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Fischer A, Martirosian P, Machann J, Fränkle B, Schick F. Frequency shifts of free water signals from compact bone: Simulations and measurements using a UTE-FID sequence. Magn Reson Med 2024; 92:257-268. [PMID: 38282291 DOI: 10.1002/mrm.30027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024]
Abstract
PURPOSE Free water in cortical bone is either contained in nearly cylindrical structures (mainly Haversian canals oriented parallel to the bone axis) or in more spherically shaped pores (lacunae). Those cavities have been reported to crucially influence bone quality and mechanical stability. Susceptibility differences between bone and water can lead to water frequency shifts dependent on the geometric characteristics. The purpose of this study is to calculate and measure the frequency distribution of the water signal in MRI in dependence of the microscopic bone geometry. METHODS Finite element modeling and analytical approaches were performed to characterize the free water components of bone. The previously introduced UTE-FID technique providing spatially resolved FID-spectra was used to measure the frequency distribution pixel-wise for different orientations of the bone axis. RESULTS The frequency difference between free water in spherical pores and in canals parallel to B0 amounts up to approximately 100 Hz at 3T. Simulated resonance frequencies showed good agreement with the findings in UTE-FID spectra. The intensity ratio of the two signal components (parallel canals and spherical pores) was found to vary between periosteal and endosteal regions. CONCLUSION Spatially resolved UTE-FID examinations allow the determination of the frequency distribution of signals from free water in cortical bone. This frequency distribution indicates the composition of the signal contributions from nearly spherical cavities and cylindrical canals which allows for further characterization of bone structure and status.
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Affiliation(s)
- Anja Fischer
- Section on Experimental Radiology, University Hospital Tübingen, Tübingen, Germany
- Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz, Center Munich at the University of Tübingen, Tübingen, Germany
- German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Petros Martirosian
- Section on Experimental Radiology, University Hospital Tübingen, Tübingen, Germany
| | - Jürgen Machann
- Section on Experimental Radiology, University Hospital Tübingen, Tübingen, Germany
- Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz, Center Munich at the University of Tübingen, Tübingen, Germany
- German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Bernd Fränkle
- Karlsruhe Institute of Technology, Institute of Mechanical Process Engineering and Mechanics, Karlsruhe, Germany
| | - Fritz Schick
- Section on Experimental Radiology, University Hospital Tübingen, Tübingen, Germany
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2
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Künstner A, Schwarting J, Witte HM, Xing P, Bernard V, Stölting S, Lohneis P, Janke F, Salehi M, Chen X, Kusch K, Sültmann H, Chteinberg E, Fischer A, Siebert R, von Bubnoff N, Merz H, Busch H, Feller AC, Gebauer N. Genome-wide DNA methylation-analysis of blastic plasmacytoid dendritic cell neoplasm identifies distinct molecular features. Leukemia 2024:10.1038/s41375-024-02240-8. [PMID: 38600314 DOI: 10.1038/s41375-024-02240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) constitutes a rare and aggressive malignancy originating from plasmacytoid dendritic cells (pDCs) with a primarily cutaneous tropism followed by dissemination to the bone marrow and other organs. We conducted a genome-wide analysis of the tumor methylome in an extended cohort of 45 BPDCN patients supplemented by WES and RNA-seq as well as ATAC-seq on selected cases. We determined the BPDCN DNA methylation profile and observed a dramatic loss of DNA methylation during malignant transformation from early and mature DCs towards BPDCN. DNA methylation profiles further differentiate between BPDCN, AML, CMML, and T-ALL exhibiting the most striking global demethylation, mitotic stress, and merely localized DNA hypermethylation in BPDCN resulting in pronounced inactivation of tumor suppressor genes by comparison. DNA methylation-based analysis of the tumor microenvironment by MethylCIBERSORT yielded two, prognostically relevant clusters (IC1 and IC2) with specific cellular composition and mutational spectra. Further, the transcriptional subgroups of BPDCN (C1 and C2) differ by DNA methylation signatures in interleukin/inflammatory signaling genes but also by higher transcription factor activity of JAK-STAT and NFkB signaling in C2 in contrast to an EZH2 dependence in C1-BPDCN. Our integrative characterization of BPDCN offers novel molecular insights and potential diagnostic applications.
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Affiliation(s)
- Axel Künstner
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Julian Schwarting
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Hanno M Witte
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Department of Hematology and Oncology, Federal Armed Forces Hospital Ulm, Oberer Eselsberg 40, 89081, Ulm, Germany
| | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Veronica Bernard
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Stephanie Stölting
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Philipp Lohneis
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Maede Salehi
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Kathrin Kusch
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Emil Chteinberg
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Nikolas von Bubnoff
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Hartmut Merz
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Alfred C Feller
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Niklas Gebauer
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany.
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
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3
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Frank D, Patnana PK, Vorwerk J, Mao L, Gopal LM, Jung N, Hennig T, Ruhnke L, Frenz JM, Kuppusamy M, Autry R, Wei L, Sun K, Mohammed Ahmed HM, Künstner A, Busch H, Müller H, Hutter S, Hoermann G, Liu L, Xie X, Al-Matary Y, Nimmagadda SC, Cano FC, Heuser M, Thol F, Göhring G, Steinemann D, Thomale J, Leitner T, Fischer A, Rad R, Röllig C, Altmann H, Kunadt D, Berdel WE, Hüve J, Neumann F, Klingauf J, Calderon V, Opalka B, Dührsen U, Rosenbauer F, Dugas M, Varghese J, Reinhardt HC, von Bubnoff N, Möröy T, Lenz G, Batcha AMN, Giorgi M, Selvam M, Wang E, McWeeney SK, Tyner JW, Stölzel F, Mann M, Jayavelu AK, Khandanpour C. Germ line variant GFI1-36N affects DNA repair and sensitizes AML cells to DNA damage and repair therapy. Blood 2023; 142:2175-2191. [PMID: 37756525 PMCID: PMC10733838 DOI: 10.1182/blood.2022015752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 09/29/2023] Open
Abstract
ABSTRACT Growth factor independence 1 (GFI1) is a DNA-binding transcription factor and a key regulator of hematopoiesis. GFI1-36N is a germ line variant, causing a change of serine (S) to asparagine (N) at position 36. We previously reported that the GFI1-36N allele has a prevalence of 10% to 15% among patients with acute myeloid leukemia (AML) and 5% to 7% among healthy Caucasians and promotes the development of this disease. Using a multiomics approach, we show here that GFI1-36N expression is associated with increased frequencies of chromosomal aberrations, mutational burden, and mutational signatures in both murine and human AML and impedes homologous recombination (HR)-directed DNA repair in leukemic cells. GFI1-36N exhibits impaired binding to N-Myc downstream-regulated gene 1 (Ndrg1) regulatory elements, causing decreased NDRG1 levels, which leads to a reduction of O6-methylguanine-DNA-methyltransferase (MGMT) expression levels, as illustrated by both transcriptome and proteome analyses. Targeting MGMT via temozolomide, a DNA alkylating drug, and HR via olaparib, a poly-ADP ribose polymerase 1 inhibitor, caused synthetic lethality in human and murine AML samples expressing GFI1-36N, whereas the effects were insignificant in nonmalignant GFI1-36S or GFI1-36N cells. In addition, mice that received transplantation with GFI1-36N leukemic cells treated with a combination of temozolomide and olaparib had significantly longer AML-free survival than mice that received transplantation with GFI1-36S leukemic cells. This suggests that reduced MGMT expression leaves GFI1-36N leukemic cells particularly vulnerable to DNA damage initiating chemotherapeutics. Our data provide critical insights into novel options to treat patients with AML carrying the GFI1-36N variant.
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Affiliation(s)
- Daria Frank
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
| | - Pradeep Kumar Patnana
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Jan Vorwerk
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Lianghao Mao
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Lavanya Mokada Gopal
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Noelle Jung
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Thorben Hennig
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Leo Ruhnke
- Department of Internal Medicine I, University Hospital Dresden, Technical University Dresden, Dresden, Germany
| | - Joris Maximillian Frenz
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Maithreyan Kuppusamy
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Robert Autry
- Hopp Children’s Cancer Center, Heidelberg, Germany
| | - Lanying Wei
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Kaiyan Sun
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Helal Mohammed Mohammed Ahmed
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Axel Künstner
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | | | | | | | - Longlong Liu
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoqing Xie
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Yahya Al-Matary
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Subbaiah Chary Nimmagadda
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Fiorella Charles Cano
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Jürgen Thomale
- Institute of Cell Biology, University Hospital Essen, Essen, Germany
| | - Theo Leitner
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research, School of Medicine, Technische Universität München, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research, School of Medicine, Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum Rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
| | | | | | | | - Wolfgang E. Berdel
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Jana Hüve
- Fluorescence Microscopy Facility Münster, Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Felix Neumann
- Fluorescence Microscopy Facility Münster, Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
- Refined Laser Systems GmbH, Münster, Germany
| | - Jürgen Klingauf
- Fluorescence Microscopy Facility Münster, Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Virginie Calderon
- Bioinformatic Core Facility, Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
| | - Bertram Opalka
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
| | - Ulrich Dührsen
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
| | - Nikolas von Bubnoff
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Georg Lenz
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Aarif M. N. Batcha
- Institute of Medical Data Processing, Biometrics and Epidemiology, Faculty of Medicine, Ludwig Maximilians University Munich, Munich, Germany
- Data Integration for Future Medicine, Ludwig Maximilian University Munich, Munich, Germany
| | - Marianna Giorgi
- Roswell Park Comprehensive Cancer Center, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY
| | - Murugan Selvam
- Roswell Park Comprehensive Cancer Center, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY
| | - Eunice Wang
- Roswell Park Comprehensive Cancer Center, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY
| | - Shannon K. McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR
| | - Jeffrey W. Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR
| | - Friedrich Stölzel
- Department of Internal Medicine I, University Hospital Dresden, Technical University Dresden, Dresden, Germany
- Department of Medicine II, Division for Stem Cell Transplantation and Cellular Immunotherapy, University Cancer Center Schleswig-Holstein, University Hospital Schleswig-Holstein Kiel, Christian Albrecht University Kiel, Kiel, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Munich, Germany
| | - Ashok Kumar Jayavelu
- Proteomics and Cancer Cell Signaling Group, Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
- Hopp Children’s Cancer Center, Heidelberg, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Munich, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Cyrus Khandanpour
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University Cancer Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
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4
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Zhou W, Fischer A, Ogwang MD, Luo W, Kerchan P, Reynolds SJ, Tenge CN, Were PA, Kuremu RT, Wekesa WN, Masalu N, Kawira E, Kinyera T, Otim I, Legason ID, Nabalende H, Ayers LW, Bhatia K, Goedert JJ, Gouveia MH, Cole N, Hicks B, Jones K, Hummel M, Schlesner M, Chagaluka G, Mutalima N, Borgstein E, Liomba GN, Kamiza S, Mkandawire N, Mitambo C, Molyneux EM, Newton R, Glaser S, Kretzmer H, Manning M, Hutchinson A, Hsing AW, Tettey Y, Adjei AA, Chanock SJ, Siebert R, Yeager M, Prokunina-Olsson L, Machiela MJ, Mbulaiteye SM. Mosaic chromosomal alterations in peripheral blood leukocytes of children in sub-Saharan Africa. Nat Commun 2023; 14:8081. [PMID: 38057307 PMCID: PMC10700489 DOI: 10.1038/s41467-023-43881-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023] Open
Abstract
In high-income countries, mosaic chromosomal alterations in peripheral blood leukocytes are associated with an elevated risk of adverse health outcomes, including hematologic malignancies. We investigate mosaic chromosomal alterations in sub-Saharan Africa among 931 children with Burkitt lymphoma, an aggressive lymphoma commonly characterized by immunoglobulin-MYC chromosomal rearrangements, 3822 Burkitt lymphoma-free children, and 674 cancer-free men from Ghana. We find autosomal and X chromosome mosaic chromosomal alterations in 3.4% and 1.7% of Burkitt lymphoma-free children, and 8.4% and 3.7% of children with Burkitt lymphoma (P-values = 5.7×10-11 and 3.74×10-2, respectively). Autosomal mosaic chromosomal alterations are detected in 14.0% of Ghanaian men and increase with age. Mosaic chromosomal alterations in Burkitt lymphoma cases include gains on chromosomes 1q and 8, the latter spanning MYC, while mosaic chromosomal alterations in Burkitt lymphoma-free children include copy-neutral loss of heterozygosity on chromosomes 10, 14, and 16. Our results highlight mosaic chromosomal alterations in sub-Saharan African populations as a promising area of research.
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Affiliation(s)
- Weiyin Zhou
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Anja Fischer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | | | - Wen Luo
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Steven J Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Constance N Tenge
- EMBLEM Study, Moi University College of Health Sciences, Eldoret, Kenya
| | - Pamela A Were
- EMBLEM Study, Academic Model Providing Access To Healthcare (AMPATH), Eldoret, Kenya
| | - Robert T Kuremu
- EMBLEM Study, Moi University College of Health Sciences, Eldoret, Kenya
| | - Walter N Wekesa
- EMBLEM Study, Moi University College of Health Sciences, Eldoret, Kenya
| | | | - Esther Kawira
- EMBLEM Study, Shirati Health, Education, and Development Foundation, Shirati, Tanzania
| | - Tobias Kinyera
- EMBLEM Study, St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Isaac Otim
- EMBLEM Study, St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Ismail D Legason
- EMBLEM Study, Kuluva Hospital, Arua, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Hadijah Nabalende
- EMBLEM Study, St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Leona W Ayers
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Kishor Bhatia
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - James J Goedert
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Mateus H Gouveia
- Center for Research on Genomics & Global Health, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Nathan Cole
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael Hummel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Berlin, Germany
- Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, D-10117, Berlin, Germany
| | - Mathias Schlesner
- Biomedical Informatics, Data Mining and Data Analytics, University of Augsburg, Augsburg, Germany
| | - George Chagaluka
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Nora Mutalima
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
- Cancer Epidemiology Unit, University of Oxford, Oxford, UK
| | - Eric Borgstein
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - George N Liomba
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Steve Kamiza
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Nyengo Mkandawire
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Collins Mitambo
- Research Department, Ministry of Health, P.O. Box 30377, Lilongwe 3, Malawi
| | - Elizabeth M Molyneux
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Robert Newton
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michelle Manning
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ann W Hsing
- Stanford Cancer Institute, Stanford University, Stanford, Palo Alto, CA, USA
| | - Yao Tettey
- Department of Pathology, University of Ghana Medical School, College of Health Sciences, P.O. Box KB 52, Korle-Bu, Accra, Ghana
| | - Andrew A Adjei
- Department of Pathology, University of Ghana Medical School, College of Health Sciences, P.O. Box KB 52, Korle-Bu, Accra, Ghana
| | - Stephen J Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Meredith Yeager
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA.
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5
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Schleussner N, Cauchy P, Franke V, Giefing M, Fornes O, Vankadari N, Assi SA, Costanza M, Weniger MA, Akalin A, Anagnostopoulos I, Bukur T, Casarotto MG, Damm F, Daumke O, Edginton-White B, Gebhardt JCM, Grau M, Grunwald S, Hansmann ML, Hartmann S, Huber L, Kärgel E, Lusatis S, Noerenberg D, Obier N, Pannicke U, Fischer A, Reisser A, Rosenwald A, Schwarz K, Sundararaj S, Weilemann A, Winkler W, Xu W, Lenz G, Rajewsky K, Wasserman WW, Cockerill PN, Scheidereit C, Siebert R, Küppers R, Grosschedl R, Janz M, Bonifer C, Mathas S. Transcriptional reprogramming by mutated IRF4 in lymphoma. Nat Commun 2023; 14:6947. [PMID: 37935654 PMCID: PMC10630337 DOI: 10.1038/s41467-023-41954-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 09/20/2023] [Indexed: 11/09/2023] Open
Abstract
Disease-causing mutations in genes encoding transcription factors (TFs) can affect TF interactions with their cognate DNA-binding motifs. Whether and how TF mutations impact upon the binding to TF composite elements (CE) and the interaction with other TFs is unclear. Here, we report a distinct mechanism of TF alteration in human lymphomas with perturbed B cell identity, in particular classic Hodgkin lymphoma. It is caused by a recurrent somatic missense mutation c.295 T > C (p.Cys99Arg; p.C99R) targeting the center of the DNA-binding domain of Interferon Regulatory Factor 4 (IRF4), a key TF in immune cells. IRF4-C99R fundamentally alters IRF4 DNA-binding, with loss-of-binding to canonical IRF motifs and neomorphic gain-of-binding to canonical and non-canonical IRF CEs. IRF4-C99R thoroughly modifies IRF4 function by blocking IRF4-dependent plasma cell induction, and up-regulates disease-specific genes in a non-canonical Activator Protein-1 (AP-1)-IRF-CE (AICE)-dependent manner. Our data explain how a single mutation causes a complex switch of TF specificity and gene regulation and open the perspective to specifically block the neomorphic DNA-binding activities of a mutant TF.
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Affiliation(s)
- Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Pierre Cauchy
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- University Medical Center Freiburg, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center, Berlin, Germany
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, 60-479, Poland
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105, Kiel, Germany
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Naveen Vankadari
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mariantonia Costanza
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, 45122, Essen, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center, Berlin, Germany
| | - Ioannis Anagnostopoulos
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken (CCCMF), Würzburg, Germany
| | - Thomas Bukur
- TRON gGmbH - Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Marco G Casarotto
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Frederik Damm
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
| | - Oliver Daumke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Structural Biology, 13125, Berlin, Germany
| | - Benjamin Edginton-White
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Michael Grau
- Department of Physics, University of Marburg, 35052, Marburg, Germany
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Stephan Grunwald
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Structural Biology, 13125, Berlin, Germany
| | - Martin-Leo Hansmann
- Frankfurt Institute of Advanced Studies, Frankfurt am Main, Germany
- Institute for Pharmacology and Toxicology, Goethe University, Frankfurt am Main, Germany
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lionel Huber
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Eva Kärgel
- Signal Transduction in Tumor Cells, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Simone Lusatis
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Daniel Noerenberg
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
| | - Nadine Obier
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ulrich Pannicke
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anja Reisser
- Department of Physics, Institute of Biophysics, Ulm University, Ulm, Germany
| | - Andreas Rosenwald
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken (CCCMF), Würzburg, Germany
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg-Hessen, Ulm, Germany
| | - Srinivasan Sundararaj
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Andre Weilemann
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Wiebke Winkler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Wendan Xu
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Georg Lenz
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Klaus Rajewsky
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, 13125, Berlin, Germany
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Claus Scheidereit
- Signal Transduction in Tumor Cells, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105, Kiel, Germany
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Ralf Küppers
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, 45122, Essen, Germany
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany.
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany.
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
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6
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Krüger J, Fischer A, Breunig M, Allgöwer C, Schulte L, Merkle J, Mulaw MA, Okeke N, Melzer MK, Morgenstern C, Azoitei N, Seufferlein T, Barth TF, Siebert R, Hohwieler M, Kleger A. DNA methylation-associated allelic inactivation regulates Keratin 19 gene expression during pancreatic development and carcinogenesis. J Pathol 2023; 261:139-155. [PMID: 37555362 DOI: 10.1002/path.6156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/29/2023] [Accepted: 06/09/2023] [Indexed: 08/10/2023]
Abstract
Within the pancreas, Keratin 19 (KRT19) labels the ductal lineage and is a determinant of pancreatic ductal adenocarcinoma (PDAC). To investigate KRT19 expression dynamics, we developed a human pluripotent stem cell (PSC)-based KRT19-mCherry reporter system in different genetic backgrounds to monitor KRT19 expression from its endogenous gene locus. A differentiation protocol to generate mature pancreatic duct-like organoids was applied. While KRT19/mCherry expression became evident at the early endoderm stage, mCherry signal was present in nearly all cells at the pancreatic endoderm (PE) and pancreatic progenitor (PP) stages. Interestingly, despite homogenous KRT19 expression, mCherry positivity dropped to 50% after ductal maturation, indicating a permanent switch from biallelic to monoallelic expression. DNA methylation profiling separated the distinct differentiation intermediates, with site-specific DNA methylation patterns occurring at the KRT19 locus during ductal maturation. Accordingly, the monoallelic switch was partially reverted upon treatment with a DNA-methyltransferase inhibitor. In human PDAC cohorts, high KRT19 levels correlate with low locus methylation and decreased survival. At the same time, activation of oncogenic KRASG12D signalling in our reporter system reversed monoallelic back to biallelic KRT19 expression in pancreatic duct-like organoids. Allelic reactivation was also detected in single-cell transcriptomes of human PDACs, which further revealed a positive correlation between KRT19 and KRAS expression. Accordingly, KRAS mutant PDACs had higher KRT19 mRNA but lower KRT19 gene locus DNA methylation than wildtype counterparts. KRT19 protein was additionally detected in plasma of PDAC patients, with higher concentrations correlating with shorter progression-free survival in gemcitabine/nabPaclitaxel-treated and opposing trends in FOLFIRINOX-treated patients. Apart from being an important pancreatic ductal lineage marker, KRT19 appears tightly controlled via a switch from biallelic to monoallelic expression during ductal lineage entry and is aberrantly expressed after oncogenic KRASG12D expression, indicating a role in PDAC development and malignancy. Soluble KRT19 might serve as a relevant biomarker to stratify treatment. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jana Krüger
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics, Ulm University & Ulm University Hospital, Ulm, Germany
| | - Markus Breunig
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, Germany
| | - Chantal Allgöwer
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, Germany
| | - Lucas Schulte
- Division of Interdisciplinary Pancreatology, Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | | | - Medhanie A Mulaw
- Unit for Single-cell Genomics, Medical Faculty, Ulm University, Ulm, Germany
| | - Nnamdi Okeke
- Institute of Human Genetics, Ulm University & Ulm University Hospital, Ulm, Germany
| | - Michael K Melzer
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, Germany
- Department of Urology, Ulm University Hospital, Ulm, Germany
| | - Clara Morgenstern
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, Germany
| | - Ninel Azoitei
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, Germany
| | - Thomas Seufferlein
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Thomas Fe Barth
- Department of Pathology, Ulm University Hospital, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University & Ulm University Hospital, Ulm, Germany
| | - Meike Hohwieler
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, Germany
| | - Alexander Kleger
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, Germany
- Division of Interdisciplinary Pancreatology, Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
- Organoid Core Facility, Ulm University, Ulm, Germany
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7
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Nagel S, Fischer A, Bens S, Hauer V, Pommerenke C, Uphoff CC, Zaborski M, Siebert R, Quentmeier H. PI3K/AKT inhibitor BEZ-235 targets CCND2 and induces G1 arrest in breast implant-associated anaplastic large cell lymphoma. Leuk Res 2023; 133:107377. [PMID: 37647808 DOI: 10.1016/j.leukres.2023.107377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/11/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023]
Abstract
Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is a mature, CD30-positive T-cell lymphoma lacking expression of the anaplastic lymphoma kinase (ALK). In contrast to ALK-positive ALCL, BIA-ALCL cells express cyclin D2 (CCND2) which controls cyclin dependent kinases 4 and 6 (CDK4/6). DNA methylation and expression analyses performed with cell lines and primary cells suggest that the expression of CCND2 in BIA-ALCL cell lines conforms to the physiological status of differentiated T-cells, and that it is not the consequence of genomic alterations as observed in other hematopoietic tumors. Using cell line model systems we show that treatment with the CDK4/6 inhibitor palbociclib effects dephosphorylation of the retinoblastoma protein (RB) and causes cell cycle arrest in G1 in BIA-ALCL. Moreover, we show that the PI3K/AKT inhibitor BEZ-235 induces dephosphorylation of the mTORC1 target S6 and of GSK3β, indicators for translational inhibition and proteasomal degradation. Consequently, CCND2 protein levels declined after stimulation with BEZ-235, RB was dephosphorylated and the cell cycle was arrested in G1. Taken together, our data imply potential application of CDK4/6 inhibitors and PI3K/AKT inhibitors for the therapy of BIA-ALCL.
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Affiliation(s)
- Stefan Nagel
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany.
| | - Anja Fischer
- Ulm University and Ulm University Medical Center, Institute of Human Genetics, Ulm, Germany
| | - Susanne Bens
- Ulm University and Ulm University Medical Center, Institute of Human Genetics, Ulm, Germany
| | - Vivien Hauer
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Claudia Pommerenke
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Braunschweig, Germany
| | - Cord C Uphoff
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Margarete Zaborski
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Reiner Siebert
- Ulm University and Ulm University Medical Center, Institute of Human Genetics, Ulm, Germany
| | - Hilmar Quentmeier
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
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8
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Reuken PA, Besteher B, Finke K, Fischer A, Holl A, Katzer K, Lehmann-Pohl K, Lemhöfer C, Nowka M, Puta C, Walter M, Weißenborn C, Stallmach A. Longterm course of neuropsychological symptoms and ME/CFS after SARS-CoV-2-infection: a prospective registry study. Eur Arch Psychiatry Clin Neurosci 2023:10.1007/s00406-023-01661-3. [PMID: 37587244 DOI: 10.1007/s00406-023-01661-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023]
Abstract
A significant proportion of patients after SARS-CoV-2 infection suffer from long-lasting symptoms. Although many different symptoms are described, the majority of patients complains about neuropsychological symptoms. Additionally, a subgroup of patients fulfills diagnostic criteria for ME/CFS. We analyzed a registry of all patients presenting in the out-patients clinic at a German university center. For patients with more than one visit, changes in reported symptoms from first to second visit were analyzed. A total of 1022 patients were included in the study, 411 of them had more than one visit. 95.5% of the patients reported a polysymptomatic disease. At the first visit 31.3% of the patients fulfilled ME/CFS criteria after a median time of 255 days post infection and and at the second visit after a median of 402 days, 19.4% still suffered from ME/CFS. Self-reported fatigue (83.7-72.7%) and concentration impairment (66.2-57.9%) decreased from first to second visit contrasting non-significant changes in the structured screening. A significant proportion of SARS-CoV-2 survivors presenting with ongoing symptoms present with ME/CFS. Although the proportion of subjective reported symptoms and their severity reduce over time, a significant proportion of patients suffer from long-lasting symptoms necessitating new therapeutic concepts.
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Affiliation(s)
- P A Reuken
- Department of Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Am Klinikum 1, 07743, Jena, Germany.
| | - B Besteher
- Department of Psychiatry and Psychotherapy, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
| | - K Finke
- Department of Neurology, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
| | - A Fischer
- Department of Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Am Klinikum 1, 07743, Jena, Germany
| | - A Holl
- Department of Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Am Klinikum 1, 07743, Jena, Germany
| | - K Katzer
- Department of Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Am Klinikum 1, 07743, Jena, Germany
| | - K Lehmann-Pohl
- Center for Sepsis Control and Care (CSCC), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
| | - C Lemhöfer
- Institute of Physical and Rehabilitation Medicine, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
| | - M Nowka
- Department of Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Am Klinikum 1, 07743, Jena, Germany
| | - C Puta
- Center for Sepsis Control and Care (CSCC), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
- Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany
- Center for Interdisciplinary Prevention of Diseases Related to Professional Activities, Jena, Germany
| | - M Walter
- Department of Psychiatry and Psychotherapy, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
| | - C Weißenborn
- Department of Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Am Klinikum 1, 07743, Jena, Germany
| | - A Stallmach
- Department of Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Am Klinikum 1, 07743, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
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9
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Kouroukli AG, Fischer A, Kretzmer H, Chteinberg E, Rajaram N, Glaser S, Kolarova J, Bashtrykov P, Mathas S, Drexler HG, Ohno H, Ammerpohl O, Jeltsch A, Siebert R, Bens S. The DNA methylation status of the TERT promoter differs between subtypes of mature B-cell lymphomas. Blood Cancer J 2023; 13:98. [PMID: 37365157 DOI: 10.1038/s41408-023-00872-0] [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: 02/10/2023] [Revised: 05/24/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Affiliation(s)
- Alexandra G Kouroukli
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Helene Kretzmer
- Computational Genomics, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Emil Chteinberg
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Nivethika Rajaram
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Stephan Mathas
- Charité - Universitätsmedizin Berlin, Hematology, Oncology and Tumor Immunology, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Group Biology of Malignant Lymphomas, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a cooperation between the MDC and the Charité, Berlin, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124, Braunschweig, Germany
| | - Hitoshi Ohno
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany.
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10
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Wedekind R, Fischer A, Mewes KR, Brenneisen P, Holtkötter O. Investigating the surfactant antagonism with the Open Source Reconstructed Epidermis (OS-Rep) model. Toxicol In Vitro 2023; 88:105557. [PMID: 36681289 DOI: 10.1016/j.tiv.2023.105557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/11/2022] [Accepted: 01/15/2023] [Indexed: 01/20/2023]
Abstract
Under the current EU chemicals legislation, in vitro test methods became the preferred methods to identify and classify the skin irritation potential of chemicals and mixtures. Among these, especially in vitro skin models are widely used. For surfactants, a well-known group of typically irritating chemicals, it is a long-standing experience that the irritation potential of a mixture of surfactants is typically lower than the irritation potential of the single surfactants, an effect usually described as surfactant antagonism. In order to evaluate if this effect can be observed in skin model systems as well, the irritation potential of the surfactants and of their mixtures was determined in the Open Source Reconstructed Epidermis (OS-REp) models. Combinations of sodium dodecyl sulfate or linear alkylbenzene sulfonate with cocoamidopropyl betain and alkyl polyglycosid, respectively, resulted in a clear decrease of the irritation potential compared to the irritation exerted by the single surfactants. The effect appeared to be primarily driven by the mixture's lower ability to damage the skin model's barrier, as shown by a reduced fluorescein permeation.
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Affiliation(s)
| | | | | | - Peter Brenneisen
- Institute of Biochemistry & Molecular Biology I, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
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11
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Fischer A, Veraar C, Sulz I, Singer P, Barazzoni R, Tarantino S, Hiesmayr M. Does bmi affect ageing? A nutritionday analysis in 178 961 patients. Clin Nutr ESPEN 2023. [DOI: 10.1016/j.clnesp.2022.09.163] [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: 03/29/2023]
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12
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Fischer A, Lersch R, de Andrade Krätzig N, Strong A, Friedrich MJ, Weber J, Engleitner T, Öllinger R, Yen HY, Kohlhofer U, Gonzalez-Menendez I, Sailer D, Kogan L, Lahnalampi M, Laukkanen S, Kaltenbacher T, Klement C, Rezaei M, Ammon T, Montero JJ, Schneider G, Mayerle J, Heikenwälder M, Schmidt-Supprian M, Quintanilla-Martinez L, Steiger K, Liu P, Cadiñanos J, Vassiliou GS, Saur D, Lohi O, Heinäniemi M, Conte N, Bradley A, Rad L, Rad R. In vivo interrogation of regulatory genomes reveals extensive quasi-insufficiency in cancer evolution. Cell Genom 2023; 3:100276. [PMID: 36950387 PMCID: PMC10025556 DOI: 10.1016/j.xgen.2023.100276] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 09/05/2022] [Accepted: 02/08/2023] [Indexed: 03/10/2023]
Abstract
In contrast to mono- or biallelic loss of tumor-suppressor function, effects of discrete gene dysregulations, as caused by non-coding (epi)genome alterations, are poorly understood. Here, by perturbing the regulatory genome in mice, we uncover pervasive roles of subtle gene expression variation in cancer evolution. Genome-wide screens characterizing 1,450 tumors revealed that such quasi-insufficiency is extensive across entities and displays diverse context dependencies, such as distinct cell-of-origin associations in T-ALL subtypes. We compile catalogs of non-coding regions linked to quasi-insufficiency, show their enrichment with human cancer risk variants, and provide functional insights by engineering regulatory alterations in mice. As such, kilo-/megabase deletions in a Bcl11b-linked non-coding region triggered aggressive malignancies, with allele-specific tumor spectra reflecting gradual gene dysregulations through modular and cell-type-specific enhancer activities. Our study constitutes a first survey toward a systems-level understanding of quasi-insufficiency in cancer and gives multifaceted insights into tumor evolution and the tissue-specific effects of non-coding mutations.
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Affiliation(s)
- Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Robert Lersch
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Alexander Strong
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Mathias J. Friedrich
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Hsi-Yu Yen
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Comparative Experimental Pathology, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Ursula Kohlhofer
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Irene Gonzalez-Menendez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - David Sailer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Liz Kogan
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Mari Lahnalampi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Saara Laukkanen
- Faculty of Medicine and Health Technology, Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University, Tampere, Finland
| | - Thorsten Kaltenbacher
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Christine Klement
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Majdaddin Rezaei
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Tim Ammon
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute of Experimental Hematology, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Juan J. Montero
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Julia Mayerle
- Medical Department II, University Hospital, LMU Munich, Munich, Germany
| | - Mathias Heikenwälder
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Experimental Hematology, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Comparative Experimental Pathology, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Pentao Liu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Li Ka Shing Faculty of Medicine, Stem Cell and Regenerative Medicine Consortium, School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), 33193 Oviedo, Spain
| | - George S. Vassiliou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0PT, UK
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Olli Lohi
- Faculty of Medicine and Health Technology, Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University, Tampere, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Nathalie Conte
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Lena Rad
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
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13
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Bredthauer C, Fischer A, Ahari AJ, Cao X, Weber J, Rad L, Rad R, Wachutka L, Gagneur J. Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens. Nucleic Acids Res 2023; 51:e21. [PMID: 36617985 PMCID: PMC9976929 DOI: 10.1093/nar/gkac1215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/06/2022] [Accepted: 12/17/2022] [Indexed: 01/10/2023] Open
Abstract
Transposon screens are powerful in vivo assays used to identify loci driving carcinogenesis. These loci are identified as Common Insertion Sites (CISs), i.e. regions with more transposon insertions than expected by chance. However, the identification of CISs is affected by biases in the insertion behaviour of transposon systems. Here, we introduce Transmicron, a novel method that differs from previous methods by (i) modelling neutral insertion rates based on chromatin accessibility, transcriptional activity and sequence context and (ii) estimating oncogenic selection for each genomic region using Poisson regression to model insertion counts while controlling for neutral insertion rates. To assess the benefits of our approach, we generated a dataset applying two different transposon systems under comparable conditions. Benchmarking for enrichment of known cancer genes showed improved performance of Transmicron against state-of-the-art methods. Modelling neutral insertion rates allowed for better control of false positives and stronger agreement of the results between transposon systems. Moreover, using Poisson regression to consider intra-sample and inter-sample information proved beneficial in small and moderately-sized datasets. Transmicron is open-source and freely available. Overall, this study contributes to the understanding of transposon biology and introduces a novel approach to use this knowledge for discovering cancer driver genes.
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Affiliation(s)
- Carl Bredthauer
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Computational Health Center, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Ata Jadid Ahari
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany
| | - Xueqi Cao
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Lena Rad
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Institute for Experimental Cancer Therapy, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Medicine II, Klinikum rechts der Isar, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Leonhard Wachutka
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany
| | - Julien Gagneur
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Computational Health Center, Helmholtz Zentrum Munich, Neuherberg, Germany.,Institute of Human Genetics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
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14
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Schuetz C, Gerke J, Ege M, Walter J, Kusters M, Worth A, Kanakry JA, Dimitrova D, Wolska-Kuśnierz B, Chen K, Unal E, Karakukcu M, Pashchenko O, Leiding J, Kawai T, Amrolia PJ, Berghuis D, Buechner J, Buchbinder D, Cowan MJ, Gennery AR, Güngör T, Heimall J, Miano M, Meyts I, Morris EC, Rivière J, Sharapova SO, Shaw PJ, Slatter M, Honig M, Veys P, Fischer A, Cavazzana M, Moshous D, Schulz A, Albert MH, Puck JM, Lankester AC, Notarangelo LD, Neven B. Hypomorphic RAG deficiency: impact of disease burden on survival and thymic recovery argues for early diagnosis and HSCT. Blood 2023; 141:713-724. [PMID: 36279417 PMCID: PMC10082356 DOI: 10.1182/blood.2022017667] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/19/2022] [Accepted: 10/04/2022] [Indexed: 11/20/2022] Open
Abstract
Patients with hypomorphic mutations in the RAG1 or RAG2 gene present with either Omenn syndrome or atypical combined immunodeficiency with a wide phenotypic range. Hematopoietic stem cell transplantation (HSCT) is potentially curative, but data are scarce. We report on a worldwide cohort of 60 patients with hypomorphic RAG variants who underwent HSCT, 78% of whom experienced infections (29% active at HSCT), 72% had autoimmunity, and 18% had granulomas pretransplant. These complications are frequently associated with organ damage. Eight individuals (13%) were diagnosed by newborn screening or family history. HSCT was performed at a median of 3.4 years (range 0.3-42.9 years) from matched unrelated donors, matched sibling or matched family donors, or mismatched donors in 48%, 22%, and 30% of the patients, respectively. Grafts were T-cell depleted in 15 cases (25%). Overall survival at 1 and 4 years was 77.5% and 67.5% (median follow-up of 39 months). Infection was the main cause of death. In univariable analysis, active infection, organ damage pre-HSCT, T-cell depletion of the graft, and transplant from a mismatched family donor were predictive of worse outcome, whereas organ damage and T-cell depletion remained significant in multivariable analysis (hazard ratio [HR] = 6.01, HR = 8.46, respectively). All patients diagnosed by newborn screening or family history survived. Cumulative incidences of acute and chronic graft-versus-host disease were 35% and 22%, respectively. Cumulative incidences of new-onset autoimmunity was 15%. Immune reconstitution, particularly recovery of naïve CD4+ T cells, was faster and more robust in patients transplanted before 3.5 years of age, and without organ damage. These findings support the indication for early transplantation.
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Affiliation(s)
- C. Schuetz
- Department of Paediatrics, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - J. Gerke
- Department of Paediatrics, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - M. Ege
- Dr. von Hauner Children’s Hospital at Ludwig-Maximilians-Universität, München, Germany
- Helmholtz Zentrum München, Neuherberg, Germany
| | - J. Walter
- Division of Allergy and Immunology, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL
- Division of Allergy and Immunology, Department of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, FL
| | - M. Kusters
- Department of Immunology and Gene therapy, Great Ormond Street Hospital, NHS Foundation trust, London, United Kingdom
| | - A. Worth
- Department of Immunology and Gene therapy, Great Ormond Street Hospital, NHS Foundation trust, London, United Kingdom
| | - J. A. Kanakry
- Experimental Transplantation and Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - D. Dimitrova
- Experimental Transplantation and Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - B. Wolska-Kuśnierz
- Department of Immunology, Children's Memorial Health Institute, Warsaw, Poland
| | - K. Chen
- Division of Allergy and Immunology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT
| | - E. Unal
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Erciyes University, Kayseri, Turkey
| | - M. Karakukcu
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Erciyes University, Kayseri, Turkey
| | - O. Pashchenko
- Department of Immunology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - J. Leiding
- Division of Allergy and Immunology, Department of Pediatrics, Johns Hopkins University, Orlando Health Arnold Pamer Hospital for Children, Orlando, FL
| | - T. Kawai
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - P. J. Amrolia
- Bone Marrow Transplant Unit, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - D. Berghuis
- Department of Pediatrics, Willem-Alexander Children’s Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - J. Buechner
- Department of Pediatric Hematology and Oncology, Oslo University Hospital, Oslo, Norway
| | - D. Buchbinder
- Division of Hematology, Children's Hospital of Orange County, Orange, CA
| | - M. J. Cowan
- Division of Allergy, Immunology, and Blood and Marrow Transplant, Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - A. R. Gennery
- Translational and Clinical Research Institute, Newcastle University, Paediatric Haematopoietic Stem Cell Transplant Unit, Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
| | - T. Güngör
- Department of Hematology/Oncology/Immunology, Gene-therapy, and Stem Cell Transplantation, University Children’s Hospital Zurich–Eleonore Foundation & Children’s Research Center, Zürich, Switzerland
| | - J. Heimall
- Division of Allergy and Immunology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
| | - M. Miano
- IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - I. Meyts
- Department of Pediatrics, Department of Microbiology and Immunology, University Hospitals Leuven, Leuven, Belgium
| | - E. C. Morris
- UCL Institute of Immunity & Transplantation, University College London Hospitals NHS Foundation Trust, Royal Free London Hospital NHS Foundation Trust, London, United Kingdom
| | - J. Rivière
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - S. O. Sharapova
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - P. J. Shaw
- Blood Transplant and Cell Therapies, Children’s Hospital at Westmead, Sydney, Australia
| | - M. Slatter
- Paediatric Immunology & HSCT, Great North Children's Hospital, Newcastle upon Tyne, United Kingdom
| | - M. Honig
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - P. Veys
- Bone Marrow Transplant Unit, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - A. Fischer
- Paediatric Immunology, Department of Immunology, Haematology and Rheumatology, Necker-Enfants Malades, Paris, France
- Institut Imagine, Paris Descartes-Sorbonne Paris Cité University, Paris, France
- Collège de France, Paris, France
| | - M. Cavazzana
- Institut Imagine, Paris Descartes-Sorbonne Paris Cité University, Paris, France
- Département de Biothérapie, Hôpital Universitaire Necker-Enfants Malades, Groupe Hospitalier Paris Centre, Assistance Publique–Hopitaux de Paris, Paris, France
- Centre d’Investigation Clinique Biothérapie, Groupe hospitalier Universitaire paris centre, Assistance Publique-Hôpitaux de Paris, INSERM CIC 1416, Paris, France
| | - D. Moshous
- Paediatric Immunology, Department of Immunology, Haematology and Rheumatology, Necker-Enfants Malades, Paris, France
- Institut Imagine, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - A. Schulz
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - M. H. Albert
- Pediatric SCT Program, Dr. von Hauner University Children’s Hospital, Ludwig-Maximilians Universität, München, Germany
| | - J. M. Puck
- Division of Allergy, Immunology, and Blood and Marrow Transplant, Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - A. C. Lankester
- Department of Pediatrics, Willem-Alexander Children’s Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - L. D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - B. Neven
- Paediatric Immunology, Department of Immunology, Haematology and Rheumatology, Necker-Enfants Malades, Paris, France
| | - Inborn Errors Working Party (IEWP) of the European Society for Immunodeficiencies (ESID) and European Society for Blood and Marrow Transplantation (EBMT) and the Primary Immune Deficiency Treatment Consortium (PIDTC)
- Department of Paediatrics, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Dr. von Hauner Children’s Hospital at Ludwig-Maximilians-Universität, München, Germany
- Helmholtz Zentrum München, Neuherberg, Germany
- Division of Allergy and Immunology, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL
- Division of Allergy and Immunology, Department of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, FL
- Department of Immunology and Gene therapy, Great Ormond Street Hospital, NHS Foundation trust, London, United Kingdom
- Experimental Transplantation and Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Department of Immunology, Children's Memorial Health Institute, Warsaw, Poland
- Division of Allergy and Immunology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Erciyes University, Kayseri, Turkey
- Department of Immunology, Pirogov Russian National Research Medical University, Moscow, Russia
- Division of Allergy and Immunology, Department of Pediatrics, Johns Hopkins University, Orlando Health Arnold Pamer Hospital for Children, Orlando, FL
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Bone Marrow Transplant Unit, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
- Department of Pediatrics, Willem-Alexander Children’s Hospital, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pediatric Hematology and Oncology, Oslo University Hospital, Oslo, Norway
- Division of Hematology, Children's Hospital of Orange County, Orange, CA
- Division of Allergy, Immunology, and Blood and Marrow Transplant, Department of Pediatrics, University of California San Francisco, San Francisco, CA
- Translational and Clinical Research Institute, Newcastle University, Paediatric Haematopoietic Stem Cell Transplant Unit, Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
- Department of Hematology/Oncology/Immunology, Gene-therapy, and Stem Cell Transplantation, University Children’s Hospital Zurich–Eleonore Foundation & Children’s Research Center, Zürich, Switzerland
- Division of Allergy and Immunology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
- IRCCS Istituto Giannina Gaslini, Genova, Italy
- Department of Pediatrics, Department of Microbiology and Immunology, University Hospitals Leuven, Leuven, Belgium
- UCL Institute of Immunity & Transplantation, University College London Hospitals NHS Foundation Trust, Royal Free London Hospital NHS Foundation Trust, London, United Kingdom
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
- Blood Transplant and Cell Therapies, Children’s Hospital at Westmead, Sydney, Australia
- Paediatric Immunology & HSCT, Great North Children's Hospital, Newcastle upon Tyne, United Kingdom
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
- Bone Marrow Transplant Unit, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
- Paediatric Immunology, Department of Immunology, Haematology and Rheumatology, Necker-Enfants Malades, Paris, France
- Institut Imagine, Paris Descartes-Sorbonne Paris Cité University, Paris, France
- Collège de France, Paris, France
- Département de Biothérapie, Hôpital Universitaire Necker-Enfants Malades, Groupe Hospitalier Paris Centre, Assistance Publique–Hopitaux de Paris, Paris, France
- Centre d’Investigation Clinique Biothérapie, Groupe hospitalier Universitaire paris centre, Assistance Publique-Hôpitaux de Paris, INSERM CIC 1416, Paris, France
- Pediatric SCT Program, Dr. von Hauner University Children’s Hospital, Ludwig-Maximilians Universität, München, Germany
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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Veraar C, Fischer A, Bernardi M, Sulz I, Mohamed M, Dworschak M, Tschernko E, Lassnigg A, Hiesmayr M. RESTING ENERGY EXPENDITURE IMPACTS ON SHORT- AND LONG-TERM MORTALITY IN CRITICALLY ILL PATIENTS AFTER CARDIAC SURGERY- A RETROSPECTIVE ANALYSIS. J Cardiothorac Vasc Anesth 2022. [DOI: 10.1053/j.jvca.2022.09.011] [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: 12/07/2022]
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16
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Fagherazzi G, Zhang L, Elbéji A, Pizzimenti M, Nazarov P, Aguayo G, Fischer A. 6Développement de nouveaux ”endpoints” cliniques à l'aide de biomarqueurs numériques basés sur la voix pour le suivi à distance, en vie réelle, de patients en recherche clinique: exemple de biomarqueurs vocaux pour le suivi du statut symptomatique de patients avec COVID-19. Rev Epidemiol Sante Publique 2022. [DOI: 10.1016/j.respe.2022.09.065] [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: 11/06/2022] Open
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17
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Kley M, Inderbinen S, Zogg M, Sellner M, Fischer A, Kędzierski J, Boudon S, Jetten A, Smieško M, Odermatt A. P10-02 Parabens and UV-filters activating retinoic acid-related orphan receptor γ(t). Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.433] [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: 11/25/2022]
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18
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Fischer A, Dai X, Kalscheur KF. Feed efficiency of lactating Holstein cows is repeatable within diet but less reproducible when changing dietary starch and forage concentrations. Animal 2022; 16:100599. [PMID: 35907383 DOI: 10.1016/j.animal.2022.100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 11/01/2022] Open
Abstract
Improving feed efficiency has become an important target for dairy farmers to produce more milk with fewer feed resources. With decreasing availability of arable land to produce feeds that are edible for human consumption, it will be important to increase the proportion of feeds in the diets for dairy cattle that are less edible for human consumption. The current research analyzed the ability of lactating dairy cows to maintain their feed efficiency when switching between a high starch diet (HS diet: 27% starch, 29% NDF, 47.1% forages on a DM basis) and a low starch diet (LS diet: 13% starch, 37% NDF, 66.4% forages on a DM basis). Sixty-two lactating Holstein cows (137 ± 23 days in milk (DIM) at the start of experiment), of which 29 were primiparous cows, were utilized in a crossover design with two 70-d experimental periods, including a 14-d adaption period for each. Feed efficiency was estimated as the individual deviation from the population average intercept in a mixed model predicting DM intake (DMI) with net energy in milk, maintenance and BW gain and loss. Repeatability was estimated within each diet by comparing feed efficiency estimated over the first 28-day period and the second 28-day period within each diet, using Pearson's and intraclass correlations, and the estimation of error of repeatability. Similarly, reproducibility was estimated by comparing the second 28-day period of one diet with the first 28-day period of the other diet. Feed efficiency was less reproducible across diets than repeatable within the same diet. This was shown by lower intraclass correlations (0.399) across diets compared to that in the HS diet (0.587) and LS diet (0.806), as well as a lower Pearson's correlation coefficient (0.418) across diets compared to that in the HS diet (0.630) and LS diet (0.809). In addition, the estimation of error of repeatability was higher (0.830 kg DM/d) across diets compared to that in the HS diet (0.761 kg DM/d) and LS diet (0.504 kg DM/d). This means that the feed efficiency of dairy cows is more likely to change after a diet change than over subsequent lactation stages. Other determinants, such as digestive processes, need to be further investigated to determine its effects on estimating feed efficiency.
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Affiliation(s)
- A Fischer
- U.S. Dairy Forage Research Center, USDA-Agricultural Research Service, Madison, WI 53706, USA
| | - X Dai
- U.S. Dairy Forage Research Center, USDA-Agricultural Research Service, Madison, WI 53706, USA
| | - K F Kalscheur
- U.S. Dairy Forage Research Center, USDA-Agricultural Research Service, Madison, WI 53706, USA.
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19
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Joshi DC, Gebresenbut GH, Fischer A, Rydh A, Häussermann U, Nordblad P, Mathieu R. 2D crystal structure and anisotropic magnetism of GdAu 6.75-xAl 0.5+x (x ≈ 0.54). Sci Rep 2022; 12:13141. [PMID: 35907933 PMCID: PMC9338926 DOI: 10.1038/s41598-022-17068-4] [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: 03/03/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
Exploration of the gold-rich part of the ternary Gd–Au–Al system afforded the intermetallic compound GdAu6.75−xAl0.5+x (x ≈ 0.54) which was structurally characterized by single crystal X-ray diffraction (Pnma, a = 18.7847(4) Å, b = 23.8208(5) Å, c = 5.3010(1) Å). GdAu6.75−xAl0.5+x crystallizes in a previously unknown structure type featuring layers of Gd2(Au, Al)29 and Gd2(Au, Al)28 clusters which are arranged as in a close-packing parallel to the ac plane. The Gd substructure corresponds to slightly corrugated 36 nets (dGd–Gd = 5.30–5.41 Å) which are stacked on top of each other along the b direction with alternating short (5.4, 5.6 Å, within layers) and long distances (6.4 Å, between layers). The title compound has been discussed with respect to a quasicrystal approximant (1/1 AC) GdAu5.3Al in the same system. The magnetic properties of GdAu6.75−xAl0.5+x were found to be reminiscent to those of some ternary ACs, with sharp peaks in the temperature dependent magnetization, and metamagnetic-like transitions. The material becomes antiferromagnetic below 25 K; magnetometry results suggest that the antiferromagnetic state is composed of ferromagnetic ac planes, coupled antiferromagnetically along the b direction.
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Affiliation(s)
- D C Joshi
- Department of Materials Science and Engineering, Uppsala University, Box 35, 751 03, Uppsala, Sweden.
| | - G H Gebresenbut
- Department of Chemistry-Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
| | - A Fischer
- Institute of Physics, Augsburg University, 86159, Augsburg, Germany
| | - A Rydh
- Department of Physics, Stockholm University, 106 91, Stockholm, Sweden
| | - U Häussermann
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91, Stockholm, Sweden
| | - P Nordblad
- Department of Materials Science and Engineering, Uppsala University, Box 35, 751 03, Uppsala, Sweden
| | - R Mathieu
- Department of Materials Science and Engineering, Uppsala University, Box 35, 751 03, Uppsala, Sweden.
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20
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Xavier C, Le Cozler Y, Depuille L, Caillot A, Lebreton A, Allain C, Delouard J, Delattre L, Luginbuhl T, Faverdin P, Fischer A. The use of 3-dimensional imaging of Holstein cows to estimate body weight and monitor the composition of body weight change throughout lactation. J Dairy Sci 2022; 105:4508-4519. [DOI: 10.3168/jds.2021-21337] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/06/2022] [Indexed: 11/19/2022]
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21
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Fischer A, Martirosian P, Benkert T, Schick F. Spatially resolved free-induction decay spectroscopy using a 3D ultra-short echo time multi-echo imaging sequence with systematic echo shifting and compensation of B 0 field drifts. Magn Reson Med 2021; 87:2099-2110. [PMID: 34866240 DOI: 10.1002/mrm.29115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 11/08/2022]
Abstract
PURPOSE Biologically interesting signals can exhibit fast transverse relaxation and frequency shifts compared to free water. For spectral assignment, a ultra-short echo time (UTE) imaging sequence was modified to provide pixel-wise free-induction decay (FID) acquisition. METHODS The UTE-FID approach presented relies on a multi-echo 3D spiral UTE sequence with six echoes per radiofrequency (RF) excitation (TEmin 0.05 ms, echo spacing 3 ms). A complex pixel-wise raw data set for FID spectroscopy is obtained by several multi-echo UTE measurements with systematic shifting of the readout by 0.25 or 0.5 ms, until the time domain is filled for 18 or 45 ms. B0 drifts are compensated by mapping and according phase correction. Autoregressive extrapolation of the signal is performed before Gaussian filtering. This method was applied to a phantom containing collagen-water solutions of different concentrations. To calculate the collagen content, a 19-peak collagen model was extracted from a non-selective FID spectrum (50% collagen solution). Proton-density-collagen-fraction (PDCF) was calculated for 10 collagen solutions (2%-50%). Furthermore, an in vivo UTE-FID spectrum of adipose tissue was recorded. RESULTS UTE-FID signal patterns agreed well with the non-spatially selective pulse-acquire FID spectrum from a sphere filled with 50% collagen. Differentiation of collagen solution from distilled water in the PDCF map was possible from 4% collagen concentration for a UTE-FID sequence with 128 × 128 × 64 matrix (voxel size 1 × 1 × 2.85 mm3 ). The mean values of the PDCF correlate linearly with collagen concentration. CONCLUSION The presented UTE-FID approach allows pixel-wise raw data acquisition similar to non-spatially selective pulse-acquire spectroscopy. Spatially resolved applications for assessment of spectra of rapidly decaying signals seem feasible.
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Affiliation(s)
- Anja Fischer
- Section on Experimental Radiology, University Hospital Tübingen, Tübingen, Germany
| | - Petros Martirosian
- Section on Experimental Radiology, University Hospital Tübingen, Tübingen, Germany
| | - Thomas Benkert
- MR Applications Predevelopment, Siemens Healthcare GmbH, Erlangen, Germany
| | - Fritz Schick
- Section on Experimental Radiology, University Hospital Tübingen, Tübingen, Germany
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22
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Mello L, Fernandes F, Fischer A. Implementation of the new QUANUM 30 tool as an internal audit methodology in a large general hospital. Phys Med 2021. [DOI: 10.1016/s1120-1797(22)00049-7] [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: 11/29/2022] Open
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23
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Fischer A, Siebenrock T, Liebau K, Hertwig A, Hahn R, Anwar M, Pesta M, Timmermann I, Brugger J, Posch M, Tamandl D, Ringl H, Hiesmayr M. Association of ct skeletal muscle area and density with age: a prospective study in 200 non-critically ill patients. Clin Nutr ESPEN 2021. [DOI: 10.1016/j.clnesp.2021.09.176] [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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24
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Fischer A, Barazzoni R, Tarantino S, Laviano A, Veraar C, Sulz I, Schneider S, Lassnigg A, Cuerda-Compes C, Pestana E, Hiesmayr M. Does bmi affect the use of enteral and parenteral nutrition in the ward: a nutritionday analysis in 191 886 adult patients. Clin Nutr ESPEN 2021. [DOI: 10.1016/j.clnesp.2021.09.062] [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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Martin P, Ducrocq V, Fischer A, Friggens NC. Combining datasets in a dynamic residual feed intake model and comparison with linear model results in lactating Holstein cattle. Animal 2021; 15:100412. [PMID: 34844182 DOI: 10.1016/j.animal.2021.100412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 10/19/2022] Open
Abstract
A new method to estimate residual feed intake (RFI) was recently developed based on a multi-trait random regression model. This approach deals with the dynamic nature of the lactation, which is in contrast with classical linear approaches. However, an issue remains: pooling data across sites and years, which implies dealing with different (and sometimes unknown) diet energy contents. This will be needed for genomic evaluation. In this study, we tested whether merging two individual datasets into a larger one can lead to valuable results in comparison to analysing them on their own with the multi-trait random regression model. Three datasets were defined: the first one with 1 063 lactations, the second one with 205 lactations from a second farm and the third one combining the data of the two first datasets (1 268 lactations). The model was applied to the three datasets to estimate individual RFI as well as variance components and correlations between the four traits included in the model (fat and protein corrected milk production, BW, feed intake and body condition score), and a fixed month-year-farm effect was used to define the contemporary group. The variance components and correlations between animal effects of the four traits were very similar irrespective of the dataset used with correlations higher than 0.94 between the different datasets. The RFI estimates for animals from their single farm only were also very similar (r > 0.95) to the ones computed from the merged dataset (Dataset 3). This highlights that the contemporary group correction in the model adequately accounts for differences between the two feeding environments. The dynamic model can thus be used to produce RFI estimates from merged datasets, at least when animals are raised in similar systems. In addition, the 205 lactations from the second farm were also used to estimate the RFI with a linear approach. The RFI estimated by the two approaches were similar when the considered period was rather short (r = 0.85 for RFI for the first 84 days of lactation) but this correlation weakened as the period length grew (r = 0.77 for RFI for the first 168 days of lactation). This weakening in correlations between the two approaches when increasing the used time-period reflects that only the dynamic model permits the regression coefficients to evolve in line with the physiological changes through the lactation. The results of this study enlarge the possibilities of use for the dynamic RFI model.
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Affiliation(s)
- P Martin
- UMR GABI, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - V Ducrocq
- UMR GABI, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - A Fischer
- PEGASE, INRAE, Institut Agro, 35590 Saint Gilles, France; Institut de l'élevage, 149 rue de Bercy, 75595 Paris, France
| | - N C Friggens
- UMR 0791 MoSAR, INRAE, AgroParisTech, Université Paris-Saclay, 75005 Paris, France
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Moustafa A, Alexander S, Pitcher N, Goldberg J, Fischer A, Planet P. 511: Longitudinal evolution and adaptation of Staphylococcus aureus in cystic fibrosis. J Cyst Fibros 2021. [DOI: 10.1016/s1569-1993(21)01935-4] [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: 10/20/2022]
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Nambiar GG, Thornell I, Stoltz D, Fischer A. 217: Pancreatic enzyme treatment of obstructive meconium from CF pigs. J Cyst Fibros 2021. [DOI: 10.1016/s1569-1993(21)01642-8] [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: 11/25/2022]
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Kienenberger Z, Farber T, Teresi M, Milavetz F, Singh S, Ode KL, Thoma T, Weiner R, Burlage K, Fischer A. 255: Patient and caregiver opinions of airway clearance methods used for cystic fibrosis. J Cyst Fibros 2021. [DOI: 10.1016/s1569-1993(21)01680-5] [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: 12/01/2022]
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Makowski L, Feld J, Koeppe J, Engelbertz C, Illner J, Kuehnemund L, Fischer A, Lange SA, Droege P, Guenster C, Gerss J, Reinecke H, Freisinger E. Sex related differences in vascular interventions and outcome of patients with critical limb threatening ischemia in a real-world cohort. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.2038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
The prevalence of critical limb threatening ischemia (CLTI) is increasing worldwide and the focus is the reduction of outcome events like death or amputation of the lower limb (LL). Sex related differences in medical supply and outcome are a current matter of debate.
Purpose
In the present study, we included patients with CLTI in an unselected “real-world” cohort and studied sex related differences in their risk profile and vascular interventions, as well as their impact on long-term outcome.
Methods
We analyzed 119,953 unselected patients of the public health insurance in Germany (AOK), which were hospitalized between 2010 and 2017 for a main diagnosis of CLTI (Rutherford stage (RF) 4–6). In our data files, a baseline period of 2 years previous index hospitalization and a follow-up period until 2018 was included.
Results
In our cohort, more than half were male CLTI patients (57% male vs. 43% female), while female CLTI patients were at higher age (median: 73.8 years male vs. 81.4 years female). Male patients had higher ratios of diabetes, dyslipidemia, smoking, cerebrovascular disease and chronic coronary syndrome, whereas female CLTI patients show a higher prevalence of hypertension, atrial fibrillation, chronic heart failure and chronic kidney disease (all p<0.001). During index hospitalisation more than one quarter of all CLTI patients suffered from rest pain (RF 4), and approximately one third for minor (RF 5) and one third for major (RF 6) tissue lost. Female patients were more often diagnosed with RF 5 (32% male vs. 36% female), while the proportion of male patients was slightly higher at RF 4 (29% male vs. 27% female) and RF 6 (39% male vs. 37% female, all p<0.001).
During index hospitalization, almost 70% underwent any diagnostic angiography and in 63% of all patients a revascularization procedure was performed. Both were carried out more often in male patients (both p<0.001).The Kaplan Meier curve showed an increased mortality rate in female patients during follow up (figure 1), while no differences were observed for the combined endpoint amputation of the LL or death. Interestingly after adjustment for age and patients risk'constellation, female gender was associated with increased overall-survival (female HR 0.95; 95%-CI 0.94–0.96, p<0.001) and amputation-free survival which is a combined endpoint of amputation of the LL or death (female HR 0.84; 95%-CI 0.83–0.85, p<0.001).
Conclusion
Female patients with CLTI were older and showed lower rates of diagnostic angiography and revascularization procedures of the LL during index hopsitalization. Nevertheless, male sex was an independent risk factor for all-cause mortality and the combined endpoint amputation of the LL or death during long-term follow-up. These results indicate that further analyses are needed to determine the various individual needs of male and female CLTI patients.
Funding Acknowledgement
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): The project upon which this publication is based was funded by The Federal Joint Committee, Innovation Committee (G-BA, Innovationsfonds, number 01VSF18051).
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Affiliation(s)
- L Makowski
- University Hospital of Munster, Cardiol, Dept. of Cardiology I - Coronary and Peripheral Vascular Disease, Heart Failure, Muenster, Germany
| | - J Feld
- University of Muenster, Institute of Biostatistics and Clinical Research, Muenster, Germany
| | - J Koeppe
- University of Muenster, Institute of Biostatistics and Clinical Research, Muenster, Germany
| | - C Engelbertz
- University Hospital of Munster, Cardiol, Dept. of Cardiology I - Coronary and Peripheral Vascular Disease, Heart Failure, Muenster, Germany
| | - J Illner
- University Hospital of Munster, Cardiol, Dept. of Cardiology I - Coronary and Peripheral Vascular Disease, Heart Failure, Muenster, Germany
| | - L Kuehnemund
- University Hospital of Munster, Cardiol, Dept. of Cardiology I - Coronary and Peripheral Vascular Disease, Heart Failure, Muenster, Germany
| | - A Fischer
- University Hospital of Munster, Cardiol, Dept. of Cardiology III - Adult Congenital and Valvular Heart Disease, Muenster, Germany, Muenster, Germany
| | - S A Lange
- University Hospital of Munster, Cardiol, Dept. of Cardiology I - Coronary and Peripheral Vascular Disease, Heart Failure, Muenster, Germany
| | - P Droege
- AOK Research Institute (WidO), Berlin, Germany
| | - C Guenster
- AOK Research Institute (WidO), Berlin, Germany
| | - J Gerss
- University of Muenster, Institute of Biostatistics and Clinical Research, Muenster, Germany
| | - H Reinecke
- University Hospital of Munster, Cardiol, Dept. of Cardiology I - Coronary and Peripheral Vascular Disease, Heart Failure, Muenster, Germany
| | - E Freisinger
- University Hospital of Munster, Cardiol, Dept. of Cardiology I - Coronary and Peripheral Vascular Disease, Heart Failure, Muenster, Germany
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Vanselow C, Hoppe O, Stöbener D, Fischer A. Stereoscopic particle image velocimetry in inhomogeneous refractive index fields of combustion flows. Appl Opt 2021; 60:8716-8727. [PMID: 34613097 DOI: 10.1364/ao.431977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Particle image velocimetry (PIV) measurements in reactive flows are disturbed by inhomogeneous refractive index fields, which cause measurement deviations in particle positions due to light refraction. The resulting measurement errors are known for standard PIV, but the measurement errors for stereoscopic PIV are still unknown. Therefore, for comparison, the velocity errors for standard and stereoscopic PIV are analyzed in premixed propane flames with different Reynolds numbers. For this purpose, ray-tracing simulations based on the time-averaged inhomogeneous refractive index fields of the studied non-swirled flame flows measured by the background-oriented Schlieren technique are performed to quantify the resulting position errors of the particles. In addition, the performance of the volumetric self-calibration relevant to tomographic PIV is analyzed with respect to the remaining position errors of the particles within the flames. The position errors cause significant standard PIV errors of 2% for the velocity component radial to the burner symmetry axis. Stereoscopic PIV measurements result in measurement errors of up to 3% radial to the burner axis and 13% for the velocity component perpendicular to the measurement plane. Due to the lower refractive index gradients in the axial direction, no significant velocity errors are observed for the axial velocity component. For the investigated flame configurations, the position errors and velocity errors increase with the Reynolds numbers. However, this dependence needs to be verified for other flame configurations such as swirled flame flows.
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Fischer A. Rasmussen, Susan. Persons of courage and renown: Tuareg actors, acting, plays, and cultural memory in northern Mali. viii, 224 pp., illus., bibliogr. Lanham, Md: Lexington Books, 2019. £73.00 (cloth). Royal Anthropological Inst 2021. [DOI: 10.1111/1467-9655.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Fischer A, Hoskin P. PO-1330 Radiotherapy toxicity in prostate cancer patients with bilateral hip prostheses. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)07781-1] [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: 10/20/2022]
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Wimmer M, Radice S, Janssen D, Fischer A. Fretting-corrosion of CoCr-alloys against TiAl6V4: The importance of molybdenum in oxidative biological environments. Wear 2021; 477:203813. [PMID: 34690379 PMCID: PMC8528050 DOI: 10.1016/j.wear.2021.203813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Periprosthetic fluids often contain reactive oxygen species, including H2O2, that are generated during inflammatory processes. Here, we investigated the fretting-corrosion behavior of CoCrX-alloys (X = Mo, Fe) in a complex protein-containing lubricant, with and without the addition of H2O2. Given the known protective role of molybdenum as an alloying element in metal degradation, we considered its effects by designing a two-way factorial experiment. The aim of the study was to investigate tribocorrosive mechanisms in modular joints of knee and hip prostheses. A previously described test-rig was used to run fretting corrosion tests of CoCrX-alloys with (X=Mo) and without (X=Fe) molybdenum against TiAl6V4 in bovine calf serum (BCS) with and without a physiological relevant H2O2 level (3 mM) in gross slip mode (4 Hz, ±50 μm, pmax=0.18 GPa, 37 °C, 50,000 cycles). Two CoCr-pins were pressed against a cylindrical TiAl6V4-rod, forming a line contact. Normal and frictional forces, the displacement, and the open circuit potential (OCP) were measured and recorded continuously. The dissipated frictional work was independent of alloy composition. The addition of H2O2 lowered the dissipated frictional work and increased wear, and this was significant in the absence of Mo. The mean OCP value was lower with Mo-containing than with Mo-free alloy in both pure BCS (p = .042), and BCS ± H2O2 (p < .0005). The wear scar was deeper for the Mo-free alloy, and this was significant (p = .013) in the presence of H2O2. These findings suggest a marked weakening of the passive film in the presence of H2O2, which is mitigated by the availability of Mo.
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Affiliation(s)
- M.A. Wimmer
- Rush University Medical Center, Chicago, IL, USA
| | - S. Radice
- Rush University Medical Center, Chicago, IL, USA
| | - D. Janssen
- University of Duisburg-Essen, Materials Science and Engineering, Duisburg, Germany
| | - A. Fischer
- Rush University Medical Center, Chicago, IL, USA
- University of Duisburg-Essen, Materials Science and Engineering, Duisburg, Germany
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Asnagli H, Novak A, Birch L, Lane R, Minet N, Laughton D, George P, De Ribains G, Latour S, Fischer A, Bourne T, Parker A. OP0034 STP938, A NOVEL, POTENT AND SELECTIVE INHIBITOR OF CTP SYNTHASE 1 (CTPS1) DEMONSTRATES EFFICACY IN RODENT MODELS OF INFLAMMATION AND ARTHRITIS. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:The final rate-limiting step in pyrimidine synthesis is the conversion of UTP to CTP which is catalyzed by cytidine triphosphate synthase 1 (CTPS1) or CTPS2. A hypomorphic mutation in the CTPS1 gene has highlighted the essential and non-redundant role of CTPS1 in T and B lymphocyte proliferation1. These patients exhibit no effects on non-hematopoietic tissues. Thus, selective inhibition of CTPS1 represents a novel targeted approach to dampen pathological T- and B-cell lympho-proliferation. STP938 is an orally bioavailable, small molecular weight, selective inhibitor of CTPS1 developed by Step Pharma.Objectives:To demonstrate the in vitro effects of CTPS1 inhibition on T and B cell proliferation and the therapeutic potential of STP938 using in vivo models of disease.Methods:The in vitro anti-proliferative activity of STP938 was investigated using cell lines and primary human PBMCs. STP938 was assessed in vivo using the DTH-KLH rat model and the mouse collagen-induced arthritis (CIA) model. For the KLH-DTH model, Lewis rats were immunized with KLH, a week later, challenged locally at the ear with KLH antigen, ear swelling was assessed after 24 hours. Blood samples were collected for detection of KLH-specific IgG levels at day 8. STP938 was given orally one-hour prior to immunization and then b.i.d. for 7 days. For the CIA model, DBA-1 mice were immunized with Collagen type II and complete Freund’s adjuvant and received a booster immunization three weeks later. STP938 was administered to mice developing signs of arthritis from Day 28 to 45 orally daily b.i.d.Results:STP938 inhibited in vitro proliferation of HEKwt but not HEK-CTPS1KO cells as well as Jurkat and human PBMCs. STP938 demonstrated a significant and dose-dependent inhibition of KLH-specific T and B cell responses in vivo. STP938 significantly reduced the disease severity in the CIA model in a dose-dependent manner as determined by clinical and histopathological readouts.Conclusion:Our preliminary in vitro and in vivo results indicate that inhibition of CTPS1 specifically blocks proliferation of cells derived from the lymphocyte lineage and reduces the T cell driven inflammatory response. These data highlight the therapeutical potential of STP938 in treating patients with autoimmune diseases such as rheumatoid arthritis.References:[1]Martin et al, JCI Insight. 2020, 12;5(5):133880Disclosure of Interests:Hélène ASNAGLI Employee of: Step Pharma, Andrew Novak: None declared, Louise Birch Shareholder of: Step Pharma, Rebecca Lane: None declared, Norbert Minet Employee of: employee as Ph D student under CIFRE grant, David Laughton: None declared, Pascal George Shareholder of: Step Pharma, Geoffroy de Ribains Shareholder of: as former employee of Step Pharma, Employee of: former employee of Step Pharma, Sylvain Latour: None declared, Alain Fischer: None declared, Tim Bourne Shareholder of: UCB, Step Pharma, Sitryx Therapeutics, Consultant of: a range of biotech companies, Employee of: former employee of Step Pharma and Sitryx Therapeutics, Andrew Parker Employee of: Step Pharma
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Eickelpasch N, Stang W, Fischer A. Status of decommissioning work at the Gundremmingen unit A power station / Kontinuierlicher Rückbau des Kernkraftwerkes Gundremmingen A. KERNTECHNIK 2021. [DOI: 10.1515/kern-1991-560614] [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: 11/15/2022]
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Muiños-Landin S, Fischer A, Holubec V, Cichos F. Reinforcement learning with artificial microswimmers. Sci Robot 2021; 6:6/52/eabd9285. [PMID: 34043550 DOI: 10.1126/scirobotics.abd9285] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/26/2021] [Indexed: 01/05/2023]
Abstract
Artificial microswimmers that can replicate the complex behavior of active matter are often designed to mimic the self-propulsion of microscopic living organisms. However, compared with their living counterparts, artificial microswimmers have a limited ability to adapt to environmental signals or to retain a physical memory to yield optimized emergent behavior. Different from macroscopic living systems and robots, both microscopic living organisms and artificial microswimmers are subject to Brownian motion, which randomizes their position and propulsion direction. Here, we combine real-world artificial active particles with machine learning algorithms to explore their adaptive behavior in a noisy environment with reinforcement learning. We use a real-time control of self-thermophoretic active particles to demonstrate the solution of a simple standard navigation problem under the inevitable influence of Brownian motion at these length scales. We show that, with external control, collective learning is possible. Concerning the learning under noise, we find that noise decreases the learning speed, modifies the optimal behavior, and also increases the strength of the decisions made. As a consequence of time delay in the feedback loop controlling the particles, an optimum velocity, reminiscent of optimal run-and-tumble times of bacteria, is found for the system, which is conjectured to be a universal property of systems exhibiting delayed response in a noisy environment.
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Affiliation(s)
- S Muiños-Landin
- Molecular Nanophotonics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany.,AIMEN Technology Centre, Smart Systems and Smart Manufacturing-Artificial Intelligence and Data Analytics Laboratory, PI. Cataboi, 36418 Pontevedra, Spain
| | - A Fischer
- Molecular Nanophotonics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany
| | - V Holubec
- Institute for Theoretical Physics, Universität Leipzig, 04103 Leipzig, Germany.,Department of Macromolecular Physics, Faculty of Mathematics and Physics, Charles University, 18000 Prague, Czech Republic
| | - F Cichos
- Molecular Nanophotonics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany.
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Del Castillo J, Russi M, Filomeno P, Kenny-Pujadas JE, Cabrera-Frola JA, Fischer A, Bongiovanni JC, Amaya J. [Experimental cadaveric study assesing protection and osteotomy guide system (BARU) in hallux valgus surgery using Reverdin-Isham technic]. Acta Ortop Mex 2021; 35:132-136. [PMID: 34731912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Hallux valgus is a high frequency disorder, affecting the first ray. Operative correction techniques have grown popularity lately. One of them is the Reverdin-Isham technique (first metatarsal medial incomplete osteotomy). Recently, a protection and osteotomy cutting guide has been developed: the BARU system. OBJECTIVE To test the usefulness of the BARU system as a protective factor for soft structures adjacent to the surgical site and guidance for osteotomy. MATERIAL AND METHODS Experimental cadaveric study. Six cadaveric feet (two fresh-frozen and four in formaldehyde solution), unapproached. Feet were numbered and intervened with RI technique, three of them with BARU system and three without it. Afterwards, dissection by two dissectors who did not know whether the BARU system had been used or not, establishing a single-blinded model. 13 structures were evaluated in each foot. Data was recovered into Microsoft Office Excel and processed with SPSS. 2 test (significative if p value < 0.05) and relative risk were calculated. RESULTS Approach using BARU system was satisfactory, with usual-size operation-ports. BARU system colocation was simple and radiological control showed adequate spatial location. The device contributed as reference for cutting direction and depth. 65 out of the 78 searched structures were found (83.3%). Six injuries were found among the assessed structures: plantar medial nerve (one injury), plantar medial artery (one injury), flexor brevis muscle (three injuries), abductor muscle (one injury). Five of these injuries occurred in non-utilizing BARU system feet. CONCLUSION Promising results in terms of protection of nearby structures, cutting guide, and ease of intervention. Avoids X-rays exposure. Not significant statistical calculations, the sample should be enlarged.
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Affiliation(s)
- J Del Castillo
- Departamento de Anatomía, Universidad de la República, Uruguay
| | - M Russi
- Sanatorio Americano, Uruguay
| | - P Filomeno
- Clínica de Traumatología y Ortopedia, Universidad de la República, Uruguay
| | | | | | - A Fischer
- Hospital Banco de Seguros del Estado, Uruguay
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John S, Weizel D, Heumann AS, Fischer A, Orlowski K, Mrkor KU, Edelmann-Nusser J, Witte K. Persisting inter-limb differences in patients following total hip arthroplasty four to five years after surgery? A preliminary cross-sectional study. BMC Musculoskelet Disord 2021; 22:230. [PMID: 33639901 PMCID: PMC7916281 DOI: 10.1186/s12891-021-04099-7] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Total hip arthroplasty (THA) is an effective procedure for patients with end-stage hip osteoarthritis. However, whether or not pre-operatively existing functional deficits are persisting several years post-surgery in the affected limb has not been thoroughly researched. Therefore, the primary aim of this preliminary study was to include patients four to five years after undergoing THA and to investigate potential differences between the operated and non-operated leg in hip strength, range of motion (ROM), balance, and gait. The secondary aim was to compare these values from the operated leg of the patients to those of the legs of healthy subjects. METHODS Sixteen patients (age: 65.20 ± 5.32 years) following unilateral THA (post-operation time: 4.7 ± 0.7 years) and ten, healthy, age-matched control subjects (age: 60.85 ± 7.57 years) were examined for maximum isometric hip muscle strength, active ROM of the hip joint, balance and gait on both limbs. Paired t-tests were used to assess the inter-limb differences in the THA group. Analyses of covariance (ANCOVA) were performed to compare groups, using age as a covariate. RESULTS The analysis of inter-limb differences in patients following THA revealed significant deficits on the operated side for hip abduction strength (p = 0.02), for hip flexion ROM (p < 0.01) and for balance in terms of the length of center of pressure (COP) (p = 0.04). Compared to values of the control subjects, the patients demonstrated significantly reduced hip strength in flexion, extension and abduction (p < 0.05) on the operated leg as well as reduced ROM measures in hip flexion, extension and abduction (p < 0.05). CONCLUSIONS The first results of this explorative study indicated that inter-limb differences as well as reduced hip strength and hip ROM compared with control subjects were still present four to five years after THA. These persisting asymmetries and deficits in patients following THA may be one explanation for the decrease in health-related quality of life (HRQoL) seen in patients over the years after surgery. Further studies are required to replicate these findings with a larger sample size. TRIAL REGISTRATION DRKS, DRKS00016945. Registered 12 March 2019 - Retrospectively registered.
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Affiliation(s)
- Stefanie John
- Sports Science, Faculty of Humanities, Otto-von-Guericke-University, Zschokkestraße 32, 39104, Magdeburg, Germany.
| | - David Weizel
- Sports Science, Faculty of Humanities, Otto-von-Guericke-University, Zschokkestraße 32, 39104, Magdeburg, Germany
| | - Anna S Heumann
- Sports Science, Faculty of Humanities, Otto-von-Guericke-University, Zschokkestraße 32, 39104, Magdeburg, Germany
| | - Anja Fischer
- Sports Science, Faculty of Humanities, Otto-von-Guericke-University, Zschokkestraße 32, 39104, Magdeburg, Germany
| | - Katja Orlowski
- Department of Computer Science and Media, Brandenburg University of Applied Sciences, Magdeburger Straße 50, 14770, Brandenburg an der Havel, Germany
| | - Kai-Uwe Mrkor
- Department of Computer Science and Media, Brandenburg University of Applied Sciences, Magdeburger Straße 50, 14770, Brandenburg an der Havel, Germany
| | - Jürgen Edelmann-Nusser
- Sports Science, Faculty of Humanities, Otto-von-Guericke-University, Zschokkestraße 32, 39104, Magdeburg, Germany
| | - Kerstin Witte
- Sports Science, Faculty of Humanities, Otto-von-Guericke-University, Zschokkestraße 32, 39104, Magdeburg, Germany
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Pittrof SL, Kaufhold L, Fischer A, Wefers D. Products Released from Structurally Different Dextrans by Bacterial and Fungal Dextranases. Foods 2021; 10:foods10020244. [PMID: 33530339 PMCID: PMC7911647 DOI: 10.3390/foods10020244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/13/2021] [Accepted: 01/21/2021] [Indexed: 12/25/2022] Open
Abstract
Dextran hydrolysis by dextranases is applied in the sugar industry and the medical sector, but it also has a high potential for use in structural analysis of dextrans. However, dextranases are produced by several organisms and thus differ in their properties. The aim of this study was to comparatively investigate the product patterns obtained from the incubation of linear as well as O3- and O4-branched dextrans with different dextranases. For this purpose, genes encoding for dextranases from Bacteroides thetaiotaomicron and Streptococcus salivarius were cloned and heterologously expressed in Escherichia coli. The two recombinant enzymes as well as two commercial dextranases from Chaetomium sp. and Penicillium sp. were subsequently used to hydrolyze structurally different dextrans. The hydrolysis products were investigated in detail by HPAEC-PAD. For dextranases from Chaetomium sp., Penicillium sp., and Bacteroides thetaiotaomicron, isomaltose was the end product of the hydrolysis from linear dextrans, whereas Penicillium sp. dextranase led to isomaltose and isomaltotetraose. In addition, the latter enzyme also catalyzed a disproportionation reaction when incubated with isomaltotriose. For O3- and O4-branched dextrans, the fungal dextranases yielded significantly different oligosaccharide patterns than the bacterial enzymes. Overall, the product patterns can be adjusted by choosing the correct enzyme as well as a defined enzyme activity.
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Affiliation(s)
- Silke L. Pittrof
- Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (S.L.P.); (L.K.); (A.F.)
| | - Larissa Kaufhold
- Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (S.L.P.); (L.K.); (A.F.)
| | - Anja Fischer
- Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (S.L.P.); (L.K.); (A.F.)
| | - Daniel Wefers
- Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (S.L.P.); (L.K.); (A.F.)
- Food Chemistry–Functional Food, Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Correspondence:
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Zapletal B, Veraar C, Sulz I, Fischer A, Mouhieddine M, Schuh C, Tarantino S, Hiesmayr M. Infections are associated with a higher substrate provision in icu patients: An icu nutritionday analysis. Clin Nutr ESPEN 2020. [DOI: 10.1016/j.clnesp.2020.09.293] [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: 11/27/2022]
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Hadjadj J, Carla C, Tusseau M, Stolzenberg M, Aladjidi N, Lega J, Jean-François V, Picard C, Walzer T, Ehl S, Fischer A, Neven B, Belot A, Rieux-Laucat F. Mutations haplo-insuffisantes du gène SOCS1 : une nouvelle cause d’auto-immunité à début précoce traitée par une thérapie ciblée. Rev Med Interne 2020. [DOI: 10.1016/j.revmed.2020.10.096] [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: 10/22/2022]
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Fischer A, Veraar C, Tarantino S, Moick S, Sulz I, Schuh C, Mouhieddine M, Hiesmayr M. Cut-off for risk increase with low bmi in hospitalized patients: A regional nutritionday analysis. Clin Nutr ESPEN 2020. [DOI: 10.1016/j.clnesp.2020.09.255] [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: 10/23/2022]
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Tombor L, John D, Glaser S, Luxan G, Forte E, Furtado M, Rosenthal N, Manavski Y, Fischer A, Muhly-Reinholz M, Looso M, Acker T, Harvey R, Abplanalp A, Dimmeler S. Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.3736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
After myocardial infarct (MI), followed by ischemia and scar formation, interstitial cells play key roles in the adaptation to injury. Endothelial cells (ECs), for instance, can clonally expand, migrate into the infarct area and facilitate crucial functions promoting revascularization, reestablishment of oxygen supply and secretion of paracrine factors. Moreover, ECs can transiently undergo changes towards a mesenchymal phenotype (Endothelial-to-mesenchymal transition; EndMT). Whether this process contributes to long-term cardiac fibrosis or helps to facilitate post-ischemic vessel growth remains controversial. Here, we aim to delineate kinetics and characteristics of phenotypic changes in ECs with single cell RNA-sequencing (scRNA-seq).
We performed a time course (homeostasis or 0 day (d), 1d, 3d, 5d, 7d, 14d, 28d post-MI) in mice and isolated the non-cardiomyocyte fraction for scRNA-seq (n=35,312 cells). Pecam1/Cdh5 double positive ECs showed expression of apoptosis, hypoxia and inflammation markers at 3d. Bioinformatic cell cycle analysis predicted high association with proliferative capacities at 3d, indicative of EC turnover post-MI. Metabolism, recently linked to regulate EndMT, was altered. We found genes of the glycolysis and the TCA-cycle pathway upregulated at 1d to 3d, and a decrease of fatty acid signaling genes. At 3d, mesenchymal markers Fn1, Vim, S100a4, Serpine1 transiently increased compared to homeostasis (>1.6-fold, p<0.05) together with a reduction of EC genes such as Pecam1. Interestingly, mesenchymal transition was transient and returned to baseline levels at 28d after MI. Cell fate trajectory analysis confirmed these findings by identifying an EC state characterized by high proliferation and mesenchymal but low EC properties. At 3d to 7d the majority of the ECs were assigned to this state, based on their transcriptomic profile.
We additionally used Cdh5-CreERT2; R26-mT/mG mice followed by scRNA-seq to trace the fate of ECs. Bioinformatic analysis of GFP-positive ECs confirmed the gain in mesenchymal marker but revealed no full transition to the mesenchymal state at later timepoints. This suggests a transient mesenchymal activation of ECs rather than a complete lineage transition. We further induced EndMT with TGF-β2 in ECs in vitro and observed reversibility of the phenotype after withdrawal of the stimulus. After treatment, ECs upregulated various mesenchymal marker genes. Withdrawal of TGF-β2 at 3d or 7d, reverted expression to baseline levels. We further determined DNA methylation of EndMT gene loci to assess if TGF-β2 leads to a true fate change but did not observe changes after TGF-β2 stimulation and withdrawal. Taken together, our data suggests that ECs undergo a transient mesenchymal activation concomitant with a metabolic adaptation early after MI but do not acquire a long-term mesenchymal fate. This activation may facilitate EC migration and clonal expansion to regenerate the vascular network.
Funding Acknowledgement
Type of funding source: Foundation. Main funding source(s): German Center of Cardiovascular Research (DZHK), Deutsche Forschungsgemeinschaft (DFG) CRC1366 Project B4
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Affiliation(s)
- L Tombor
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - D John
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - S.F Glaser
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - G Luxan
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - E Forte
- The Jackson Lab, Bar Harbor, United States of America
| | - M Furtado
- The Jackson Lab, Bar Harbor, United States of America
| | - N Rosenthal
- The Jackson Lab, Bar Harbor, United States of America
| | - Y Manavski
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - A Fischer
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - M Muhly-Reinholz
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - M Looso
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - T Acker
- Justus-Liebig University of Giessen, Giessen, Germany
| | - R Harvey
- Victor Chang Cardiac Research Institute, Sydney, Australia
| | - A Abplanalp
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - S Dimmeler
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
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Buchholz E, Berulava T, Elerdashvili V, Pena T, Lbik D, Mohamed B, Bohnsack K, Bohnsack M, Hasenfuss G, Fischer A, Toischer K. m6A RNA methylation contributes to translational control in heart failure progression. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.3587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background/Introduction
Heart failure, characterized by reduced cardiac function and left ventricular dilatation, is a leading cause of hospital admission and mortality. Among increased apoptosis and fibrosis, the progression of heart failure is accompanied by changes in gene expression. There is increasing evidence, that also epigenetic processes such as DNA and histone modifications, long non-coding RNAs and transcription factors orchestrate aberrant gene expression in heart failure. Among these epigenetic processes, N6-methyladenosine (m6A) is the most prevalent modification found in all classes of RNA. Such m6A patterns in for example mRNA can have influence on various mechanisms such as splicing, transport, storage or decay of mRNAs. Due to its reversible and dynamic nature regulated via methyltransferases (mainly the METTL3/METTL14/WTAP-complex) and demethylases (mainly FTO and ALkBH5) it adds a new layer of epigenetic regulation.
Purpose
Changes in epigenetic processes are important mechanisms in heart failure progression. We aimed to elucidate the potential role of m6A methylation in heart failure development.
Methods
We analysed m6A methylation in different stages of heart failure progression in mouse and human tissue via methylated RNA immunoprecipitation (meRIP) followed by next generation sequencing (NGS). With polysome fractionation followed by NGS, we studied a potential link between polysomal occupancy and m6a RNA methylation.
Results
We found that approximately one quarter of all RNA transcripts in healthy mouse and human tissue carry m6A RNA methylation. During progression to heart failure we found that changes in m6A methylation exceed changes in gene expression in both, mouse and human. RNAs with altered m6A levels were mainly linked to metabolic and regulatory pathways, whereas changes in expression represented changes in structural plasticity. Furthermore, we found a link between m6A RNA methylation and altered RNA translation. Interestingly, transcripts with unchanged expression level but a differential change in their methylation level also showed differential polysomal occupancy. We could show a corresponding change in protein level, which points to a potential new mechanism of transcription-independent modulation of translation. The importance of m6A methylation was furthermore confirmed in a cardiomyocyte specific knock-out of the RNA demethylase FTO in mice where it lead to impaired cardiac function compared to control mice.
Conclusions
We could show that the m6A landscape is altered in heart hypertrophy and heart failure. Methylation changes exceed expression changes in disease progression and lead to changes in protein abundance, which uncovers a new transcription-independent mechanism of translation regulation. Therefore, our data suggest that targeting epitranscriptomic mechansims, such as m6A methylation, might be a an interesting approach for thereapeutic interventions.
Funding Acknowledgement
Type of funding source: Public grant(s) – EU funding. Main funding source(s): SFB 1002 Modulatory Units in Heart Failure
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Affiliation(s)
- E Buchholz
- University Medical Center Goettingen, Cardiology, Goettingen, Germany
| | - T Berulava
- German Center for Neurodegenerative Diseases, Goettingen, Germany
| | - V Elerdashvili
- German Center for Neurodegenerative Diseases, Goettingen, Germany
| | - T Pena
- German Center for Neurodegenerative Diseases, Goettingen, Germany
| | - D Lbik
- University Medical Center Goettingen, Cardiology, Goettingen, Germany
| | - B.A Mohamed
- University Medical Center Goettingen, Cardiology, Goettingen, Germany
| | - K.E Bohnsack
- University Medical Center Goettingen, Institute for Molecular Biology, Goettingen, Germany
| | - M.T Bohnsack
- University Medical Center Goettingen, Institute for Molecular Biology, Goettingen, Germany
| | - G Hasenfuss
- University Medical Center Goettingen, Cardiology, Goettingen, Germany
| | - A Fischer
- German Center for Neurodegenerative Diseases, Goettingen, Germany
| | - K Toischer
- University Medical Center Goettingen, Cardiology, Goettingen, Germany
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Mittelstadt S, Grube M, Hartkopf A, Engler T, Walter CB, Oberlechner E, Krämer B, Grischke EM, Brucker SY, Fischer A, Staebler A, Kommoss S. Charakterisierung von Langzeitüberleberinnen nach Ovarialkarzinom im Patientenkollektiv der Universitätsfrauenklinik Tübingen. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1718208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
| | - M Grube
- Universitätsfrauenklinik Tübingen
| | | | - T Engler
- Universitätsfrauenklinik Tübingen
| | | | | | - B Krämer
- Universitätsfrauenklinik Tübingen
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Grube M, Krämer P, Chiu D, Bosse T, Scheunhage D, Koebel M, Singh N, Manchanda R, Hammond R, Heitz F, Harter P, du Bois A, Ataseven B, Neudeck N, Beschorner C, Fischer A, Greif K, Krämer B, Brucker S, Talhouk A, Anglesio M, Staebler A, Kommoss S. Immunhistochemische Expression von L1CAM in endometrioiden Ovarialkarzinomen – Ein neuer prognostischer Marker? Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1718139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- M Grube
- Universitätsfrauenklinik Tübingen
| | - P Krämer
- Universitätsfrauenklinik Tübingen
| | - D Chiu
- Department of Obstetrics and Gynecology, University of British Columbia
| | - T Bosse
- Leiden University Medical Center
| | | | - M Koebel
- Department of Pathology and Laboratory Medicine, University of Calgary
| | - N Singh
- Dept of Cellular Pathology, BartsHealth NHS Trust
| | - R Manchanda
- Dept of Cellular Pathology, BartsHealth NHS Trust
| | - R Hammond
- Dept of Cellular Pathology, BartsHealth NHS Trust
| | | | | | | | | | - N Neudeck
- Institut für Pathologie, Universitätsklinikum Tübingen
| | - C Beschorner
- Institut für Pathologie, Universitätsklinikum Tübingen
| | - A Fischer
- Institut für Pathologie, Universitätsklinikum Tübingen
| | - K Greif
- Institut für Pathologie, Universitätsklinikum Tübingen
| | - B Krämer
- Universitätsfrauenklinik Tübingen
| | | | - A Talhouk
- Department of Obstetrics and Gynecology, University of British Columbia
| | - M Anglesio
- Department of Obstetrics and Gynecology, University of British Columbia
| | - A Staebler
- Institut für Pathologie, Universitätsklinikum Tübingen
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Wupper S, Fischer A, Luersen K, Ipharraguerre IR, Chikamoto K, Furune T, Ishida Y, Terao K, Rimbach G. Effects of dietary gamma-cyclodextrin on voluntary activity and muscle strength in mice. J Physiol Pharmacol 2020; 71. [PMID: 32991317 DOI: 10.26402/jpp.2020.3.08] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/30/2020] [Indexed: 11/03/2022]
Abstract
Gamma-cyclodextrin (γCD) is a cyclic oligosaccharide consisting of eight α-(1,4)-linked glucopyranose subunits, which is often used in the food and pharmaceutical industries. However, little is known regarding the metabolic activity of "empty" γCD per se. Therefore, in the present study young C57BL/6 male mice received a control diet (CON) or an experimental diet that was supplemented with 12.88% γCD exchanged against corn starch. After 6 weeks of treatment, the voluntary wheel running activity was monitored and the muscle strength of mice was measured by employing Kondziela's inverted screen test and forelimb grip strength assay. The γCD-treated mice covered a significantly larger distance per night (CON 8.6 km, γCD 12.4 km) and were significantly longer active (CON 340 min, γCD 437 min). Moreover, γCD-treated mice significantly performed better at the inverted screen test indicated by an enhanced Kondziela score (CON 3.10, γCD 4.63). These data suggest that dietary γCD leads to an increased endurance. We also found a slightly anti-glycemic effect of γCD during oral glucose tolerance test. However, our mice from the γCD group exhibited no difference in terms of GLUT2 protein level in ileum tissue nor increased muscle glycogen storage. Furthermore, γCD exhibited no DPP-4 inhibitory activity in vitro. By analysing candidate muscle genes and proteins related to endurance and muscle performance we did not observe any differences in terms of Sirt1, Pgc1α, Cpt1b, Mef2c, Myh1 and Myh2 gene expression levels as well as total oxidative phosphorylation (OXPHOS), mtTFA and GLUT4 protein expression levels in skeletal muscle in response to γCD. We could not fully establish the exact underlying molecular mechanisms of the fitness improvement by dietary γCD which warrants further investigations.
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Affiliation(s)
- S Wupper
- Institute of Human Nutrition and Food Science, University of Kiel, Kiel, Germany.
| | - A Fischer
- Institute of Human Nutrition and Food Science, University of Kiel, Kiel, Germany
| | - K Luersen
- Institute of Human Nutrition and Food Science, University of Kiel, Kiel, Germany
| | - I R Ipharraguerre
- Institute of Human Nutrition and Food Science, University of Kiel, Kiel, Germany
| | - K Chikamoto
- CycloChem Bio Co., Ltd., 7-4-5 Minatojima-minamimachi, Chuo-ku, Kobe, Japan
| | - T Furune
- CycloChem Bio Co., Ltd., 7-4-5 Minatojima-minamimachi, Chuo-ku, Kobe, Japan
| | - Y Ishida
- CycloChem Bio Co., Ltd., 7-4-5 Minatojima-minamimachi, Chuo-ku, Kobe, Japan
| | - K Terao
- CycloChem Bio Co., Ltd., 7-4-5 Minatojima-minamimachi, Chuo-ku, Kobe, Japan
| | - G Rimbach
- Institute of Human Nutrition and Food Science, University of Kiel, Kiel, Germany
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Becker T, Weberpals J, Jegg AM, So WV, Fischer A, Weisser M, Schmich F, Rüttinger D, Bauer-Mehren A. An enhanced prognostic score for overall survival of patients with cancer derived from a large real-world cohort. Ann Oncol 2020; 31:1561-1568. [PMID: 32739409 DOI: 10.1016/j.annonc.2020.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND By understanding prognostic biomarkers, we gain insights into disease biology and may improve design, conduct, and data analysis of clinical trials and real-world data. In this context, we used the Flatiron Health Electronic Health Record-derived deidentified database that provides treatment outcome and biomarker data from >280 oncology centers in the USA, organized into 17 cohorts defined by cancer type. PATIENTS AND METHODS In 122 694 patients, we analyzed demographic, clinical, routine hematology, and blood chemistry parameters within a Cox proportional hazard framework to derive a multivariable prognostic risk model for overall survival (OS), the 'Real wOrld PROgnostic score (ROPRO)'. We validated ROPRO in two independent phase I and III clinical studies. RESULTS A total of 27 variables contributed independently and homogeneously across cancer indications to OS. In the largest cohort (advanced non-small-cell lung cancer), for example, patients with elevated ROPRO scores (upper 10%) had a 7.91-fold (95% confidence interval 7.45-8.39) increased death hazard compared with patients with low scores (lower 10%). Median survival was 23.9 months (23.3-24.5) in the lowest ROPRO quartile Q1, 14.8 months (14.4-15.2) in Q2, 9.4 months (9.1-9.7) in Q3, and 4.7 months (4.6-4.8) in Q4. The ROPRO model performance indicators [C-index = 0.747 (standard error 0.001), 3-month area under the curve (AUC) = 0.822 (0.819-0.825)] strongly outperformed those of the Royal Marsden Hospital Score [C-index = 0.54 (standard error 0.0005), 3-month AUC = 0.579 (0.577-0.581)]. We confirmed the high prognostic relevance of ROPRO in clinical Phase 1 and III trials. CONCLUSIONS The ROPRO provides improved prognostic power for OS. In oncology clinical development, it has great potential for applications in patient stratification, patient enrichment strategies, data interpretation, and early decision-making in clinical studies.
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Affiliation(s)
- T Becker
- Data Science, Pharma Research and Development, Roche Innovation Center Munich, Munich, Germany
| | - J Weberpals
- Data Science, Pharma Research and Development, Roche Innovation Center Munich, Munich, Germany
| | - A M Jegg
- Early Clinical Development Oncology, Pharma Research and Development, Roche Innovation Center Munich, Munich, Germany
| | - W V So
- Data Science, Pharma Research and Development, Roche Innovation Center New York, New York, USA
| | - A Fischer
- Data Science, Pharma Research and Development, Roche Innovation Center Munich, Munich, Germany
| | - M Weisser
- Early Clinical Development Oncology, Pharma Research and Development, Roche Innovation Center Munich, Munich, Germany
| | - F Schmich
- Data Science, Pharma Research and Development, Roche Innovation Center Munich, Munich, Germany
| | - D Rüttinger
- Early Clinical Development Oncology, Pharma Research and Development, Roche Innovation Center Munich, Munich, Germany
| | - A Bauer-Mehren
- Data Science, Pharma Research and Development, Roche Innovation Center Munich, Munich, Germany.
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Fischer A, Klein P, Radulescu P, Gulsun M, Mohamed Ali A, R.S V, Schoebinger M, Sahbaee P, Sharma P, Schoepf U. Deep Learning Based Automated Coronary Labeling For Structured Reporting Of Coronary CT Angiography In Accordance With SCCT Guidelines. J Cardiovasc Comput Tomogr 2020. [DOI: 10.1016/j.jcct.2020.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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