dal Soglio
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Nelly Sabbaghian
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Mona K Wu
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Stefano Zannella
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Marc R Fabian
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Reiner Siebert
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - Jan Menke
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - John R Priest
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
| | - William D Foulkes
- From the Departments of Human Genetics (M.A.-R., M.K.W., W.D.F.), Pharmacology (D.P.), Oncology (M.R.F., W.D.F.), and Biochemistry (M.R.F.), and the Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital (M.A.-R., D.P., N.S., M.K.W., M.R.F., W.D.F.), McGill University, the Department of Pathology, Montreal Children's Hospital (V.-H.N.), the Department of Radiology (K.M.), and the Cancer Research Program, Research Institute (W.D.F.), McGill University Health Centre, and the Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine (D.B.-D.S.) - all in Montreal; the Department of Pediatrics, Endocrinology Unit, Sapienza University, Rome (M.S.), and Centro Diagnostico Italiano, Milan (S.Z.) - both in Italy; the Department of Pediatrics and Adolescent Medicine, Faculty of Medicine (M.K.), and the Institute for Diagnostic and Interventional Radiology, Faculty of Medicine (J.M.), Georg-August University, Göttingen, the Department of Pediatric Surgery, St. Bernward Krankenhaus Hildesheim, Hildesheim (S.G.), and the Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm (R.W., C.L., R.S.) - all in Germany; and Minneapolis (J.R.P.)
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Hüllein J, Słabicki M, Rosolowski M, Jethwa A, Habringer S, Tomska K, Kurilov R, Lu J, Scheinost S, Wagener R, Huang Z, Lukas M, Yavorska O, Helfrich H, Scholtysik R, Bonneau K, Tedesco D, Küppers R, Klapper W, Pott C, Stilgenbauer S, Burkhardt B, Löffler M, Trümper LH, Hummel M, Brors B, Zapatka M, Siebert R, Kreuz M, Keller U, Huber W, Zenz T. MDM4 Is Targeted by 1q Gain and Drives Disease in Burkitt Lymphoma. Cancer Res 2019; 79:3125-3138. [DOI: 10.1158/0008-5472.can-18-3438] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/11/2019] [Accepted: 04/15/2019] [Indexed: 11/16/2022]
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López C, Kleinheinz K, Aukema SM, Rohde M, Bernhart SH, Hübschmann D, Wagener R, Toprak UH, Raimondi F, Kreuz M, Waszak SM, Huang Z, Sieverling L, Paramasivam N, Seufert J, Sungalee S, Russell RB, Bausinger J, Kretzmer H, Ammerpohl O, Bergmann AK, Binder H, Borkhardt A, Brors B, Claviez A, Doose G, Feuerbach L, Haake A, Hansmann ML, Hoell J, Hummel M, Korbel JO, Lawerenz C, Lenze D, Radlwimmer B, Richter J, Rosenstiel P, Rosenwald A, Schilhabel MB, Stein H, Stilgenbauer S, Stadler PF, Szczepanowski M, Weniger MA, Zapatka M, Eils R, Lichter P, Loeffler M, Möller P, Trümper L, Klapper W, Hoffmann S, Küppers R, Burkhardt B, Schlesner M, Siebert R. Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma. Nat Commun 2019; 10:1459. [PMID: 30926794 PMCID: PMC6440956 DOI: 10.1038/s41467-019-08578-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/18/2019] [Indexed: 12/17/2022] Open
Abstract
Burkitt lymphoma (BL) is the most common B-cell lymphoma in children. Within the International Cancer Genome Consortium (ICGC), we performed whole genome and transcriptome sequencing of 39 sporadic BL. Here, we unravel interaction of structural, mutational, and transcriptional changes, which contribute to MYC oncogene dysregulation together with the pathognomonic IG-MYC translocation. Moreover, by mapping IGH translocation breakpoints, we provide evidence that the precursor of at least a subset of BL is a B-cell poised to express IGHA. We describe the landscape of mutations, structural variants, and mutational processes, and identified a series of driver genes in the pathogenesis of BL, which can be targeted by various mechanisms, including IG-non MYC translocations, germline and somatic mutations, fusion transcripts, and alternative splicing. Burkitt lymphoma (BL) is the most common pediatric B-cell lymphoma. Here, within the International Cancer Genome Consortium, the authors performed whole genome and transcriptome sequencing of 39 sporadic BL, describing the landscape of mutations, structural variants, and mutational processes that underpin this disease how alterations on different cellular levels cooperate in deregulating key pathways and complexes.
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Affiliation(s)
- Cristina López
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, 69120, Heidelberg, Germany
| | - Sietse M Aukema
- Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany.,Hematopathology Section, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Marius Rohde
- Pediatric Hematology and Oncology, University Hospital Giessen, 35392, Giessen, Germany
| | - Stephan H Bernhart
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany.,Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany.,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, 04107, Leipzig, Germany
| | - Daniel Hübschmann
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Pediatric Immunology, Hematology and Oncology, University Hospital, 69120, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Division of Stem Cells and Cancer, Heidelberg, Germany and Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Umut H Toprak
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Francesco Raimondi
- Cell Networks, Bioquant and Biochemistry CenterBiochemie Zentrum Heidelberg (BZH), University of Heidelberg, 69120, Heidelberg, Germany
| | - Markus Kreuz
- Institute for Medical Informatics Statistics and Epidemiology, 04107, Leipzig, Germany
| | | | - Zhiqin Huang
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Lina Sieverling
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany.,Division of Applied Bioinformatics (G200), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Medical Faculty Heidelberg, Heidelberg University, 69120, Heidelber, Germany
| | - Julian Seufert
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | | | - Robert B Russell
- Cell Networks, Bioquant and Biochemistry CenterBiochemie Zentrum Heidelberg (BZH), University of Heidelberg, 69120, Heidelberg, Germany
| | - Julia Bausinger
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Helene Kretzmer
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany.,Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany.,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, 04107, Leipzig, Germany.,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anke K Bergmann
- Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany.,Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Hans Binder
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany.,Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany
| | - Arndt Borkhardt
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics (G200), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Alexander Claviez
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Gero Doose
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany.,Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany.,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, 04107, Leipzig, Germany
| | - Lars Feuerbach
- Division of Applied Bioinformatics (G200), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Andrea Haake
- Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Martin-Leo Hansmann
- Senckenberg Institute of Pathology, University of Frankfurt Medical School, 60590, Frankfurt am Main, Germany
| | - Jessica Hoell
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Michael Hummel
- Institute of Pathology, Charité - University Medicine Berlin, 10117, Berlin, Germany
| | - Jan O Korbel
- Genome Biology Unit, EMBL Heidelberg, 69117, Heidelberg, Germany
| | - Chris Lawerenz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Dido Lenze
- Institute of Pathology, Charité - University Medicine Berlin, 10117, Berlin, Germany
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Julia Richter
- Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany.,Hematopathology Section, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Andreas Rosenwald
- Institute of Pathology, Comprehensive Cancer Center Mainfranken, University of Würzburg, 97080, Würzburg, Germany
| | - Markus B Schilhabel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | | | | | - Peter F Stadler
- Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany
| | | | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, 45147, Essen, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, 69120, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Markus Loeffler
- Institute for Medical Informatics Statistics and Epidemiology, 04107, Leipzig, Germany
| | - Peter Möller
- Institute of Pathology, University of Ulm and University Hospital of Ulm, 89081, Ulm, Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August-University of Göttingen, 37075, Göttingen, Germany
| | - Wolfram Klapper
- Hematopathology Section, Christian-Albrechts-University, 24105, Kiel, Germany
| | | | - Steve Hoffmann
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany.,Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany.,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, 04107, Leipzig, Germany.,Computational Biology, Leibniz Institute on Ageing-Fritz Lipmann Institut (FLI), 07745, Jena, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, 45147, Essen, Germany
| | - Birgit Burkhardt
- University Hospital Münster - Pediatric Hematology and Oncology, 48149, Münster, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. .,Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany. .,Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany.
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36
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Kock L, Hillmer M, Wagener R, Soglio DB, Sabbaghian N, Siebert R, Priest JR, Miller M, Foulkes WD. Further evidence that full gene deletions of
DICER1
predispose to DICER1 syndrome. Genes Chromosomes Cancer 2019; 58:602-604. [DOI: 10.1002/gcc.22728] [Citation(s) in RCA: 6] [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] [Received: 11/30/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 11/09/2022] Open
Affiliation(s)
- Leanne Kock
- Department of Human GeneticsMcGill University Montréal Québec Canada
- Lady Davis InstituteSegal Cancer Centre, Jewish General Hospital Montréal Québec Canada
| | - Morten Hillmer
- Institute of Human GeneticsUlm University and Ulm University Medical Centre Ulm Germany
| | - Rabea Wagener
- Institute of Human GeneticsUlm University and Ulm University Medical Centre Ulm Germany
| | - Dorothée Bouron‐Dal Soglio
- Department of PathologyCHU Sainte Justine Montréal Québec Canada
- Department of Pathology and Cellular Biology, Faculty of MedicineUniversité de Montréal Montréal Québec Canada
| | - Nelly Sabbaghian
- Lady Davis InstituteSegal Cancer Centre, Jewish General Hospital Montréal Québec Canada
| | - Reiner Siebert
- Institute of Human GeneticsUlm University and Ulm University Medical Centre Ulm Germany
| | | | - Michal Miller
- Department of PediatricsGeisinger Medical Centre Danville Pennsylvania
| | - William D. Foulkes
- Department of Human GeneticsMcGill University Montréal Québec Canada
- Lady Davis InstituteSegal Cancer Centre, Jewish General Hospital Montréal Québec Canada
- Department of Medical GeneticsResearch Institute of the McGill University Health Centre Montreal Québec Canada
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37
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Vogt J, Wagener R, Montesinos-Rongen M, Ammerpohl O, Paulus W, Deckert M, Siebert R. Array-based profiling of the lymphoma cell DNA methylome does not unequivocally distinguish primary lymphomas of the central nervous system from non-CNS diffuse large B-cell lymphomas. Genes Chromosomes Cancer 2018; 58:66-69. [PMID: 30284345 DOI: 10.1002/gcc.22687] [Citation(s) in RCA: 9] [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: 08/02/2018] [Revised: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 02/02/2023] Open
Abstract
Primary lymphomas of the central nervous system (PCNSL) are diffuse large B-cell lymphomas (DLBCLs) confined to the central nervous system (CNS). We here performed array-based DNA methylation analyses of 26 PCNSL and 78 DLBCL and validated our findings in an independent dataset. We identified 2847 CpGs differentially methylated between PCNSL and non-CNS-DLBCL. Neither a supervised analysis using these CpGs nor application of 3 CpG classifiers selected for class separation unambiguously separated PCNSL from non-CNS-DLBCL. Remarkably, 6/78 non-CNS-DLBCL consistently segregated with PCNSL, which displayed molecular features typical for PCNSL. Our findings suggest that a subset of non-CNS-DLBCL exists which molecularly resembles PCNSL.
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Affiliation(s)
- Julia Vogt
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Martina Deckert
- Institute of Neuropathology, University Hospital of Cologne, Cologne, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
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38
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Merk DJ, Ohli J, Merk ND, Thatikonda V, Morrissy S, Schoof M, Schmid SN, Harrison L, Filser S, Ahlfeld J, Erkek S, Raithatha K, Andreska T, Weißhaar M, Launspach M, Neumann JE, Shakarami M, Plenker D, Marra MA, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJM, Lutz B, Ertl-Wagner B, Rossi A, Wagener R, Siebert R, Jung A, Eberhart CG, Lach B, Sendtner M, Pfister SM, Taylor MD, Chavez L, Kool M, Schüller U. Opposing Effects of CREBBP Mutations Govern the Phenotype of Rubinstein-Taybi Syndrome and Adult SHH Medulloblastoma. Dev Cell 2018; 44:709-724.e6. [PMID: 29551561 DOI: 10.1016/j.devcel.2018.02.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 10/06/2017] [Revised: 01/08/2018] [Accepted: 02/12/2018] [Indexed: 10/17/2022]
Abstract
Recurrent mutations in chromatin modifiers are specifically prevalent in adolescent or adult patients with Sonic hedgehog-associated medulloblastoma (SHH MB). Here, we report that mutations in the acetyltransferase CREBBP have opposing effects during the development of the cerebellum, the primary site of origin of SHH MB. Our data reveal that loss of Crebbp in cerebellar granule neuron progenitors (GNPs) during embryonic development of mice compromises GNP development, in part by downregulation of brain-derived neurotrophic factor (Bdnf). Interestingly, concomitant cerebellar hypoplasia was also observed in patients with Rubinstein-Taybi syndrome, a congenital disorder caused by germline mutations of CREBBP. By contrast, loss of Crebbp in GNPs during postnatal development synergizes with oncogenic activation of SHH signaling to drive MB growth, thereby explaining the enrichment of somatic CREBBP mutations in SHH MB of adult patients. Together, our data provide insights into time-sensitive consequences of CREBBP mutations and corresponding associations with human diseases.
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Affiliation(s)
- Daniel J Merk
- Center for Neuropathology, Ludwig-Maximilians-University, 81377 Munich, Germany; Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Neurobiology, Harvard Medical School, Boston, MA 02215, USA
| | - Jasmin Ohli
- Center for Neuropathology, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Natalie D Merk
- Munich Center for Integrated Protein Science at the Chemistry Department, Technical University, 85747 Munich, Germany
| | - Venu Thatikonda
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sorana Morrissy
- Arthur and Sonia Labatt Brain Tumour Research Centre and Division of Neurosurgery, Hospital for Sick Children (HSC), Toronto, ON M5G 1L7, Canada; Program in Developmental and Stem Cell Biology, HSC, Toronto, ON M5G 1X8, Canada
| | - Melanie Schoof
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), Hamburg 20251, Germany
| | - Susanne N Schmid
- Center for Neuropathology, Ludwig-Maximilians-University, 81377 Munich, Germany; Department of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Luke Harrison
- Center for Neuropathology, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Severin Filser
- German Center for Neurodegenerative Diseases (DZNE), Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Julia Ahlfeld
- Center for Neuropathology, Ludwig-Maximilians-University, 81377 Munich, Germany; Division of Clinical Pharmacology, Department of Internal Medicine IV, Ludwig-Maximilians-University, 80337 Munich, Germany
| | - Serap Erkek
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; German Cancer Consortium (DKTK), Core Center Heidelberg, 69120 Heidelberg, Germany
| | - Kaamini Raithatha
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Thomas Andreska
- Institute for Clinical Neurobiology, University of Würzburg, 97078 Würzburg, Germany
| | - Marc Weißhaar
- Center for Neuropathology, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Michael Launspach
- Center for Neuropathology, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Julia E Neumann
- Center for Neuropathology, Ludwig-Maximilians-University, 81377 Munich, Germany; Institute of Neuropathology, University Medical Center, Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Mehdi Shakarami
- Walter Brendel Center of Experimental Medicine, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Dennis Plenker
- Department of Translational Genomics, University of Cologne, 50931 Cologne, Germany
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC VSZ 4S6, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Yisu Li
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC VSZ 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC VSZ 4S6, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC VSZ 4S6, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC VSZ 4S6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC VSZ 4S6, Canada
| | - Beat Lutz
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Birgit Ertl-Wagner
- Institute of Clinical Radiology, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Andrea Rossi
- Department of Pediatric Neuroradiology, Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Rabea Wagener
- Institute of Human Genetics, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany; Institute for Human Genetics, Ulm University and Ulm University Medical Center, 89081 Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany; Institute for Human Genetics, Ulm University and Ulm University Medical Center, 89081 Ulm, Germany
| | - Andreas Jung
- Institute of Pathology, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Charles G Eberhart
- Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Boleslaw Lach
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Michael Sendtner
- Institute for Clinical Neurobiology, University of Würzburg, 97078 Würzburg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), Core Center Heidelberg, 69120 Heidelberg, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Michael D Taylor
- Arthur and Sonia Labatt Brain Tumour Research Centre and Division of Neurosurgery, Hospital for Sick Children (HSC), Toronto, ON M5G 1L7, Canada; Program in Developmental and Stem Cell Biology, HSC, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lukas Chavez
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), Core Center Heidelberg, 69120 Heidelberg, Germany
| | - Ulrich Schüller
- Center for Neuropathology, Ludwig-Maximilians-University, 81377 Munich, Germany; Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), Hamburg 20251, Germany; Institute of Neuropathology, University Medical Center, Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, 20246 Hamburg, Germany.
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39
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de Kock L, Geoffrion D, Rivera B, Wagener R, Sabbaghian N, Bens S, Ellezam B, Bouron-Dal Soglio D, Ordóñez J, Sacharow S, Polo Nieto JF, Guillerman RP, Vujanic GM, Priest JR, Siebert R, Foulkes WD. Multiple DICER1-related tumors in a child with a large interstitial 14q32 deletion. Genes Chromosomes Cancer 2018; 57:223-230. [DOI: 10.1002/gcc.22523] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 02/04/2023] Open
Affiliation(s)
- Leanne de Kock
- Department of Human Genetics; McGill University; Montréal Québec Canada
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital; Montréal Québec Canada
| | - Dominique Geoffrion
- Department of Human Genetics; McGill University; Montréal Québec Canada
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital; Montréal Québec Canada
| | - Barbara Rivera
- Department of Human Genetics; McGill University; Montréal Québec Canada
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital; Montréal Québec Canada
| | - Rabea Wagener
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center; Ulm Germany
| | - Nelly Sabbaghian
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital; Montréal Québec Canada
| | - Susanne Bens
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center; Ulm Germany
| | - Benjamin Ellezam
- Department of Pathology; CHU Sainte Justine; Quebec Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine; Université de Montréal; Montréal Québec Canada
| | - Dorothée Bouron-Dal Soglio
- Department of Pathology; CHU Sainte Justine; Quebec Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine; Université de Montréal; Montréal Québec Canada
| | - Jessica Ordóñez
- The Dr. John T. Macdonald Foundation Department of Human Genetics; University of Miami; Miami Florida USA
- Division of Clinical Genetics; Center for Genomic Medicine, Miami Cancer Institute; Miami Florida USA
| | - Stephanie Sacharow
- The Dr. John T. Macdonald Foundation Department of Human Genetics; University of Miami; Miami Florida USA
- Division of Genetics and Genomics; Boston Children's Hospital; Boston Massachusetts USA
| | | | - R. Paul Guillerman
- Department of Pediatric Radiology; Texas Children's Hospital; Houston Texas USA
| | | | | | - Reiner Siebert
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center; Ulm Germany
| | - William D. Foulkes
- Department of Human Genetics; McGill University; Montréal Québec Canada
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital; Montréal Québec Canada
- Department of Medical Genetics; Research Institute of the McGill University Health Centre; Montreal Quebec Canada
- Program in Cancer Genetics, Departments of Oncology and Human Genetics; McGill University; Montreal Quebec Canada
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40
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Rivera B, Di Iorio M, Frankum J, Nadaf J, Fahiminiya S, Arcand SL, Burk DL, Grapton D, Tomiak E, Hastings V, Hamel N, Wagener R, Aleynikova O, Giroux S, Hamdan FF, Dionne-Laporte A, Zogopoulos G, Rousseau F, Berghuis AM, Provencher D, Rouleau GA, Michaud JL, Mes-Masson AM, Majewski J, Bens S, Siebert R, Narod SA, Akbari MR, Lord CJ, Tonin PN, Orthwein A, Foulkes WD. Functionally Null RAD51D Missense Mutation Associates Strongly with Ovarian Carcinoma. Cancer Res 2017; 77:4517-4529. [PMID: 28646019 DOI: 10.1158/0008-5472.can-17-0190] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 01/24/2017] [Revised: 03/23/2017] [Accepted: 06/06/2017] [Indexed: 11/16/2022]
Abstract
RAD51D is a key player in DNA repair by homologous recombination (HR), and RAD51D truncating variant carriers have an increased risk for ovarian cancer. However, the contribution of nontruncating RAD51D variants to cancer predisposition remains uncertain. Using deep sequencing and case-control genotyping studies, we show that in French Canadians, the missense RAD51D variant c.620C>T;p.S207L is highly prevalent and is associated with a significantly increased risk for ovarian high-grade serous carcinoma (HGSC; 3.8% cases vs. 0.2% controls). The frequency of the p.S207L variant did not significantly differ from that of controls in breast, endometrial, pancreas, or colorectal adenocarcinomas. Functionally, we show that this mutation impairs HR by disrupting the RAD51D-XRCC2 interaction and confers PARP inhibitor sensitivity. These results highlight the importance of a functional RAD51D-XRCC2 interaction to promote HR and prevent the development of HGSC. This study identifies c.620C>T;p.S207L as the first bona fide pathogenic RAD51D missense cancer susceptibility allele and supports the use of targeted PARP-inhibitor therapies in ovarian cancer patients carrying deleterious missense RAD51D variants. Cancer Res; 77(16); 4517-29. ©2017 AACR.
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Affiliation(s)
- Barbara Rivera
- Department of Human Genetics, McGill University, Montreal, Canada
- Lady Davis Institute, Montreal, Canada
| | - Massimo Di Iorio
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Jessica Frankum
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Canada
- Genome Quebec Innovation Centre, Montreal, Canada
| | - Somayyeh Fahiminiya
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Suzanna L Arcand
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - David L Burk
- Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Eva Tomiak
- Department of Genetics, University of Ottawa, Children's Hospital of Eastern Ontario, Canada
| | - Valerie Hastings
- Department of Genetics, University of Ottawa, Children's Hospital of Eastern Ontario, Canada
| | - Nancy Hamel
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Rabea Wagener
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Olga Aleynikova
- Department of pathology, Jewish General Hospital, Montreal, Canada
| | - Sylvie Giroux
- University of Laval and CHU Research Centre, Quebec; Canada
| | - Fadi F Hamdan
- CHU Sainte-Justine Research Center, Montreal, Canada
| | | | - George Zogopoulos
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
- The Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | | | | | - Diane Provencher
- Centre de recherche du CHUM and Institut du cancer de Montréal, University of Montreal, Montreal, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | | | - Anne-Marie Mes-Masson
- Centre de recherche du CHUM and Institut du cancer de Montréal, University of Montreal, Montreal, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Canada
- Genome Quebec Innovation Centre, Montreal, Canada
| | - Susanne Bens
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Steven A Narod
- Dalla Lana School of Public Health, Toronto, Canada
- Women's College Hospital, Toronto, Canada
| | - Mohammad R Akbari
- Dalla Lana School of Public Health, Toronto, Canada
- Women's College Hospital, Toronto, Canada
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Patricia N Tonin
- Department of Human Genetics, McGill University, Montreal, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
- Department of Medicine, McGill University, Montreal, Canada
| | - Alexandre Orthwein
- Lady Davis Institute, Montreal, Canada
- Department of Oncology, McGill University, Montreal, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Canada.
- Lady Davis Institute, Montreal, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
- Department of Medical Genetics, Research Institute, McGill University Health Centre, Montreal, Canada
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41
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Rivera B, Iorio MRD, Frankum J, Nadaf J, Fahiminiya S, Arcand SL, Burk D, Grapton D, Tomiak E, Hastings V, Hamel N, Wagener R, Aleynikova O, Giroux S, Hamdan FF, Orthwein A, Zogopoulos G, Rousseau F, Berghuis A, Provencher DM, Rouleau GA, Michaud JL, Mes-Masson AM, Majewski J, Bens S, Siebert R, Narod S, Akbari M, Lord CJ, Tonin PN, Dionne-Laporte A, Foulkes WD. Abstract 2479: A functionally null RAD51D missense mutation is strongly associated with ovarian carcinoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2479] [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
Background and goal: RAD51D is a key player in DNA repair by homologous recombination (HR) and carriers of truncating RAD51D mutations have an increased risk for ovarian cancer (OC). However, the contribution of non-truncating RAD51D variants to cancer predisposition remains uncertain. We sought to fully characterize the previously described missense RAD51D variant c.620C>T;p.S207L in order to elucidate its role in OC.
Methods: A clinical panel screening was used to identify the RAD51D variant c.620C>T;p.S207L in two French Canadian (FC) kindred affected with familial High Grade Serous Cancer (HGSC) of the ovary or endometrium. High resolution melting, TaqMan genotyping and Sanger sequencing were used to genotype the p.S207L variant in a series of unselected cases of HGSC of the ovary and endometrium, breast, pancreas and colorectal cancer and healthy controls, all of a FC origin. Whole exome sequencing (WES) was performed to study the genetic signature characterizing RAD51D associated tumors. RAD51 foci formation and CRISPR-Cas9-stimulated and HR-mediated gene targeting assays were used to assess HR activity of RAD51D-S207L mutated CHO cells. HR activity in RAD51D-S207L mutated human cells was tested by a DR-GFP assay. The effect of RAD51D p.S207L on RAD51D-XRCC2 interactions was analyzed by co-immunoprecipitation and quantified in-vivo in a single cell colocalization assay. Sensitivity to PARP inhibitors (PARPi) was evaluated in a cell survival assay.
Results: Using deep sequencing and case-control genotyping studies, we showed that the missense RAD51D variant c.620C>T;p.S207L is over-represented in the French Canadian population affected by HGSC of the ovary (3.8% cases vs 0.002% controls; p < 0.0001).The frequency of the p.S207L variant did not differ from that of controls in breast, endometrial, pancreas and colorectal adenocarcinomas. A common haplotype shared by all the carriers suggested a founder origin for c.620C>T;p.S207L mutation. WES analysis of RAD51D tumor profiles revealed the presence of signature 3 which is known to be associated with HR defects. Functionally, we show that this mutation impairs HR by disrupting the RAD51D-XRCC2 interaction and confers PARP-inhibitor sensitivity to CHO cells.
Conclusions: This work identifies RAD51D p.S207L as the first bona fide pathogenic missense susceptibility allele for HGSC of the ovary and supports the use of targeted PARPi therapies in OC patients carrying missense RAD51D mutations.
Citation Format: Barbara Rivera, Massimo R. Di Iorio, Jessica Frankum, Javad Nadaf, Somayyeh Fahiminiya, Suzanna L. Arcand, David Burk, Damien Grapton, Eva Tomiak, Valerie Hastings, Nancy Hamel, Rabea Wagener, Olga Aleynikova, Sylvie Giroux, Fadi F. Hamdan, Alexandre Orthwein, George Zogopoulos, Francois Rousseau, Albert Berghuis, Diane M. Provencher, Guy A. Rouleau, Jacques L. Michaud, Anne-Marie Mes-Masson, Jacek Majewski, Susanne Bens, Reiner Siebert, Steven Narod, Mohammad Akbari, Chris J. Lord, Patricia N. Tonin, Alexandre Dionne-Laporte, William D. Foulkes. A functionally null RAD51D missense mutation is strongly associated with ovarian carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2479. doi:10.1158/1538-7445.AM2017-2479
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Affiliation(s)
| | | | | | - Javad Nadaf
- 1McGill University, Montreal, Quebec, Canada
| | - Somayyeh Fahiminiya
- 3The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Suzanna L. Arcand
- 3The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - David Burk
- 1McGill University, Montreal, Quebec, Canada
| | | | - Eva Tomiak
- 5University of Ottawa, Children's Hospital of Eastern Ontario, Ontario, Ontario, Canada
| | - Valerie Hastings
- 5University of Ottawa, Children's Hospital of Eastern Ontario, Ontario, Ontario, Canada
| | - Nancy Hamel
- 3The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Rabea Wagener
- 6University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | | | - Sylvie Giroux
- 8University of Laval and CHU Research Centre, Montreal, Quebec, Canada
| | - Fadi F. Hamdan
- 9CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | | | - George Zogopoulos
- 3The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Francois Rousseau
- 8University of Laval and CHU Research Centre, Montreal, Quebec, Canada
| | | | - Diane M. Provencher
- 10Centre de recherche du CHUM and Institut du cancer de Montréal, University of Montreal, Montreal, Quebec, Canada
| | - Guy A. Rouleau
- 11Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | - Anne-Marie Mes-Masson
- 10Centre de recherche du CHUM and Institut du cancer de Montréal, University of Montreal, Montreal, Quebec, Canada
| | | | - Susanne Bens
- 6University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Reiner Siebert
- 6University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Steven Narod
- 12Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - Mohammad Akbari
- 12Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - Chris J. Lord
- 2The Institute of Cancer Research, London, United Kingdom
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Wagener R, Kretzmer H, Ammerpohl O, López C, Rohde M, Carillo-De-Santa-Pau E, Salaverria I, Szczepanowski M, Burkhardt B, Hummel M, Klapper W, Küppers R, Löffler M, Möller P, Neequaye J, Wößmann W, Lichter P, Stunnenberg H, Trümper L, Mbulaiteye S, Hoffman S, Siebert R. PROFILING OF DNA METHYLATION IN EPIDEMIOLOGICAL AND CLINICAL SUBGROUPS OF BURKITT LYMPHOMA IN THE FRAMEWORK OF THE MMML: ICGC AND BLUEPRINT CONSORTIA. Hematol Oncol 2017. [DOI: 10.1002/hon.2437_94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- R. Wagener
- University of Ulm; Institute of Human Genetics; Ulm Germany
| | - H. Kretzmer
- LIFE Research Center for Civilization Diseases, University of Leipzig; Transcriptome Bioinformatics Group; Leipzig Germany
| | - O. Ammerpohl
- Christian-Albrechts-University; Campus Kiel, Institute of Human Genetics; Kiel Germany
| | - C. López
- University of Ulm; Institute of Human Genetics; Ulm Germany
| | - M. Rohde
- Justus-Liebig-University Giessen; Department od Pediatric Hematology and Oncology; Giessen Germany
| | - E. Carillo-De-Santa-Pau
- Spanish National Cancer Research Centre (CNIO); Structural Biology and BioComputing Programme; Madrid Spain
| | - I. Salaverria
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Hematopathology Unit, Hospital Clínic; Barcelona Spain
| | - M. Szczepanowski
- University Hospital Schleswig-Holstein Campus Kiel; Clinic of Internal Medicine II, Hematology Laboratory Section; Kiel Germany
| | - B. Burkhardt
- University Hospital Münster; Department of Pediatric Hematology and Oncology; Münster Germany
| | - M. Hummel
- Charité - University Medicine Berlin; Institute of Pathology; Berlin Germany
| | - W. Klapper
- University Hospital Schleswig-Holstein Campus Kiel/ Christian-Albrechts University Kiel; Institute of Hematopathology; Kiel Germany
| | - R. Küppers
- University of Duisburg-Essen; Institute of Cell Biology (Cancer Research); Essen Germany
| | - M. Löffler
- IMISE; Institute for Medical Informatics Statistics and Epidemiology; Leipzig Germany
| | - P. Möller
- Medical Faculty of the Ulm University; Institute of Pathology; Ulm Germany
| | - J. Neequaye
- University of Ghana Medical School; Department of Child Health; Accra Ghana
| | - W. Wößmann
- Justus-Liebig-University; 16 NHL-BFM Study Centre and Department of Paediatric Haematology and Oncology; Giessen Germany
| | - P. Lichter
- German Cancer Research Center; Division of Molecular Genetics; Heidelberg Germany
| | - H. Stunnenberg
- Radboud University; Molecular Biology, NCMLS, FNWI; Njimegen Netherlands
| | - L. Trümper
- Georg-August-University of Göttingen; Department of Hematology and Oncology; Göttingen Germany
| | - S.M. Mbulaiteye
- National Cancer Institute; National Institutes of Health, Division of Cancer Epidemiology and Genetics; Rockville USA
| | - S. Hoffman
- LIFE Research Center for Civilization Diseases, University of Leipzig; Transcriptome Bioinformatics Group; Leipzig Germany
| | - R. Siebert
- University of Ulm; Institute of Human Genetics; Ulm Germany
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Bens S, Kolarova J, Kreuz M, Bernhart S, Kretzmer H, Wagener R, Küppers R, Ammerpohl O, Burkhardt B, Hoffmann S, Hummel M, Klapper W, Lichter P, Löffler M, Möller P, Radlwimmer B, Rosenstiel P, Stein H, Trümper L, Siebert R. COMPREHENSIVE EPIGENETIC AND TRANSCRIPTIONAL SURVEY OF THE “IMPRINTOME” IN NORMAL B-CELLS AND GERMINAL CENTER DERIVED B-CELL LYMPHOMAS OF THE MMML AND ICGC MMML-SEQ NETWORKS. Hematol Oncol 2017. [DOI: 10.1002/hon.2438_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- S. Bens
- Institute of Human Genetics; Ulm University; Ulm Germany
| | - J. Kolarova
- Institute of Human Genetics; Ulm University; Ulm Germany
| | - M. Kreuz
- Institute of Medical Informatics Statistics and Epidemiology; University Leipzig; Leipzig Germany
| | - S. Bernhart
- Bioinformatics Group Department of Computer Science; University Leipzig; Leipzig Germany
| | - H. Kretzmer
- Transcriptome Bioinformatics Group LIFE Research Center for Civilization Diseases; University Leipzig; Leipzig Germany
| | - R. Wagener
- Institute of Human Genetics; Ulm University; Ulm Germany
| | - R. Küppers
- Institute of Cell Biology (Cancer Research); University of Duisburg-Essen; Essen Germany
| | - O. Ammerpohl
- Institute of Human Genetics; Christian-Albrechts-University Kiel; Kiel Germany
| | - B. Burkhardt
- Department of Pediatric Hematology and Oncology; University Hospital Münster; Münster Germany
| | - S. Hoffmann
- Transcriptome Bioinformatics Group LIFE Research Center for Civilization Diseases; University Leipzig; Leipzig Germany
| | - M. Hummel
- Institute of Pathology; Charité-University Medicine Berlin; Berlin Germany
| | - W. Klapper
- Section of Hematopathology Institute of Pathology; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts-University Kiel; Kiel Germany
| | - P. Lichter
- Division of Molecular Genetics; German Cancer Research Center; Heidelberg Germany
| | - M. Löffler
- Institute of Medical Informatics Statistics and Epidemiology; University Leipzig; Leipzig Germany
| | - P. Möller
- Institute of Pathology; Medical Faculty of the Ulm University; Ulm Germany
| | - B. Radlwimmer
- Division of Molecular Genetics; German Cancer Research Center; Heidelberg Germany
| | - P. Rosenstiel
- Institute of Clinical Molecular Biology; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts-University Kiel; Kiel Germany
| | - H. Stein
- Pathodiagnostik Berlin; Berlin Reference Center for Lymphomas and Hematopathology; Berlin Germany
| | - L. Trümper
- Department of Hematology and Medical Oncology; University Medicine Göttingen; Göttingen Germany
| | - R. Siebert
- Institute of Human Genetics; Ulm University; Ulm Germany
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Huebschmann D, Kleinheinz K, Wagener R, Kretzmer H, Toprak U, Bernhart S, Lopez Gonzales C, Kreuz M, Eils R, Hansmann M, Hoffmann S, Hummel M, Klapper W, Lawerenz C, Loeffler M, Möller P, Richter J, Rosenstiel P, Rosenwald A, Stilgenbauer S, Weniger M, Trümper L, Küppers R, Schlesner M, Siebert R. MUTATIONAL SIGNATURES IN GERMINAL CENTER DERIVED B-CELL LYMPHOMAS FROM ADULT PATIENTS ANALYZED IN THE ICGC MMML-SEQ CONSORTIUM. Hematol Oncol 2017. [DOI: 10.1002/hon.2437_95] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- D. Huebschmann
- Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - K. Kleinheinz
- Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - R. Wagener
- Medicine; Institute of Human Genetics; Ulm Germany
| | - H. Kretzmer
- University Leipzig; Leipzig Research Center for Civilization Diseases; Leipzig Germany
| | - U.H. Toprak
- Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - S.H. Bernhart
- University Leipzig; Leipzig Research Center for Civilization Diseases; Leipzig Germany
| | | | - M. Kreuz
- Leipzig University; Institute for Medical Informatics Statistics and Epidemiology; Leipzig Germany
| | - R. Eils
- Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - M. Hansmann
- University of Frankfurt Medical School; Senckenberg Institute of Pathology; Frankfurt am Main Germany
| | - S. Hoffmann
- University Leipzig; Leipzig Research Center for Civilization Diseases; Leipzig Germany
| | - M. Hummel
- University Medicine Berlin; Institute of Pathology, Charité; Berlin Germany
| | - W. Klapper
- University Hospital Schleswig-Holstein Campus Kiel; Section of Hematopathology Institute of Pathology; Kiel Germany
| | - C. Lawerenz
- Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - M. Loeffler
- Leipzig University; Institute for Medical Informatics Statistics and Epidemiology; Leipzig Germany
| | - P. Möller
- Medical Faculty of the Ulm University; Institute of Pathology; Ulm Germany
| | - J. Richter
- University Hospital Schleswig-Holstein Campus Kiel; Section of Hematopathology Institute of Pathology; Kiel Germany
| | - P. Rosenstiel
- University Hospital Schleswig-Holstein Campus Kiel; Institute of Clinical Molecular Biology; Kiel Germany
| | - A. Rosenwald
- University of Wuerzburg; institute of Pathology; Würzburg Germany
| | - S. Stilgenbauer
- University Medical Center Ulm; Department for Internal Medicine III, Hematology, Oncology and Rheumatology and infectious diseases; Ulm Germany
| | - M. Weniger
- University of Duisburg-Essen; Medical School, Institute of Cell Biology (Cancer Research); Essen Germany
| | - L. Trümper
- Georg August University of Göttingen; Department of Hematology and Oncology; Göttingen Germany
| | - R. Küppers
- University of Duisburg-Essen; Medical School, Institute of Cell Biology (Cancer Research); Essen Germany
| | - M. Schlesner
- Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - R. Siebert
- Medicine; Institute of Human Genetics; Ulm Germany
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Siebert R, Gerhäuser C, Simon R, Wagener R, Weber UD, Sauter G, Plass C, Lichter P. Internationales Krebsgenomkonsortium (ICGC). MED GENET-BERLIN 2017. [DOI: 10.1007/s11825-017-0117-7] [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: 10/20/2022]
Abstract
Zusammenfassung
Die Katalogisierung genomischer, epigenetischer und transkriptioneller Veränderungen in Tumorzellen sowie die Integration disponierender oder klinisch relevanter Keimbahnvarianten ist die Voraussetzung für die zukünftige Anwendung präzisionsmedizinischer Ansätze in der Onkologie. Das Internationale Krebsgenomkonsortium (International Cancer Genome Consortium, ICGC) hat sich deshalb zum Ziel gesetzt, auf verschiedenen OMICs-Ebenen die wesentlichen Aberrationen in den 50 häufigsten und sozioökonomisch relevanten Tumorentitäten zu beschreiben. Dazu werden die Tumoren nach standardisierten Protokollen mittels sequenzierungsbasierter Verfahren analysiert. Die erhobenen Daten sind unter bestimmten Bedingungen auch Wissenschaftlern außerhalb des ICGC zugänglich. Auch wenn die Datensammlung noch nicht abgeschlossen ist, konnten entitätenspezifische und -übergreifende Analysen u. a. bereits Mutationssignaturen oder neue Driververänderungen und pathogene Signalwege identifizieren.
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Affiliation(s)
- Reiner Siebert
- Aff1 0000 0004 1936 9748 grid.6582.9 Institut für Humangenetik Universität Ulm & Universitätsklinikum Ulm Albert-Einstein-Allee 11 89081 Ulm Deutschland
| | - Clarissa Gerhäuser
- Aff2 0000 0004 0492 0584 grid.7497.d Deutsches Krebsforschungszentrum (DKFZ) Heidelberg Deutschland
| | - Ronald Simon
- Aff3 0000 0001 2180 3484 grid.13648.38 Universitätsklinikum Hamburg-Eppendorf Hamburg Deutschland
| | - Rabea Wagener
- Aff1 0000 0004 1936 9748 grid.6582.9 Institut für Humangenetik Universität Ulm & Universitätsklinikum Ulm Albert-Einstein-Allee 11 89081 Ulm Deutschland
| | - Ursula D. Weber
- Aff2 0000 0004 0492 0584 grid.7497.d Deutsches Krebsforschungszentrum (DKFZ) Heidelberg Deutschland
| | - Guido Sauter
- Aff3 0000 0001 2180 3484 grid.13648.38 Universitätsklinikum Hamburg-Eppendorf Hamburg Deutschland
| | - Christoph Plass
- Aff2 0000 0004 0492 0584 grid.7497.d Deutsches Krebsforschungszentrum (DKFZ) Heidelberg Deutschland
| | - Peter Lichter
- Aff2 0000 0004 0492 0584 grid.7497.d Deutsches Krebsforschungszentrum (DKFZ) Heidelberg Deutschland
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Sabatelli P, Sardone F, Traina F, Merlini L, Santi S, Wagener R, Faldini C. TGF-β1 differentially modulates the collagen VI α5 and α6 chains in human tendon cultures. J BIOL REG HOMEOS AG 2016; 30:107-113. [PMID: 28002907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Collagen VI is a microfibrillar collagen with a potential regulatory role in tendon repair mechanism. We studied the expression of collagen VI α5 and α6 chains in normal human tendon fibroblast cultures, both under basal condition and in response to TGF-β1, a potent regulator of tendon healing. Under basal condition, we found that the α5 chain was expressed, although to a lesser extent with respect to the α3 chain; in contrast, the α6 chain was absent. The treatment with TGFβ1 induced an opposite effect on the expression of the α5 and α6 chains; in fact, while the α5 chain was dramatically reduced, the α6 chain was induced and released in the culture medium. These data indicate that collagen VI α5 and α6 chains are differentially involved in tendon matrix homeostasis. The α6 chain may represent a new potential biomarker for monitoring TGFβ1-related events in tendon, as healing and fibrotic scar formation.
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Affiliation(s)
- P Sabatelli
- National Research Council of Italy, Institute of Molecular Genetics, Bologna, Italy
- IOR-IRCCS, SC Laboratory of Musculoskeletal Cell Biology, Bologna, Italy
| | - F Sardone
- National Research Council of Italy, Institute of Molecular Genetics, Bologna, Italy
- IOR-IRCCS, SC Laboratory of Musculoskeletal Cell Biology, Bologna, Italy
| | - F Traina
- University of Bologna, Rizzoli Orthopaedic Institute, Bologna, Italy
| | - L Merlini
- DIBINEM-Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - S Santi
- National Research Council of Italy, Institute of Molecular Genetics, Bologna, Italy
- IOR-IRCCS, SC Laboratory of Musculoskeletal Cell Biology, Bologna, Italy
| | - R Wagener
- Center for Biochemistry, Center for Molecular Medicine (CMMC) and Cologne Center for Musculoskeletal Biomechanics (CCMB), University of Cologne, Germany
| | - C Faldini
- University of Bologna, Rizzoli Orthopaedic Institute, Bologna, Italy
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47
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Szczepanowski M, Masqué-Soler N, Schlesner M, Haake A, Richter J, Wagener R, Burkhardt B, Kreuz M, Siebert R, Klapper W. Immunohistochemical detection of inhibitor of DNA binding 3 mutational variants in mature aggressive B-cell lymphoma. Haematologica 2016; 101:e259-61. [PMID: 26992947 DOI: 10.3324/haematol.2015.138701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Monika Szczepanowski
- Institute of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein Campus Kiel, Christian-Albrechts University Kiel, Germany
| | - Neus Masqué-Soler
- Institute of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein Campus Kiel, Christian-Albrechts University Kiel, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Germany
| | - Andrea Haake
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Müenster, Germany
| | - Julia Richter
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Müenster, Germany
| | - Rabea Wagener
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Müenster, Germany
| | - Birgit Burkhardt
- NHL-BFM Study Center and Department of Pediatric Hematology and Oncology, University Children's Hospital, Müenster, Germany
| | - Markus Kreuz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Müenster, Germany
| | | | - Wolfram Klapper
- Institute of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein Campus Kiel, Christian-Albrechts University Kiel, Germany
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48
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Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Humme M, Karsch D, Kerstens HH, Klapper W, Kreuz M, Lawerenz C, Lenzek D, Loeffler M, López C, MacLeod RA, Martens JH, Kulis M, Martín-Subero JI, Möller P, Nage I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nat Genet 2015; 47:1316-1325. [PMID: 26437030 PMCID: PMC5444523 DOI: 10.1038/ng.3413] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [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: 06/01/2015] [Accepted: 09/08/2015] [Indexed: 12/14/2022]
Abstract
Although Burkitt lymphomas and follicular lymphomas both have features of germinal center B cells, they are biologically and clinically quite distinct. Here we performed whole-genome bisulfite, genome and transcriptome sequencing in 13 IG-MYC translocation-positive Burkitt lymphoma, nine BCL2 translocation-positive follicular lymphoma and four normal germinal center B cell samples. Comparison of Burkitt and follicular lymphoma samples showed differential methylation of intragenic regions that strongly correlated with expression of associated genes, for example, genes active in germinal center dark-zone and light-zone B cells. Integrative pathway analyses of regions differentially methylated in Burkitt and follicular lymphomas implicated DNA methylation as cooperating with somatic mutation of sphingosine phosphate signaling, as well as the TCF3-ID3 and SWI/SNF complexes, in a large fraction of Burkitt lymphomas. Taken together, our results demonstrate a tight connection between somatic mutation, DNA methylation and transcriptional control in key B cell pathways deregulated differentially in Burkitt lymphoma and other germinal center B cell lymphomas.
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Affiliation(s)
- Helene Kretzmer
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Stephan H. Bernhart
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Wei Wang
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Andrea Haake
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Marc A. Weniger
- German ICGC MMML-Seq-project
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Anke K. Bergmann
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
- BLUEPRINT project
| | - Matthew J. Betts
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Enrique Carrillo-de-Santa-Pau
- BLUEPRINT project
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Gero Doose
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Jana Gutwein
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Julia Richter
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Volker Hovestadt
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Bingding Huang
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Daniel Rico
- BLUEPRINT project
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Frank Jühling
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Qianhao Lu
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Christian Otto
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Rabea Wagener
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Judith Arnolds
- Department of Otorhinolaryngology, University of Duisburg-Essen, Essen, Germany
| | - Birgit Burkhardt
- German ICGC MMML-Seq-project
- University Hospital Muenster - Pediatric Hematology and Oncology, Münster Germany
| | - Alexander Claviez
- German ICGC MMML-Seq-project
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Hans G. Drexler
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sonja Eberth
- German ICGC MMML-Seq-project
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Department of Hematology and Oncology, Georg-Augusts-University of Göttingen, Göttingen, Germany
| | - Roland Eils
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Paul Flicek
- BLUEPRINT project
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Siegfried Haas
- German ICGC MMML-Seq-project
- Friedrich-Ebert Hospital Neumuenster, Clinics for Haematology, Oncology and Nephrology, Neumünster, Germany
| | - Michael Humme
- German ICGC MMML-Seq-project
- Institute of Pathology, Charité – University Medicine Berlin, Berlin, Germany
| | - Dennis Karsch
- German ICGC MMML-Seq-project
- Department of Internal Medicine II: Hematology and Oncology, University Medical Centre, Campus Kiel, Kiel, Germany
| | - Hinrik H.D. Kerstens
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Wolfram Klapper
- German ICGC MMML-Seq-project
- Hematopathology Section, Christian-Albrechts-University, Kiel, Germany
| | - Markus Kreuz
- German ICGC MMML-Seq-project
- BLUEPRINT project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Chris Lawerenz
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Dido Lenzek
- German ICGC MMML-Seq-project
- Institute of Pathology, Charité – University Medicine Berlin, Berlin, Germany
| | - Markus Loeffler
- German ICGC MMML-Seq-project
- BLUEPRINT project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Cristina López
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Roderick A.F. MacLeod
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Joost H.A. Martens
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Marta Kulis
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - José Ignacio Martín-Subero
- BLUEPRINT project
- Departamento de Anatomía Patológica, Farmacología y Microbiología, Universitat de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Peter Möller
- German ICGC MMML-Seq-project
- Institute of Pathology, Medical Faculty of the Ulm University, Ulm, Germany
| | - Inga Nage
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Simone Picelli
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Inga Vater
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Marius Rohde
- German ICGC MMML-Seq-project
- University Hospital Giessen, Pediatric Hematology and Oncology, Giessen, Germany
| | - Philip Rosenstiel
- German ICGC MMML-Seq-project
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Maciej Rosolowski
- German ICGC MMML-Seq-project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Robert B. Russell
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Markus Schilhabel
- German ICGC MMML-Seq-project
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Matthias Schlesner
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Peter F. Stadler
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
- RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany
| | | | - Lorenz Trümper
- German ICGC MMML-Seq-project
- Department of Hematology and Oncology, Georg-Augusts-University of Göttingen, Göttingen, Germany
| | - Hendrik G. Stunnenberg
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Ralf Küppers
- German ICGC MMML-Seq-project
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
- BLUEPRINT project
| | - Ole Ammerpohl
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Peter Lichter
- German ICGC MMML-Seq-project
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Reiner Siebert
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
- BLUEPRINT project
| | - Steve Hoffmann
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
- BLUEPRINT project
| | - Bernhard Radlwimmer
- German ICGC MMML-Seq-project
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
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Wagener R, Aukema SM, Schlesner M, Haake A, Burkhardt B, Claviez A, Drexler HG, Hummel M, Kreuz M, Loeffler M, Rosolowski M, López C, Möller P, Richter J, Rohde M, Betts MJ, Russell RB, Bernhart SH, Hoffmann S, Rosenstiel P, Schilhabel M, Szczepanowski M, Trümper L, Klapper W, Siebert R. ThePCBP1gene encoding poly(rc) binding protein i is recurrently mutated in Burkitt lymphoma. Genes Chromosomes Cancer 2015; 54:555-64. [DOI: 10.1002/gcc.22268] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 05/11/2015] [Indexed: 12/19/2022] Open
Affiliation(s)
- Rabea Wagener
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Sietse M. Aukema
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Matthias Schlesner
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics; Heidelberg Germany
| | - Andrea Haake
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Birgit Burkhardt
- Non-Hodgkin Lymphoma Berlin-Frankfurt-Münster Group Study Center, Department of Pediatric Hematology and Oncology, University Children's Hospital; Münster Germany
| | - Alexander Claviez
- Department of Pediatrics; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University; Kiel Germany
| | - Hans G. Drexler
- Leibniz-Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH; Braunschweig Germany
| | - Michael Hummel
- Institute of Pathology, Campus Benjamin Franklin, Charité-Universitätsmedizin; Berlin Germany
| | - Markus Kreuz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig; Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig; Germany
| | - Maciej Rosolowski
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig; Germany
| | - Cristina López
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Peter Möller
- Institute of Pathology, Universitätsklinikum Ulm; Ulm Germany
| | - Julia Richter
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Marius Rohde
- Department of Pediatric Hematology and Oncology; Justus Liebig University; Giessen Germany
| | - Matthew J. Betts
- Cell Networks, Bioquant, University of Heidelberg; Heidelberg Germany
| | - Robert B. Russell
- Cell Networks, Bioquant, University of Heidelberg; Heidelberg Germany
| | - Stephan H. Bernhart
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig; Leipzig Germany
| | - Steve Hoffmann
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig; Leipzig Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Markus Schilhabel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Monika Szczepanowski
- Institute of Hematopathology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology; Georg-August University of Göttingen; Germany
| | - Wolfram Klapper
- Institute of Hematopathology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
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50
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Wagener R, Lenz M, Schuldt B, Lenz I, Schuppert A, Siebert R, Müller FJ. Investigation of potential traces of pluripotency in germinal-center-derived B-cell lymphomas driven by MYC. Blood Cancer J 2015; 5:e317. [PMID: 26024287 PMCID: PMC4476019 DOI: 10.1038/bcj.2015.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- R Wagener
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - M Lenz
- 1] Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany [2] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - B Schuldt
- 1] Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany [2] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - I Lenz
- Zentrum für Integrative Psychiatrie, University Hospital Schleswig-Holstein, Kiel, Germany
| | - A Schuppert
- 1] Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany [2] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - R Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - F-J Müller
- Zentrum für Integrative Psychiatrie, University Hospital Schleswig-Holstein, Kiel, Germany
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