1
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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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2
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Goyal A, Bauer J, Hey J, Papageorgiou DN, Stepanova E, Daskalakis M, Scheid J, Dubbelaar M, Klimovich B, Schwarz D, Märklin M, Roerden M, Lin YY, Ma T, Mücke O, Rammensee HG, Lübbert M, Loayza-Puch F, Krijgsveld J, Walz JS, Plass C. DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts. Nat Commun 2023; 14:6731. [PMID: 37872136 PMCID: PMC10593957 DOI: 10.1038/s41467-023-42417-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 10/04/2022] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Immunotherapies targeting cancer-specific neoantigens have revolutionized the treatment of cancer patients. Recent evidence suggests that epigenetic therapies synergize with immunotherapies, mediated by the de-repression of endogenous retroviral element (ERV)-encoded promoters, and the initiation of transcription. Here, we use deep RNA sequencing from cancer cell lines treated with DNA methyltransferase inhibitor (DNMTi) and/or Histone deacetylase inhibitor (HDACi), to assemble a de novo transcriptome and identify several thousand ERV-derived, treatment-induced novel polyadenylated transcripts (TINPATs). Using immunopeptidomics, we demonstrate the human leukocyte antigen (HLA) presentation of 45 spectra-validated treatment-induced neopeptides (t-neopeptides) arising from TINPATs. We illustrate the potential of the identified t-neopeptides to elicit a T-cell response to effectively target cancer cells. We further verify the presence of t-neopeptides in AML patient samples after in vivo treatment with the DNMT inhibitor Decitabine. Our findings highlight the potential of ERV-derived neoantigens in epigenetic and immune therapies.
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Affiliation(s)
- Ashish Goyal
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jens Bauer
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Joschka Hey
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German-Israeli Helmholtz Research School in Cancer Biology, Heidelberg, Germany
- German Center for Lung Research, (DZL) partner site Heidelberg, Heidelberg, Germany
| | - Dimitris N Papageorgiou
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Ekaterina Stepanova
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Daskalakis
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern, University Hospital, University of Bern, Bern, Switzerland
| | - Jonas Scheid
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Marissa Dubbelaar
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Boris Klimovich
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Dominic Schwarz
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Märklin
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Malte Roerden
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Yu-Yu Lin
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Ma
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Oliver Mücke
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Lübbert
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fabricio Loayza-Puch
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Center for Lung Research, (DZL) partner site Heidelberg, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
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3
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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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4
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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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5
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Hey J, Halperin C, Hartmann M, Mayer S, Schönung M, Lipka DB, Scherz-Shouval R, Plass C. DNA methylation landscape of tumor-associated macrophages reveals pathways, transcription factors and prognostic value relevant to triple-negative breast cancer patients. Int J Cancer 2023; 152:1226-1242. [PMID: 36408934 DOI: 10.1002/ijc.34364] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 07/15/2022] [Revised: 10/17/2022] [Accepted: 11/03/2022] [Indexed: 11/23/2022]
Abstract
The accumulation of myeloid cells, particularly tumor-associated macrophages (TAMs), characterizes the tumor microenvironment (TME) of many solid cancers, including breast cancer. Compared to healthy tissue-resident macrophages, TAMs acquire distinct transcriptomes and tumor-promoting functions by largely unknown mechanisms. Here, we hypothesize the involvement of TME signaling and subsequent epigenetic reprogramming of TAMs. Using the 4T1 mouse model of triple-negative breast cancer, we demonstrate that the presence of cancer cells significantly alters the DNA methylation landscape of macrophages and, to a lesser extent, bone marrow-derived monocytes (BMDMs). TAM methylomes, dissected into BMDM-originating and TAM-specific epigenetic programs, implicated transcription factors (TFs) and signaling pathways involved in TAM reprogramming, correlated with cancer-specific gene expression patterns. Utilizing published single-cell gene expression data, we linked microenvironmentally-derived signals to the cancer-specific DNA methylation landscape of TAMs. These integrative analyses highlighted the role of altered cytokine production in the TME (eg, TGF-β, IFN-γ and CSF1) on the induction of specific TFs (eg, FOSL2, STAT1 and RUNX3) responsible for the epigenetic reprogramming of TAMs. DNA methylation deconvolution identified a TAM-specific signature associated with the identified signaling pathways and TFs, corresponding with severe tumor grade and poor prognosis of breast cancer patients. Similarly, immunosuppressive TAM functions were identified, such as induction of the immune inhibitory receptor-ligand PD-L1 by DNA hypomethylation of Cd274. Collectively, these results provide strong evidence that the epigenetic landscapes of macrophages and monocytes are perturbed by the presence of breast cancer, pointing to molecular mechanisms of TAM reprogramming, impacting patient outcomes.
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Affiliation(s)
- Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Coral Halperin
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Mark Hartmann
- Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Shimrit Mayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Maximilian Schönung
- Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Heidelberg, Germany.,Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Daniel B Lipka
- Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Ruth Scherz-Shouval
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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6
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Hey J, Llamazares Prada M, Plass C. HDAC6 score: to treat or not to treat? Nat Cancer 2023; 4:156-158. [PMID: 36585451 DOI: 10.1038/s43018-022-00494-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Cancer-Transitional Research and Exchange Program, German-Israeli Helmholtz Research School in Cancer Biology, Heidelberg, Germany.,Translational Lung Research Center (TLRC), member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Maria Llamazares Prada
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Lung Research Center (TLRC), member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Cancer-Transitional Research and Exchange Program, German-Israeli Helmholtz Research School in Cancer Biology, Heidelberg, Germany. .,Translational Lung Research Center (TLRC), member of the German Center for Lung Research (DZL), Heidelberg, Germany.
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7
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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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8
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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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9
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Meier R, Greve G, Zimmer D, Bresser H, Berberich B, Langova R, Stomper J, Rubarth A, Feuerbach L, Lipka DB, Hey J, Grüning B, Brors B, Duyster J, Plass C, Becker H, Lübbert M. The antileukemic activity of decitabine upon PML/RARA-negative AML blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation. Blood Cancer J 2022; 12:122. [PMID: 35995769 PMCID: PMC9395383 DOI: 10.1038/s41408-022-00715-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/03/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
The prognosis of AML patients with adverse genetics, such as a complex, monosomal karyotype and TP53 lesions, is still dismal even with standard chemotherapy. DNA-hypomethylating agent monotherapy induces an encouraging response rate in these patients. When combined with decitabine (DAC), all-trans retinoic acid (ATRA) resulted in an improved response rate and longer overall survival in a randomized phase II trial (DECIDER; NCT00867672). The molecular mechanisms governing this in vivo synergism are unclear. We now demonstrate cooperative antileukemic effects of DAC and ATRA on AML cell lines U937 and MOLM-13. By RNA-sequencing, derepression of >1200 commonly regulated transcripts following the dual treatment was observed. Overall chromatin accessibility (interrogated by ATAC-seq) and, in particular, at motifs of retinoic acid response elements were affected by both single-agent DAC and ATRA, and enhanced by the dual treatment. Cooperativity regarding transcriptional induction and chromatin remodeling was demonstrated by interrogating the HIC1, CYP26A1, GBP4, and LYZ genes, in vivo gene derepression by expression studies on peripheral blood blasts from AML patients receiving DAC + ATRA. The two drugs also cooperated in derepression of transposable elements, more effectively in U937 (mutated TP53) than MOLM-13 (intact TP53), resulting in a “viral mimicry” response. In conclusion, we demonstrate that in vitro and in vivo, the antileukemic and gene-derepressive epigenetic activity of DAC is enhanced by ATRA.
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Affiliation(s)
- Ruth Meier
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gabriele Greve
- Institute of Genetic Epidemiology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dennis Zimmer
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Helena Bresser
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bettina Berberich
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ralitsa Langova
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Bioscience, University of Heidelberg, Heidelberg, Germany
| | - Julia Stomper
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anne Rubarth
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lars Feuerbach
- Division of Applied Bioinformatics, 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.,Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Justus Duyster
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, Freiburg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heiko Becker
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Lübbert
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, Freiburg, Germany.
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10
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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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11
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Stubbs M, Hey J, Fung A, Maynard J, Parnell B, Sinha A. P.21 A multidisciplinary safety checklist to facilitate continuous fetal heart monitoring during labour epidural analgesia insertion. Int J Obstet Anesth 2022. [DOI: 10.1016/j.ijoa.2022.103317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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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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13
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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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14
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Zanetti C, Kumar R, Ender J, Godavarthy PS, Hartmann M, Hey J, Breuer K, Weissenberger ES, Minciacchi VR, Karantanou C, Gu Z, Roberts KG, Metzler M, Stock W, Mullighan CG, Bloomfield CD, Filmann N, Bankov K, Hartmann S, Hasserjian RP, Cousins AF, Halsey C, Plass C, Lipka DB, Krause DS. The age of the bone marrow microenvironment influences B-cell acute lymphoblastic leukemia progression via CXCR5-CXCL13. Blood 2021; 138:1870-1884. [PMID: 34424946 PMCID: PMC8767790 DOI: 10.1182/blood.2021011557] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 03/02/2021] [Accepted: 08/05/2021] [Indexed: 12/17/2022] Open
Abstract
B-cell acute lymphoblastic leukemia (B-ALL) occurs most commonly in children, whereas chronic myeloid leukemia is more frequent in adults. The myeloid bias of hematopoiesis in elderly individuals has been considered causative, but the age of the bone marrow microenvironment (BMM) may be contributory. Using various murine models of B-ALL in young vs old mice, we recapitulated B-ALL preponderance in children vs adults. We showed differential effects of young vs old BM macrophages on B-ALL cell function. Molecular profiling using RNA- and ATAC-sequencing revealed pronounced differences in young vs old BMM-derived macrophages and enrichment for gene sets associated with inflammation. In concordance with the role of C-X-C motif chemokine (CXCL) 13 for disease-associated B-cell chemoattraction, we found CXCL13 to be highly expressed in young macrophages on a translational compared with a transcriptional level. Inhibition of CXCL13 in BM macrophages impaired leukemia cell migration and decreased the proliferation of cocultured B-ALL cells, whereas recombinant CXCL13 increased pAKT and B-ALL cell expansion. Pretreatment of B-ALL-initiating cells with CXCL13 accelerated B-ALL progression. Deficiency of Cxcr5, the receptor for CXCL13, on B-ALL-initiating cells prolonged murine survival, whereas high expression of CXCR5 in pediatric B-ALL may predict central nervous system relapse. CXCL13 staining was increased in bone sections from pediatric compared with adult patients with B-ALL. Taken together, our study shows that the age of the BMM and, in particular, BM macrophages influence the leukemia phenotype. The CXCR5-CXCL13 axis may act as prognostic marker and an attractive novel target for the treatment of B-ALL.
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Affiliation(s)
- Costanza Zanetti
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Rahul Kumar
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Joscha Ender
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Parimala S Godavarthy
- Department of Internal Medicine II, Hematology, Oncology, University Hospital Tübingen, Tübingen, Germany
| | - Mark Hartmann
- Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German-Israeli Helmholtz Research School in Cancer Biology, Heidelberg, Germany
- Faculty of Biosciences, Ruprecht Karls University of Heidelberg, Heidelberg, Germany
| | - Kersten Breuer
- Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Eva S Weissenberger
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Valentina R Minciacchi
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Christina Karantanou
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Zhaohui Gu
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Kathryn G Roberts
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Markus Metzler
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Wendy Stock
- Department of Hematology and Oncology, University of Chicago, Chicago, IL
| | | | | | | | - Katrin Bankov
- Department of Pathology, Goethe University, Frankfurt am Main, Germany
| | - Sylvia Hartmann
- Department of Pathology, Goethe University, Frankfurt am Main, Germany
| | - Robert P Hasserjian
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Antony F Cousins
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christina Halsey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christoph Plass
- Cancer Epigenetics Group, Division of Epigenomics and Cancer Risk Factors, DKFZ, Heidelberg, Germany
| | - Daniel B Lipka
- Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Faculty of Medicine, Otto von Guericke University, Magdeburg, Germany
| | - Daniela S Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Frankfurt Cancer Institute, Frankfurt am Main, Germany; and
- Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
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15
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Bacher H, Schweyen R, Olms C, Arnold C, Setz J, Hey J. 10-Year Clinical Comparative Study of Ceramic and Composite Veneered Metal Crowns. Eur J Prosthodont Restor Dent 2021; 29. [PMID: 33769724 DOI: 10.1922/ejprd_2148bacher11] [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] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The rejection of composite veneerings in fixed partial dentures is primarily caused by the inadequacy of the bonds between the metal framework and the composite veneering. The development of improved veneering composites necessitates an investigation of their clinical suitability compared with ceramic materials. Nineteen patients with at least two suitable, adjacent natural teeth for crowning were treated with 64 high noble alloy crowns. The adjacent crowns were veneered with ceramic (IPS inline) and composite materials (SR Adoro). Seven follow-up examinations were carried out over a period of 10 years. The crowns were investigated for mechanical defects, periodontal parameters, and discolorations. The survival rates of the ceramic veneered metal crowns (CeMCs) and composite veneered metal crowns (CoMCs) at the 10-year follow-up were 87.1 and 87.9%, respectively. The success rates of the crowns after 10 years were 83.9% for CeMCs and 51.5% for CoMCs (log-rank test, p = 0.009). No significant differences between the groups were found in the periodontal parameters (Kruskal-Wallis one-way analysis of variance, ANOVA p ⟩ 0.05). After 10 years, discoloration patterns of the two materials differed significantly (Mann-Whitney-U-test, p = 0.017). Thus, despite the improvements associated with CoMCs, CeMCs remain the gold standard for veneered metal crowns.
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Affiliation(s)
- H Bacher
- Martin-Luther-University Halle-Wittenberg, Department of Prosthodontics, Magdeburger Str. 16, 06112 Halle, Germany
| | - R Schweyen
- Martin-Luther-University Halle-Wittenberg, Department of Prosthodontics, Magdeburger Str. 16, 06112 Halle, Germany
| | - C Olms
- University of Leipzig, Department of Prosthodontics and Material Science, Liebigstr. 12, 04103 Leipzig, Germany
| | - C Arnold
- Martin-Luther-University Halle-Wittenberg, Department of Prosthodontics, Magdeburger Str. 16, 06112 Halle, Germany
| | - J Setz
- Martin-Luther-University Halle-Wittenberg, Department of Prosthodontics, Magdeburger Str. 16, 06112 Halle, Germany
| | - J Hey
- Charité - Universitätsmedizin Berlin, Department of Prosthodontics, Geriatric Dentistry and Craniomandibular Disorders, Assmannshauser Strasse 4-6, 14197 Berlin
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16
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Touzart A, Mayakonda A, Smith C, Hey J, Toth R, Cieslak A, Andrieu GP, Tran Quang C, Latiri M, Ghysdael J, Spicuglia S, Dombret H, Ifrah N, Macintyre E, Lutsik P, Boissel N, Plass C, Asnafi V. Epigenetic analysis of patients with T-ALL identifies poor outcomes and a hypomethylating agent-responsive subgroup. Sci Transl Med 2021; 13:13/595/eabc4834. [PMID: 34039737 DOI: 10.1126/scitranslmed.abc4834] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/10/2020] [Accepted: 05/07/2021] [Indexed: 12/14/2022]
Abstract
Adult "T cell" acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy that is associated with poor outcomes, requiring additional therapeutic options. The DNA methylation landscapes of adult T-ALL remain undercharacterized. Here, we systematically analyzed the DNA methylation profiles of normal thymic-sorted T cell subpopulations and 143 primary adult T-ALLs as part of the French GRAALL 2003-2005 trial. Our results indicated that T-ALL is epigenetically heterogeneous consisting of five subtypes (C1-C5), which were either associated with co-occurring DNA methyltransferase 3 alpha (DNMT3A)/isocitrate dehydrogenase [NADP(+)] 2 (IDH2) mutations (C1), TAL bHLH transcription factor 1, erythroid differentiation factor (TAL1) deregulation (C2), T cell leukemia homeobox 3 (TLX3) (C3), TLX1/in cis-homeobox A9 (HOXA9) (C4), or in trans-HOXA9 overexpression (C5). Integrative analysis of DNA methylation and gene expression identified potential cluster-specific oncogenes and tumor suppressor genes. In addition to an aggressive hypomethylated subgroup (C1), our data identified an unexpected subset of hypermethylated T-ALL (C5) associated with poor outcome and primary therapeutic response. Using mouse xenografts, we demonstrated that hypermethylated T-ALL samples exhibited therapeutic responses to the DNA hypomethylating agent 5-azacytidine, which significantly (survival probability; P = 0.001 for C3, 0.01 for C4, and 0.0253 for C5) delayed tumor progression. These findings suggest that epigenetic-based therapies may provide an alternative treatment option in hypermethylated T-ALL.
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Affiliation(s)
- Aurore Touzart
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Université de Paris (Descartes), 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
| | - Anand Mayakonda
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Charlotte Smith
- Université de Paris (Descartes), 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
| | - Joschka Hey
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany.,Germany-Israeli Helmholtz Research School in Cancer Biology, 69120 Heidelberg, Germany
| | - Reka Toth
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Agata Cieslak
- Université de Paris (Descartes), 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
| | - Guillaume P Andrieu
- Université de Paris (Descartes), 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
| | - Christine Tran Quang
- Institut Curie, Orsay, France.,CNRS UMR3348, Institut Curie, Orsay, France.,INSERM 1278, Centre Universitaire, Orsay, France.,PSL Research University, Paris, France.,Paris-Saclay, 91400 Orsay, France
| | - Mehdi Latiri
- Université de Paris (Descartes), 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
| | - Jacques Ghysdael
- Institut Curie, Orsay, France.,CNRS UMR3348, Institut Curie, Orsay, France.,INSERM 1278, Centre Universitaire, Orsay, France.,PSL Research University, Paris, France.,Paris-Saclay, 91400 Orsay, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), Equipe labellisée Ligue, UMR1090, 13288 Marseille, France
| | - Hervé Dombret
- Université Paris Diderot, Institut Universitaire d'Hématologie, EA-3518, Assistance Publique-Hôpitaux de Paris, University Hospital Saint-Louis, 75010 Paris, France
| | - Norbert Ifrah
- PRES LUNAM, CHU Angers service des Maladies du Sang et INSERM U 892, 49933 Angers, France
| | - Elizabeth Macintyre
- Université de Paris (Descartes), 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
| | - Pavlo Lutsik
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Cancer Research Consortium (DKTK), 69120 Heidelberg, Germany
| | - Nicolas Boissel
- Université Paris Diderot, Institut Universitaire d'Hématologie, EA-3518, Assistance Publique-Hôpitaux de Paris, University Hospital Saint-Louis, 75010 Paris, France
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. .,German Cancer Research Consortium (DKTK), 69120 Heidelberg, Germany
| | - Vahid Asnafi
- Université de Paris (Descartes), 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.
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17
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Mayakonda A, Schönung M, Hey J, Batra RN, Feuerstein-Akgoz C, Köhler K, Lipka DB, Sotillo R, Plass C, Lutsik P, Toth R. Methrix: an R/bioconductor package for systematic aggregation and analysis of bisulfite sequencing data. Bioinformatics 2020; 36:5524-5525. [PMID: 33346800 DOI: 10.1093/bioinformatics/btaa1048] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/20/2020] [Accepted: 12/08/2020] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Whole genome bisulfite sequencing (WGBS), measures DNA methylation at base pair resolution resulting in large bedGraph like coverage files. Current options for processing such files are hindered by discrepancies in file format specification, speed and memory requirements. RESULTS We developed methrix, an R package, which provides a toolset for systematic analysis of large datasets. Core functionality of the package includes a comprehensive bedGraph or similar tab-separated text file reader - which summarizes methylation calls based on annotated reference indices, infers and collapses strands, and handles uncovered reference CpG sites while facilitating a flexible input file format specification. Additional optimized functions for quality control filtering, sub-setting, and visualization allow user-friendly and effective processing of WGBS results. Easy integration with tools for differentially methylated region (DMR) calling and annotation further eases the analysis of genome-wide methylation data. Overall, methrix enriches established WGBS workflows by bringing together computational efficiency and versatile functionality. AVAILABILITY AND IMPLEMENTATION Methrix is implemented as an R package, made available under MIT license at https://github.com/CompEpigen/methrix and can be installed from the Bioconductor repository. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anand Mayakonda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Maximilian Schönung
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,German-Israeli Helmholtz Research School in Cancer Biology, Germany
| | - Rajbir Nath Batra
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Clarissa Feuerstein-Akgoz
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Kristin Köhler
- Bioinformatics Bachelor program, Free University Berlin, Berlin, 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
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Research Consortium (DKTK), Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Reka Toth
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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18
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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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19
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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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20
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Schweyen R, Beuer F, Bochskanl M, Hey J. Implementing a new curriculum for computer-assisted restorations in prosthetic dentistry. Eur J Dent Educ 2018; 22:e237-e247. [PMID: 28653464 DOI: 10.1111/eje.12278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/28/2017] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Computer-aided design/computer-aided manufacturing (CAD/CAM) of fixed prosthetic restorations has gained popularity in the last decade. However, this field of dentistry has not been integrated in the dental curriculum at most universities. MATERIAL AND METHODS According to the method of Kern, a curriculum was designed and established on a voluntary basis in the prosthetic education of a German dental school. The success of the implementation was measured by evaluation carried out by the participants on a visual analogue scale. Furthermore, the clinical performance of the fabricated restorations was evaluated. RESULTS Ninety-four percent of all students participated in the CAD/CAM curriculum indicating considerable interest. Nearly half of all students used the acquired knowledge to design crowns for their patients. All restorations fabricated by participants of the new CAD/CAM programme showed good clinical performance. DISCUSSION By phasing-in the CAD/CAM training programme, independent CAD/CAM-based fabrication of all-ceramic crowns increased student's self-confidence in tooth preparation. A tendency was found that students using CAD/CAM technology prepared more teeth than their fellow students who did not use CAD/CAM technology. Further studies are required to investigate the influence of independent CAD/CAM-based single-crown fabrication on the quality of the preparation.
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Affiliation(s)
- R Schweyen
- Department of Prosthodontics, University of Halle, Halle, Germany
| | - F Beuer
- Department of Prosthodontics, Charité - University of Berlin, Berlin, Germany
| | - M Bochskanl
- Department of Prosthodontics, University of Halle, Halle, Germany
| | - J Hey
- Department of Prosthodontics, University of Halle, Halle, Germany
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Papadimitriou-Olivgeris M, Bartzavali C, Christofidou M, Bereksi N, Hey J, Zambardi G, Spiliopoulou I. Performance of chromID® CARBA medium for carbapenemases-producing Enterobacteriaceae detection during rectal screening. Eur J Clin Microbiol Infect Dis 2013; 33:35-40. [PMID: 23912722 DOI: 10.1007/s10096-013-1925-6] [Citation(s) in RCA: 33] [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: 05/31/2013] [Accepted: 07/03/2013] [Indexed: 10/26/2022]
Abstract
Chromogenic chromID® CARBA medium was compared with CDC method and MacConkey agar with imipenem for its performance in detecting carbapenemase-producing Enterobacteriaceae (CPE) during a faecal screening surveillance program. Double rectal swabs were collected from patients hospitalized in the ICU. One swab was inoculated onto the solid media chromID® CARBA and MacConkey agar with imipenem, while the other was tested according to CDC protocol. Suspected colonies from all procedures were identified to species level and tested for their susceptibility to carbapenems by phenotypic tests. All carbapenem non-susceptible isolates were tested by the modified Hodge test (MHT) and synergy tests. Positive results were confirmed by PCR testing for carbapenemase gene detection. Performance of all three procedures applied was statistically analyzed as compared to MHT and PCR results for the presence of carbapenemase-encoding genes. Out of 177 rectal samples tested, 86 samples were found to contain one or more CPE verified by molecular detection of carbapenemase encoding genes among isolated Enterobacteriaceae. Sensitivity of chromID® CARBA was 96.5 % in clinical samples. Specificity was 91.2 % at the reading level and 100.0 % after Gram staining. chromID® CARBA performed with high accuracy among the phenotypic methods applied, giving early results.
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Schweyen R, Hey J, Fränzel W, Vordermark D, Hildebrandt G, Kuhnt T. [Radiation-related caries: etiology and possible preventive strategies. What should the radiotherapist know?]. Strahlenther Onkol 2011; 188:21-8. [PMID: 22189435 DOI: 10.1007/s00066-011-0011-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Accepted: 06/30/2011] [Indexed: 11/30/2022]
Abstract
BACKGROUND After radiation treatment of head-and-neck cancer, the impairment of patient's quality of life still remains an issue. After completion of the treatment course, a substantial number of patients develop so-called radiation caries. In addition, almost 50% of all cases of infectious osteoradionecrosis (iORN) of the jaws are directly associated with radiation caries. This review addresses our current knowledge on the etiology and pathogenesis of radiation caries including possible preventive strategies. MATERIALS AND METHODS A PubMed search using the terms "radiation caries" ("radiation related caries", "radiation related damage to dentition") and "radiogenic caries" ("postradiation caries", "dental complications and radiotherapy") was performed. The analysis of its content focused on the etiology, the pathogenesis, and the available knowledge on prophylaxis as well as treatment of radiation caries. RESULTS For this review, 60 publications were selected. As main causal factors for radiogenic caries, either indirect impairment, resulting from alterations in the oral environment (e.g., radiation-induced xerostomia) or direct radiation-induced damage in teeth hard tissues are discussed. Radiation caries remains a lifelong threat and, therefore, requires permanent prevention programs. CONCLUSION To enable optimal medical care of the patients during the time course of radiotherapy as well as afterwards, close interdisciplinary cooperation between radiotherapists, oral surgeons, otorhinolaryngologists, and dentists is absolutely essential.
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Affiliation(s)
- R Schweyen
- Universitätspoliklinik für Prothetik, Martin-Luther-Universität Halle-Wittenberg, Halle-Wittenberg, Deutschland
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Hey J, Leusser D, Kratzert D, Kling C, Stalke D. Evaluating electron delocalization: the need for aromaticity descriptors. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311088581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Kuhnt T, Seidel J, Setz J, Gerlach R, Vordermark D, Gernhardt C, Hey J. Recovery of the Parotid Gland Function after Radiotherapy of Head and Neck Cancer. Int J Radiat Oncol Biol Phys 2010. [DOI: 10.1016/j.ijrobp.2010.07.1033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
The species problem is the long-standing failure of biologists to agree on how we should identify species and how we should define the word 'species'. The innumerable attacks on the problem have turned the often-repeated question 'what are species?' into a philosophical conundrum. Today, the preferred form of attack is the well-crafted argument, and debaters seem to have stopped inquiring about what new information is needed to solve the problem. However, our knowledge is not complete and we have overlooked something. The species problem can be overcome if we understand our own role, as conflicted investigators, in causing the problem.
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Abstract
Levels and patterns of human DNA sequence variation vary widely among loci. However, some of this variation may be due to the different populations used in different studies. So far, few studies of diverse human populations have compared different genetic loci for the same samples of populations and individuals. Here, we present new polymorphism data from intron 4 of the Factor IX gene (FIX) sequenced in diverse Old World populations. An explicit comparison is made with another X-linked gene, PDHA1, for which the sampling of individuals was very similar. Despite having a similar amount of divergence from chimpanzees, as do other nuclear genes, FIX has comparatively much less DNA sequence variation among humans. Nucleotide diversity at FIX is the lowest among the existing non-Y chromosome nuclear gene datasets and is less than 10% of the diversity found at PDHA1. Estimates of effective population size based on FIX are 8,558, about half of the value obtained for PDHA1, and the time to the most recent common ancestry among human FIX gene copies (282,000 years) is one of the most recent estimates reported for human genes. Analyses presented here suggest a history for the FIX region that includes recent positive directional selection, or background, selection. The general conclusion emerging is that very large variations can exist between the histories of similar genomic regions, even when sampling differences are minimized.
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Affiliation(s)
- E E Harris
- Universidade de São Paulo, Cidade Universitaria, Departamento de Biologia, Instituto de Biociências, Rua do Matão-Travessa 14 number 321, CEP 05508-900, São Paulo, Brazil.
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Kliman RM, Andolfatto P, Coyne JA, Depaulis F, Kreitman M, Berry AJ, McCarter J, Wakeley J, Hey J. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 2000; 156:1913-31. [PMID: 11102384 PMCID: PMC1461354 DOI: 10.1093/genetics/156.4.1913] [Citation(s) in RCA: 299] [Impact Index Per Article: 12.5] [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: 11/14/2022] Open
Abstract
The origins and divergence of Drosophila simulans and close relatives D. mauritiana and D. sechellia were examined using the patterns of DNA sequence variation found within and between species at 14 different genes. D. sechellia consistently revealed low levels of polymorphism, and genes from D. sechellia have accumulated mutations at a rate that is approximately 50% higher than the same genes from D. simulans. At synonymous sites, D. sechellia has experienced a significant excess of unpreferred codon substitutions. Together these observations suggest that D. sechellia has had a reduced effective population size for some time, and that it is accumulating slightly deleterious mutations as a result. D. simulans and D. mauritiana are both highly polymorphic and the two species share many polymorphisms, probably since the time of common ancestry. A simple isolation speciation model, with zero gene flow following incipient species separation, was fitted to both the simulans/mauritiana divergence and the simulans/sechellia divergence. In both cases the model fit the data quite well, and the analyses revealed little evidence of gene flow between the species. The exception is one gene copy at one locus in D. sechellia, which closely resembled other D. simulans sequences. The overall picture is of two allopatric speciation events that occurred quite near one another in time.
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Affiliation(s)
- R M Kliman
- Department of Genetics, Rutgers University, Piscataway, New Jersey 08854-8082, USA
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Affiliation(s)
- M A Noor
- Department of Biological Sciences, Louisiana State University, Baton Rouge 70803, USA.
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Hey J, Harris E. Origins of modern humans still look recent. Curr Biol 2000; 10:R8-9. [PMID: 10660285 DOI: 10.1016/s0960-9822(99)00274-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Abstract
The issue of whether the malaria parasite Plasmodium falciparum is effectively clonal, as some argue, or undergoes outcrossing at a high rate, as many others believe, has been controversial. Recent data support the latter view, though no doubt the puzzle has not yet been laid to rest.
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Affiliation(s)
- J Hey
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Ashworth Labs, King's Buildings, West Mains Road, Edinburgh, EH9 3JT, Scotland, UK.
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Abstract
The domestication of all major crop plants occurred during a brief period in human history about 10,000 years ago. During this time, ancient agriculturalists selected seed of preferred forms and culled out seed of undesirable types to produce each subsequent generation. Consequently, favoured alleles at genes controlling traits of interest increased in frequency, ultimately reaching fixation. When selection is strong, domestication has the potential to drastically reduce genetic diversity in a crop. To understand the impact of selection during maize domestication, we examined nucleotide polymorphism in teosinte branched1, a gene involved in maize evolution. Here we show that the effects of selection were limited to the gene's regulatory region and cannot be detected in the protein-coding region. Although selection was apparently strong, high rates of recombination and a prolonged domestication period probably limited its effects. Our results help to explain why maize is such a variable crop. They also suggest that maize domestication required hundreds of years, and confirm previous evidence that maize was domesticated from Balsas teosinte of southwestern Mexico.
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Affiliation(s)
- R L Wang
- Department of Plant Biology, University of Minnesota, St Paul 55108, USA
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Abstract
Diverse African and non-African samples of the X-linked PDHA1 (pyruvate dehydrogenase E1 alpha subunit) locus revealed a fixed DNA sequence difference between the two sample groups. The age of onset of population subdivision appears to be about 200 thousand years ago. This predates the earliest modern human fossils, suggesting the transformation to modern humans occurred in a subdivided population. The base of the PDHA1 gene tree is relatively ancient, with an estimated age of 1.86 million years, a late Pliocene time associated with early species of Homo. PDHA1 revealed very low variation among non-Africans, but in other respects the data are consistent with reports from other X-linked and autosomal haplotype data sets. Like these other genes, but in conflict with microsatellite and mitochondrial data, PDHA1 does not show evidence of human population expansion.
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Affiliation(s)
- E E Harris
- Department of Genetics, Rutgers University, Nelson Biological Labs, 604 Allison Road, Piscataway, NJ 08854-8082, USA
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Aslanian R, Brown JE, Shih NY, wa Mutahi M, Green MJ, She S, Del Prado M, West R, Hey J. 4-[(1H-imidazol-4-yl) methyl] benzamidines and benzylamidines: novel antagonists of the histamine H3 receptor. Bioorg Med Chem Lett 1998; 8:2263-8. [PMID: 9873525 DOI: 10.1016/s0960-894x(98)00399-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A series of amidine substituted phenyl-, benzyl-, and phenethylimidazoles based on the known H3 agonist SK&F 91606 (4) has been synthesized and tested as ligands for the histamine H3 receptor. Insertion of a phenyl ring between the imidazole ring and the amidine moiety produces antagonists. The benzyl series was found to be the most potent and was further investigated. Compounds 9c and 18 (entries 5 and 12, Table 1) are potent ligands for the H3 receptor with K(i) values of 16 nM and 7.2 nM respectively. In vivo, both compounds were shown to be equipotent to thioperamide (2), the standard H3 antagonist.
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Affiliation(s)
- R Aslanian
- Schering-Plough Research Institute, Kenilworth, NJ 07033, USA
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Abstract
If multiple linked polymorphisms are under natural selection, then conflicts arise and the efficiency of natural selection is hindered relative to the case of no linkage. This simple interaction between linkage and natural selection creates an opportunity for mutations that raise the level of recombination to increase in frequency and have an enhanced chance of fixation. This important finding by S. Otto and N. Barton means that mutations that raise the recombination rate, but are otherwise neutral, will be selectively favored under fairly general circumstances of multilocus selection and linkage. The effect described by Otto and Barton, which was limited to neutral modifiers, can also be extended to include all modifiers of recombination, both beneficial and deleterious. Computer simulations show that beneficial mutations that also increase recombination have an increased chance of fixation. Similarly, deleterious mutations that also decrease recombination have an increased chance of fixation. The results suggest that a simple model of recombination modifiers, including both neutral and pleiotropic modifiers, is a necessary explanation for the evolutionary origin of recombination.
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Affiliation(s)
- J Hey
- Department of Genetics, Rutgers University, Nelson Biological Labs, Piscataway, New Jersey 08854-8082, USA.
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Abstract
The divergence of Drosophila pseudoobscura and close relatives D. persimilis and D. pseudoobscura bogotana has been studied using comparative DNA sequence data from multiple nuclear loci. New data from the Hsp82 and Adh regions, in conjunction with existing data from Adh and the Period locus, are examined in the light of various models of speciation. The principal finding is that the three loci present very different histories, with Adh indicating large amounts of recent gene flow among the taxa, while little or no gene flow is apparent in the data from the other loci. The data were compared with predictions from several isolation models of divergence. These models include no gene flow, and they were found to be incompatible with the data. Instead the DNA data, taken together with other evidence, seem consistent with divergence models in which natural selection acts against gene flow at some loci more than at others. This family of models includes some sympatric and parapatric speciation models, as well as models of secondary contact and subsequent reinforcement of sexual isolation.
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Affiliation(s)
- R L Wang
- Biological Sciences, Rutgers University, Nelson Labs, Piscataway, New Jersey 08855-1059, USA
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Abstract
Population genetic models often use a population recombination parameter 4Nc, where N is the effective population size and c is the recombination rate per generation. In many ways 4Nc is comparable to 4Nu, the population mutation rate. Both combine genome level and population level processes, and together they describe the rate of production of genetic variation in a population. However, 4Nc is more difficult to estimate. For a population sample of DNA sequences, historical recombination can only be detected if polymorphisms exist, and even then most recombination events are not detectable. This paper describes an estimator of 4Nc, hereafter designated gamma (gamma), that was developed using a coalescent model for a sample of four DNA sequences with recombination. The reliability of gamma was assessed using multiple coalescent simulations. In general gamma has low to moderate bias, and the reliability of gamma is comparable, though less, than that for a widely used estimator of 4Nu. If there exists an independent estimate of the recombination rate (per generation, per base pair), gamma can be used to estimate the effective population size or the neutral mutation rate.
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Affiliation(s)
- J Hey
- Department of Ecology, Evolution and Natural Resources, Nelson Laboratories, Rutgers University, Piscataway, New Jersey 08855-1059, USA.
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Abstract
The expected numbers of different categories of polymorphic sites are derived for two related models of population history the isolation model, in which an ancestral population splits into two descendents, and the size-change model, in which a single population undergoes an instantaneous change in size. For the isolation model, the observed numbers of shared, fixed, and exclusive polymorphic sites are used to estimate the relative sizes of the three populations, ancestral plus two descendent, as well as the time of the split. For the size change model, the numbers of sites segregating at particular frequencies in the sample are used to estimate the relative sizes of the ancestral and descendent populations plus the time the change took place. Parameters are estimated by choosing values that most closely equate expectations with observations. Computer simulations show that current and historical population parameters can be estimated accurately. The methods are applied to DNA data from two species of Drosophila and to some human mitochondrial DNA sequences.
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Affiliation(s)
- J Wakeley
- Department of Biological Sciences, Rutgers University, Piscataway, New Jersey 08855-1059, USA.
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Abstract
Human mitochondrial DNA (mtDNA) sequences reveal an abundance of polymorphic sites in which the frequencies of the segregating bases are very different. A typical polymorphism involves one base at low frequency and the other base at high frequency. In contrast, nuclear gene data sets tend to show an excess of polymorphisms in which both segregating bases are at intermediate frequencies. A new statistical test of this difference finds significant differences between mtDNA and nuclear gene data sets reported in the literature. However, differences in the polymorphism patterns could be caused by different sample origins for the different data sets. To examine the mtDNA-nuclear difference more closely, DNA sequences were generated from a portion of the X-linked pyruvate dehydrogenase E1 alpha subunit (PDHA1) locus and from a portion of mitochondrial control region I (CRI) from each of eight individuals, four from sub-Saharan Africa. The two genes revealed a significant difference in the site frequency distribution of polymorphic sites. PDHA1 revealed an excess of intermediate-frequency polymorphisms, while CRI showed an excess of sites with the low-high frequency pattern. The discrepancy suggests that mitochondrial variation has been shaped by natural selection, and may not be ideal for some questions on human origins.
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Affiliation(s)
- J Hey
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, Piscataway 08855-1059, USA.
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Abstract
Thirty-five period locus sequences from Drosophila pseudoobscura and its siblings species, D. p. bogotana, D. persimilis, and D. miranda, were studied. A large amount of variation was found within D. pseudoobscura and D. persimilis, consistent with histories of large effective population sizes. D. p. bogotana, however, has a severe reduction in diversity. Combined analysis of per with two other loci, in both D. p. bogotana and D. pseudoobscura, strongly suggest this reduction is due to recent directional selection at or near per within D. p. bogotana. Since D. p. bogotana is highly variable and shares variation with D. pseudoobscura at other loci, the low level of variation at per within D. p. bogotana can not be explained by a small effective population size or by speciation via founder event. Both D. pseudoobscura and D. persimilis have considerable intraspecific gene flow. A large portion of one D. persimilis sequence appears to have arisen via introgression from D. pseudoobscura. The time of this event appears to be well after the initial separation of these two species. The estimated times since speciation are one mya for D. pseudoobscura and D. persimilis and 2 mya since the formation of D. miranda.
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Affiliation(s)
- R L Wang
- Department of Biological Sciences, Rutgers University, Piscataway, New Jersey 08855-1059, USA
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Abstract
The virilis phylad of the Drosophila virilis group consists of five closely related taxa: D. virilis, D. lummei, D. novamexicana, D. americana americana and D. americana texana. DNA sequences from a 2.1-kb pair portion of the period locus were generated in four to eight individuals from each of the five taxa. We found evidence of recombination and high levels of variation within species. We found no evidence of recent natural selection. Surprisingly there was no evidence of divergence between D. a. americana and D. a. texana, and they collectively appear to have had a large historical effective population size. The ranges of these two taxa overlap in a large hybrid zone that has been delineated in the eastern U.S. on the basis of the geographic pattern of a chromosomal fusion. Also surprisingly, D. novamexicana appears to consist of two distinct groups each with low population size and no gene flow between them.
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Affiliation(s)
- H Hilton
- Department of Biological Sciences, Rutgers University, Piscataway, NJ 08855-1059, USA.
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Price JW, Anton G, Arends J, Beulertz W, Bock A, Breuer M, Büchler K, Clajus M, Detemple P, Hey J, Krämer D, Meyer W, Nefkens BM, Nöldeke G, Schneider W, Zucht B. eta meson photoproduction on hydrogen near threshold. Phys Rev C Nucl Phys 1995; 51:R2283-R2287. [PMID: 9970384 DOI: 10.1103/physrevc.51.r2283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Abstract
Codon bias varies widely among the loci of Drosophila melanogaster, and some of this diversity has been explained by variation in the strength of natural selection. A study of correlations between intron and coding region base composition shows that variation in mutation pattern also contributes to codon bias variation. This finding is corroborated by an analysis of variance (ANOVA), which shows a tendency for introns from the same gene to be similar in base composition. The strength of base composition correlations between introns and codon third positions is greater for genes with low codon bias than for genes with high codon bias. This pattern can be explained by an overwhelming effect of natural selection, relative to mutation, in highly biased loci. In particular, this correlation is absent when examining fourfold degenerate sites of highly biased genes. In general, it appears that selection acts more strongly in choosing among fourfold degenerate codons than among twofold degenerate codons. Although the results indicate regional variation in mutational bias, no evidence is found for large scale regions of compositional homogeneity.
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Affiliation(s)
- R M Kliman
- Department of Biological Sciences, Rutgers University, Piscataway, New Jersey 08855-1059
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Mrzljak RI, Bond AM, Cardwell TJ, Cattrall RW, Newman OMG, Champion BR, Hey J. Efficient procedures for the voltammetric determination of total arsenic in zinc and cadmium plant electrolyte process streams and in industrial effluents. Analyst 1994. [DOI: 10.1039/an9941901051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Synonymous codons are not used equally in many organisms, and the extent of codon bias varies among loci. Earlier studies have suggested that more highly expressed loci in Drosophila melanogaster are more biased, consistent with findings from several prokaryotes and unicellular eukaryotes that codon bias is partly due to natural selection for translational efficiency. We link this model of varying selection intensity to the population-genetics prediction that the effectiveness of natural selection is decreased under reduced recombination. In analyses of 385 D. melanogaster loci, we find that codon bias is reduced in regions of low recombination (i.e., near centromeres and telomeres and on the fourth chromosome). The effect does not appear to be a linear function of recombination rate; rather, it seems limited to regions with the very lowest levels of recombination. The large majority of the genome apparently experiences recombination at a sufficiently high rate for effective natural selection against suboptimal codons. These findings support models of the Hill-Robertson effect and genetic hitchhiking and are largely consistent with multiple reports of low levels of DNA sequence variation in regions of low recombination.
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Affiliation(s)
- R M Kliman
- Nelson Labs, Rutgers University, Piscataway, New Jersey 08855-1059
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Abstract
Two regions of the genome, a 1-kbp portion of the zeste locus and a 1.1-kbp portion of the yolk protein 2 locus, were sequenced in six individuals from each of four species: Drosophila melanogaster, D. simulans, D. mauritiana, and D. sechellia. The species and strains were the same as those of a previous study of a 1.9-kbp region of the period locus. No evidence was found for recent balancing or directional selection or for the accumulation of selected differences between species. Yolk protein 2 has a high level of amino acid replacement variation and a low level of synonymous variation, while zeste has the opposite pattern. This contrast is consistent with information on gene function and patterns of codon bias. Polymorphism levels are consistent with a ranking of effective population sizes, from low to high, in the following order: D. sechellia, D. melanogaster, D.mauritiana, and D. simulans. The apparent species relationships are very similar to those suggested by the period locus study. In particular, D. simulans appears to be a large population that is still segregating variation that arose before the separation of D. mauritiana and D. sechellia. It is estimated that the separation of ancestral D. melanogaster from the other species occurred 2.5-3.4 Mya. The separations of D. sechellia and D. mauritiana from ancestral D. simulans appear to have occurred 0.58-0.86 Mya, with D. mauritiana having diverged from ancestral D. simulans 0.1 Myr more recently than D. sechellia.
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Affiliation(s)
- J Hey
- Department of Biological Sciences, Rutgers University, Piscataway, New Jersey 08855
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50
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Abstract
A 1.9-kilobase region of the period locus was sequenced in six individuals of Drosophila melanogaster and from six individuals of each of three sibling species: Drosophila simulans, Drosophila sechellia and Drosophila mauritiana. Extensive genealogical analysis of 174 polymorphic sites reveals a complex history. It appears that D. simulans, as a large population still segregating very old lineages, gave rise to the island species D. mauritiana and D. sechellia. Rather than considering these speciation events as having produced "sister" taxa, it seems more appropriate to consider D. simulans a parent species to D. sechellia and D. mauritiana. The order, in time, of these two phylogenetic events remains unclear. D. mauritiana supports a large number of polymorphisms, many of which are shared with D. simulans, and so appears to have begun and persisted as a large population. In contrast, D. sechellia has very little variation and seems to have experienced a severe population bottleneck. Alternatively, the low variation in D. sechellia could be due to recent directional selection and genetic hitchhiking at or near the per locus.
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Affiliation(s)
- R M Kliman
- Department of Biological Sciences, Nelson Laboratories, Rutgers University, Piscataway, New Jersey 08855-1059
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