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Lipka DB, Witte T, Toth R, Yang J, Wiesenfarth M, Nöllke P, Fischer A, Brocks D, Gu Z, Park J, Strahm B, Wlodarski M, Yoshimi A, Claus R, Lübbert M, Busch H, Boerries M, Hartmann M, Schönung M, Kilik U, Langstein J, Wierzbinska JA, Pabst C, Garg S, Catalá A, De Moerloose B, Dworzak M, Hasle H, Locatelli F, Masetti R, Schmugge M, Smith O, Stary J, Ussowicz M, van den Heuvel-Eibrink MM, Assenov Y, Schlesner M, Niemeyer C, Flotho C, Plass C. RAS-pathway mutation patterns define epigenetic subclasses in juvenile myelomonocytic leukemia. Nat Commun 2017; 8:2126. [PMID: 29259247 PMCID: PMC5736667 DOI: 10.1038/s41467-017-02177-w] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 11/13/2017] [Indexed: 01/15/2023] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is an aggressive myeloproliferative disorder of early childhood characterized by mutations activating RAS signaling. Established clinical and genetic markers fail to fully recapitulate the clinical and biological heterogeneity of this disease. Here we report DNA methylome analysis and mutation profiling of 167 JMML samples. We identify three JMML subgroups with unique molecular and clinical characteristics. The high methylation group (HM) is characterized by somatic PTPN11 mutations and poor clinical outcome. The low methylation group is enriched for somatic NRAS and CBL mutations, as well as for Noonan patients, and has a good prognosis. The intermediate methylation group (IM) shows enrichment for monosomy 7 and somatic KRAS mutations. Hypermethylation is associated with repressed chromatin, genes regulated by RAS signaling, frequent co-occurrence of RAS pathway mutations and upregulation of DNMT1 and DNMT3B, suggesting a link between activation of the DNA methylation machinery and mutational patterns in JMML.
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MESH Headings
- Antineoplastic Agents/therapeutic use
- Biopsy
- Child
- Child, Preschool
- Chromatin/genetics
- Chromatin/metabolism
- DNA (Cytosine-5-)-Methyltransferase 1/metabolism
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- DNA Mutational Analysis
- Epigenomics
- Female
- Gene Expression Regulation, Leukemic
- Hematopoietic Stem Cell Transplantation
- Humans
- Infant
- Leukemia, Myelomonocytic, Juvenile/genetics
- Leukemia, Myelomonocytic, Juvenile/mortality
- Leukemia, Myelomonocytic, Juvenile/pathology
- Leukemia, Myelomonocytic, Juvenile/therapy
- Male
- Mutation
- Noonan Syndrome/genetics
- Noonan Syndrome/pathology
- Prognosis
- Prospective Studies
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/metabolism
- Proto-Oncogene Proteins c-cbl
- Proto-Oncogene Proteins p21(ras)/genetics
- Proto-Oncogene Proteins p21(ras)/metabolism
- Signal Transduction/genetics
- Up-Regulation
- DNA Methyltransferase 3B
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Affiliation(s)
- Daniel B Lipka
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany.
- Department of Hematology and Oncology, Medical Center, Otto-von-Guericke-University, Leipziger Strasse 44, 39120, Magdeburg, Germany.
- Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke-University, Leipziger Strasse 44, 39120, Magdeburg, Germany.
| | - Tania Witte
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
- Cancer Epigenetics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Reka Toth
- Computational Epigenomics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Jing Yang
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Manuel Wiesenfarth
- Division of Biostatistics, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Peter Nöllke
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
| | - Alexandra Fischer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
| | - David Brocks
- Cancer Epigenetics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Jeongbin Park
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Brigitte Strahm
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
| | - Marcin Wlodarski
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), 79106, Freiburg, Germany
| | - Ayami Yoshimi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
| | - Rainer Claus
- Division of Hematology, Oncology and Stem Cell Transplantation, University Medical Center, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Michael Lübbert
- Division of Hematology, Oncology and Stem Cell Transplantation, University Medical Center, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Hauke Busch
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Strasse 17, 79104, Freiburg, Germany
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Melanie Boerries
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Strasse 17, 79104, Freiburg, Germany
- German Cancer Consortium (DKTK), 79106, Freiburg, Germany
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Mark Hartmann
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Maximilian Schönung
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Umut Kilik
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Jens Langstein
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Justyna A Wierzbinska
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
- Cancer Epigenetics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Caroline Pabst
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, INF 410, 69120, Heidelberg, Germany
| | - Swati Garg
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, INF 410, 69120, Heidelberg, Germany
| | - Albert Catalá
- Department of Hematology and Oncology, Hospital Sant Joan de Déu, Passeig de Sant Joan de Déu, 2, 08950, Esplugues de Llobrega, Barcelona, Spain
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, De Pintelaan 185, 9000, Ghent, Belgium
| | - Michael Dworzak
- St. Anna Children's Hospital and Children's Cancer Research Institute, Medical University of Vienna, Zimmermannplatz 10, 1090, Vienna, Austria
| | - Henrik Hasle
- Department of Pediatrics, Aarhus University Hospital Skejby, Palle Juul-Jensens Boulevard 82, 8200, Aarhus, Denmark
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Bambino Gesú Children's Hospital, University of Pavia, Piazza S. Onofrio 4, Rome, 00165, Italy
| | - Riccardo Masetti
- Department of Pediatric Oncology and Hematology, University of Bologna, Via Massarenti 11, 40138, Bologna, Italy
| | - Markus Schmugge
- Department of Hematology and Oncology, University Children's Hospital, Steinwiesstrasse 75, 8032, Zurich, Switzerland
| | - Owen Smith
- Department of Paediatric Oncology and Haematology, Our Lady's Children's Hospital Crumlin, Dublin, 12, Ireland
| | - Jan Stary
- Department of Pediatric Hematology and Oncology, Charles University and University Hospital Motol, V Úvalu 84, 150 06, Prague 5, Czech Republic
| | - Marek Ussowicz
- Department of Pediatric Hematology, Oncology and BMT, Wroclaw Medical University, ul. Borowska 213, 50-556, Wroclaw, Poland
| | | | - Yassen Assenov
- Computational Epigenomics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Charlotte Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), 79106, Freiburg, Germany
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), 79106, Freiburg, Germany
| | - Christoph Plass
- Cancer Epigenetics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany.
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
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