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Kaasinen E, Kuismin O, Rajamäki K, Ristolainen H, Aavikko M, Kondelin J, Saarinen S, Berta DG, Katainen R, Hirvonen EAM, Karhu A, Taira A, Tanskanen T, Alkodsi A, Taipale M, Morgunova E, Franssila K, Lehtonen R, Mäkinen M, Aittomäki K, Palotie A, Kurki MI, Pietiläinen O, Hilpert M, Saarentaus E, Niinimäki J, Junttila J, Kaikkonen K, Vahteristo P, Skoda RC, Seppänen MRJ, Eklund KK, Taipale J, Kilpivaara O, Aaltonen LA. Impact of constitutional TET2 haploinsufficiency on molecular and clinical phenotype in humans. Nat Commun 2019; 10:1252. [PMID: 30890702 PMCID: PMC6424975 DOI: 10.1038/s41467-019-09198-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/25/2019] [Indexed: 12/15/2022] Open
Abstract
Clonal hematopoiesis driven by somatic heterozygous TET2 loss is linked to malignant degeneration via consequent aberrant DNA methylation, and possibly to cardiovascular disease via increased cytokine and chemokine expression as reported in mice. Here, we discover a germline TET2 mutation in a lymphoma family. We observe neither unusual predisposition to atherosclerosis nor abnormal pro-inflammatory cytokine or chemokine expression. The latter finding is confirmed in cells from three additional unrelated TET2 germline mutation carriers. The TET2 defect elevates blood DNA methylation levels, especially at active enhancers and cell-type specific regulatory regions with binding sequences of master transcription factors involved in hematopoiesis. The regions display reduced methylation relative to all open chromatin regions in four DNMT3A germline mutation carriers, potentially due to TET2-mediated oxidation. Our findings provide insight into the interplay between epigenetic modulators and transcription factor activity in hematological neoplasia, but do not confirm the putative role of TET2 in atherosclerosis.
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Affiliation(s)
- Eevi Kaasinen
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, SE 171 77, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77, Stockholm, Sweden
| | - Outi Kuismin
- Department of Clinical Genetics, Oulu University Hospital, FI-90029, Oulu, Finland
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, FI-90014, Oulu, Finland
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, FI-00014, Helsinki, Finland
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
- Clinicum, University of Helsinki, FI-00014, Helsinki, Finland
| | - Heikki Ristolainen
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Mervi Aavikko
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Johanna Kondelin
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Silva Saarinen
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Davide G Berta
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Riku Katainen
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Elina A M Hirvonen
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Auli Karhu
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Aurora Taira
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Tomas Tanskanen
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Amjad Alkodsi
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Minna Taipale
- Department of Biosciences and Nutrition, Karolinska Institutet, SE 171 77, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77, Stockholm, Sweden
| | - Ekaterina Morgunova
- Department of Biosciences and Nutrition, Karolinska Institutet, SE 171 77, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77, Stockholm, Sweden
| | - Kaarle Franssila
- HUSLAB, Helsinki University Hospital, FI-00029, Helsinki, Finland
| | - Rainer Lehtonen
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Markus Mäkinen
- Cancer and Translational Medicine Research Unit, University of Oulu, FI-90014, Oulu, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, FI-00029, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, FI-00014, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Department of Neurology and Department of Psychiatry, Massachusetts General Hospital, Boston, 02114, MA, USA
- The Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA
| | - Mitja I Kurki
- Analytic and Translational Genetics Unit, Department of Medicine, Department of Neurology and Department of Psychiatry, Massachusetts General Hospital, Boston, 02114, MA, USA
| | - Olli Pietiläinen
- The Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA
| | - Morgane Hilpert
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, CH-4031, Switzerland
| | - Elmo Saarentaus
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, FI-00014, Helsinki, Finland
| | - Jaakko Niinimäki
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, FI-90014, Oulu, Finland
- Research Unit of Medical Imaging, Physics and Technology, Faculty of Medicine, University of Oulu, FI-90014, Oulu, Finland
| | - Juhani Junttila
- Research Unit of Internal Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, FI-90014, Oulu, Finland
| | - Kari Kaikkonen
- Research Unit of Internal Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, FI-90014, Oulu, Finland
| | - Pia Vahteristo
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
| | - Radek C Skoda
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, CH-4031, Switzerland
| | - Mikko R J Seppänen
- Adult Immunodeficiency Unit, Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, FI-00029, Helsinki, Finland
- Rare Diseases Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, FI-00029, Helsinki, Finland
| | - Kari K Eklund
- Clinicum, University of Helsinki, FI-00014, Helsinki, Finland
- Department of Rheumatology, Helsinki University Hospital, FI-00029, Helsinki, Finland
- ORTON Orthopaedic Hospital, FI-00280, Helsinki, Finland
| | - Jussi Taipale
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, SE 171 77, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77, Stockholm, Sweden
| | - Outi Kilpivaara
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland.
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland.
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, FI-00014, Helsinki, Finland.
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, FI-00014, Helsinki, Finland.
- Department of Biosciences and Nutrition, Karolinska Institutet, SE 171 77, Stockholm, Sweden.
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Hirvonen EAM, Pitkänen E, Hemminki K, Aaltonen LA, Kilpivaara O. Whole-exome sequencing identifies novel candidate predisposition genes for familial polycythemia vera. Hum Genomics 2017; 11:6. [PMID: 28427458 PMCID: PMC5397753 DOI: 10.1186/s40246-017-0102-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/09/2017] [Indexed: 12/12/2022] Open
Abstract
Background Polycythemia vera (PV), characterized by massive production of erythrocytes, is one of the myeloproliferative neoplasms. Most patients carry a somatic gain-of-function mutation in JAK2, c.1849G > T (p.Val617Phe), leading to constitutive activation of JAK-STAT signaling pathway. Familial clustering is also observed occasionally, but high-penetrance predisposition genes to PV have remained unidentified. Results We studied the predisposition to PV by exome sequencing (three cases) in a Finnish PV family with four patients. The 12 shared variants (maximum allowed minor allele frequency <0.001 in Finnish population in ExAC database) predicted damaging in silico and absent in an additional control set of over 500 Finns were further validated by Sanger sequencing in a fourth affected family member. Three novel predisposition candidate variants were identified: c.1254C > G (p.Phe418Leu) in ZXDC, c.1931C > G (p.Pro644Arg) in ATN1, and c.701G > A (p.Arg234Gln) in LRRC3. We also observed a rare, predicted benign germline variant c.2912C > G (p.Ala971Gly) in BCORL1 in all four patients. Somatic mutations in BCORL1 have been reported in myeloid malignancies. We further screened the variants in eight PV patients in six other Finnish families, but no other carriers were found. Conclusions Exome sequencing provides a powerful tool for the identification of novel variants, and understanding the familial predisposition of diseases. This is the first report on Finnish familial PV cases, and we identified three novel candidate variants that may predispose to the disease. Electronic supplementary material The online version of this article (doi:10.1186/s40246-017-0102-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elina A M Hirvonen
- Genome-Scale Biology Research Program, Research Programs Unit and Department of Medical and Clinical Genetics, Medicum, University of Helsinki, P.O. Box 63, 00014, Helsinki, Finland
| | - Esa Pitkänen
- Genome-Scale Biology Research Program, Research Programs Unit and Department of Medical and Clinical Genetics, Medicum, University of Helsinki, P.O. Box 63, 00014, Helsinki, Finland
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lauri A Aaltonen
- Genome-Scale Biology Research Program, Research Programs Unit and Department of Medical and Clinical Genetics, Medicum, University of Helsinki, P.O. Box 63, 00014, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, SE-17177, Stockholm, Sweden
| | - Outi Kilpivaara
- Genome-Scale Biology Research Program, Research Programs Unit and Department of Medical and Clinical Genetics, Medicum, University of Helsinki, P.O. Box 63, 00014, Helsinki, Finland.
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