1
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Bakr A, Corte GD, Veselinov O, Kelekçi S, Chen MJM, Lin YY, Sigismondo G, Iacovone M, Cross A, Syed R, Jeong Y, Sollier E, Liu CS, Lutsik P, Krijgsveld J, Weichenhan D, Plass C, Popanda O, Schmezer P. ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response. Nucleic Acids Res 2024:gkae233. [PMID: 38587186 DOI: 10.1093/nar/gkae233] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/27/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
AT-rich interaction domain protein 1A (ARID1A), a SWI/SNF chromatin remodeling complex subunit, is frequently mutated across various cancer entities. Loss of ARID1A leads to DNA repair defects. Here, we show that ARID1A plays epigenetic roles to promote both DNA double-strand breaks (DSBs) repair pathways, non-homologous end-joining (NHEJ) and homologous recombination (HR). ARID1A is accumulated at DSBs after DNA damage and regulates chromatin loops formation by recruiting RAD21 and CTCF to DSBs. Simultaneously, ARID1A facilitates transcription silencing at DSBs in transcriptionally active chromatin by recruiting HDAC1 and RSF1 to control the distribution of activating histone marks, chromatin accessibility, and eviction of RNAPII. ARID1A depletion resulted in enhanced accumulation of micronuclei, activation of cGAS-STING pathway, and an increased expression of immunomodulatory cytokines upon ionizing radiation. Furthermore, low ARID1A expression in cancer patients receiving radiotherapy was associated with higher infiltration of several immune cells. The high mutation rate of ARID1A in various cancer types highlights its clinical relevance as a promising biomarker that correlates with the level of immune regulatory cytokines and estimates the levels of tumor-infiltrating immune cells, which can predict the response to the combination of radio- and immunotherapy.
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Affiliation(s)
- Ali Bakr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Giuditta Della Corte
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Olivera Veselinov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Simge Kelekçi
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Mei-Ju May Chen
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Yu-Yu Lin
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
| | - Marika Iacovone
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Alice Cross
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Rabail Syed
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Yunhee Jeong
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Etienne Sollier
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Chun-Shan Liu
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), INF280, 69120 Heidelberg, Germany
| | - Odilia Popanda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Peter Schmezer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
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2
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Waraky A, Östlund A, Nilsson T, Weichenhan D, Lutsik P, Bähr M, Hey J, Tunali G, Adamsson J, Jacobsson S, Morsy MHA, Li S, Fogelstrand L, Plass C, Palmqvist L. Aberrant MNX1 expression associated with t(7;12)(q36;p13) pediatric acute myeloid leukemia induces the disease through altering histone methylation. Haematologica 2024; 109:725-739. [PMID: 37317878 PMCID: PMC10905087 DOI: 10.3324/haematol.2022.282255] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 06/05/2023] [Indexed: 06/16/2023] Open
Abstract
Certain subtypes of acute myeloid leukemia (AML) in children have inferior outcome, such as AML with translocation t(7;12)(q36;p13) leading to an MNX1::ETV6 fusion along with high expression of MNX1. We have identified the transforming event in this AML and possible ways of treatment. Retroviral expression of MNX1 was able to induce AML in mice, with similar gene expression and pathway enrichment to t(7;12) AML patient data. Importantly, this leukemia was only induced in immune incompetent mice using fetal but not adult hematopoietic stem and progenitor cells. The restriction in transforming capacity to cells from fetal liver is in alignment with t(7;12)(q36;p13) AML being mostly seen in infants. Expression of MNX1 led to increased histone 3 lysine 4 mono-, di- and trimethylation, reduction in H3K27me3, accompanied with changes in genome-wide chromatin accessibility and genome expression, likely mediated through MNX1 interaction with the methionine cycle and methyltransferases. MNX1 expression increased DNA damage, depletion of the Lin-/Sca1+/c-Kit+ population and skewing toward the myeloid lineage. These effects, together with leukemia development, were prevented by pre-treatment with the S-adenosylmethionine analog Sinefungin. In conclusion, we have shown the importance of MNX1 in development of AML with t(7;12), supporting a rationale for targeting MNX1 and downstream pathways.
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Affiliation(s)
- Ahmed Waraky
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, and; Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg
| | - Anders Östlund
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg
| | - Tina Nilsson
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg
| | - Marion Bähr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg
| | - Gürcan Tunali
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg
| | - Jenni Adamsson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg
| | - Susanna Jacobsson
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg
| | | | - Susann Li
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg
| | - Linda Fogelstrand
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, and; Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg
| | - Lars Palmqvist
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, and; Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg.
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3
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Schöpf J, Uhrig S, Heilig CE, Lee KS, Walther T, Carazzato A, Dobberkau AM, Weichenhan D, Plass C, Hartmann M, Diwan GD, Carrero ZI, Ball CR, Hohl T, Kindler T, Rudolph-Hähnel P, Helm D, Schneider M, Nilsson A, Øra I, Imle R, Banito A, Russell RB, Jones BC, Lipka DB, Glimm H, Hübschmann D, Hartmann W, Fröhling S, Scholl C. Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions. Nat Commun 2024; 15:51. [PMID: 38168093 PMCID: PMC10761971 DOI: 10.1038/s41467-023-44360-2] [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: 03/23/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Linking clinical multi-omics with mechanistic studies may improve the understanding of rare cancers. We leverage two precision oncology programs to investigate rhabdomyosarcoma with FUS/EWSR1-TFCP2 fusions, an orphan malignancy without effective therapies. All tumors exhibit outlier ALK expression, partly accompanied by intragenic deletions and aberrant splicing resulting in ALK variants that are oncogenic and sensitive to ALK inhibitors. Additionally, recurrent CKDN2A/MTAP co-deletions provide a rationale for PRMT5-targeted therapies. Functional studies show that FUS-TFCP2 blocks myogenic differentiation, induces transcription of ALK and truncated TERT, and inhibits DNA repair. Unlike other fusion-driven sarcomas, TFCP2-rearranged tumors exhibit genomic instability and signs of defective homologous recombination. DNA methylation profiling demonstrates a close relationship with undifferentiated sarcomas. In two patients, sarcoma was preceded by benign lesions carrying FUS-TFCP2, indicating stepwise sarcomagenesis. This study illustrates the potential of linking precision oncology with preclinical research to gain insight into the classification, pathogenesis, and therapeutic vulnerabilities of rare cancers.
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Affiliation(s)
- Julia Schöpf
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sebastian Uhrig
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg, and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christoph E Heilig
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kwang-Seok Lee
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Tatjana Walther
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Alexander Carazzato
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Anna Maria Dobberkau
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | | | | | - Mark Hartmann
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Gaurav D Diwan
- Bioquant, Heidelberg University, Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Zunamys I Carrero
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Claudia R Ball
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD, Dresden, Germany
- Faculty of Biology, TUD Dresden University of Technology, Dresden, Germany
| | - Tobias Hohl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Thomas Kindler
- University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hematology, Medical Oncology and Pneumology, University Medical Center, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Patricia Rudolph-Hähnel
- University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hematology, Medical Oncology and Pneumology, University Medical Center, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Dominic Helm
- Proteomics Core Facility, DKFZ, Heidelberg, Germany
| | | | - Anna Nilsson
- Pediatric Oncology and Coagulation, Karolinska University Hospital, Stockholm, Sweden
| | - Ingrid Øra
- Pediatric Oncology and Hematology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Roland Imle
- Soft-Tissue Sarcoma Junior Research Group, DKFZ, Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ana Banito
- Soft-Tissue Sarcoma Junior Research Group, DKFZ, Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
| | - Robert B Russell
- Bioquant, Heidelberg University, Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Barbara C Jones
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD, Dresden, Germany
- Translational Functional Cancer Genomics, DKFZ, Heidelberg, Germany
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg, and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Wolfgang Hartmann
- Gerhard Domagk Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
| | - Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
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4
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Schmutz M, Zucknick M, Schlenk RF, Mertens D, Benner A, Weichenhan D, Mücke O, Döhner K, Plass C, Bullinger L, Claus R. Predictive value of DNA methylation patterns in AML patients treated with an azacytidine containing induction regimen. Clin Epigenetics 2023; 15:171. [PMID: 37885041 PMCID: PMC10601277 DOI: 10.1186/s13148-023-01580-z] [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: 06/25/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a heterogeneous disease with a poor prognosis. Dysregulation of the epigenetic machinery is a significant contributor to disease development. Some AML patients benefit from treatment with hypomethylating agents (HMAs), but no predictive biomarkers for therapy response exist. Here, we investigated whether unbiased genome-wide assessment of pre-treatment DNA-methylation profiles in AML bone marrow blasts can help to identify patients who will achieve a remission after an azacytidine-containing induction regimen. RESULTS A total of n = 155 patients with newly diagnosed AML treated in the AMLSG 12-09 trial were randomly assigned to a screening and a refinement and validation cohort. The cohorts were divided according to azacytidine-containing induction regimens and response status. Methylation status was assessed for 664,227 500-bp-regions using methyl-CpG immunoprecipitation-seq, resulting in 1755 differentially methylated regions (DMRs). Top regions were distilled and included genes such as WNT10A and GATA3. 80% of regions identified as a hit were represented on HumanMethlyation 450k Bead Chips. Quantitative methylation analysis confirmed 90% of these regions (36 of 40 DMRs). A classifier was trained using penalized logistic regression and fivefold cross validation containing 17 CpGs. Validation based on mass spectra generated by MALDI-TOF failed (AUC 0.59). However, discriminative ability was maintained by adding neighboring CpGs. A recomposed classifier with 12 CpGs resulted in an AUC of 0.77. When evaluated in the non-azacytidine containing group, the AUC was 0.76. CONCLUSIONS Our analysis evaluated the value of a whole genome methyl-CpG screening assay for the identification of informative methylation changes. We also compared the informative content and discriminatory power of regions and single CpGs for predicting response to therapy. The relevance of the identified DMRs is supported by their association with key regulatory processes of oncogenic transformation and support the idea of relevant DMRs being enriched at distinct loci rather than evenly distribution across the genome. Predictive response to therapy could be established but lacked specificity for treatment with azacytidine. Our results suggest that a predictive epigenotype carries its methylation information at a complex, genome-wide level, that is confined to regions, rather than to single CpGs. With increasing application of combinatorial regimens, response prediction may become even more complicated.
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Affiliation(s)
- Maximilian Schmutz
- Hematology and Oncology, Medical Faculty, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manuela Zucknick
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo, Norway
| | - Richard F Schlenk
- NCT-Trial Center, National Center of Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Mertens
- Cooperation Unit "Mechanisms of Leukemogenesis", German Cancer Research Center, Heidelberg, Germany
- Division of Chronic Lymphocytic Leukemia, Department of Internal Medicine III, Ulm University Medical Center, Ulm, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Mücke
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Bullinger
- German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- Department of Hematology, Oncology, and Cancer Immunology, Campus Virchow Klinikum, Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Rainer Claus
- Hematology and Oncology, Medical Faculty, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany.
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Pathology, Medical Faculty, University of Augsburg, Augsburg, Germany.
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5
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Schwartz U, Llamazares Prada M, Pohl ST, Richter M, Tamas R, Schuler M, Keller C, Mijosek V, Muley T, Schneider MA, Quast K, Hey J, Heußel CP, Warth A, Winter H, Serçin Ö, Karmouty-Quintana H, Jyothula SS, Patel MK, Herth F, Koch I, Petrosino G, Titimeaua A, Mardin BR, Weichenhan D, Jurkowski TP, Imbusch CD, Brors B, Benes V, Jung B, Wyatt D, Stahl HF, Plass C, Jurkowska RZ. High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD. EMBO J 2023:e111272. [PMID: 37143403 DOI: 10.15252/embj.2022111272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 03/14/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. Considering its environmental cause, we hypothesized that COPD will be associated with altered epigenetic signaling in lung cells. We generated genome-wide DNA methylation maps at single CpG resolution of primary human lung fibroblasts (HLFs) across COPD stages. We show that the epigenetic landscape is changed early in COPD, with DNA methylation changes occurring predominantly in regulatory regions. RNA sequencing of matched fibroblasts demonstrated dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization. Data integration identified 110 candidate regulators of disease phenotypes that were linked to fibroblast repair processes using phenotypic screens. Our study provides high-resolution multi-omic maps of HLFs across COPD stages. We reveal novel transcriptomic and epigenetic signatures associated with COPD onset and progression and identify new candidate regulators involved in the pathogenesis of chronic lung diseases. The presence of various epigenetic factors among the candidates demonstrates that epigenetic regulation in COPD is an exciting research field that holds promise for novel therapeutic avenues for patients.
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Affiliation(s)
- Uwe Schwartz
- BioMed X Institute, Heidelberg, Germany
- NGS Analysis Center Biology and Pre-Clinical Medicine, University of Regensburg, Regensburg, Germany
| | - Maria Llamazares Prada
- BioMed X Institute, Heidelberg, Germany
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Stephanie T Pohl
- BioMed X Institute, Heidelberg, Germany
- Division of Biomedicine, School of Biosciences, Cardiff University, Cardiff, UK
| | | | | | - Michael Schuler
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Corinna Keller
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | - Thomas Muley
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Heidelberg Lung Biobank, Thoraxklinik,, University Hospital Heidelberg, Heidelberg, Germany
| | - Marc A Schneider
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Heidelberg Lung Biobank, Thoraxklinik,, University Hospital Heidelberg, Heidelberg, Germany
| | - Karsten Quast
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Claus P Heußel
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik, University of Heidelberg, Heidelberg, Germany
- Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Arne Warth
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Heidelberg Lung Biobank, Thoraxklinik,, University Hospital Heidelberg, Heidelberg, Germany
- Pathological Institute, University Hospital Heidelberg, Heidelberg, Germany
| | - Hauke Winter
- Translational Research Unit, Heidelberg Lung Biobank, Thoraxklinik,, University Hospital Heidelberg, Heidelberg, Germany
- Department of Surgery, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Soma Sk Jyothula
- Center for Advanced Cardiopulmonary Therapies and Transplantation, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Manish K Patel
- Center for Advanced Cardiopulmonary Therapies and Transplantation, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Felix Herth
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Heidelberg Lung Biobank, Thoraxklinik,, University Hospital Heidelberg, Heidelberg, Germany
- Department of Pneumology and Critical Care Medicine and Translational Research Unit, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Ina Koch
- Asklepios Biobank for Lung Diseases, Department of Thoracic Surgery, Asklepios Fachkliniken München-Gauting, German Center for Lung Research (DZL), Munich, Germany
| | | | - Alexandru Titimeaua
- Division of Biomedicine, School of Biosciences, Cardiff University, Cardiff, UK
| | | | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Vladimir Benes
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Birgit Jung
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - David Wyatt
- Biotherapeutics Discovery, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Heiko F Stahl
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Renata Z Jurkowska
- BioMed X Institute, Heidelberg, Germany
- Division of Biomedicine, School of Biosciences, Cardiff University, Cardiff, UK
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Schoepf J, Uhrig S, Heilig CE, Lee KS, Walther T, Carazzato A, Dobberkau AM, Weichenhan D, Plass C, Hartmann M, Diwan G, Carrero Z, Ball CR, Hohl T, Kindler T, Rudolph-Hähnel P, Nilsson A, Øra I, Imle R, Banito A, Russell R, Jones BC, Lipka DB, Glimm H, Hübschmann D, Hartmann W, Fröhling S, Scholl C. Abstract 4544: Genomic, transcriptomic, functional, and mechanistic characterization of rhabdomyosarcoma with FUS-TFCP2 or EWSR1-TFCP2 fusions. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4544] [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: 04/07/2023]
Abstract
Abstract
Rhabdomyosarcoma (RMS) is a soft-tissue sarcoma subtype composed of malignant immature precursor cells with myogenic differentiation defined by aberrant expression of the transcription factors MYOD1 and MYOG. Four subtypes are distinguished, characterized by considerable clinical, histologic, and genetic heterogeneity. RMS with fusions of the transcription factor TFCP2 to either FUS or EWSR1 has only recently been observed, but its classification and pathogenesis are unclear. We studied the clinical course, histopathology, and molecular landscape of 12 cases of this new RMS type and determined the functional properties of tumor-specific genetic alterations. Unusually for gene fusion-driven sarcomas, most tumors had highly rearranged genomes, including chromothripsis, and signs of defective homologous recombination DNA repair. All tumors were characterized by extremely high expression of a truncated TERT variant and the receptor tyrosine kinase ALK. The latter was additionally affected by intragenic deletions (33%), which resulted, together with aberrant splicing events, in the expression of shortened ALK variants (58%). Three ALK variants were oncogenic in immortalized cells in vitro and after xenotransplantation in mice and responded variably to different ALK inhibitors. Additional recurrent alterations included CDKN2A/MTAP co-deletions (67%) and mutations in PAPPA2 (25%) encoding an IGFBP5-specific proteinase. DNA methylation analysis of FUS/EWSR1-TFCP2 RMS, along with 19 other soft-tissue sarcoma types, revealed a close relationship with undifferentiated sarcoma but not with other RMS subtypes, suggesting that FUS/EWSR1-TFCP2 RMS is a distinct sarcoma entity possibly arising from a different cell of origin than other RMS types. Transduction of TFCP2 fusions into immortalized human cells conferred anchorage-independent growth and blocked late myogenic differentiation. Genes significantly induced in these cells were also highly expressed in patient tumors, including ALK, TERT, and two known regulators of skeletal muscle cells, IGFBP5 and PTH1R. ACT-seq demonstrated direct binding of FUS-TFCP2 to the ALK and TERT gene loci outside their regular promoters, which correlated with the expression of alternative transcript variants. Finally, FUS-TFCP2 appeared to induce a defect in DNA double-strand repair in immortalized cells, rendering them sensitive to treatment with cisplatin. Together, our study gives insights into the pathogenesis of a new RMS subtype defined by FUS-TFCP2 or EWSR1-TFCP2 fusions and suggests entry points for therapeutic intervention with DNA-damaging agents, ALK inhibitors, and, in the case of additional CDKN2A/MTAP co-deletion, drugs targeting PRMT5.
Citation Format: Julia Schoepf, Sebastian Uhrig, Christoph E. Heilig, Kwang-Seok Lee, Tatjana Walther, Alexander Carazzato, Anna Maria Dobberkau, Dieter Weichenhan, Christoph Plass, Mark Hartmann, Gaurav Diwan, Zunamys Carrero, Claudia R. Ball, Tobias Hohl, Thomas Kindler, Patricia Rudolph-Hähnel, Anna Nilsson, Ingrid Øra, Roland Imle, Ana Banito, Robert Russell, Barbara C. Jones, Daniel B. Lipka, Hanno Glimm, Daniel Hübschmann, Wolfgang Hartmann, Stefan Fröhling, Claudia Scholl. Genomic, transcriptomic, functional, and mechanistic characterization of rhabdomyosarcoma with FUS-TFCP2 or EWSR1-TFCP2 fusions. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4544.
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Affiliation(s)
- Julia Schoepf
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | | | - Christoph E. Heilig
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Kwang-Seok Lee
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Tatjana Walther
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Alexander Carazzato
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Anna Maria Dobberkau
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | | | | | - Mark Hartmann
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Gaurav Diwan
- 3Heidelberg University Biochemistry Centre, Heidelberg University, Heidelberg, Germany
| | - Zunamys Carrero
- 4National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Claudia R. Ball
- 4National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Tobias Hohl
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Thomas Kindler
- 5University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Anna Nilsson
- 6Pediatric Oncology and Coagulation, Karolinska University Hospital, Stockholm, Sweden
| | - Ingrid Øra
- 7Pediatric Oncology and Hematology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Roland Imle
- 2German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ana Banito
- 2German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Robert Russell
- 3Heidelberg University Biochemistry Centre, Heidelberg University, Heidelberg, Germany
| | - Barbara C. Jones
- 8Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Daniel B. Lipka
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Hanno Glimm
- 4National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Daniel Hübschmann
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Wolfgang Hartmann
- 9Gerhard Domagk Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Stefan Fröhling
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Claudia Scholl
- 1German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
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7
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Weichenhan D, Riedel A, Meinen C, Basic A, Toth R, Bähr M, Lutsik P, Hey J, Sollier E, Toprak UH, Kelekçi S, Lin YY, Hakobyan M, Touzart A, Goyal A, Wierzbinska JA, Schlesner M, Westermann F, Lipka DB, Plass C. Translocation t(6;7) in AML-M4 cell line GDM-1 results in MNX1 activation through enhancer-hijacking. Leukemia 2023; 37:1147-1150. [PMID: 36949154 PMCID: PMC10169647 DOI: 10.1038/s41375-023-01865-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 03/24/2023]
Affiliation(s)
- Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Riedel
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Charlotte Meinen
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alisa Basic
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Reka Toth
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Marion Bähr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Oncology KU Leuven, Leuven, Belgium
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Etienne Sollier
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Umut H Toprak
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simge Kelekçi
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Yu-Yu Lin
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mariam Hakobyan
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Aurore Touzart
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Université de Paris Cité, Institut Necker Enfants-Malades (INEM), Institut National de la Santé et de la Recherche Médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Ashish Goyal
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Justyna A Wierzbinska
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Matthias Schlesner
- Faculty of Applied Informatics, University of Augsburg, Augsburg, Germany
| | - Frank Westermann
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
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8
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Oeing CU, Pepin ME, Saul KB, Agircan AS, Assenov Y, Merkel TS, Sedaghat-Hamedani F, Weis T, Meder B, Guan K, Plass C, Weichenhan D, Siede D, Backs J. Indirect epigenetic testing identifies a diagnostic signature of cardiomyocyte DNA methylation in heart failure. Basic Res Cardiol 2023; 118:9. [PMID: 36939901 PMCID: PMC10027651 DOI: 10.1007/s00395-022-00954-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 03/21/2023]
Abstract
Precision-based molecular phenotyping of heart failure must overcome limited access to cardiac tissue. Although epigenetic alterations have been found to underlie pathological cardiac gene dysregulation, the clinical utility of myocardial epigenomics remains narrow owing to limited clinical access to tissue. Therefore, the current study determined whether patient plasma confers indirect phenotypic, transcriptional, and/or epigenetic alterations to ex vivo cardiomyocytes to mirror the failing human myocardium. Neonatal rat ventricular myocytes (NRVMs) and single-origin human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and were treated with blood plasma samples from patients with dilated cardiomyopathy (DCM) and donor subjects lacking history of cardiovascular disease. Following plasma treatments, NRVMs and hiPSC-CMs underwent significant hypertrophy relative to non-failing controls, as determined via automated high-content screening. Array-based DNA methylation analysis of plasma-treated hiPSC-CMs and cardiac biopsies uncovered robust, and conserved, alterations in cardiac DNA methylation, from which 100 sites were validated using an independent cohort. Among the CpG sites identified, hypo-methylation of the ATG promoter was identified as a diagnostic marker of HF, wherein cg03800765 methylation (AUC = 0.986, P < 0.0001) was found to out-perform circulating NT-proBNP levels in differentiating heart failure. Taken together, these findings support a novel approach of indirect epigenetic testing in human HF.
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Affiliation(s)
- Christian U Oeing
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
- Department of Internal Medicine and Cardiology, Charité University Medicine, DZHK (German Center for Cardiovascular Research), Partner site Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Mark E Pepin
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Kerstin B Saul
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Ayça Seyhan Agircan
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Yassen Assenov
- Cancer Epigenomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Tobias S Merkel
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Farbod Sedaghat-Hamedani
- Department of Cardiology, University of Heidelberg, DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Tanja Weis
- Department of Cardiology, University of Heidelberg, DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Benjamin Meder
- Department of Cardiology, University of Heidelberg, DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Kaomei Guan
- Institute of Pharmacology and Toxicology, Technische Universität Medical Centre Dresden, Dresden, Germany
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- Cancer Epigenomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Dominik Siede
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Johannes Backs
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany.
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9
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Boonsanay V, Mosa MH, Looso M, Weichenhan D, Ceteci F, Pudelko L, Lechel A, Michel CS, Künne C, Farin HF, Plass C, Greten FR. Loss of SUV420H2-Dependent Chromatin Compaction Drives Right-Sided Colon Cancer Progression. Gastroenterology 2023; 164:214-227. [PMID: 36402192 PMCID: PMC9889219 DOI: 10.1053/j.gastro.2022.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND & AIMS Epigenetic processes regulating gene expression contribute markedly to epithelial cell plasticity in colorectal carcinogenesis. The lysine methyltransferase SUV420H2 comprises an important regulator of epithelial plasticity and is primarily responsible for trimethylation of H4K20 (H4K20me3). Loss of H4K20me3 has been suggested as a hallmark of human cancer due to its interaction with DNMT1. However, the role of Suv4-20h2 in colorectal cancer is unknown. METHODS We examined the alterations in histone modifications in patient-derived colorectal cancer organoids. Patient-derived colorectal cancer organoids and mouse intestinal organoids were genetically manipulated for functional studies in patient-derived xenograft and orthotopic transplantation. Gene expression profiling, micrococcal nuclease assay, and chromatin immunoprecipitation were performed to understand epigenetic regulation of chromatin states and gene expression in patient-derived and mouse intestinal organoids. RESULTS We found that reduced H4K20me3 levels occurred predominantly in right-sided patient-derived colorectal cancer organoids, which were associated with increased chromatin accessibility. Re-compaction of chromatin by methylstat, a histone demethylase inhibitor, resulted in reduced growth selectively in subcutaneously grown tumors derived from right-sided cancers. Using mouse intestinal organoids, we confirmed that Suv4-20h2-mediated H4K20me3 is required for maintaining heterochromatin compaction and to prevent R-loop formation. Cross-species comparison of Suv4-20h2-depleted murine organoids with right-sided colorectal cancer organoids revealed a large overlap of gene signatures involved in chromatin silencing, DNA methylation, and stemness/Wnt signaling. CONCLUSIONS Loss of Suv4-20h2-mediated H4K20me3 drives right-sided colorectal tumorigenesis through an epigenetically controlled mechanism of chromatin compaction. Our findings unravel a conceptually novel approach for subtype-specific therapy of this aggressive form of colorectal cancer.
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Affiliation(s)
- Verawan Boonsanay
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mohammed H. Mosa
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mario Looso
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Fatih Ceteci
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lorenz Pudelko
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Andre Lechel
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Christian S. Michel
- Department of Hematology, Medical Oncology, and Pneumology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Carsten Künne
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Henner F. Farin
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany,German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany,German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | - Florian R. Greten
- Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Germany,German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany,Correspondence Address correspondence to: Florian R. Greten, MD, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Strasse 42-44, 60596 Frankfurt am Main, Germany.
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10
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Thürmann L, Klös M, Mackowiak SD, Bieg M, Bauer T, Ishaque N, Messingschlager M, Herrmann C, Röder S, Bauer M, Schäuble S, Faessler E, Hahn U, Weichenhan D, Mücke O, Plass C, Borte M, von Mutius E, Stangl GI, Lauener R, Karvonen AM, Divaret-Chauveau A, Riedler J, Heinrich J, Standl M, von Berg A, Schaaf B, Herberth G, Kabesch M, Eils R, Trump S, Lehmann I. Global hypomethylation in childhood asthma identified by genome-wide DNA-methylation sequencing preferentially affects enhancer regions. Allergy 2023. [PMID: 36704932 DOI: 10.1111/all.15658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/21/2022] [Accepted: 12/29/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND Childhood asthma is a result of a complex interaction of genetic and environmental components causing epigenetic and immune dysregulation, airway inflammation and impaired lung function. Although different microarray based EWAS studies have been conducted, the impact of epigenetic regulation in asthma development is still widely unknown. We have therefore applied unbiased whole genome bisulfite sequencing (WGBS) to characterize global DNA-methylation profiles of asthmatic children compared to healthy controls. METHODS Peripheral blood samples of 40 asthmatic and 42 control children aged 5-15 years from three birth cohorts were sequenced together with paired cord blood samples. Identified differentially methylated regions (DMRs) were categorized in genotype-associated, cell-type-dependent, or prenatally primed. Network analysis and subsequent natural language processing of DMR-associated genes was complemented by targeted analysis of functional translation of epigenetic regulation on the transcriptional and protein level. RESULTS In total, 158 DMRs were identified in asthmatic children compared to controls of which 37% were related to the eosinophil content. A global hypomethylation was identified affecting predominantly enhancer regions and regulating key immune genes such as IL4, IL5RA, and EPX. These DMRs were confirmed in n = 267 samples and could be linked to aberrant gene expression. Out of the 158 DMRs identified in the established phenotype, 56 were perturbed already at birth and linked, at least in part, to prenatal influences such as tobacco smoke exposure or phthalate exposure. CONCLUSION This is the first epigenetic study based on whole genome sequencing to identify marked dysregulation of enhancer regions as a hallmark of childhood asthma.
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Affiliation(s)
- Loreen Thürmann
- Associated Member of the German Center for Lung Research, Unit for Molecular Epidemiology, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Klös
- Associated Member of the German Center for Lung Research, Unit for Molecular Epidemiology, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sebastian D Mackowiak
- Associated Member of the German Center for Lung Research, Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Bieg
- Associated Member of the German Center for Lung Research, Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tobias Bauer
- German Cancer Research Center (DKFZ), Division of Theoretical Bioinformatics and Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Naveed Ishaque
- Associated Member of the German Center for Lung Research, Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Marey Messingschlager
- Associated Member of the German Center for Lung Research, Unit for Molecular Epidemiology, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Carl Herrmann
- Health Data Science Unit, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Röder
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Mario Bauer
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Sascha Schäuble
- Friedrich-Schiller-University Jena, Jena University Language & Information Engineering (JULIE) Lab, Jena, Germany.,Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Systems Biology and Bioinformatics Unit, Jena, Germany
| | - Erik Faessler
- Friedrich-Schiller-University Jena, Jena University Language & Information Engineering (JULIE) Lab, Jena, Germany
| | - Udo Hahn
- Friedrich-Schiller-University Jena, Jena University Language & Information Engineering (JULIE) Lab, Jena, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Mücke
- Division of Cancer Epigenetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Munich, Germany
| | - Michael Borte
- Children's Hospital, Municipal Hospital "St. Georg", Leipzig, Germany
| | - Erika von Mutius
- German Center for Lung Research (DZL), Heidelberg, Munich, Germany.,Dr. von Hauner Children's Hospital, Ludwig Maximilian University Munich, Munich, Germany.,Helmholtz Zentrum München-German Research Center for Environmental Health, Institute for Asthma and Allergy Prevention, Neuherberg, Germany
| | - Gabriele I Stangl
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Halle (Saale), Germany
| | - Roger Lauener
- Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Anne M Karvonen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Amandine Divaret-Chauveau
- Pediatric Allergy Department, Children's Hospital, University Hospital of Nancy, Vandoeuvre les Nancy, France.,UMR 6249 Chrono-Environment, Centre National de la Recherche Scientifique and University of Franche-Comté, Besançon, France.,EA3450 Development, Adaptation and Handicap, University of Lorraine, Nancy, France
| | | | - Joachim Heinrich
- German Center for Lung Research (DZL), Heidelberg, Munich, Germany.,Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU, Munich, Germany.,Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Marie Standl
- German Center for Lung Research (DZL), Heidelberg, Munich, Germany.,Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Andrea von Berg
- Department of Pediatrics, Research Institute, Marien-Hospital Wesel, Wesel, Germany
| | - Beate Schaaf
- Pediatric Outpatient Department, Bad Honnef, Germany
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Roland Eils
- Associated Member of the German Center for Lung Research, Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.,Health Data Science Unit, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Munich, Germany
| | - Saskia Trump
- Associated Member of the German Center for Lung Research, Unit for Molecular Epidemiology, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Irina Lehmann
- Associated Member of the German Center for Lung Research, Unit for Molecular Epidemiology, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Center for Lung Research (DZL), Heidelberg, Munich, Germany
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Smith C, Goyal A, Weichenhan D, Allemand E, Mayakonda A, Toprak U, Riedel A, Balducci E, Manojkumar M, Pejkovska A, Mücke O, Sollier E, Bakr A, Breuer K, Lutsik P, Hermine O, Spicuglia S, Asnafi V, Plass C, Touzart A. TAL1 activation in T-Cell acute lymphoblastic leukemia: A novel oncogenic 3' neoenhancer. Haematologica 2023; 108:1259-1271. [PMID: 36632736 PMCID: PMC10153542 DOI: 10.3324/haematol.2022.281583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Indexed: 01/13/2023] Open
Abstract
T-cell acute lymphocytic leukemia protein 1 (TAL1) is one of the most frequently deregulated oncogenes in T-cell acute lymphoblastic leukemia (T-ALL). Its deregulation can occur through diverse in cis-alterations, including SIL-TAL1 microdeletions, translocations with Tcell Receptor (TCR) loci and, more recently described upstream intergenic non-coding mutations. These mutations consist of recurrent focal microinsertions that create an oncogenic neo-enhancer accompanied with activating epigenetic marks. This observation laid the groundwork for an innovative paradigm, the activation of proto-oncogenes via genomic alterations of non-coding intergenic regions. However, for the majority of TAL1 expressing (TAL1+) T-ALLs, the deregulation mechanism remains "unresolved". We took advantage of H3K27ac and H3K4me3 ChIP-seq data of eight T-ALLs, including five TAL1+ cases and identified a putative novel oncogenic neo-enhancer downstream of TAL1 in an "unresolved" monoallelic TAL1+ case. A rare but recurrent somatic heterozygous microinsertion within this region creates a de novo binding site for MYB transcription factor (TF). Here, we demonstrate that this mutation leads to increased enhancer activity, gain of active epigenetic marks and TAL1 activation via recruitment of MYB. These results highlight the diversity of non-coding mutations that can drive oncogene activation.
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Affiliation(s)
- Charlotte Smith
- Université de Paris Cité, Institut Necker Enfants-Malades (INEM), Institut National de la Santé et de la Recherche Médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75743 Paris
| | - Ashish Goyal
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Eric Allemand
- Université de Paris Cité, Institut Imagine, Inserm U1163, Paris
| | - Anand Mayakonda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Umut Toprak
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg
| | - Anna Riedel
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Estelle Balducci
- Université de Paris Cité, Institut Necker Enfants-Malades (INEM), Institut National de la Santé et de la Recherche Médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75743 Paris
| | - Manisha Manojkumar
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Anastasija Pejkovska
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Oliver Mücke
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Etienne Sollier
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Ali Bakr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Kersten Breuer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Olivier Hermine
- Université de Paris Cité, Institut Imagine, Inserm U1163, Paris, France; Department of Hematology, Hôpital Necker Enfants Malades, AP-HP, Faculté de Médecine Paris Descartes, Paris
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), Equipe labellisée Ligue, UMR1090, 13288 Marseille
| | - Vahid Asnafi
- Université de Paris Cité, Institut Necker Enfants-Malades (INEM), Institut National de la Santé et de la Recherche Médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75743 Paris
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; German Cancer Research Consortium (DKTK), 69120 Heidelberg.
| | - Aurore Touzart
- Université de Paris Cité, Institut Necker Enfants-Malades (INEM), Institut National de la Santé et de la Recherche Médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75743 Paris, France; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg.
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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 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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, 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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, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, 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, Akbani R, von Mering C, 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. 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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14
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Halperin C, Hey J, Weichenhan D, Stein Y, Mayer S, Lutsik P, Plass C, Scherz-Shouval R. Global DNA Methylation Analysis of Cancer-Associated Fibroblasts Reveals Extensive Epigenetic Rewiring Linked with RUNX1 Upregulation in Breast Cancer Stroma. Cancer Res 2022; 82:4139-4152. [PMID: 36287637 DOI: 10.1158/0008-5472.can-22-0209] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 08/10/2022] [Accepted: 09/14/2022] [Indexed: 12/14/2022]
Abstract
Cancer cells recruit and rewire normal fibroblasts in their microenvironment to become protumorigenic cancer-associated fibroblasts (CAF). These CAFs are genomically stable, yet their transcriptional programs are distinct from those of their normal counterparts. Transcriptional regulation plays a major role in this reprogramming, but the extent to which epigenetic modifications of DNA also contribute to the rewiring of CAF transcription is not clear. Here we address this question by dissecting the epigenetic landscape of breast CAFs. Applying tagmentation-based whole-genome bisulfite sequencing in a mouse model of breast cancer, we found that fibroblasts undergo massive DNA methylation changes as they transition into CAFs. Transcriptional and epigenetic analyses revealed RUNX1 as a potential mediator of this process and identified a RUNX1-dependent stromal gene signature. Coculture and mouse models showed that both RUNX1 and its stromal signature are induced as normal fibroblasts transition into CAFs. In breast cancer patients, RUNX1 was upregulated in CAFs, and expression of the RUNX1 signature was associated with poor disease outcome, highlighting the relevance of these findings to human disease. This work presents a comprehensive genome-wide map of DNA methylation in CAFs and reveals a previously unknown facet of the dynamic plasticity of the stroma. SIGNIFICANCE The first genome-wide map of DNA methylation in breast cancer-associated fibroblasts unravels a previously unknown facet of the dynamic plasticity of the stroma, with far-reaching therapeutic implications.
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Affiliation(s)
- Coral Halperin
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yaniv Stein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Shimrit Mayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ruth Scherz-Shouval
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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15
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Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH, Wojciechowski M, Rażew M, Mayyas IM, Kardailsky O, Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan D, Jurkowska RZ, Krueger F, Plass C, Zacharias M, Bochtler M, Hore TA, Jurkowski TP. Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function. Sci Adv 2022; 8:eabm2427. [PMID: 36070377 PMCID: PMC9451156 DOI: 10.1126/sciadv.abm2427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic domain of mammalian TET enzymes favor CGs embedded within basic helix-loop-helix and basic leucine zipper domain transcription factor-binding sites, with up to 250-fold preference in vitro. Crystal structures and molecular dynamics calculations show that sequence preference is caused by intrasubstrate interactions and CG flanking sequence indirectly affecting enzyme conformation. TET sequence preferences are physiologically relevant as they explain the rates of DNA demethylation in TET-rescue experiments in culture and in vivo within the zygote and germ line. Most and least favorable TET motifs represent DNA sites that are bound by methylation-sensitive immediate-early transcription factors and octamer-binding transcription factor 4 (OCT4), respectively, illuminating TET function in transcriptional responses and pluripotency support.
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Affiliation(s)
- Mirunalini Ravichandran
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 1301, San Francisco, CA 94143, USA
- Universität Stuttgart, Abteilung Biochemie, Institute für Biochemie und Technische Biochemie, Allmandring 31, Stuttgart D-70569, Germany
| | - Dominik Rafalski
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Claudia I. Davies
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | | | - Xinsheng Nan
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | | | - Annika Kotter
- Johannes-Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Sciences, Staudingerweg 5, 55128 Mainz, Germany
| | - Katarzyna Misztal
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Andrew H. Wang
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | - Marek Wojciechowski
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Michał Rażew
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Issam M. Mayyas
- University of Otago, Department of Pathology, Dunedin 9016, New Zealand
| | - Olga Kardailsky
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | - Uwe Schwartz
- University of Regensburg, Computational Core Unit, 93053 Regensburg, Germany
| | - Krzysztof Zembrzycki
- Institute of Fundamental Technological Research, Department of Biosystems and Soft Matter PAS, Pawińskiego 5B, Warsaw, Poland
| | - Ian M. Morison
- University of Otago, Department of Pathology, Dunedin 9016, New Zealand
| | - Mark Helm
- Johannes-Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Sciences, Staudingerweg 5, 55128 Mainz, Germany
| | - Dieter Weichenhan
- German Cancer Research Center (DKFZ), Division of Cancer Epigenomics, Heidelberg, Germany
| | - Renata Z. Jurkowska
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Christoph Plass
- German Cancer Research Center (DKFZ), Division of Cancer Epigenomics, Heidelberg, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, James-Franck Str. 1, 85748 Garching, Germany
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS (IBB), Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Timothy A. Hore
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | - Tomasz P. Jurkowski
- Universität Stuttgart, Abteilung Biochemie, Institute für Biochemie und Technische Biochemie, Allmandring 31, Stuttgart D-70569, Germany
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
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16
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Kadouri N, Givony T, Nevo S, Hey J, Ben Dor S, Damari G, Dassa B, Dobes J, Weichenhan D, Bähr M, Paulsen M, Haffner-Krausz R, Mall MA, Plass C, Goldfarb Y, Abramson J. Transcriptional regulation of the thymus master regulator Foxn1. Sci Immunol 2022; 7:eabn8144. [PMID: 36026441 DOI: 10.1126/sciimmunol.abn8144] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
FOXN1 is a transcription factor critical for the development of both thymic epithelial cell (TEC) and hair follicle cell (HFC) compartments. However, mechanisms controlling its expression remain poorly understood. To address this question, we performed thorough analyses of the evolutionary conservation and chromatin status of the Foxn1 locus in different tissues and states and identified several putative cis-regulatory regions unique to TECs versus HFCs. Furthermore, experiments using genetically modified mice with specific deletions in the Foxn1 locus and additional bioinformatic analyses helped us identify key regions and transcription factors involved in either positive or negative regulation of Foxn1 in both TECs and HFCs. Specifically, we identified SIX1 and FOXN1 itself as key factors inducing Foxn1 expression in embryonic and neonatal TECs. Together, our data provide important mechanistic insights into the transcriptional regulation of the Foxn1 gene in TEC versus HFC and highlight the role of FOXN1 in its autoregulation.
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Affiliation(s)
- Noam Kadouri
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Givony
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shir Nevo
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Shifra Ben Dor
- Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Golda Damari
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Jan Dobes
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marion Bähr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michelle Paulsen
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
| | | | - Marcus A Mall
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany.,Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yael Goldfarb
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
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17
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Chen Y, Toth R, Chocarro S, Weichenhan D, Hey J, Lutsik P, Sawall S, Stathopoulos GT, Plass C, Sotillo R. Club cells employ regeneration mechanisms during lung tumorigenesis. Nat Commun 2022; 13:4557. [PMID: 35931677 PMCID: PMC9356049 DOI: 10.1038/s41467-022-32052-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 10/10/2021] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
The high plasticity of lung epithelial cells, has for many years, confounded the correct identification of the cell-of-origin of lung adenocarcinoma (LUAD), one of the deadliest malignancies worldwide. Here, we employ lineage-tracing mouse models to investigate the cell of origin of Eml4-Alk LUAD, and show that Club and Alveolar type 2 (AT2) cells give rise to tumours. We focus on Club cell originated tumours and find that Club cells experience an epigenetic switch by which they lose their lineage fidelity and gain an AT2-like phenotype after oncogenic transformation. Single-cell transcriptomic analyses identified two trajectories of Club cell evolution which are similar to the ones used during lung regeneration, suggesting that lung epithelial cells leverage on their plasticity and intrinsic regeneration mechanisms to give rise to a tumour. Together, this study highlights the role of Club cells in LUAD initiation, identifies the mechanism of Club cell lineage infidelity, confirms the presence of these features in human tumours, and unveils key mechanisms conferring LUAD heterogeneity.
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Affiliation(s)
- Yuanyuan Chen
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Reka Toth
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Bioinformatics Platform, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Sara Chocarro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Stefan Sawall
- X-Ray Imaging and CT, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Georgios T Stathopoulos
- Comprehensive Pneumology Center (CPC) and Institute for Lung Biology and Disease (iLBD), Helmholtz Center Munich-German Research Center for Environmental Health (HMGU), Max-Lebsche-Platz 31, 81377, Munich, Bavaria, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TRLC), Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), 69120, Heidelberg, Germany
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. .,German Center for Lung Research (DZL), Heidelberg, Germany. .,Translational Lung Research Center Heidelberg (TRLC), Heidelberg, Germany. .,German Consortium for Translational Cancer Research (DKTK), 69120, Heidelberg, Germany.
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18
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Liu CS, Rioja I, Bakr A, Veldwijk MR, Sperk E, Herskind C, Weichenhan D, Prinjha RK, Plass C, Schmezer P, Popanda O. Selective inhibitors of bromodomain BD1 and BD2 of BET proteins modulate radiation-induced pro-fibrotic fibroblast responses. Int J Cancer 2022; 151:275-286. [PMID: 35239184 DOI: 10.1002/ijc.33989] [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: 10/29/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022]
Abstract
Radiotherapy can induce various adverse effects including fibrosis in cancer patients. Radiation-induced aberrant expression of pro-fibrotic genes has been associated with dysregulated epigenetic mechanisms. Pan-BET (bromodomain and extra-terminal domain) inhibitors, such as JQ1 and I-BET151, have been reported to attenuate the pro-fibrotic response after irradiation. Despite their profound pre-clinical efficacy, the clinical utility of pan-inhibitors is limited due to observed cyto-toxicicities. Recently, inhibitors were developed that selectively target the first (BD1) and second (BD2) bromodomain of the BET proteins (iBET-BD1 (GSK778) and iBET-BD2 (GSK046)). Here, their potential to attenuate radiation-induced fibroblast activation with low-toxicity was investigated. Our results indicated that cell proliferation and cell cycle progression in fibroblasts from BJ cells and six donors were reduced when treated with I-BET151 and iBET-BD1, but not with iBET-BD2. After irradiation, induction of DGKA and pro-fibrotic markers, especially COL1A1 and ACTA2, was attenuated with all BET inhibitors. H3K27ac enrichment was similar at the DGKA enhancer region after I-BET151 treatment and irradiation, but was reduced at the COL1A1 transcription start site and the ACTA2 enhancer site. iBET-BD2 did not change H3K27ac levels in these regions. BRD4 occupancy at these regions was not altered by any of the compounds. Cell migration activity was measured as a characteristic independent of extracellular matrix production and was un-changed in fibroblasts after irradiation and BET inhibitor-treatment. In conclusion, iBET-BD2 efficiently suppressed radiation-induced expression of DGKA and pro-fibrotic markers without showing cyto-toxicity. Thus BD2-selective targeting is a promising new therapeutic avenue for further investigations to prevent or attenuate radiotherapy-induced fibrosis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Chun-Shan Liu
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Experimental Hepatology, Inflammation and Cancer Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Inmaculada Rioja
- Immuno-Epigenetics, Immunology Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Ali Bakr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marlon R Veldwijk
- Cellular and Molecular Radiation Oncology Lab, Department of Radiation Oncology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Elena Sperk
- Cellular and Molecular Radiation Oncology Lab, Department of Radiation Oncology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carsten Herskind
- Cellular and Molecular Radiation Oncology Lab, Department of Radiation Oncology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rab K Prinjha
- Immuno-Epigenetics, Immunology Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Schmezer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Odilia Popanda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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19
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Goeppert B, Stichel D, Toth R, Fritzsche S, Loeffler MA, Schlitter AM, Neumann O, Assenov Y, Vogel MN, Mehrabi A, Hoffmann K, Köhler B, Springfeld C, Weichenhan D, Plass C, Esposito I, Schirmacher P, von Deimling A, Roessler S. Integrative analysis reveals early and distinct genetic and epigenetic changes in intraductal papillary and tubulopapillary cholangiocarcinogenesis. Gut 2022; 71:391-401. [PMID: 33468537 PMCID: PMC8762040 DOI: 10.1136/gutjnl-2020-322983] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE A detailed understanding of the molecular alterations in different forms of cholangiocarcinogenesis is crucial for a better understanding of cholangiocarcinoma (CCA) and may pave the way to early diagnosis and better treatment options. DESIGN We analysed a clinicopathologically well-characterised patient cohort (n=54) with high-grade intraductal papillary (IPNB) or tubulopapillary (ITPN) neoplastic precursor lesions of the biliary tract and correlated the results with an independent non-IPNB/ITPN associated CCA cohort (n=294). The triplet sample set of non-neoplastic biliary epithelium, precursor and invasive CCA was analysed by next generation sequencing, DNA copy number and genome-wide methylation profiling. RESULTS Patients with invasive CCA arising from IPNB/ITPN had better prognosis than patients with CCA not associated with IPNB/ITPN. ITPN was localised mostly intrahepatic, whereas IPNB was mostly of extrahepatic origin. IPNB/ITPN were equally associated with small-duct and large-duct type intrahepatic CCA. IPNB exhibited mutational profiles of extrahepatic CCA, while ITPN had significantly fewer mutations. Most mutations were shared between precursor lesions and corresponding invasive CCA but ROBO2 mutations occurred exclusively in invasive CCA and CTNNB1 mutations were mainly present in precursor lesions. In addition, IPNB and ITPN differed in their DNA methylation profiles and analyses of latent methylation components suggested that IPNB and ITPN may have different cells-of-origin. CONCLUSION Integrative analysis revealed that IPNB and ITPN harbour distinct early genetic alterations, IPNB are enriched in mutations typical for extrahepatic CCA, whereas ITPN exhibited few genetic alterations and showed distinct epigenetic profiles. In conclusion, IPNB/ITPN may represent a distinctive, intermediate form of intrahepatic and extrahepatic cholangiocarcinogenesis.
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Affiliation(s)
- Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany .,Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany,Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Reka Toth
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sarah Fritzsche
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | - Olaf Neumann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Yassen Assenov
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Monika Nadja Vogel
- Diagnostic and Interventional Radiology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Arianeb Mehrabi
- Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany,Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Katrin Hoffmann
- Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany,Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Bruno Köhler
- Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany,Department of Medical Oncology, National Center of Tumor Diseases, Heidelberg, Germany
| | - Christoph Springfeld
- Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany,Department of Medical Oncology, National Center of Tumor Diseases, Heidelberg, Germany
| | - Dieter Weichenhan
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany,Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Irene Esposito
- Institute of Pathology, Heinrich-Heine-Universitat Dusseldorf, Dusseldorf, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany,Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany,Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany .,Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany
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20
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Mundy-Bosse BL, Weigel C, Wu YZ, Abdelbaky S, Youssef Y, Casas SB, Polley N, Ernst G, Young KA, McConnell KK, Nalin AP, Wu KG, Broughton M, Lordo MR, Altynova E, Hegewisch-Solloa E, Enriquez-Vera DY, Dueñas D, Barrionuevo C, Yu SC, Saleem A, Suarez CJ, Briercheck EL, Molina-Kirsch H, Loughran TP, Weichenhan D, Plass C, Reneau JC, Mace EM, Gamboa FV, Weinstock DM, Natkunam Y, Caligiuri MA, Mishra A, Porcu P, Baiocchi RA, Brammer JE, Freud AG, Oakes CC. Identification and targeting of the developmental blockade in extranodal natural killer/T cell lymphoma. Blood Cancer Discov 2022; 3:154-169. [PMID: 35247900 PMCID: PMC9414823 DOI: 10.1158/2643-3230.bcd-21-0098] [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: 06/15/2021] [Revised: 12/01/2021] [Accepted: 01/24/2022] [Indexed: 11/16/2022] Open
Abstract
Extranodal natural killer/T-cell lymphoma (ENKTL) is an aggressive, rare lymphoma of natural killer (NK) cell origin with poor clinical outcomes. Here we used phenotypic and molecular profiling, including epigenetic analyses, to investigate how ENKTL ontogeny relates to normal NK-cell development. We demonstrate that neoplastic NK cells are stably, but reversibly, arrested at earlier stages of NK-cell maturation. Genes downregulated in the most epigenetic immature tumors were associated with polycomb silencing along with genomic gain and overexpression of EZH2. ENKTL cells exhibited genome-wide DNA hypermethylation. Tumor-specific DNA methylation gains were associated with polycomb-marked regions, involving extensive gene silencing and loss of transcription factor binding. To investigate therapeutic targeting, we treated novel patient-derived xenograft (PDX) models of ENKTL with the DNA hypomethylating agent, 5-azacytidine. Treatment led to reexpression of NK-cell developmental genes, phenotypic NK-cell differentiation, and prolongation of survival. These studies lay the foundation for epigenetic-directed therapy in ENKTL. SIGNIFICANCE Through epigenetic and transcriptomic analyses of ENKTL, a rare, aggressive malignancy, along with normal NK-cell developmental intermediates, we identified that extreme DNA hypermethylation targets genes required for NK-cell development. Disrupting this epigenetic blockade in novel PDX models led to ENKTL differentiation and improved survival. This article is highlighted in the In This Issue feature, p. 85.
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Affiliation(s)
- Bethany L. Mundy-Bosse
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
- Corresponding Authors: Bethany L. Mundy-Bosse, The Ohio State University James Comprehensive Cancer Center, 882 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-688-6564; E-mail: ; Aharon G. Freud, The Ohio State University James Comprehensive Cancer Center, 892 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-293-7904; E-mail: ; and Christopher C. Oakes, The Ohio State University James Comprehensive Cancer Center, 455 OSU CCC/Wiseman Hall, 410 West 12th Avenue, Columbus, OH 43210. Phone: 614-685-9284; E-mail:
| | - Christoph Weigel
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Yue-Zhong Wu
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Salma Abdelbaky
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Youssef Youssef
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Susana Beceiro Casas
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Nicholas Polley
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Gabrielle Ernst
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Karen A. Young
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Kathleen K. McConnell
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Ansel P. Nalin
- Medical Scientist Training Program, The Ohio State University, Columbus, Ohio
| | - Kevin G. Wu
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Megan Broughton
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Matthew R. Lordo
- Medical Scientist Training Program, The Ohio State University, Columbus, Ohio
| | - Ekaterina Altynova
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Everardo Hegewisch-Solloa
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | | | - Daniela Dueñas
- Instituto Nacional de Enfermedades Neoplasticas, Lima, Peru
| | | | - Shan-Chi Yu
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Atif Saleem
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carlos J. Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Edward L. Briercheck
- Department of Medicine, Division of Hematology and Medical Oncology, Fred Hutchinson Cancer Research Institute and the University of Washington, Seattle, Washington
| | | | - Thomas P. Loughran
- Division of Hematology, Department of Medicine, University of Virginia Cancer Center, Charlottesville, Virginia
| | - Dieter Weichenhan
- Division of Epigenomics, The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics, The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John C. Reneau
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Emily M. Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Fabiola Valvert Gamboa
- Department of Medical Oncology, Liga Nacional Contra el Cáncer, Guatemala City, Guatemala
| | - David M. Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Michael A. Caligiuri
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, California
| | - Anjali Mishra
- Division of Hematologic Malignancies and Hematopoietic Stem Cell Transplantation, Department of Medical Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Pierluigi Porcu
- Division of Hematologic Malignancies and Hematopoietic Stem Cell Transplantation, Department of Medical Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Robert A. Baiocchi
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Jonathan E. Brammer
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Aharon G. Freud
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
- Department of Pathology, The Ohio State University, Columbus, Ohio
- Corresponding Authors: Bethany L. Mundy-Bosse, The Ohio State University James Comprehensive Cancer Center, 882 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-688-6564; E-mail: ; Aharon G. Freud, The Ohio State University James Comprehensive Cancer Center, 892 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-293-7904; E-mail: ; and Christopher C. Oakes, The Ohio State University James Comprehensive Cancer Center, 455 OSU CCC/Wiseman Hall, 410 West 12th Avenue, Columbus, OH 43210. Phone: 614-685-9284; E-mail:
| | - Christopher C. Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
- Corresponding Authors: Bethany L. Mundy-Bosse, The Ohio State University James Comprehensive Cancer Center, 882 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-688-6564; E-mail: ; Aharon G. Freud, The Ohio State University James Comprehensive Cancer Center, 892 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-293-7904; E-mail: ; and Christopher C. Oakes, The Ohio State University James Comprehensive Cancer Center, 455 OSU CCC/Wiseman Hall, 410 West 12th Avenue, Columbus, OH 43210. Phone: 614-685-9284; E-mail:
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21
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Schönrock A, Heinzelmann E, Steffl B, Demirdizen E, Narayanan A, Krunic D, Bähr M, Park JW, Schmidt C, Özduman K, Pamir MN, Wick W, Bestvater F, Weichenhan D, Plass C, Taranda J, Mall M, Turcan Ş. OUP accepted manuscript. Neuro Oncol 2022; 24:1911-1924. [PMID: 35468210 PMCID: PMC9629421 DOI: 10.1093/neuonc/noac110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) is an aggressive tumor that frequently exhibits gain of chromosome 7, loss of chromosome 10, and aberrantly activated receptor tyrosine kinase signaling pathways. Previously, we identified Mesenchyme Homeobox 2 (MEOX2), a gene located on chromosome 7, as an upregulated transcription factor in GBM. Overexpressed transcription factors can be involved in driving GBM. Here, we aimed to address the role of MEOX2 in GBM. METHODS Patient-derived GBM tumorspheres were used to constitutively knockdown or overexpress MEOX2 and subjected to in vitro assays including western blot to assess ERK phosphorylation. Cerebral organoid models were used to investigate the role of MEOX2 in growth initiation. Intracranial mouse implantation models were used to assess the tumorigenic potential of MEOX2. RNA-sequencing, ACT-seq, and CUT&Tag were used to identify MEOX2 target genes. RESULTS MEOX2 enhanced ERK signaling through a feed-forward mechanism. We identified Ser155 as a putative ERK-dependent phosphorylation site upstream of the homeobox-domain of MEOX2. S155A substitution had a major effect on MEOX2 protein levels and altered its subnuclear localization. MEOX2 overexpression cooperated with p53 and PTEN loss in cerebral organoid models of human malignant gliomas to induce cell proliferation. Using high-throughput genomics, we identified putative transcriptional target genes of MEOX2 in patient-derived GBM tumorsphere models and a fresh frozen GBM tumor. CONCLUSIONS We identified MEOX2 as an oncogenic transcription regulator in GBM. MEOX2 increases proliferation in cerebral organoid models of GBM and feeds into ERK signaling that represents a core signaling pathway in GBM.
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Affiliation(s)
| | | | | | | | - Ashwin Narayanan
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Damir Krunic
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marion Bähr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Claudia Schmidt
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Koray Özduman
- Department of Neurosurgery, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - M Necmettin Pamir
- Department of Neurosurgery, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Bestvater
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julian Taranda
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Şevin Turcan
- Corresponding Author: Şevin Turcan, PhD, Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, Heidelberg, Germany ()
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22
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Bakr A, Hey J, Sigismondo G, Liu CS, Sadik A, Goyal A, Cross A, Iyer RL, Müller P, Trauernicht M, Breuer K, Lutsik P, Opitz C, Krijgsveld J, Weichenhan D, Plass C, Popanda O, Schmezer P. ID3 promotes homologous recombination via non-transcriptional and transcriptional mechanisms and its loss confers sensitivity to PARP inhibition. Nucleic Acids Res 2021; 49:11666-11689. [PMID: 34718742 PMCID: PMC8599806 DOI: 10.1093/nar/gkab964] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/23/2021] [Accepted: 10/05/2021] [Indexed: 12/13/2022] Open
Abstract
The inhibitor of DNA-binding 3 (ID3) is a transcriptional regulator that limits interaction of basic helix-loop-helix transcription factors with their target DNA sequences. We previously reported that ID3 loss is associated with mutational signatures linked to DNA repair defects. Here we demonstrate that ID3 exhibits a dual role to promote DNA double-strand break (DSB) repair, particularly homologous recombination (HR). ID3 interacts with the MRN complex and RECQL helicase to activate DSB repair and it facilitates RAD51 loading and downstream steps of HR. In addition, ID3 promotes the expression of HR genes in response to ionizing radiation by regulating both chromatin accessibility and activity of the transcription factor E2F1. Consistently, analyses of TCGA cancer patient data demonstrate that low ID3 expression is associated with impaired HR. The loss of ID3 leads to sensitivity of tumor cells to PARP inhibition, offering new therapeutic opportunities in ID3-deficient tumors.
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Affiliation(s)
- Ali Bakr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
- Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
| | - Chun-Shan Liu
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Ahmed Sadik
- DKTK Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ashish Goyal
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Alice Cross
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
- Imperial College London, London, SW7 2AZ, UK
| | - Ramya Lakshmana Iyer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Patrick Müller
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Max Trauernicht
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Kersten Breuer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Christiane A Opitz
- DKTK Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Neurology Clinic and National Center for Tumor Diseases, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
- Heidelberg University, Medical Faculty, INF672, 69120, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), INF280, 69120 Heidelberg, Germany
| | - Odilia Popanda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Peter Schmezer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
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23
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Boldrin E, Gaffo E, Niedermayer A, Boer JM, Zimmermann M, Weichenhan D, Claus R, Münch V, Sun Q, Enzenmüller S, Seyfried F, Demir S, Zinngrebe J, Cario G, Schrappe M, Den Boer ML, Plass C, Debatin KM, Te Kronnie G, Bortoluzzi S, Meyer LH. MicroRNA-497/195 is tumor suppressive and cooperates with CDKN2A/B in pediatric acute lymphoblastic leukemia. Blood 2021; 138:1953-1965. [PMID: 34098582 DOI: 10.1182/blood.2020007591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 05/24/2021] [Indexed: 11/20/2022] Open
Abstract
We previously identified an association of rapid engraftment of patient-derived leukemia cells transplanted into NOD/SCID mice with early relapse in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). In a search for the cellular and molecular profiles associated with this phenotype, we investigated the expression of microRNAs (miRNAs) in different engraftment phenotypes and patient outcomes. We found high expression of miR-497 and miR-195 (hereafter miR-497/195) in patient-derived xenograft samples with slow engraftment derived from patients with favorable outcome. In contrast, epigenetic repression and low expression of these miRNAs was observed in rapidly engrafting samples associated with early relapse. Overexpression of miR-497/195 in patient-derived leukemia cells suppressed in vivo growth of leukemia and prolonged recipient survival. Conversely, inhibition of miR-497/195 led to increased leukemia cell growth. Key cell cycle regulators were downregulated upon miR-497/195 overexpression, and we identified cyclin-dependent kinase 4 (CDK4)- and cyclin-D3 (CCND3)-mediated control of G1/S transition as a principal mechanism for the suppression of BCP-ALL progression by miR-497/195. The critical role for miR-497/195-mediated cell cycle regulation was underscored by finding (in an additional independent series of patient samples) that high expression of miR-497/195 together with a full sequence for CDKN2A and CDKN2B (CDKN2A/B) was associated with excellent outcome, whereas deletion of CDKN2A/B together with low expression of miR-497/195 was associated with clearly inferior relapse-free survival. These findings point to the cooperative loss of cell cycle regulators as a new prognostic factor indicating possible therapeutic targets for pediatric BCP-ALL.
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Affiliation(s)
- Elena Boldrin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
- Department of Biology, University of Padua, Padua, Italy
| | - Enrico Gaffo
- Department of Molecular Medicine, Padua University, Padua, Italy
| | - Alexandra Niedermayer
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Judith M Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Martin Zimmermann
- Department of Pediatric Hematology and Oncology, Medical School Hannover, Hannover, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Rainer Claus
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
- Department of Hematology/Oncology, Augsburg University Medical Center, Augsburg, Germany
| | - Vera Münch
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Qian Sun
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Stefanie Enzenmüller
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Felix Seyfried
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Salih Demir
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Julia Zinngrebe
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Gunnar Cario
- Pediatric Hematology and Oncology, University Hospital Schleswig Holstein, Campus Kiel, Germany
| | - Martin Schrappe
- Pediatric Hematology and Oncology, University Hospital Schleswig Holstein, Campus Kiel, Germany
| | - Monique L Den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Klaus-Michael Debatin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Geertruij Te Kronnie
- Department of Women's and Children's Health, Padua University, Padua, Italy; and
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, Padua University, Padua, Italy
- Interdepartmental Research Center for Innovative Biotechnologies, Padua University, Padua, Italy
| | - Lüder Hinrich Meyer
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
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24
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Hey J, Paulsen M, Toth R, Weichenhan D, Butz S, Schatterny J, Liebers R, Lutsik P, Plass C, Mall MA. Epigenetic reprogramming of airway macrophages promotes polarization and inflammation in muco-obstructive lung disease. Nat Commun 2021; 12:6520. [PMID: 34764283 PMCID: PMC8586227 DOI: 10.1038/s41467-021-26777-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 10/29/2020] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
Lung diseases, such as cystic fibrosis and COPD, are characterized by mucus obstruction and chronic airway inflammation, but their mechanistic link remains poorly understood. Here, we focus on the function of the mucostatic airway microenvironment on epigenetic reprogramming of airway macrophages (AM) and resulting transcriptomic and phenotypical changes. Using a mouse model of muco-obstructive lung disease (Scnn1b-transgenic), we identify epigenetically controlled, differentially regulated pathways and transcription factors involved in inflammatory responses and macrophage polarization. Functionally, AMs from Scnn1b-transgenic mice have reduced efferocytosis and phagocytosis, and excessive inflammatory responses upon lipopolysaccharide challenge, mediated through enhanced Irf1 function and expression. Ex vivo stimulation of wild-type AMs with native mucus impairs efferocytosis and phagocytosis capacities. In addition, mucus induces gene expression changes, comparable with those observed in AMs from Scnn1b-transgenic mice. Our data show that mucostasis induces epigenetic reprogramming of AMs, leading to changes favoring tissue damage and disease progression. Targeting these altered AMs may support therapeutic approaches in patients with muco-obstructive lung diseases.
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Affiliation(s)
- Joschka Hey
- grid.7497.d0000 0004 0492 0584Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Ruprecht Karl University of Heidelberg, Heidelberg, Germany ,grid.452624.3Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Michelle Paulsen
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany. .,Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany. .,Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Reka Toth
- grid.7497.d0000 0004 0492 0584Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- grid.7497.d0000 0004 0492 0584Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simone Butz
- grid.452624.3Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
| | - Jolanthe Schatterny
- grid.452624.3Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
| | - Reinhard Liebers
- grid.7497.d0000 0004 0492 0584Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.461742.2Present Address: National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Pavlo Lutsik
- grid.7497.d0000 0004 0492 0584Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.
| | - Marcus A. Mall
- grid.452624.3Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany ,grid.452624.3German Center for Lung Research (DZL), Associated Partner, Berlin, Germany
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25
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Català-Moll F, Ferreté-Bonastre AG, Li T, Weichenhan D, Lutsik P, Ciudad L, Álvarez-Prado ÁF, Rodríguez-Ubreva J, Klemann C, Speckmann C, Vilas-Zornoza A, Abolhassani H, Martínez-Gallo M, Dieli-Crimi R, Rivière JG, Martín-Nalda A, Colobran R, Soler-Palacín P, Kracker S, Hammarström L, Prosper F, Durandy A, Grimbacher B, Plass C, Ballestar E. Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction. Nucleic Acids Res 2021; 49:5057-5073. [PMID: 33950194 PMCID: PMC8136777 DOI: 10.1093/nar/gkab322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/07/2020] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Activation-induced deaminase (AID) initiates antibody diversification in germinal center B cells by deaminating cytosines, leading to somatic hypermutation and class-switch recombination. Loss-of-function mutations in AID lead to hyper-IgM syndrome type 2 (HIGM2), a rare human primary antibody deficiency. AID-mediated deamination has been proposed as leading to active demethylation of 5-methycytosines in the DNA, although evidence both supports and casts doubt on such a role. In this study, using whole-genome bisulfite sequencing of HIGM2 B cells, we investigated direct AID involvement in active DNA demethylation. HIGM2 naïve and memory B cells both display widespread DNA methylation alterations, of which ∼25% are attributable to active DNA demethylation. For genes that undergo active demethylation that is impaired in HIGM2 individuals, our analysis indicates that AID is not directly involved. We demonstrate that the widespread alterations in the DNA methylation and expression profiles of HIGM2 naïve B cells result from premature overstimulation of the B-cell receptor prior to the germinal center reaction. Our data support a role for AID in B cell central tolerance in preventing the expansion of autoreactive cell clones, affecting the correct establishment of DNA methylation patterns.
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Affiliation(s)
- Francesc Català-Moll
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Anna G Ferreté-Bonastre
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Ángel F Álvarez-Prado
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Christian Klemann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Carsten Speckmann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- Faculty of Medicine, Center for Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Germany
| | - Amaya Vilas-Zornoza
- Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
| | - Hassan Abolhassani
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, SE 14186 Stockholm , Sweden
| | - Mónica Martínez-Gallo
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
| | - Romina Dieli-Crimi
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
| | - Jacques G Rivière
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Andrea Martín-Nalda
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Roger Colobran
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona (UAB), Bellaterra, Catalonia, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Sven Kracker
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, SE 14186 Stockholm , Sweden
| | - Felipe Prosper
- Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
| | - Anne Durandy
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- German Center for Infection Research (DZIF), Satellite Center Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs University, Freiburg, Germany
- RESIST, Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany
- Institute of Immunity & Transplantation, Royal Free Hospital, University College London, UK
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
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26
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Lother A, Bondareva O, Saadatmand AR, Pollmeier L, Härdtner C, Hilgendorf I, Weichenhan D, Eckstein V, Plass C, Bode C, Backs J, Hein L, Gilsbach R. Diabetes changes gene expression but not DNA methylation in cardiac cells. J Mol Cell Cardiol 2021; 151:74-87. [PMID: 33197445 DOI: 10.1016/j.yjmcc.2020.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 05/30/2020] [Revised: 10/22/2020] [Accepted: 11/08/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Diabetes mellitus is a worldwide epidemic that causes high mortality due to cardiovascular complications, in particular heart failure. Diabetes is associated with profound pathophysiological changes in the heart. The aim of this study was to investigate the impact of diabetes on gene expression and DNA methylation in cardiac cells. METHODS AND RESULTS Transcriptome analysis of heart tissue from mice with streptozotocin-induced diabetes revealed only 39 genes regulated, whereas cell type-specific analysis of the diabetic heart was more sensitive and more specific than heart tissue analysis and revealed a total of 3205 differentially regulated genes in five cell types. Whole genome DNA methylation analysis with basepair resolution of distinct cardiac cell types identified highly specific DNA methylation signatures of genic and regulatory regions. Interestingly, despite marked changes in gene expression, DNA methylation remained stable in streptozotocin-induced diabetes. Integrated analysis of cell type-specific gene expression enabled us to assign the particular contribution of single cell types to the pathophysiology of the diabetic heart. Finally, analysis of gene regulation revealed ligand-receptor pairs as potential mediators of heterocellular interaction in the diabetic heart, with fibroblasts and monocytes showing the highest degree of interaction. CONCLUSION In summary, cell type-specific analysis reveals differentially regulated gene programs that are associated with distinct biological processes in diabetes. Interestingly, despite these changes in gene expression, cell type-specific DNA methylation signatures of genic and regulatory regions remain stable in diabetes. Analysis of heterocellular interactions in the diabetic heart suggest that the interplay between fibroblasts and monocytes is of pivotal importance.
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Affiliation(s)
- Achim Lother
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Germany; Heart Center Freiburg University, Department of Cardiology and Angiology I, Faculty of Medicine, University of Freiburg, Germany
| | - Olga Bondareva
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Germany
| | - Ali R Saadatmand
- Institute of Experimental Cardiology, Heidelberg University, Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Luisa Pollmeier
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Germany
| | - Carmen Härdtner
- Heart Center Freiburg University, Department of Cardiology and Angiology I, Faculty of Medicine, University of Freiburg, Germany
| | - Ingo Hilgendorf
- Heart Center Freiburg University, Department of Cardiology and Angiology I, Faculty of Medicine, University of Freiburg, Germany
| | - Dieter Weichenhan
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Eckstein
- Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Bode
- Heart Center Freiburg University, Department of Cardiology and Angiology I, Faculty of Medicine, University of Freiburg, Germany
| | - Johannes Backs
- Institute of Experimental Cardiology, Heidelberg University, Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Ralf Gilsbach
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Germany; Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany; German Centre of Cardiovascular Research (DZHK), partner site RheinMain, Frankfurt am Main, Germany.
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27
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Greve G, Schüler J, Grüning BA, Berberich B, Stomper J, Zimmer D, Gutenkunst L, Bönisch U, Meier R, Blagitko-Dorfs N, Grishina O, Pfeifer D, Weichenhan D, Plass C, Lübbert M. Decitabine Induces Gene Derepression on Monosomic Chromosomes: In Vitro and In Vivo Effects in Adverse-Risk Cytogenetics AML. Cancer Res 2020; 81:834-846. [PMID: 33203699 DOI: 10.1158/0008-5472.can-20-1430] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/21/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022]
Abstract
Hypomethylating agents (HMA) have become the backbone of nonintensive acute myeloid leukemia/myelodysplastic syndrome (AML/MDS) treatment, also by virtue of their activity in patients with adverse genetics, for example, monosomal karyotypes, often with losses on chromosome 7, 5, or 17. No comparable activity is observed with cytarabine, a cytidine analogue without DNA-hypomethylating properties. As evidence exists for compounding hypermethylation and gene silencing of hemizygous tumor suppressor genes (TSG), we thus hypothesized that this effect may preferentially be reversed by the HMAs decitabine and azacitidine. An unbiased RNA-sequencing approach was developed to interrogate decitabine-induced transcriptome changes in AML cell lines with or without a deletion of chromosomes 7q, 5q or 17p. HMA treatment preferentially upregulated several hemizygous TSG in this genomic region, significantly derepressing endogenous retrovirus (ERV)3-1, with promoter demethylation, enhanced chromatin accessibility, and increased H3K4me3 levels. Decitabine globally reactivated multiple transposable elements, with activation of the dsRNA sensor RIG-I and interferon regulatory factor (IRF)7. Induction of ERV3-1 and RIG-I mRNA was also observed during decitabine treatment in vivo in serially sorted peripheral blood AML blasts. In patient-derived monosomal karyotype AML murine xenografts, decitabine treatment resulted in superior survival rates compared with cytarabine. Collectively, these data demonstrate preferential gene derepression and ERV reactivation in AML with chromosomal deletions, providing a mechanistic explanation that supports the clinical observation of superiority of HMA over cytarabine in this difficult-to-treat patient group. SIGNIFICANCE: These findings unravel the molecular mechanism underlying the intriguing clinical activity of HMAs in AML/MDS patients with chromosome 7 deletions and other monosomal karyotypes.See related commentary by O'Hagan et al., p. 813.
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Affiliation(s)
- Gabriele Greve
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Schüler
- Charles River Discovery Research Services Germany GmbH, Freiburg, Germany
| | - Björn A Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Bettina Berberich
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Stomper
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dennis Zimmer
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lea Gutenkunst
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ulrike Bönisch
- Deep Sequencing Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ruth Meier
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Clinic for Pediatric and Adolescent Medicine Klinikum Karlsruhe, Karlsruhe, Germany
| | - Nadja Blagitko-Dorfs
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Olga Grishina
- Clinical Trials Unit, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Lübbert
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,DKTK Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
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28
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Schönung M, Hess J, Bawidamann P, Stäble S, Hey J, Langstein J, Assenov Y, Weichenhan D, Lutsik P, Lipka DB. AmpliconDesign - an interactive web server for the design of high-throughput targeted DNA methylation assays. Epigenetics 2020; 16:933-939. [PMID: 33100132 DOI: 10.1080/15592294.2020.1834921] [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] [Indexed: 01/16/2023] Open
Abstract
Targeted analysis of DNA methylation patterns based on bisulfite-treated genomic DNA (BT-DNA) is considered as a gold-standard for epigenetic biomarker development. Existing software tools facilitate primer design, primer quality control or visualization of primer localization. However, high-throughput design of primers for BT-DNA amplification is hampered by limits in throughput and functionality of existing tools, requiring users to repeatedly perform specific tasks manually. Consequently, the design of PCR primers for BT-DNA remains a tedious and time-consuming process. To bridge this gap, we developed AmpliconDesign, a webserver providing a scalable and user-friendly platform for the design and analysis of targeted DNA methylation studies based on BT-DNA, e.g. deep amplicon bisulfite sequencing (ampBS-seq) or EpiTYPER MassArray. Core functionality of the web server includes high-throughput primer design and binding site validation based on in silico bisulfite-converted DNA sequences, prediction of fragmentation patterns for EpiTYPER MassArray, an interactive quality control as well as a streamlined analysis workflow for ampBS-seq.
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Affiliation(s)
- Maximilian Schönung
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Jana Hess
- Saarland University, Saarbrücken, Germany
| | - Pascal Bawidamann
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Sina Stäble
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Division of Experimental Hematology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joschka Hey
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German-Israeli Helmholtz Research School in Cancer Biology
| | - Jens Langstein
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Yassen Assenov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel B Lipka
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany
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29
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Lutsik P, Baude A, Mancarella D, Öz S, Kühn A, Toth R, Hey J, Toprak UH, Lim J, Nguyen VH, Jiang C, Mayakonda A, Hartmann M, Rosemann F, Breuer K, Vonficht D, Grünschläger F, Lee S, Schuhmacher MK, Kusevic D, Jauch A, Weichenhan D, Zustin J, Schlesner M, Haas S, Park JH, Park YJ, Oppermann U, Jeltsch A, Haller F, Fellenberg J, Lindroth AM, Plass C. Globally altered epigenetic landscape and delayed osteogenic differentiation in H3.3-G34W-mutant giant cell tumor of bone. Nat Commun 2020; 11:5414. [PMID: 33110075 PMCID: PMC7591516 DOI: 10.1038/s41467-020-18955-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 04/09/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
The neoplastic stromal cells of giant cell tumor of bone (GCTB) carry a mutation in H3F3A, leading to a mutant histone variant, H3.3-G34W, as a sole recurrent genetic alteration. We show that in patient-derived stromal cells H3.3-G34W is incorporated into the chromatin and associates with massive epigenetic alterations on the DNA methylation, chromatin accessibility and histone modification level, that can be partially recapitulated in an orthogonal cell line system by the introduction of H3.3-G34W. These epigenetic alterations affect mainly heterochromatic and bivalent regions and provide possible explanations for the genomic instability, as well as the osteolytic phenotype of GCTB. The mutation occurs in differentiating mesenchymal stem cells and associates with an impaired osteogenic differentiation. We propose that the observed epigenetic alterations reflect distinct differentiation stages of H3.3 WT and H3.3 MUT stromal cells and add to H3.3-G34W-associated changes. The histone variant mutation H3.3-G34W occurs in the majority of giant cell tumor of bone (GCTB). By profiling patient-derived GCTB tumor cells, the authors show that this mutation associates with epigenetic alterations in heterochromatic and bivalent regions that contribute to an impaired osteogenic differentiation and the osteolytic phenotype of GCTB.
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Affiliation(s)
- Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Annika Baude
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Daniela Mancarella
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Simin Öz
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Alexander Kühn
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Reka Toth
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Umut H Toprak
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Jinyeong Lim
- Graduate School of Cancer Science and Policy, Cancer Biomedical Science, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea, Republic of Korea
| | - Viet Ha Nguyen
- Graduate School of Cancer Science and Policy, Cancer Biomedical Science, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea, Republic of Korea
| | - Chao Jiang
- Botnar Research Centre, Oxford NIHR BRC, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK
| | - Anand Mayakonda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Mark Hartmann
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) & German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Felix Rosemann
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Kersten Breuer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Dominik Vonficht
- Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine-HI-STEM gGmbH, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Florian Grünschläger
- Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine-HI-STEM gGmbH, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Suman Lee
- Graduate School of Cancer Science and Policy, Cancer Biomedical Science, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea, Republic of Korea
| | - Maren Kirstin Schuhmacher
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Denis Kusevic
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Anna Jauch
- Institute of Human Genetics, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 366, 69120, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Jozef Zustin
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20251, Hamburg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Simon Haas
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine-HI-STEM gGmbH, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Joo Hyun Park
- Department of Nutritional Science and Food Management, Ewha Womans University, 52 Ewhayeodae-gil, Daehyeon-dong, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Yoon Jung Park
- Department of Nutritional Science and Food Management, Ewha Womans University, 52 Ewhayeodae-gil, Daehyeon-dong, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Udo Oppermann
- Botnar Research Centre, Oxford NIHR BRC, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.,FRIAS-Freiburg Institute of Advanced Studies, Albert Ludwig University of Freiburg, Alberstrasse 19, 79104, Freiburg, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Florian Haller
- Institute of Pathology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nürnberg, Krankenstrasse 8, 91054, Erlangen, Germany
| | - Jörg Fellenberg
- Department of Experimental Orthopaedics, Orthopaedic University Hospital Heidelberg, Ruprecht Karl University of Heidelberg, Schlierbacher Landstrasse 200a, 69118, Heidelberg, Germany
| | - Anders M Lindroth
- Graduate School of Cancer Science and Policy, Cancer Biomedical Science, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea, Republic of Korea.
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. .,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
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30
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Espinet E, Gu Z, Imbusch CD, Giese NA, Büscher M, Safavi M, Weisenburger S, Klein C, Vogel V, Falcone M, Insua-Rodríguez J, Reitberger M, Thiel V, Kossi SO, Muckenhuber A, Sarai K, Lee AYL, Backx E, Zarei S, Gaida MM, Rodríguez-Paredes M, Donato E, Yen HY, Eils R, Schlesner M, Pfarr N, Hackert T, Plass C, Brors B, Steiger K, Weichenhan D, Arda HE, Rooman I, Kopp JL, Strobel O, Weichert W, Sprick MR, Trumpp A. Aggressive PDACs Show Hypomethylation of Repetitive Elements and the Execution of an Intrinsic IFN Program Linked to a Ductal Cell of Origin. Cancer Discov 2020; 11:638-659. [PMID: 33060108 DOI: 10.1158/2159-8290.cd-20-1202] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 11/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive desmoplasia, which challenges the molecular analyses of bulk tumor samples. Here we FACS-purified epithelial cells from human PDAC and normal pancreas and derived their genome-wide transcriptome and DNA methylome landscapes. Clustering based on DNA methylation revealed two distinct PDAC groups displaying different methylation patterns at regions encoding repeat elements. Methylationlow tumors are characterized by higher expression of endogenous retroviral transcripts and double-stranded RNA sensors, which lead to a cell-intrinsic activation of an interferon signature (IFNsign). This results in a protumorigenic microenvironment and poor patient outcome. Methylationlow/IFNsignhigh and Methylationhigh/IFNsignlow PDAC cells preserve lineage traits, respective of normal ductal or acinar pancreatic cells. Moreover, ductal-derived Kras G12D/Trp53 -/- mouse PDACs show higher expression of IFNsign compared with acinar-derived counterparts. Collectively, our data point to two different origins and etiologies of human PDACs, with the aggressive Methylationlow/IFNsignhigh subtype potentially targetable by agents blocking intrinsic IFN signaling. SIGNIFICANCE: The mutational landscapes of PDAC alone cannot explain the observed interpatient heterogeneity. We identified two PDAC subtypes characterized by differential DNA methylation, preserving traits from normal ductal/acinar cells associated with IFN signaling. Our work suggests that epigenetic traits and the cell of origin contribute to PDAC heterogeneity.This article is highlighted in the In This Issue feature, p. 521.
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Affiliation(s)
- Elisa Espinet
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany. .,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Zuguang Gu
- Bioinformatics and Omics Data Analytics, DKFZ, Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, DKFZ and NCT, Heidelberg, Germany
| | - Nathalia A Giese
- Department of General and Visceral Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Magdalena Büscher
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mariam Safavi
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Silke Weisenburger
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Corinna Klein
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
| | - Vanessa Vogel
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
| | - Mattia Falcone
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Jacob Insua-Rodríguez
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Manuel Reitberger
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Vera Thiel
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Steffi O Kossi
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
| | | | - Karnjit Sarai
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alex Y L Lee
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elyne Backx
- Laboratory of Molecular and Medical Oncology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Soheila Zarei
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthias M Gaida
- Institute of Pathology, University Hospital of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center JGU Mainz, Mainz, Germany
| | | | - Elisa Donato
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Hsi-Yu Yen
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Roland Eils
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany.,Digital Health Centre, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany.,Health Data Science Unit, University Hospital and University of Heidelberg, Heidelberg, Germany
| | | | - Nicole Pfarr
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Thilo Hackert
- Department of General and Visceral Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Benedikt Brors
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Applied Bioinformatics, DKFZ and NCT, Heidelberg, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Dieter Weichenhan
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - H Efsun Arda
- Laboratory of Receptor Biology and Gene Expression, Center of Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Ilse Rooman
- Laboratory of Molecular and Medical Oncology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Janel L Kopp
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Oliver Strobel
- Department of General and Visceral Surgery, University Hospital Heidelberg, Heidelberg, Germany.,National Center of Tumor Diseases, NCT, Heidelberg, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Martin R Sprick
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Andreas Trumpp
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany. .,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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31
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Weichenhan D, Lipka DB, Lutsik P, Goyal A, Plass C. Epigenomic technologies for precision oncology. Semin Cancer Biol 2020; 84:60-68. [PMID: 32822861 DOI: 10.1016/j.semcancer.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/15/2022]
Abstract
Epigenetic patterns in a cell control the expression of genes and consequently determine the phenotype of a cell. Cancer cells possess altered epigenomes which include aberrant patterns of DNA methylation, histone tail modifications, nucleosome positioning and of the three-dimensional chromatin organization within a nucleus. These altered epigenetic patterns are potential useful biomarkers to detect cancer cells and to classify tumor types. In addition, the cancer epigenome dictates the response of a cancer cell to therapeutic intervention and, therefore its knowledge, will allow to predict response to different therapeutic approaches. Here we review the current state-of-the-art technologies that have been developed to decipher epigenetic patterns on the genomic level and discuss how these methods are potentially useful for precision oncology.
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Affiliation(s)
- Dieter Weichenhan
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg & German Cancer Research Center, Im Neuenheimer Feld 581, D-69120, Heidelberg, Germany; Faculty of Medicine, Medical Center, Otto-von-Guericke-University, Leipziger Straße 44, D-39120, Magdeburg, Germany.
| | - Pavlo Lutsik
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Ashish Goyal
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Christoph Plass
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
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32
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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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Klös M, Thürmann L, Bauer M, Heinrich J, Standl M, von Berg A, Schaaf B, Weichenhan D, Mücke O, Plass C, Röder S, Herberth G, Sack U, Borte M, Stangl GI, Eils R, Trump S, Lehmann I. Longitudinal trends of serum IgE and IL5RA expression throughout childhood are associated with asthma but not with persistent wheeze. Allergy 2019; 74:2002-2006. [PMID: 31012487 DOI: 10.1111/all.13837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/11/2019] [Accepted: 03/21/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Matthias Klös
- Molecular Epidemiology Unit Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, associated partner of the German Center for Lung Research (DZL) Berlin Germany
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Loreen Thürmann
- Molecular Epidemiology Unit Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, associated partner of the German Center for Lung Research (DZL) Berlin Germany
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Mario Bauer
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Joachim Heinrich
- Institute and Clinic for Occupational, Social and Environmental Medicine University HospitalLMU Munich Germany
- Institute of Epidemiology Helmholtz Zentrum München ‐ German ResearchCenter for Environmental Health Neuherberg Germany
| | - Marie Standl
- Institute of Epidemiology Helmholtz Zentrum München ‐ German ResearchCenter for Environmental Health Neuherberg Germany
| | - Andrea von Berg
- Department of Pediatrics Research Institute Marien‐Hospital Wesel Wesel Germany
| | - Beate Schaaf
- Pediatric Outpatient Department Bad Honnef Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics German Cancer Research Center (DKFZ)Heidelberg Germany
| | - Oliver Mücke
- Division of Cancer Epigenomics German Cancer Research Center (DKFZ)Heidelberg Germany
| | - Christoph Plass
- Division of Cancer Epigenomics German Cancer Research Center (DKFZ)Heidelberg Germany
| | - Stefan Röder
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Gunda Herberth
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Ulrich Sack
- Medical Faculty Institute for Clinical Immunology University of Leipzig Leipzig Germany
| | - Michael Borte
- Children's HospitalMunicipal Hospital “St. Georg” Leipzig Germany
| | - Gabriele I. Stangl
- Institute of Agricultural and Nutritional Sciences Martin Luther University Halle‐Wittenberg Halle Germany
| | - Roland Eils
- Center for Digital Health Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, associated partner of the German Center for Lung Research (DZL) Berlin Germany
- Heidelberg University HospitalHealth Data Science Unit Heidelberg Germany
| | - Saskia Trump
- Molecular Epidemiology Unit Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, associated partner of the German Center for Lung Research (DZL) Berlin Germany
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Irina Lehmann
- Molecular Epidemiology Unit Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, associated partner of the German Center for Lung Research (DZL) Berlin Germany
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
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Schmitt K, Molfenter B, Laureano NK, Tawk B, Bieg M, Hostench XP, Weichenhan D, Ullrich ND, Shang V, Richter D, Stögbauer F, Schroeder L, de Bem Prunes B, Visioli F, Rados PV, Jou A, Plath M, Federspil PA, Thierauf J, Döscher J, Weissinger SE, Hoffmann TK, Wagner S, Wittekindt C, Ishaque N, Eils R, Klussmann JP, Holzinger D, Plass C, Abdollahi A, Freier K, Weichert W, Zaoui K, Hess J. Somatic mutations and promotor methylation of the ryanodine receptor 2 is a common event in the pathogenesis of head and neck cancer. Int J Cancer 2019; 145:3299-3310. [PMID: 31135957 DOI: 10.1002/ijc.32481] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 11/23/2018] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 12/31/2022]
Abstract
Genomic sequencing projects unraveled the mutational landscape of head and neck squamous cell carcinoma (HNSCC) and provided a comprehensive catalog of somatic mutations. However, the limited number of significant cancer-related genes obtained so far only partially explains the biological complexity of HNSCC and hampers the development of novel diagnostic biomarkers and therapeutic targets. We pursued a multiscale omics approach based on whole-exome sequencing, global DNA methylation and gene expression profiling data derived from tumor samples of the HIPO-HNC cohort (n = 87), and confirmed new findings with datasets from The Cancer Genome Atlas (TCGA). Promoter methylation was confirmed by MassARRAY analysis and protein expression was assessed by immunohistochemistry and immunofluorescence staining. We discovered a set of cancer-related genes with frequent somatic mutations and high frequency of promoter methylation. This included the ryanodine receptor 2 (RYR2), which showed variable promoter methylation and expression in both tumor samples and cell lines. Immunohistochemical staining of tissue sections unraveled a gradual loss of RYR2 expression from normal mucosa via dysplastic lesion to invasive cancer and indicated that reduced RYR2 expression in adjacent tissue and precancerous lesions might serve as risk factor for unfavorable prognosis and upcoming malignant conversion. In summary, our data indicate that impaired RYR2 function by either somatic mutation or epigenetic silencing is a common event in HNSCC pathogenesis. Detection of RYR2 expression and/or promoter methylation might enable risk assessment for malignant conversion of dysplastic lesions.
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Affiliation(s)
- Katrin Schmitt
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Britta Molfenter
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Natalia Koerich Laureano
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Oral Pathology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Bouchra Tawk
- Division of Molecular and Translational Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, and Translational Radiation Oncology, German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), and Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Xavier Pastor Hostench
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), and Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Dieter Weichenhan
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nina D Ullrich
- Institute of Physiology and Pathophysiology, Division of Cardiovascular Physiology, Heidelberg University, Heidelberg, Germany
| | - Viny Shang
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniela Richter
- Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden, Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fabian Stögbauer
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Lea Schroeder
- Division of Molecular Diagnostics of Oncogenic Infections, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bianca de Bem Prunes
- Oral Pathology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Fernanda Visioli
- Oral Pathology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Adriana Jou
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michaela Plath
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Philippe A Federspil
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Julia Thierauf
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Johannes Döscher
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Ulm, Ulm, Germany
| | | | - Thomas K Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Ulm, Ulm, Germany
| | - Steffen Wagner
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Giessen, Germany
| | - Claus Wittekindt
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Giessen, Germany
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), and Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), and Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Jens P Klussmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, Cologne, Germany
| | - Dana Holzinger
- Division of Molecular Diagnostics of Oncogenic Infections, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amir Abdollahi
- Division of Molecular and Translational Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, and Translational Radiation Oncology, German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kolja Freier
- Department of Oral and Maxillofacial Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich (TUM), and German Cancer Consortium (DKTK) partner site, Munich, Germany
| | - Karim Zaoui
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Jochen Hess
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Souren NY, Gerdes LA, Lutsik P, Gasparoni G, Beltrán E, Salhab A, Kümpfel T, Weichenhan D, Plass C, Hohlfeld R, Walter J. DNA methylation signatures of monozygotic twins clinically discordant for multiple sclerosis. Nat Commun 2019; 10:2094. [PMID: 31064978 PMCID: PMC6504952 DOI: 10.1038/s41467-019-09984-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [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: 07/17/2018] [Accepted: 04/03/2019] [Indexed: 12/25/2022] Open
Abstract
Multiple sclerosis (MS) is an inflammatory, demyelinating disease of the central nervous system with a modest concordance rate in monozygotic twins, which strongly argues for involvement of epigenetic factors. We observe highly similar peripheral blood mononuclear cell-based methylomes in 45 MS-discordant monozygotic twins. Nevertheless, we identify seven MS-associated differentially methylated positions (DMPs) of which we validate two, including a region in the TMEM232 promoter and ZBTB16 enhancer. In CD4 + T cells we find an MS-associated differentially methylated region in FIRRE. Additionally, 45 regions show large methylation differences in individual pairs, but they do not clearly associate with MS. Furthermore, we present epigenetic biomarkers for current interferon-beta treatment, and extensive validation shows that the ZBTB16 DMP is a signature for prior glucocorticoid treatment. Taken together, this study represents an important reference for epigenomic MS studies, identifies new candidate epigenetic markers, and highlights treatment effects and genetic background as major confounders. Monozygotic (MZ) twins are ideal to study the influence of non-genetic factors on complex phenotypes. Here, Souren et al. perform an EWAS in peripheral blood mononuclear cells from 45 MZ twins discordant for multiple sclerosis and identify disease and treatment-associated epigenetic markers.
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Affiliation(s)
- Nicole Y Souren
- Department of Genetics/Epigenetics, Saarland University, 66123, Saarbrücken, Germany.
| | - Lisa A Gerdes
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians University Munich, 81377, Munich, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Gilles Gasparoni
- Department of Genetics/Epigenetics, Saarland University, 66123, Saarbrücken, Germany
| | - Eduardo Beltrán
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians University Munich, 81377, Munich, Germany
| | - Abdulrahman Salhab
- Department of Genetics/Epigenetics, Saarland University, 66123, Saarbrücken, Germany
| | - Tania Kümpfel
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians University Munich, 81377, Munich, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Reinhard Hohlfeld
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians University Munich, 81377, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), 80336, Munich, Germany
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, 66123, Saarbrücken, Germany.
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36
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Goeppert B, Toth R, Singer S, Albrecht T, Lipka DB, Lutsik P, Brocks D, Baehr M, Muecke O, Assenov Y, Gu L, Endris V, Stenzinger A, Mehrabi A, Schirmacher P, Plass C, Weichenhan D, Roessler S. Integrative Analysis Defines Distinct Prognostic Subgroups of Intrahepatic Cholangiocarcinoma. Hepatology 2019; 69:2091-2106. [PMID: 30615206 PMCID: PMC6594081 DOI: 10.1002/hep.30493] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is the second most common primary liver cancer. It is defined by cholangiocytic differentiation and has poor prognosis. Recently, epigenetic processes have been shown to play an important role in cholangiocarcinogenesis. We performed an integrative analysis on 52 iCCAs using both genetic and epigenetic data with a specific focus on DNA methylation components. We found recurrent isocitrate dehydrogenase 1 (IDH1) and IDH2 (28%) gene mutations, recurrent arm-length copy number alterations (CNAs), and focal alterations such as deletion of 3p21 or amplification of 12q15, which affect BRCA1 Associated Protein 1, polybromo 1, and mouse double minute 2 homolog. DNA methylome analysis revealed excessive hypermethylation of iCCA, affecting primarily the bivalent genomic regions marked with both active and repressive histone modifications. Integrative clustering of genetic and epigenetic data identified four iCCA subgroups with prognostic relevance further designated as IDH, high (H), medium (M), and low (L) alteration groups. The IDH group consisted of all samples with IDH1 or IDH2 mutations and showed, together with the H group, a highly disrupted genome, characterized by frequent deletions of chromosome arms 3p and 6q. Both groups showed excessive hypermethylation with distinct patterns. The M group showed intermediate characteristics regarding both genetic and epigenetic marks, whereas the L group exhibited few methylation changes and mutations and a lack of CNAs. Methylation-based latent component analysis of cell-type composition identified differences among these four groups. Prognosis of the H and M groups was significantly worse than that of the L group. Conclusion: Using an integrative genomic and epigenomic analysis approach, we identified four major iCCA subgroups with widespread genomic and epigenomic differences and prognostic implications. Furthermore, our data suggest differences in the cell-of-origin of the iCCA subtypes.
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Affiliation(s)
- Benjamin Goeppert
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany,Liver Cancer Center HeidelbergHeidelbergGermany
| | - Reka Toth
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Stephan Singer
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany,Institute of PathologyErnst‐Moritz‐Arndt UniversityGreifswaldGermany
| | - Thomas Albrecht
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany
| | - Daniel B. Lipka
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Pavlo Lutsik
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - David Brocks
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Marion Baehr
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Oliver Muecke
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Yassen Assenov
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Lei Gu
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany,Boston Children's HospitalBostonMA
| | - Volker Endris
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany
| | | | - Arianeb Mehrabi
- Liver Cancer Center HeidelbergHeidelbergGermany,Department of General Visceral and Transplantation SurgeryUniversity Hospital HeidelbergHeidelbergGermany
| | - Peter Schirmacher
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany,Liver Cancer Center HeidelbergHeidelbergGermany,German Consortium for Translational Cancer ResearchHeidelbergGermany
| | - Christoph Plass
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany,German Consortium for Translational Cancer ResearchHeidelbergGermany
| | - Dieter Weichenhan
- Division of Cancer EpigenomicsGerman Cancer Research CenterHeidelbergGermany
| | - Stephanie Roessler
- Institute of PathologyUniversity Clinic of HeidelbergHeidelbergGermany,Liver Cancer Center HeidelbergHeidelbergGermany
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37
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Delacher M, Schmidl C, Herzig Y, Breloer M, Hartmann W, Brunk F, Kägebein D, Träger U, Hofer AC, Bittner S, Weichenhan D, Imbusch CD, Hotz-Wagenblatt A, Hielscher T, Breiling A, Federico G, Gröne HJ, Schmid RM, Rehli M, Abramson J, Feuerer M. Rbpj expression in regulatory T cells is critical for restraining T H2 responses. Nat Commun 2019; 10:1621. [PMID: 30962454 PMCID: PMC6453958 DOI: 10.1038/s41467-019-09276-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 04/13/2018] [Accepted: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
The transcriptional regulator Rbpj is involved in T-helper (TH) subset polarization, but its function in Treg cells remains unclear. Here we show that Treg-specific Rbpj deletion leads to splenomegaly and lymphadenopathy despite increased numbers of Treg cells with a polyclonal TCR repertoire. A specific defect of Rbpj-deficient Treg cells in controlling TH2 polarization and B cell responses is observed, leading to the spontaneous formation of germinal centers and a TH2-associated immunoglobulin class switch. The observed phenotype is environment-dependent and can be induced by infection with parasitic nematodes. Rbpj-deficient Treg cells adopt open chromatin landscapes and gene expression profiles reminiscent of tissue-derived TH2-polarized Treg cells, with a prevailing signature of the transcription factor Gata-3. Taken together, our study suggests that Treg cells require Rbpj to specifically restrain TH2 responses, including their own excessive TH2-like differentiation potential. Transcriptional regulator Rbpj is involved in T-helper subset differentiation. Here the authors show that expression of Rbpj in regulatory T cells is required to both regulate TH2 responses and regulate Treg TH2 differentiation potential.
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Affiliation(s)
- Michael Delacher
- Chair for Immunology, University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany.,Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany.,Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Christian Schmidl
- Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
| | - Yonatan Herzig
- Department of Immunology, Weizmann Institute of Science, 234 Herzl Street, 76100, Rehovot, Israel
| | - Minka Breloer
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359, Hamburg, Germany
| | - Wiebke Hartmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359, Hamburg, Germany
| | - Fabian Brunk
- Division of Developmental Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Danny Kägebein
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ulrike Träger
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ann-Cathrin Hofer
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Sebastian Bittner
- Chair for Immunology, University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany.,Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
| | - Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Achim Breiling
- Division of Epigenetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Giuseppina Federico
- Division of Cellular and Molecular Pathology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Hermann-Josef Gröne
- Division of Cellular and Molecular Pathology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Roland M Schmid
- Department of Internal Medicine, Technical University of Munich, Ismaninger Straße 22, 81675, Munich, Germany
| | - Michael Rehli
- Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany.,Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
| | - Jakub Abramson
- Department of Immunology, Weizmann Institute of Science, 234 Herzl Street, 76100, Rehovot, Israel
| | - Markus Feuerer
- Chair for Immunology, University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany. .,Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany. .,Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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38
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Haller F, Bieg M, Will R, Körner C, Weichenhan D, Bott A, Ishaque N, Lutsik P, Moskalev EA, Mueller SK, Bähr M, Woerner A, Kaiser B, Scherl C, Haderlein M, Kleinheinz K, Fietkau R, Iro H, Eils R, Hartmann A, Plass C, Wiemann S, Agaimy A. Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands. Nat Commun 2019; 10:368. [PMID: 30664630 PMCID: PMC6341107 DOI: 10.1038/s41467-018-08069-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023] Open
Abstract
The molecular pathogenesis of salivary gland acinic cell carcinoma (AciCC) is poorly understood. The secretory Ca-binding phosphoprotein (SCPP) gene cluster at 4q13 encodes structurally related phosphoproteins of which some are specifically expressed at high levels in the salivary glands and constitute major components of saliva. Here we report on recurrent rearrangements [t(4;9)(q13;q31)] in AciCC that translocate active enhancer regions from the SCPP gene cluster to the region upstream of Nuclear Receptor Subfamily 4 Group A Member 3 (NR4A3) at 9q31. We show that NR4A3 is specifically upregulated in AciCCs, and that active chromatin regions and gene expression signatures in AciCCs are highly correlated with the NR4A3 transcription factor binding motif. Overexpression of NR4A3 in mouse salivary gland cells increases expression of known NR4A3 target genes and has a stimulatory functional effect on cell proliferation. We conclude that NR4A3 is upregulated through enhancer hijacking and has important oncogenic functions in AciCC.
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MESH Headings
- Acinar Cells/metabolism
- Acinar Cells/pathology
- Animals
- Carcinoma, Acinar Cell/genetics
- Carcinoma, Acinar Cell/metabolism
- Carcinoma, Acinar Cell/pathology
- Cell Proliferation
- Chromatin/chemistry
- Chromatin/metabolism
- Chromosomes, Human, Pair 4/chemistry
- Chromosomes, Human, Pair 4/metabolism
- Chromosomes, Human, Pair 9/chemistry
- Chromosomes, Human, Pair 9/metabolism
- Cohort Studies
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Enhancer Elements, Genetic
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Neoplastic
- Genetic Loci
- Humans
- Male
- Mice
- Multigene Family
- Primary Cell Culture
- Receptors, Steroid/genetics
- Receptors, Steroid/metabolism
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/metabolism
- Salivary Gland Neoplasms/genetics
- Salivary Gland Neoplasms/metabolism
- Salivary Gland Neoplasms/pathology
- Salivary Glands/metabolism
- Salivary Glands/pathology
- Salivary Proteins and Peptides/genetics
- Salivary Proteins and Peptides/metabolism
- Translocation, Genetic
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Affiliation(s)
- Florian Haller
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstr. 8-10, 91054, Erlangen, Germany.
| | - Matthias Bieg
- Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117, Berlin, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Rainer Will
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Cindy Körner
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Alexander Bott
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Naveed Ishaque
- Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117, Berlin, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Evgeny A Moskalev
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstr. 8-10, 91054, Erlangen, Germany
| | - Sarina K Mueller
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Waldstrasse 1, 91054, Erlangen, Germany
| | - Marion Bähr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Angelika Woerner
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Birgit Kaiser
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Claudia Scherl
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Waldstrasse 1, 91054, Erlangen, Germany
| | - Marlen Haderlein
- Department of Radiation Therapy, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Universitätsstrasse 27, 91054, Erlangen, Germany
| | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Rainer Fietkau
- Department of Radiation Therapy, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Universitätsstrasse 27, 91054, Erlangen, Germany
| | - Heinrich Iro
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Waldstrasse 1, 91054, Erlangen, Germany
| | - Roland Eils
- Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117, Berlin, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Health Data Science Unit, University Hospital Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg, German Center for Lung Research, University of Heidelberg, Im Neuenheimer Feld 156, 69120 Heidelberg, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstr. 8-10, 91054, Erlangen, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Stefan Wiemann
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstr. 8-10, 91054, Erlangen, Germany
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39
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Abstract
DNA methylation changes are dynamic processes which occur at cytosines of CpG dinucleotides and contribute to normal development but also to diseases. DNA methylation changes are most effective in promoters and enhancers, the former frequently being CpG-rich and the latter, in contrast, CpG-poor. Many genome-wide methods for DNA methylation analysis interrogate predominantly CpG-rich regions and, hence, spare enhancers and other potentially important genomic regions. Whole genome bisulfite sequencing (WGBS), in contrast, analyzes the DNA methylome in its entirety. Standard tagmentation-based whole genome bisulfite sequencing (TWGBS) is a Tn5 transposon-based method which requires only 30 ng of human input DNA and, hence, is particularly suited for precious biological samples like cells sorted by flow cytometry or laser capture microdissected tissue specimens. In the standard version, tagmentation generates DNA fragments flanked by uniform sequencing adapters. In a subsequent step, the non-covalently bound adapter oligonucleotide needs to be replaced by a novel oligonucleotide to provide the proper adapter sequence for the reverse strand in paired-end sequencing. The presented protocol describes an improved, simplified version of TWGBS where the inefficient oligo-replacement is circumvented by usage of a sequencing-compatible transposase-adapter complex. Consequently, genomic DNA of only a few hundred human cells is required to interrogate the complete human DNA methylome.
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Affiliation(s)
- Dieter Weichenhan
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Charles D Imbusch
- Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Qi Wang
- Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benedikt Brors
- Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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40
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Gerhauser C, Favero F, Risch T, Simon R, Feuerbach L, Assenov Y, Heckmann D, Sidiropoulos N, Waszak SM, Hübschmann D, Urbanucci A, Girma EG, Kuryshev V, Klimczak LJ, Saini N, Stütz AM, Weichenhan D, Böttcher LM, Toth R, Hendriksen JD, Koop C, Lutsik P, Matzk S, Warnatz HJ, Amstislavskiy V, Feuerstein C, Raeder B, Bogatyrova O, Schmitz EM, Hube-Magg C, Kluth M, Huland H, Graefen M, Lawerenz C, Henry GH, Yamaguchi TN, Malewska A, Meiners J, Schilling D, Reisinger E, Eils R, Schlesner M, Strand DW, Bristow RG, Boutros PC, von Kalle C, Gordenin D, Sültmann H, Brors B, Sauter G, Plass C, Yaspo ML, Korbel JO, Schlomm T, Weischenfeldt J. Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories. Cancer Cell 2018; 34:996-1011.e8. [PMID: 30537516 PMCID: PMC7444093 DOI: 10.1016/j.ccell.2018.10.016] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [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: 05/26/2018] [Revised: 08/17/2018] [Accepted: 10/29/2018] [Indexed: 12/28/2022]
Abstract
Identifying the earliest somatic changes in prostate cancer can give important insights into tumor evolution and aids in stratifying high- from low-risk disease. We integrated whole genome, transcriptome and methylome analysis of early-onset prostate cancers (diagnosis ≤55 years). Characterization across 292 prostate cancer genomes revealed age-related genomic alterations and a clock-like enzymatic-driven mutational process contributing to the earliest mutations in prostate cancer patients. Our integrative analysis identified four molecular subgroups, including a particularly aggressive subgroup with recurrent duplications associated with increased expression of ESRP1, which we validate in 12,000 tissue microarray tumors. Finally, we combined the patterns of molecular co-occurrence and risk-based subgroup information to deconvolve the molecular and clinical trajectories of prostate cancer from single patient samples.
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Affiliation(s)
- Clarissa Gerhauser
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Francesco Favero
- Finsen Laboratory, Rigshospitalet, DK-2200, Copenhagen, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Thomas Risch
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Ronald Simon
- Department of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Lars Feuerbach
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Yassen Assenov
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Doreen Heckmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Nikos Sidiropoulos
- Finsen Laboratory, Rigshospitalet, DK-2200, Copenhagen, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Sebastian M Waszak
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69120 Heidelberg, Germany
| | - Daniel Hübschmann
- Division of Theoretical Bioinformatics, 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, Heidelberg 69120, Germany; Department of Pediatric Immunology, Hematology and Oncology, University Hospital, Heidelberg 69120, Germany
| | - Alfonso Urbanucci
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forskningsparken, University of Oslo, 0316 Oslo, Norway; Institute for Cancer Genetics and Informatics, Oslo University Hospital, 0316 Oslo, Norway; Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, 0316 Oslo, Norway
| | - Etsehiwot G Girma
- Finsen Laboratory, Rigshospitalet, DK-2200, Copenhagen, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Vladimir Kuryshev
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Durham, 27709 NC, USA
| | - Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, 27709 NC, USA
| | - Adrian M Stütz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69120 Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lisa-Marie Böttcher
- Department of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Reka Toth
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Josephine D Hendriksen
- Finsen Laboratory, Rigshospitalet, DK-2200, Copenhagen, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Christina Koop
- Department of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Pavlo Lutsik
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sören Matzk
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Hans-Jörg Warnatz
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Vyacheslav Amstislavskiy
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Clarissa Feuerstein
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Benjamin Raeder
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69120 Heidelberg, Germany
| | - Olga Bogatyrova
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | | | - Claudia Hube-Magg
- Department of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Martina Kluth
- Department of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Hartwig Huland
- Martini-Clinic Prostate Cancer Center at the University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg, Germany
| | - Markus Graefen
- Martini-Clinic Prostate Cancer Center at the University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg, Germany
| | - Chris Lawerenz
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Gervaise H Henry
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390-9110, USA
| | - Takafumi N Yamaguchi
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
| | - Alicia Malewska
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390-9110, USA
| | - Jan Meiners
- Department of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Daniela Schilling
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; NCT Trial Center, National Center for Tumor Diseases and German Cancer Research Center, 69120 Heidelberg, Germany
| | - Eva Reisinger
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, 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, Heidelberg 69120, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Douglas W Strand
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390-9110, USA
| | - Robert G Bristow
- Manchester Cancer Research Centre, University of Manchester, 555 Wilmslow Road, Manchester, UK
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Christof von Kalle
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Division of Translational Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Dmitry Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, 27709 NC, USA
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Benedikt Brors
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Guido Sauter
- Department of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Marie-Laure Yaspo
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69120 Heidelberg, Germany.
| | - Thorsten Schlomm
- Martini-Clinic Prostate Cancer Center at the University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg, Germany; Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany.
| | - Joachim Weischenfeldt
- Finsen Laboratory, Rigshospitalet, DK-2200, Copenhagen, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen, DK-2200, Copenhagen, Denmark; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69120 Heidelberg, Germany; Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany.
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41
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Stomper J, Ihorst G, Suciu S, Sander PN, Becker H, Wijermans PW, Plass C, Weichenhan D, Bissé E, Claus R, Lübbert M. Fetal hemoglobin induction during decitabine treatment of elderly patients with high-risk myelodysplastic syndrome or acute myeloid leukemia: a potential dynamic biomarker of outcome. Haematologica 2018; 104:59-69. [PMID: 30171030 PMCID: PMC6312014 DOI: 10.3324/haematol.2017.187278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 12/30/2017] [Accepted: 08/28/2018] [Indexed: 12/18/2022] Open
Abstract
Hematologic responses to hypomethylating agents are often delayed in patients with myelodysplastic syndrome or acute myeloid leukemia. Fetal hemoglobin is a potential novel bio-marker of response: recently, we demonstrated that a high fetal hemoglobin level prior to decitabine treatment was associated with superior outcome. Here we investigated whether early fetal hemoglobin induction during decitabine treatment also had prognostic value, and studied the potential of decitabine to induce erythroid differentiation and fetal hemoglobin expression in vitro Fetal hemoglobin levels were measured by high-performance liquid chromatography in patients with higher-risk myelodysplastic syndrome (n=16) and acute myeloid leukemia (n=37) before treatment and after each course of decitabine. Levels above 1.0% were considered induced. Patients achieving complete or partial remission as best response had attained a median fetal hemoglobin of 1.9% after two courses of treatment, whereas the median value in patients who did not reach complete or partial remission was 0.8% (P=0.015). Fetal hemoglobin induction after two courses of decitabine treatment was associated with early platelet doubling (P=0.006), and its subsequent decrease with hematologic relapse. In patients with myelodysplastic syndrome, induction of fetal hemoglobin after course 2 of treatment was associated with longer overall survival: median of 22.9 versus 7.3 months in patients with or without induction of fetal hemoglobin, respectively [hazard ratio=0.2 (95% confidence interval: 0.1-0.9); P=0.03]. In vitro decitabine treatment of two bi-potential myeloid leukemia cell lines (K562 and HEL) resulted in induction of an erythroid (not megakaryocytic) differentiation program, and of fetal hemoglobin mRNA and protein, associated with GATA1 gene demethylation and upregulation. In conclusion, fetal hemoglobin may provide a useful dynamic biomarker during hypomethylating agent therapy in patients with myelodysplastic syndrome or acute myeloid leukemia.
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Affiliation(s)
- Julia Stomper
- Department of Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine and Medical Center, University of Freiburg, Germany
| | - Gabriele Ihorst
- Clinical Trials Unit, Faculty of Medicine and Medical Center, University of Freiburg, Germany
| | | | - Philipp N Sander
- Department of Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine and Medical Center, University of Freiburg, Germany.,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Heiko Becker
- Department of Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine and Medical Center, University of Freiburg, Germany
| | | | - Christoph Plass
- DKFZ Heidelberg, Division of Epigenomics and Cancer Risk Factors, Heidelberg, Germany.,German Cancer Research Consortium (DKTK), Heidelberg, Germany
| | - Dieter Weichenhan
- DKFZ Heidelberg, Division of Epigenomics and Cancer Risk Factors, Heidelberg, Germany
| | - Emmanuel Bissé
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Germany
| | - Rainer Claus
- Department of Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine and Medical Center, University of Freiburg, Germany.,Department of Internal Medicine II, Hematology/Oncology, Augsburg Medical Center, Germany
| | - Michael Lübbert
- Department of Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine and Medical Center, University of Freiburg, Germany .,German Cancer Research Consortium (DKTK), Freiburg, Germany
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42
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Schlereth K, Weichenhan D, Bauer T, Heumann T, Giannakouri E, Lipka D, Jaeger S, Schlesner M, Aloy P, Eils R, Plass C, Augustin HG. The transcriptomic and epigenetic map of vascular quiescence in the continuous lung endothelium. eLife 2018; 7:34423. [PMID: 29749927 PMCID: PMC5947988 DOI: 10.7554/elife.34423] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/11/2018] [Indexed: 12/21/2022] Open
Abstract
Maintenance of a quiescent and organotypically-differentiated layer of blood vessel-lining endothelial cells (EC) is vital for human health. Yet, the molecular mechanisms of vascular quiescence remain largely elusive. Here we identify the genome-wide transcriptomic program controlling the acquisition of quiescence by comparing lung EC of infant and adult mice, revealing a prominent regulation of TGFß family members. These transcriptomic changes are distinctly accompanied by epigenetic modifications, measured at single CpG resolution. Gain of DNA methylation affects developmental pathways, including NOTCH signaling. Conversely, loss of DNA methylation preferentially occurs in intragenic clusters affecting intronic enhancer regions of genes involved in TGFβ family signaling. Functional experiments prototypically validated the strongly epigenetically regulated inhibitors of TGFβ family signaling SMAD6 and SMAD7 as regulators of EC quiescence. These data establish the transcriptional and epigenetic landscape of vascular quiescence that will serve as a foundation for further mechanistic studies of vascular homeostasis and disease-associated activation. The vascular system is made up of vessels including arteries, capillaries and veins that carry blood throughout the body. The inner surfaces of these blood vessels are lined with a thin layer of cells, called endothelial cells, which form a barrier and a communicating interface between the circulation and the surrounding tissue. Early in an organism’s life, when the vascular system is still growing, endothelial cells increase in number by dividing into more cells. In adulthood, as the vascular system reaches its full size, the endothelial cells maintain a stable number. As a result, an adult’s vascular system has a resting layer of endothelial cells that does not divide. This is known as vascular quiescence, and scientists know little about how the body achieves and maintains it. To unravel the mechanisms controlling vascular quiescence, Schlereth et al. studied endothelial cells taken from blood vessels in the lungs of newborn and adult mice. By comparing all the genes present at both developmental stages, the changes of gene activity in these cells could be measured. The results showed that the activity of genes strongly correlated with so called epigenetic changes in the genes involved in vascular quiescence. These are DNA modifications that can alter the function of a gene without affecting its underlying sequence. Two genes in particular (Smad6 and Smad7) appeared to play an important role in vascular quiescence. Their corresponding proteins, SMAD6 and SMAD7, inhibit another group of proteins (TGFβ family) important for cell growth. The results showed that the endothelial cells in adult mice produced more SMAD6 and SMAD7 than in young mice. Therefore, endothelial cells of adult mice stop to increase in number and to migrate. For the first time ever, Schlereth et al. have provided an extensive comparative analysis of gene activity and epigenetic changes to study vascular quiescence. The findings open a new chapter of vascular biology and will serve as a foundation for future research into the mechanisms of vascular quiescence. Problems in maintaining a resting layer of cells may lead to vascular dysfunction, which is associated with a wide range of diseases, such as stroke, heart disease and cancer making it a leading cause of death. In future, scientists may be able to develop new treatments that target specific molecules to help the body achieve a resting blood vessel system.
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Affiliation(s)
- Katharina Schlereth
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.,Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Tobias Bauer
- Division of Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Tina Heumann
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.,Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Evangelia Giannakouri
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.,Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Daniel Lipka
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Samira Jaeger
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, Germany.,Bioinformatics and Omics Data Analytics, German Cancer Research Center, Heidelberg, Germany
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.,Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany.,German Cancer Consortium, Heidelberg, Germany
| | - Hellmut G Augustin
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.,Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), Heidelberg, Germany.,German Cancer Consortium, Heidelberg, Germany
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43
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Daskalakis M, Brocks D, Sheng YH, Islam MS, Ressnerova A, Assenov Y, Milde T, Oehme I, Witt O, Goyal A, Kühn A, Hartmann M, Weichenhan D, Jung M, Plass C. Reactivation of endogenous retroviral elements via treatment with DNMT- and HDAC-inhibitors. Cell Cycle 2018; 17:811-822. [PMID: 29633898 DOI: 10.1080/15384101.2018.1442623] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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: 12/28/2022] Open
Abstract
Inhibitors of DNA methyltransferases (DNMTis) or histone deacetylases (HDACis) are epigenetic drugs which are investigated since decades. Several have been approved and are applied in the treatment of hematopoietic and lymphatic malignancies, although their mode of action has not been fully understood. Two recent findings improved mechanistic insights: i) activation of human endogenous retroviral elements (HERVs) with concomitant synthesis of double-stranded RNAs (dsRNAs), and ii) massive activation of promoters from long terminal repeats (LTRs) which originated from past HERV invasions. These dsRNAs activate an antiviral response pathway followed by apoptosis. LTR promoter activation leads to synthesis of non-annotated transcripts potentially encoding novel or cryptic proteins. Here, we discuss the current knowledge of the molecular effects exerted by epigenetic drugs with a focus on DNMTis and HDACis. We highlight the role in LTR activation and provide novel data from both in vitro and in vivo epigenetic drug treatment.
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Affiliation(s)
- Michael Daskalakis
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - David Brocks
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Yi-Hua Sheng
- b School of Pharmacy, College of Medicine , National Taiwan University , Taipei , Taiwan
| | - Md Saiful Islam
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Alzbeta Ressnerova
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Yassen Assenov
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Till Milde
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Ina Oehme
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Olaf Witt
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Ashish Goyal
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Alexander Kühn
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Mark Hartmann
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,g Regulation of Cellular Differentiation Group , German Cancer Research Center , Heidelberg , Germany
| | - Dieter Weichenhan
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Manfred Jung
- h Institute of Pharmaceutical Sciences, University of Freiburg , Germany
| | - Christoph Plass
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
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44
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Schliesser MG, Claus R, Hielscher T, Grimm C, Weichenhan D, Blaes J, Wiestler B, Hau P, Schramm J, Sahm F, Weiß EK, Weiler M, Baer C, Schmidt-Graf F, Schackert G, Westphal M, Hertenstein A, Roth P, Galldiks N, Hartmann C, Pietsch T, Felsberg J, Reifenberger G, Sabel MC, Winkler F, von Deimling A, Meisner C, Vajkoczy P, Platten M, Weller M, Plass C, Wick W. Prognostic relevance of miRNA-155 methylation in anaplastic glioma. Oncotarget 2018; 7:82028-82045. [PMID: 27880937 PMCID: PMC5347671 DOI: 10.18632/oncotarget.13452] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/13/2016] [Indexed: 02/03/2023] Open
Abstract
The outcome of patients with anaplastic gliomas varies considerably depending on single molecular markers, such as mutations of the isocitrate dehydrogenase (IDH) genes, as well as molecular classifications based on epigenetic or genetic profiles. Remarkably, 98% of the RNA within a cell is not translated into proteins. Of those, especially microRNAs (miRNAs) have been shown not only to have a major influence on physiologic processes but also to be deregulated and prognostic in malignancies.To find novel survival markers and treatment options we performed unbiased DNA methylation screens that revealed 12 putative miRNA promoter regions with differential DNA methylation in anaplastic gliomas. Methylation of these candidate regions was validated in different independent patient cohorts revealing a set of miRNA promoter regions with prognostic relevance across data sets. Of those, miR-155 promoter methylation and miR-155 expression were negatively correlated and especially the methylation showed superior correlation with patient survival compared to established biomarkers.Functional examinations in malignant glioma cells further cemented the relevance of miR-155 for tumor cell viability with transient and stable modifications indicating an onco-miRNA activity. MiR-155 also conferred resistance towards alkylating temozolomide and radiotherapy as consequence of nuclear factor (NF)κB activation.Preconditioning glioma cells with an NFκB inhibitor reduced therapy resistance of miR-155 overexpressing cells. These cells resembled tumors with a low methylation of the miR-155 promoter and thus mir-155 or NFκB inhibition may provide treatment options with a special focus on patients with IDH wild type tumors.
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Affiliation(s)
- Maximilian Georg Schliesser
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rainer Claus
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Diagnostic and Interventional Neuroradiology, Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christiane Grimm
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas Blaes
- Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benedikt Wiestler
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Hau
- Neurology Clinic, Regensburg University, Regensburg, Germany
| | - Johannes Schramm
- Neurosurgery Clinic, University of Bonn Medical Center, TU Munich, Munich, Germany
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisa K Weiß
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Markus Weiler
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of General Neurology, University Hospital Tübingen, Germany
| | - Constance Baer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Friederike Schmidt-Graf
- Department of General Neurology, University Hospital Tübingen, Germany.,Neurology Clinic, TU Munich, Munich, Germany
| | | | - Manfred Westphal
- Neurosurgery Clinic, University Clinic Hamburg, Eppendorf, Germany
| | - Anne Hertenstein
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Roth
- Department of General Neurology, University Hospital Tübingen, Germany.,Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | | | - Christian Hartmann
- Department of Neuropathology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany
| | - Torsten Pietsch
- Department of Neuropathology, Heinrich-Heine-University, Germany
| | - Joerg Felsberg
- Department of Neurosurgery, Heinrich-Heine-University, Germany.,Neurosurgery Clinic, Charité, Berlin, Germany
| | - Guido Reifenberger
- Department of Neurosurgery, Heinrich-Heine-University, Germany.,Neurosurgery Clinic, Charité, Berlin, Germany
| | | | - Frank Winkler
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Peter Vajkoczy
- Department Hematology, Oncology and Stem Cell Transplantation, University Hospital Freiburg, Germany
| | - Michael Platten
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of General Neurology, University Hospital Tübingen, Germany
| | - Michael Weller
- Department of General Neurology, University Hospital Tübingen, Germany.,Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Wick
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of General Neurology, University Hospital Tübingen, Germany
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45
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Gilsbach R, Schwaderer M, Preissl S, Grüning BA, Kranzhöfer D, Schneider P, Nührenberg TG, Mulero-Navarro S, Weichenhan D, Braun C, Dreßen M, Jacobs AR, Lahm H, Doenst T, Backofen R, Krane M, Gelb BD, Hein L. Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo. Nat Commun 2018; 9:391. [PMID: 29374152 PMCID: PMC5786002 DOI: 10.1038/s41467-017-02762-z] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [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: 02/13/2017] [Accepted: 12/22/2017] [Indexed: 02/04/2023] Open
Abstract
Epigenetic mechanisms and transcription factor networks essential for differentiation of cardiac myocytes have been uncovered. However, reshaping of the epigenome of these terminally differentiated cells during fetal development, postnatal maturation, and in disease remains unknown. Here, we investigate the dynamics of the cardiac myocyte epigenome during development and in chronic heart failure. We find that prenatal development and postnatal maturation are characterized by a cooperation of active CpG methylation and histone marks at cis-regulatory and genic regions to shape the cardiac myocyte transcriptome. In contrast, pathological gene expression in terminal heart failure is accompanied by changes in active histone marks without major alterations in CpG methylation and repressive chromatin marks. Notably, cis-regulatory regions in cardiac myocytes are significantly enriched for cardiovascular disease-associated variants. This study uncovers distinct layers of epigenetic regulation not only during prenatal development and postnatal maturation but also in diseased human cardiac myocytes.
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Affiliation(s)
- Ralf Gilsbach
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Martin Schwaderer
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Sebastian Preissl
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Björn A Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110, Freiburg, Germany
| | - David Kranzhöfer
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Pedro Schneider
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Thomas G Nührenberg
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- Department for Cardiology und Angiology II, University Heart Center Freiburg • Bad Krozingen, 79189, Bad Krozingen, Germany
| | - Sonia Mulero-Navarro
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6542, USA
| | - Dieter Weichenhan
- Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Christian Braun
- Forensic Institute, Ludwig-Maximilians-University, 80046, Munich, Germany
| | - Martina Dreßen
- Department of Cardiovascular Surgery, German Heart Center, Technische Universität München, 80636, Munich, Germany
- Insure (Institute for Translational Cardiac Surgery), Department of Cardiovascular Surgery, German Heart Center, Technische Universität München, 80636, Munich, Germany
| | - Adam R Jacobs
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Harald Lahm
- Department of Cardiovascular Surgery, German Heart Center, Technische Universität München, 80636, Munich, Germany
- Insure (Institute for Translational Cardiac Surgery), Department of Cardiovascular Surgery, German Heart Center, Technische Universität München, 80636, Munich, Germany
| | - Torsten Doenst
- Department of Cardiothoracic Surgery, Jena University Hospital, Friedrich-Schiller-University, 07740, Jena, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110, Freiburg, Germany
| | - Markus Krane
- Department of Cardiovascular Surgery, German Heart Center, Technische Universität München, 80636, Munich, Germany
- Insure (Institute for Translational Cardiac Surgery), Department of Cardiovascular Surgery, German Heart Center, Technische Universität München, 80636, Munich, Germany
- DZHK (German Center for Cardiovascular Research) - Partner Site Munich Heart Alliance, Munich, 60046, Germany
| | - Bruce D Gelb
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6542, USA
- Department of Genetics and Genomic Sciences & Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
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46
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Weichenhan D, Wang Q, Adey A, Wolf S, Shendure J, Eils R, Plass C. Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing. Methods Mol Biol 2018; 1708:105-122. [PMID: 29224141 DOI: 10.1007/978-1-4939-7481-8_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aberrations of the DNA methylome contribute to onset and progression of diseases. Whole genome bisulfite sequencing (WGBS) is the only analytical method covering the complete methylome. Alternative methods requiring less DNA than WGBS analyze only a minor portion of the methylome and do not cover important regulatory features like enhancers and noncoding RNAs. In tagmentation-based WGBS (TWGBS), several DNA and time-consuming steps of the conventional WGBS library preparation are circumvented by the use of a hyperactive transposase, which simultaneously fragments DNA and appends sequencing adapters. TWGBS requires only nanogram amounts of DNA and, thus, is well suited to study precious biological specimens such as sorted cells or micro-dissected tissue samples.
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Affiliation(s)
- Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Qi Wang
- Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrew Adey
- Department of Molecular & Medical Genetics and the Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Stephan Wolf
- Core Facility High Throughput Sequencing, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Roland Eils
- Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
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47
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Thürmann L, Grützmann K, Klös M, Bieg M, Winter M, Polte T, Bauer T, Schick M, Bewerunge-Hudler M, Röder S, Bauer M, Wissenbach DK, Sack U, Weichenhan D, Mücke O, Plass C, Borte M, von Bergen M, Lehmann I, Eils R, Trump S. Early-onset childhood atopic dermatitis is related to NLRP2 repression. J Allergy Clin Immunol 2017; 141:1482-1485.e16. [PMID: 29233739 DOI: 10.1016/j.jaci.2017.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 11/17/2017] [Accepted: 11/21/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Loreen Thürmann
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany
| | - Konrad Grützmann
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany; Center for Molecular Tumor Diagnostics at the National Center for Tumor Diseases, partner site Dresden, Dresden, Germany
| | - Matthias Klös
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcus Winter
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany
| | - Tobias Polte
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany
| | - Tobias Bauer
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schick
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Bewerunge-Hudler
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Röder
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany
| | - Mario Bauer
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany
| | - Dirk K Wissenbach
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany; Institute of Forensic Medicine, University Hospital Jena, Jena, Germany
| | - Ulrich Sack
- Institute of Clinical Immunology, University Hospital Leipzig, Leipzig, Germany
| | - Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Mücke
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Borte
- Municipal Hospital "St. Georg" Children's Hospital, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany; Department of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
| | - Irina Lehmann
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany.
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg, German Center for Lung Research, University of Heidelberg, Heidelberg, Germany
| | - Saskia Trump
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research Leipzig, Leipzig, Germany.
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48
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Delacher M, Imbusch CD, Weichenhan D, Breiling A, Hotz-Wagenblatt A, Träger U, Hofer AC, Kägebein D, Wang Q, Frauhammer F, Mallm JP, Bauer K, Herrmann C, Lang PA, Brors B, Plass C, Feuerer M. Erratum: Corrigendum: Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues. Nat Immunol 2017; 18:1361. [DOI: 10.1038/ni1217-1361b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, Li J, Zhang B, Hou Y, Laudato S, Lipka DB, Schott J, Bierhoff H, Assenov Y, Helf M, Ressnerova A, Islam MS, Lindroth AM, Haas S, Essers M, Imbusch CD, Brors B, Oehme I, Witt O, Lübbert M, Mallm JP, Rippe K, Will R, Weichenhan D, Stoecklin G, Gerhäuser C, Oakes CC, Wang T, Plass C. Erratum: DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Nat Genet 2017; 49:1661. [PMID: 29074949 DOI: 10.1038/ng1117-1661c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This corrects the article DOI: 10.1038/ng.3889.
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50
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Wolf C, Garding A, Filarsky K, Bahlo J, Robrecht S, Becker N, Zucknick M, Rouhi A, Weigel A, Claus R, Weichenhan D, Eichhorst B, Fischer K, Hallek M, Kuchenbauer F, Plass C, Döhner H, Stilgenbauer S, Lichter P, Mertens D. NFATC1 activation by DNA hypomethylation in chronic lymphocytic leukemia correlates with clinical staging and can be inhibited by ibrutinib. Int J Cancer 2017; 142:322-333. [PMID: 28921505 DOI: 10.1002/ijc.31057] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/31/2017] [Indexed: 12/22/2022]
Abstract
B cell receptor (BCR) signaling is a key for survival of chronic lymphocytic leukemia (CLL) cells, and BCR signaling inhibitors are clinically active. However, relapse and resistance to treatment require novel treatment options. To detect novel candidate therapeutic targets, we performed a genome-wide DNA methylation screen with custom arrays and identified aberrant promoter DNA methylation in 2,192 genes. The transcription factor NFATC1 that is a downstream effector of BCR signaling was among the top hypomethylated genes and was concomitantly transcriptionally upregulated in CLL. Intriguingly, NFATC1 promoter DNA hypomethylation levels were significantly variant in clinical trial cohorts from different disease progression stages and furthermore correlated with Binet disease staging and thymidine kinase levels, strongly suggesting a central role of NFATC1 in CLL development. Functionally, DNA hypomethylation at NFATC1 promoter inversely correlated with RNA levels of NFATC1 and dysregulation correlated with expression of target genes BCL-2, CCND1 and CCR7. The inhibition of the NFAT regulator calcineurin with tacrolimus and cyclosporin A and the BCR signaling inhibitor ibrutinib significantly reduced NFAT activity in leukemic cell lines, and NFAT inhibition resulted in increased apoptosis of primary CLL cells. In summary, our results indicate that the aberrant activation of NFATC1 by DNA hypomethylation and BCR signaling plays a major role in the pathomechanism of CLL.
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Affiliation(s)
- Christine Wolf
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angela Garding
- Signaling to Chromatin Laboratory, Institute of Molecular Biology, Mainz, Germany
| | - Katharina Filarsky
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jasmin Bahlo
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Köln, Germany
| | - Sandra Robrecht
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Köln, Germany
| | - Natalia Becker
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manuela Zucknick
- Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Arefeh Rouhi
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Anja Weigel
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Rainer Claus
- Department Medical Clinic II, Klinikum Augsburg, Augsburg, Germany
| | - Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Eichhorst
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Köln, Germany
| | - Kirsten Fischer
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Köln, Germany
| | - Michael Hallek
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Köln, Germany
| | | | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | | | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Mertens
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University of Ulm, Ulm, Germany
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