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Winter S, Götze KS, Hecker JS, Metzeler KH, Guezguez B, Woods K, Medyouf H, Schäffer A, Schmitz M, Wehner R, Glauche I, Roeder I, Rauner M, Hofbauer LC, Platzbecker U. Clonal hematopoiesis and its impact on the aging osteo-hematopoietic niche. Leukemia 2024; 38:936-946. [PMID: 38514772 DOI: 10.1038/s41375-024-02226-6] [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: 11/16/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Clonal hematopoiesis (CH) defines a premalignant state predominantly found in older persons that increases the risk of developing hematologic malignancies and age-related inflammatory diseases. However, the risk for malignant transformation or non-malignant disorders is variable and difficult to predict, and defining the clinical relevance of specific candidate driver mutations in individual carriers has proved to be challenging. In addition to the cell-intrinsic mechanisms, mutant cells rely on and alter cell-extrinsic factors from the bone marrow (BM) niche, which complicates the prediction of a mutant cell's fate in a shifting pre-malignant microenvironment. Therefore, identifying the insidious and potentially broad impact of driver mutations on supportive niches and immune function in CH aims to understand the subtle differences that enable driver mutations to yield different clinical outcomes. Here, we review the changes in the aging BM niche and the emerging evidence supporting the concept that CH can progressively alter components of the local BM microenvironment. These alterations may have profound implications for the functionality of the osteo-hematopoietic niche and overall bone health, consequently fostering a conducive environment for the continued development and progression of CH. We also provide an overview of the latest technology developments to study the spatiotemporal dependencies in the CH BM niche, ideally in the context of longitudinal studies following CH over time. Finally, we discuss aspects of CH carrier management in clinical practice, based on work from our group and others.
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Affiliation(s)
- Susann Winter
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Katharina S Götze
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine III, Technical University of Munich (TUM), School of Medicine and Health, Munich, Germany
- German MDS Study Group (D-MDS), Leipzig, Germany
| | - Judith S Hecker
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine III, Technical University of Munich (TUM), School of Medicine and Health, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich (TUM), Munich, Germany
| | - Klaus H Metzeler
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology, Cellular Therapy, Hemostaseology and Infectious Disease, University of Leipzig Medical Center, Leipzig, Germany
| | - Borhane Guezguez
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology and Oncology, University Medical Center Mainz, Mainz, Germany
| | - Kevin Woods
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology and Oncology, University Medical Center Mainz, Mainz, Germany
| | - Hind Medyouf
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Frankfurt am Main, Germany
| | - Alexander Schäffer
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Marc Schmitz
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Rebekka Wehner
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Ingo Roeder
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Martina Rauner
- Division of Endocrinology, Diabetes and Bone Diseases, Department of Medicine III, and Center for Healthy Aging, University Medical Center, TU Dresden, Dresden, Germany
| | - Lorenz C Hofbauer
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Division of Endocrinology, Diabetes and Bone Diseases, Department of Medicine III, and Center for Healthy Aging, University Medical Center, TU Dresden, Dresden, Germany.
| | - Uwe Platzbecker
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German MDS Study Group (D-MDS), Leipzig, Germany.
- Department of Hematology, Cellular Therapy, Hemostaseology and Infectious Disease, University of Leipzig Medical Center, Leipzig, Germany.
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Stumpf J, Anders L, Siepmann T, Schwöbel J, Karger C, Lindner T, Faulhaber-Walter R, Langer T, Escher K, Anding-Rost K, Seidel H, Hüther J, Pistrosch F, Martin H, Schewe J, Stehr T, Meistring F, Paliege A, Schneider D, Bast I, Steglich A, Gembardt F, Kessel F, Kröger H, Arndt P, Sradnick J, Frank K, Skrzypczyk S, Anft M, Klimova A, Mauer R, Roeder I, Tonn T, Babel N, Hugo C. 9-Month observational Dia-Vacc study of vaccine type influence on SARS-CoV-2 immunity in dialysis and kidney transplant patients. Vaccine 2024; 42:120-128. [PMID: 38114410 DOI: 10.1016/j.vaccine.2023.12.034] [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: 06/26/2023] [Revised: 12/05/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND SARS-CoV-2mRNA vaccination related seroconversion rates are reduced in dialysis and kidney transplant patients. METHODS We evaluated nine months follow up data in our observational Dia-Vacc study exploring specific cellular (interferon-γ release assay) or/and humoral immune responses after 2x SARS-CoV-2mRNA vaccination in 880 participants including healthy medical personnel (125-MP), dialysis patients (595-DP), kidney transplant recipients (111-KTR), and apheresis patients (49-AP) with positive seroconversion (de novo IgA or IgG antibody positivity by ELISA) after eight weeks. FINDINGS Nine months after first vaccination, receptor binding domain (RBD) antibodies were still positive in 90 % of MP, 86 % of AP, but only 55 %/48 % of DP/KTR, respectively. Seroconversion remained positive in 100 % of AP and 99·2 % of MP, but 86 %/81 % of DP/KTR, respectively. Compared to MP, DP but not KTR or AP were at risk for a strong RBD decline, while KTR kept lowest RBD values over time. By multivariate analysis, BNT162b2mRNA versus 1273-mRNA vaccine type was an independent risk factor for a strong decline of RBD antibodies. Within the DP group, only time on dialysis was another (inverse) risk factor for the DP group. Compared to humoral immunity, T-cell immunity decline was less prominent. INTERPRETATION While seroconverted KTR reach lowest RBD values over time, DP are at specific risk for a strong decline of RBD antibodies after successful SARS-CoV-2mRNA vaccination, which also depends on the vaccine type being used. Therefore, booster vaccinations for DP should be considered earlier compared to normal population.
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Affiliation(s)
- Julian Stumpf
- Medizinische Klinik und Poliklinik III, Universitätsklinikum, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; KfH-Nierenzentrum Dresden, Dresden, Germany
| | | | - Torsten Siepmann
- KfH-Nierenzentrum am Klinikum Chemnitz, Krankenhaus Küchwald, Chemnitz, Germany
| | | | - Claudia Karger
- KfH-Nierenzentrum am Klinikum St. Georg, Leipzig, Germany
| | - Tom Lindner
- Division of Nephrology, University Hospital Leipzig, Leipzig, Germany
| | | | | | - Katja Escher
- KfH-Gesundheitszentrum Aue, Aue-Bad-Schlema, Germany
| | | | - Harald Seidel
- KfH-Nierenzentrum am Vogtland Krankenhaus Plauen, Plauen, Germany
| | | | | | - Heike Martin
- Nephrologisches Zentrum Zwickau, Zwickau, Germany
| | - Jens Schewe
- Dialyse- und Nierenambulanz Sebnitz, Sebnitz, Germany
| | | | - Frank Meistring
- KfH-Nierenzentrum am Städtischen Klinikum Görlitz, Görlitz, Germany
| | - Alexander Paliege
- Medizinische Klinik und Poliklinik III, Universitätsklinikum, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Daniel Schneider
- Medizinische Klinik und Poliklinik III, Universitätsklinikum, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Anne Steglich
- Medizinische Klinik und Poliklinik III, Universitätsklinikum, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Florian Gembardt
- Medizinische Klinik und Poliklinik III, Universitätsklinikum, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Friederike Kessel
- Medizinische Klinik und Poliklinik III, Universitätsklinikum, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Hannah Kröger
- Medizinische Klinik und Poliklinik III, Universitätsklinikum, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Patrick Arndt
- Medizinische Klinik und Poliklinik III, Universitätsklinikum, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Jan Sradnick
- Medizinische Klinik und Poliklinik III, Universitätsklinikum, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Kerstin Frank
- Institut für Transfusionsmedizin Plauen, DRK-Blutspendedienst Nord-Ost gemeinnützige GmbH, Plauen, Germany
| | - Sarah Skrzypczyk
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Germany
| | - Moritz Anft
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Germany
| | - Anna Klimova
- National Center for Tumor Diseases (NCT) Partner Site Dresden, Dresden, Germany
| | - René Mauer
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry (IMB), Technische Universität, Dresden, Germany
| | - Ingo Roeder
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry (IMB), Technische Universität, Dresden, Germany
| | - Torsten Tonn
- Institute for Transfusion Medicine, German Red Cross Blood Donation Service North-East, Dresden, Germany; Faculty of Medicine Carl Gustav Carus, Transfusion Medicine, Technische Universität, Dresden, Germany
| | - Nina Babel
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, and Institute of Medical Immunology, Germany
| | - Christian Hugo
- Medizinische Klinik und Poliklinik III, Universitätsklinikum, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; KfH-Nierenzentrum Dresden, Dresden, Germany.
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3
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Schmäche T, Fohgrub J, Klimova A, Laaber K, Drukewitz S, Merboth F, Hennig A, Seidlitz T, Herbst F, Baenke F, Ada AM, Groß T, Wenzel C, Ball CR, Praetorius C, Schmidt T, Ringelband-Schilling B, Koschny R, Stenzinger A, Roeder I, Jaeger D, Zeissig S, Welsch T, Aust D, Glimm H, Folprecht G, Weitz J, Haag GM, Stange DE. Stratifying esophago-gastric cancer treatment using a patient-derived organoid-based threshold. Mol Cancer 2024; 23:10. [PMID: 38200602 PMCID: PMC10777586 DOI: 10.1186/s12943-023-01919-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND AND AIMS This study sought to determine the value of patient-derived organoids (PDOs) from esophago-gastric adenocarcinoma (EGC) for response prediction to neoadjuvant chemotherapy (neoCTx). METHODS Endoscopic biopsies of patients with locally advanced EGC (n = 120) were taken into culture and PDOs expanded. PDOs' response towards the single substances of the FLOT regimen and the combination treatment were correlated to patients' pathological response using tumor regression grading. A classifier based on FLOT response of PDOs was established in an exploratory cohort (n = 13) and subsequently confirmed in an independent validation cohort (n = 13). RESULTS EGC PDOs reflected patients' diverse responses to single chemotherapeutics and the combination regimen FLOT. In the exploratory cohort, PDOs response to single 5-FU and FLOT combination treatment correlated with the patients' pathological response (5-FU: Kendall's τ = 0.411, P = 0.001; FLOT: Kendall's τ = 0.694, P = 2.541e-08). For FLOT testing, a high diagnostic precision in receiver operating characteristic (ROC) analysis was reached with an AUCROC of 0.994 (CI 0.980 to 1.000). The discriminative ability of PDO-based FLOT testing allowed the definition of a threshold, which classified in an independent validation cohort FLOT responders from non-responders with high sensitivity (90%), specificity (100%) and accuracy (92%). CONCLUSION In vitro drug testing of EGC PDOs has a high predictive accuracy in classifying patients' histological response to neoadjuvant FLOT treatment. Taking into account the high rate of successful PDO expansion from biopsies, the definition of a threshold that allows treatment stratification paves the way for an interventional trial exploring PDO-guided treatment of EGC patients.
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Affiliation(s)
- Tim Schmäche
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Juliane Fohgrub
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Anna Klimova
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Institute for Medical Informatics and Biometry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Karin Laaber
- German Cancer Research Center (DKFZ) Heidelberg, Translational Functional Cancer Genomics, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Stephan Drukewitz
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), Technical University Dresden, Dresden, Germany
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Felix Merboth
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany
| | - Alexander Hennig
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Therese Seidlitz
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany
| | - Friederike Herbst
- German Cancer Research Center (DKFZ) Heidelberg, Translational Functional Cancer Genomics, Heidelberg, Germany
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Franziska Baenke
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany
| | - Anne-Marlen Ada
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany
| | - Thomas Groß
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), Technical University Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Carina Wenzel
- Institute of Pathology, University Hospital Carl Gustav CarusTechnische Universität Dresden, Dresden, Germany
| | - Claudia R Ball
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav CarusTechnische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), partner side Dresden, Dresden, Germany
- TUD Dresden University of Technology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Christian Praetorius
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Thomas Schmidt
- Department of General, Visceral and Transplantation Surgery, University Hospital of Heidelberg, Heidelberg, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Cologne, Germany
| | - Barbara Ringelband-Schilling
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany
| | - Ronald Koschny
- Department of Gastroenterology and Hepatology, University Hospital of Heidelberg, Heidelberg, Germany
| | | | - Ingo Roeder
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Institute for Medical Informatics and Biometry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Dirk Jaeger
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor-Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Zeissig
- Department of Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
- Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Thilo Welsch
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany
- Department of General, Visceral, and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniela Aust
- Institute of Pathology, University Hospital Carl Gustav CarusTechnische Universität Dresden, Dresden, Germany
- Tumour- and Normal Tissue Bank of the University Cancer Center (UCC), University Hospital Carl Gustav Carus, Medical Faculty, Technische Universität Dresden, Dresden, Germany
| | - Hanno Glimm
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Translational Functional Cancer Genomics, Heidelberg, Germany
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav CarusTechnische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), partner side Dresden, Dresden, Germany
| | - Gunnar Folprecht
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Department of Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Jürgen Weitz
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Georg M Haag
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor-Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel E Stange
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, 01307, Germany.
- National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany.
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4
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Hoffmann K, Pelz A, Karg E, Gottschalk A, Zerjatke T, Schuster S, Böhme H, Glauche I, Roeder I. Data integration between clinical research and patient care: A framework for context-depending data sharing and in silico predictions. PLOS Digit Health 2023; 2:e0000140. [PMID: 37186586 PMCID: PMC10184916 DOI: 10.1371/journal.pdig.0000140] [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] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
The transfer of new insights from basic or clinical research into clinical routine is usually a lengthy and time-consuming process. Conversely, there are still many barriers to directly provide and use routine data in the context of basic and clinical research. In particular, no coherent software solution is available that allows a convenient and immediate bidirectional transfer of data between concrete treatment contexts and research settings. Here, we present a generic framework that integrates health data (e.g., clinical, molecular) and computational analytics (e.g., model predictions, statistical evaluations, visualizations) into a clinical software solution which simultaneously supports both patient-specific healthcare decisions and research efforts, while also adhering to the requirements for data protection and data quality. Specifically, our work is based on a recently established generic data management concept, for which we designed and implemented a web-based software framework that integrates data analysis, visualization as well as computer simulation and model prediction with audit trail functionality and a regulation-compliant pseudonymization service. Within the front-end application, we established two tailored views: a clinical (i.e., treatment context) perspective focusing on patient-specific data visualization, analysis and outcome prediction and a research perspective focusing on the exploration of pseudonymized data. We illustrate the application of our generic framework by two use-cases from the field of haematology/oncology. Our implementation demonstrates the feasibility of an integrated generation and backward propagation of data analysis results and model predictions at an individual patient level into clinical decision-making processes while enabling seamless integration into a clinical information system or an electronic health record.
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Affiliation(s)
- Katja Hoffmann
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Anne Pelz
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Elena Karg
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Andrea Gottschalk
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Thomas Zerjatke
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Silvio Schuster
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Heiko Böhme
- National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
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5
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Karg E, Baldow C, Zerjatke T, Clark RE, Roeder I, Fassoni AC, Glauche I. Modelling of immune response in chronic myeloid leukemia patients suggests potential for treatment reduction prior to cessation. Front Oncol 2022; 12:1028871. [PMID: 36568156 PMCID: PMC9769401 DOI: 10.3389/fonc.2022.1028871] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Discontinuation of tyrosine kinase inhibitor (TKI) treatment is emerging as the main therapy goal for Chronic Myeloid Leukemia (CML) patients. The DESTINY trial showed that TKI dose reduction prior to cessation can lead to an increased number of patients achieving sustained treatment free remission (TFR). However, there has been no systematic investigation to evaluate how dose reduction regimens can further improve the success of TKI stop trials. Methods Here, we apply an established mathematical model of CML therapy to investigate different TKI dose reduction schemes prior to therapy cessation and evaluate them with respect to the total amount of drug used and the expected TFR success. Results Our systematic analysis confirms clinical findings that the overall time of TKI treatment is a major determinant of TFR success, while highlighting that lower dose TKI treatment for the same duration is equally sufficient for many patients. Our results further suggest that a stepwise dose reduction prior to TKI cessation can increase the success rate of TFR, while substantially reducing the amount of administered TKI. Discussion Our findings illustrate the potential of dose reduction schemes prior to treatment cessation and suggest corresponding and clinically testable strategies that are applicable to many CML patients.
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Affiliation(s)
- Elena Karg
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Christoph Baldow
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Thomas Zerjatke
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Richard E. Clark
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany,National Center for Tumor Diseases (NCT), Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden–Rossendorf (HZDR), Dresden, Germany
| | - Artur C. Fassoni
- Instituto de Matemática e Computação, Universidade Federal de Itajubá (UNIFEI), Itajubá, Brazil
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany,*Correspondence: Ingmar Glauche,
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6
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Salmon M, White HE, Zizkova H, Gottschalk A, Motlova E, Cerveira N, Colomer D, Coriu D, Franke GN, Gottardi E, Izzo B, Jurcek T, Lion T, Schäfer V, Venturi C, Vigneri P, Zawada M, Zuna J, Hovorkova L, Koblihova J, Klamova H, Markova MS, Srbova D, Benesova A, Polivkova V, Zackova D, Mayer J, Roeder I, Glauche I, Ernst T, Hochhaus A, Polakova KM, Cross NCP. Impact of BCR::ABL1 transcript type on RT-qPCR amplification performance and molecular response to therapy. Leukemia 2022; 36:1879-1886. [PMID: 35676453 PMCID: PMC9252903 DOI: 10.1038/s41375-022-01612-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 12/03/2022]
Abstract
Several studies have reported that chronic myeloid leukaemia (CML) patients expressing e14a2 BCR::ABL1 have a faster molecular response to therapy compared to patients expressing e13a2. To explore the reason for this difference we undertook a detailed technical comparison of the commonly used Europe Against Cancer (EAC) BCR::ABL1 reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assay in European Treatment and Outcome Study (EUTOS) reference laboratories (n = 10). We found the amplification ratio of the e13a2 amplicon was 38% greater than e14a2 (p = 0.015), and the amplification efficiency was 2% greater (P = 0.17). This subtle difference led to measurable transcript-type dependent variation in estimates of residual disease which could be corrected by (i) taking the qPCR amplification efficiency into account, (ii) using alternative RT-qPCR approaches or (iii) droplet digital PCR (ddPCR), a technique which is relatively insensitive to differences in amplification kinetics. In CML patients, higher levels of BCR::ABL1/GUSB were identified at diagnosis for patients expressing e13a2 (n = 67) compared to e14a2 (n = 78) when analysed by RT-qPCR (P = 0.0005) but not ddPCR (P = 0.5). These data indicate that widely used RT-qPCR assays result in subtly different estimates of disease depending on BCR::ABL1 transcript type; these differences are small but may need to be considered for optimal patient management.
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Affiliation(s)
- Matthew Salmon
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Helen E White
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Hana Zizkova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Andrea Gottschalk
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Eliska Motlova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Nuno Cerveira
- Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Dolors Colomer
- Pathology Department, Hospital Clinic, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBERONC, Barcelona, Spain
| | - Daniel Coriu
- Fundeni Clinical Institute, Hematology Department, Bucharest, Romania.,Hematology Department, Faculty of Medicine, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Georg N Franke
- University of Leipzig Medical Center, Department for Hematology, Cellular Therapies and Hemostaseology, Leipzig, Germany
| | - Enrico Gottardi
- Laboratory of Chemical and Clinical Analysis "Area 3" A.O.U San Luigi Gonzaga-Orbassano, Turin, Italy
| | - Barbara Izzo
- Department of Molecular Medicine and Medical Biotechnology University 'Federico II' and CEINGE - Advanced Biotechnologies, Naples, Italy
| | - Tomas Jurcek
- Center of Molecular Biology and Gene Therapy, Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Thomas Lion
- Labdia Labordiagnostik / St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Vivien Schäfer
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, University of Jena, Jena, Germany
| | - Claudia Venturi
- IRCSS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Paolo Vigneri
- University of Catania, Department of Clinical and Experimental Medicine, Center of Experimental Oncology and Hematology, Catania, Italy
| | | | - Jan Zuna
- CLIP, Dept. of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Lenka Hovorkova
- CLIP, Dept. of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jitka Koblihova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Hana Klamova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | | | - Dana Srbova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Adela Benesova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Vaclava Polivkova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Daniela Zackova
- Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Mayer
- Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany. Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Thomas Ernst
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, University of Jena, Jena, Germany
| | - Andreas Hochhaus
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, University of Jena, Jena, Germany
| | | | - Nicholas C P Cross
- Faculty of Medicine, University of Southampton, Southampton, UK. .,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK.
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7
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Sidorova OA, Sayed S, Paszkowski-Rogacz M, Seifert M, Camgöz A, Roeder I, Bornhäuser M, Thiede C, Buchholz F. RNAi-Mediated Screen of Primary AML Cells Nominates MDM4 as a Therapeutic Target in NK-AML with DNMT3A Mutations. Cells 2022; 11:cells11050854. [PMID: 35269477 PMCID: PMC8909053 DOI: 10.3390/cells11050854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/22/2022] Open
Abstract
DNA-methyltransferase 3A (DNMT3A) mutations belong to the most frequent genetic aberrations found in adult acute myeloid leukemia (AML). Recent evidence suggests that these mutations arise early in leukemogenesis, marking leukemic progenitors and stem cells, and persist through consolidation chemotherapy, providing a pool for AML relapse. Currently, there are no therapeutic approaches directed specifically against this cell population. To unravel therapeutically actionable targets in mutant DNMT3A-driven AML cells, we have performed a focused RNAi screen in a panel of 30 primary AML samples, all carrying a DNMT3A R882 mutation. As one of the strongest hits, we identified MDM4 as a gene essential for proliferation of primary DNMT3AWT/R882X AML cells. We analyzed a publicly available RNA-Seq dataset of primary normal karyotype (NK) AML samples and found a trend towards MDM4 transcript overexpression particularly in DNMT3A-mutant samples. Moreover, we found that the MDM2/4 inhibitor ALRN-6924 impairs growth of DNMT3AWT/R882X primary cells in vitro by inducing cell cycle arrest through upregulation of p53 target genes. Our results suggest that MDM4 inhibition is a potential target in NK-AML patients bearing DNMT3A R882X mutations.
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Affiliation(s)
- Olga Alexandra Sidorova
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
| | - Shady Sayed
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, 01307 Dresden, Germany; (M.S.); (I.R.)
| | - Aylin Camgöz
- Hopp Children’s Cancer Center Heidelberg, 69120 Heidelberg, Germany;
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, 01307 Dresden, Germany; (M.S.); (I.R.)
| | - Martin Bornhäuser
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
- National Center for Tumor Diseases (NCT/UCC), 01307 Dresden, Germany
- Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf (HZDR), 01328 Dresden, Germany
- Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
| | - Christian Thiede
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
- National Center for Tumor Diseases (NCT/UCC), 01307 Dresden, Germany
- Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf (HZDR), 01328 Dresden, Germany
- Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
- National Center for Tumor Diseases (NCT/UCC), 01307 Dresden, Germany
- Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf (HZDR), 01328 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
- Correspondence:
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8
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Schwarz A, Roeder I, Seifert M. Comparative Gene Expression Analysis Reveals Similarities and Differences of Chronic Myeloid Leukemia Phases. Cancers (Basel) 2022; 14:cancers14010256. [PMID: 35008420 PMCID: PMC8750437 DOI: 10.3390/cancers14010256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 12/25/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a slowly progressing blood cancer that primarily affects elderly people. Without successful treatment, CML progressively develops from the chronic phase through the accelerated phase to the blast crisis, and ultimately to death. Nowadays, the availability of targeted tyrosine kinase inhibitor (TKI) therapies has led to long-term disease control for the vast majority of patients. Nevertheless, there are still patients that do not respond well enough to TKI therapies and available targeted therapies are also less efficient for patients in accelerated phase or blast crises. Thus, a more detailed characterization of molecular alterations that distinguish the different CML phases is still very important. We performed an in-depth bioinformatics analysis of publicly available gene expression profiles of the three CML phases. Pairwise comparisons revealed many differentially expressed genes that formed a characteristic gene expression signature, which clearly distinguished the three CML phases. Signaling pathway expression patterns were very similar between the three phases but differed strongly in the number of affected genes, which increased with the phase. Still, significant alterations of MAPK, VEGF, PI3K-Akt, adherens junction and cytokine receptor interaction signaling distinguished specific phases. Our study also suggests that one can consider the phase-wise CML development as a three rather than a two-step process. This is in accordance with the phase-specific expression behavior of 24 potential major regulators that we predicted by a network-based approach. Several of these genes are known to be involved in the accumulation of additional mutations, alterations of immune responses, deregulation of signaling pathways or may have an impact on treatment response and survival. Importantly, some of these genes have already been reported in relation to CML (e.g., AURKB, AZU1, HLA-B, HLA-DMB, PF4) and others have been found to play important roles in different leukemias (e.g., CDCA3, RPL18A, PRG3, TLX3). In addition, increased expression of BCL2 in the accelerated and blast phase indicates that venetoclax could be a potential treatment option. Moreover, a characteristic signaling pathway signature with increased expression of cytokine and ECM receptor interaction pathway genes distinguished imatinib-resistant patients from each individual CML phase. Overall, our comparative analysis contributes to an in-depth molecular characterization of similarities and differences of the CML phases and provides hints for the identification of patients that may not profit from an imatinib therapy, which could support the development of additional treatment strategies.
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Affiliation(s)
- Annemarie Schwarz
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, D-01307 Dresden, Germany; (A.S.); (I.R.)
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, D-01307 Dresden, Germany; (A.S.); (I.R.)
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany: German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany; Helmholtz-Zentrum Dresden—Rossendorf (HZDR), D-01328 Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, D-01307 Dresden, Germany; (A.S.); (I.R.)
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany: German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany; Helmholtz-Zentrum Dresden—Rossendorf (HZDR), D-01328 Dresden, Germany
- Correspondence:
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9
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Hoffmann H, Baldow C, Zerjatke T, Gottschalk A, Wagner S, Karg E, Niehaus S, Roeder I, Glauche I, Scherf N. How to predict relapse in leukemia using time series data: A comparative in silico study. PLoS One 2021; 16:e0256585. [PMID: 34780493 PMCID: PMC8592437 DOI: 10.1371/journal.pone.0256585] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022] Open
Abstract
Risk stratification and treatment decisions for leukemia patients are regularly based on clinical markers determined at diagnosis, while measurements on system dynamics are often neglected. However, there is increasing evidence that linking quantitative time-course information to disease outcomes can improve the predictions for patient-specific treatment responses. We designed a synthetic experiment simulating response kinetics of 5,000 patients to compare different computational methods with respect to their ability to accurately predict relapse for chronic and acute myeloid leukemia treatment. Technically, we used clinical reference data to first fit a model and then generate de novo model simulations of individual patients' time courses for which we can systematically tune data quality (i.e. measurement error) and quantity (i.e. number of measurements). Based hereon, we compared the prediction accuracy of three different computational methods, namely mechanistic models, generalized linear models, and deep neural networks that have been fitted to the reference data. Reaching prediction accuracies between 60 and close to 100%, our results indicate that data quality has a higher impact on prediction accuracy than the specific choice of the particular method. We further show that adapted treatment and measurement schemes can considerably improve the prediction accuracy by 10 to 20%. Our proof-of-principle study highlights how computational methods and optimized data acquisition strategies can improve risk assessment and treatment of leukemia patients.
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Affiliation(s)
- Helene Hoffmann
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Christoph Baldow
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Thomas Zerjatke
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Andrea Gottschalk
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Sebastian Wagner
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Elena Karg
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Sebastian Niehaus
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
- AICURA Medical GmbH, Berlin, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
- National Center of Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Nico Scherf
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
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10
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Oberbeck S, Schrader A, Warner K, Jungherz D, Crispatzu G, von Jan J, Chmielewski M, Ianevski A, Diebner HH, Mayer P, Kondo Ados A, Wahnschaffe L, Braun T, Müller TA, Wagle P, Bouska A, Neumann T, Pützer S, Varghese L, Pflug N, Thelen M, Makalowski J, Riet N, Göx HJM, Rappl G, Altmüller J, Kotrová M, Persigehl T, Hopfinger G, Hansmann ML, Schlößer H, Stilgenbauer S, Dürig J, Mougiakakos D, von Bergwelt-Baildon M, Roeder I, Hartmann S, Hallek M, Moriggl R, Brüggemann M, Aittokallio T, Iqbal J, Newrzela S, Abken H, Herling M. Noncanonical effector functions of the T-memory-like T-PLL cell are shaped by cooperative TCL1A and TCR signaling. Blood 2020; 136:2786-2802. [PMID: 33301031 PMCID: PMC7731789 DOI: 10.1182/blood.2019003348] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 09/26/2019] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
T-cell prolymphocytic leukemia (T-PLL) is a poor-prognostic neoplasm. Differentiation stage and immune-effector functions of the underlying tumor cell are insufficiently characterized. Constitutive activation of the T-cell leukemia 1A (TCL1A) oncogene distinguishes the (pre)leukemic cell from regular postthymic T cells. We assessed activation-response patterns of the T-PLL lymphocyte and interrogated the modulatory impact by TCL1A. Immunophenotypic and gene expression profiles revealed a unique spectrum of memory-type differentiation of T-PLL with predominant central-memory stages and frequent noncanonical patterns. Virtually all T-PLL expressed a T-cell receptor (TCR) and/or CD28-coreceptor without overrepresentation of specific TCR clonotypes. The highly activated leukemic cells also revealed losses of negative-regulatory TCR coreceptors (eg, CTLA4). TCR stimulation of T-PLL cells evoked higher-than-normal cell-cycle transition and profiles of cytokine release that resembled those of normal memory T cells. More activated phenotypes and higher TCL1A correlated with inferior clinical outcomes. TCL1A was linked to the marked resistance of T-PLL to activation- and FAS-induced cell death. Enforced TCL1A enhanced phospho-activation of TCR kinases, second-messenger generation, and JAK/STAT or NFAT transcriptional responses. This reduced the input thresholds for IL-2 secretion in a sensitizer-like fashion. Mice of TCL1A-initiated protracted T-PLL development resembled such features. When equipped with epitope-defined TCRs or chimeric antigen receptors, these Lckpr-hTCL1Atg T cells gained a leukemogenic growth advantage in scenarios of receptor stimulation. Overall, we propose a model of T-PLL pathogenesis in which TCL1A enhances TCR signals and drives the accumulation of death-resistant memory-type cells that use amplified low-level stimulatory input, and whose loss of negative coregulators additionally maintains their activated state. Treatment rationales are provided by combined interception in TCR and survival signaling.
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MESH Headings
- Animals
- Humans
- Immunologic Memory
- Leukemia, Prolymphocytic, T-Cell/genetics
- Leukemia, Prolymphocytic, T-Cell/immunology
- Leukemia, Prolymphocytic, T-Cell/pathology
- Mice
- Mice, Knockout
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Signal Transduction/genetics
- Signal Transduction/immunology
- T-Lymphocytes/immunology
- T-Lymphocytes/pathology
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Affiliation(s)
- S Oberbeck
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - A Schrader
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - K Warner
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- Senckenberg Institute of Pathology, Goethe University, Frankfurt am Main, Germany
| | - D Jungherz
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - G Crispatzu
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - J von Jan
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - M Chmielewski
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - A Ianevski
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - H H Diebner
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry Dresden, Technische Universität Dresden, Dresden, Germany
| | - P Mayer
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - A Kondo Ados
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - L Wahnschaffe
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - T Braun
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - T A Müller
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - P Wagle
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
| | - A Bouska
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - T Neumann
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - S Pützer
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - L Varghese
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - N Pflug
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
| | - M Thelen
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - J Makalowski
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - N Riet
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - H J M Göx
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
| | - G Rappl
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - J Altmüller
- Cologne Center for Genomics, Institute of Human Genetics, UoC, Cologne, Germany
| | - M Kotrová
- Medical Department II of Hematology and Oncology, University Hospital of Schleswig Holstein, Campus Kiel, Kiel, Germany
| | - T Persigehl
- Department of Radiology, UoC, Cologne, Germany
| | - G Hopfinger
- Center for Oncology and Hematology, Kaiser-Franz-Josef-Spital, Vienna, Austria
| | - M L Hansmann
- Senckenberg Institute of Pathology, Goethe University, Frankfurt am Main, Germany
| | - H Schlößer
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - S Stilgenbauer
- Department III of Internal Medicine, University Hospital Ulm, Ulm, Germany
| | - J Dürig
- Clinic for Hematology, University Hospital Essen, Essen, Germany
| | - D Mougiakakos
- Department of Medicine 5, Hematology, and Oncology, University Hospital Erlangen, Erlangen, Germany
| | | | - I Roeder
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry Dresden, Technische Universität Dresden, Dresden, Germany
| | - S Hartmann
- Senckenberg Institute of Pathology, Goethe University, Frankfurt am Main, Germany
| | - M Hallek
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - R Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
- Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, Vienna, Austria; and
| | - M Brüggemann
- Medical Department II of Hematology and Oncology, University Hospital of Schleswig Holstein, Campus Kiel, Kiel, Germany
| | - T Aittokallio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - J Iqbal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - S Newrzela
- Senckenberg Institute of Pathology, Goethe University, Frankfurt am Main, Germany
| | - H Abken
- RCI Regensburg Center for Interventional Immunology, Regensburg, Germany
| | - M Herling
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
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11
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Roeder I, Glauche I. Overlooking the obvious? On the potential of treatment alterations to predict patient-specific therapy response. Exp Hematol 2020; 94:26-30. [PMID: 33246016 DOI: 10.1016/j.exphem.2020.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/08/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022]
Abstract
Prognostic or therapeutic classification of diseases is often based on clinical or genetic characteristics at diagnosis or response landmarks determined at a certain time point of treatment. On the other hand, there are more and more means, such as molecular markers and sensor data, that allow for quantification of disease or therapeutic parameters over time. Although a general value of time-resolved disease monitoring is widely accepted, the full potential of using the available information on disease and treatment dynamics in the context of outcome prediction or individualized treatment optimization still seems to be, at least partially, overlooked. Within this Perspective, we summarize the conceptual idea of using dynamic information to obtain a better understanding of complex pathophysiological processes within their particular "host environment," which also allows us to intrinsically map patient-specific heterogeneity. Specifically, we discuss to which extent treatment alterations can provide additional information to understand a patient's individual condition and use this information to further adapt the therapeutic strategy. This conceptual discussion is illustrated by using examples from myeloid leukemias to which we recently applied this concept using statistical and mathematical modeling.
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Affiliation(s)
- Ingo Roeder
- Technische Universität Dresden, Carl Gustav Carus Faculty of Medicine, Institute for Medical Informatics and Biometry, Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Core Unit: Data Management and Analytics, Dresden, Germany.
| | - Ingmar Glauche
- Technische Universität Dresden, Carl Gustav Carus Faculty of Medicine, Institute for Medical Informatics and Biometry, Dresden, Germany
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12
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Hoffmann H, Thiede C, Glauche I, Bornhaeuser M, Roeder I. Differential response to cytotoxic therapy explains treatment dynamics of acute myeloid leukaemia patients: insights from a mathematical modelling approach. J R Soc Interface 2020; 17:20200091. [PMID: 32900301 DOI: 10.1098/rsif.2020.0091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Disease response and durability of remission are very heterogeneous in patients with acute myeloid leukaemia (AML). There is increasing evidence that the individual risk of early relapse can be predicted based on the initial treatment response. However, it is unclear how such a correlation is linked to functional aspects of AML progression and treatment. We suggest a mathematical model in which leukaemia-initiating cells and normal/healthy haematopoietic stem and progenitor cells reversibly change between an active state characterized by proliferation and chemosensitivity and a quiescent state, in which the cells do not divide, but are also insensitive to chemotherapy. Applying this model to 275 molecular time courses of nucleophosmin 1-mutated patients, we conclude that the differential chemosensitivity of the leukaemia-initiating cells together with the cells' intrinsic proliferative capacity is sufficient to reproduce both, early relapse as well as long-lasting remission. We can, furthermore, show that the model parameters associated with individual chemosensitivity and proliferative advantage of the leukaemic cells are closely linked to the patients' time to relapse, while a reliable prediction based on early response only is not possible based on the currently available data. Although we demonstrate with our approach, that the complete response data is sufficient to quantify the aggressiveness of the disease, further investigations are necessary to study how an intensive early sampling strategy may prospectively improve risk assessment and help to optimize individual treatments.
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Affiliation(s)
- H Hoffmann
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - C Thiede
- Medical Clinic and Polyclinic I, University Hospital Dresden Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - I Glauche
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - M Bornhaeuser
- Medical Clinic and Polyclinic I, University Hospital Dresden Carl Gustav Carus, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - I Roeder
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
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13
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Machova Polakova K, Zizkova H, Zuna J, Motlova E, Hovorkova L, Gottschalk A, Glauche I, Koblihova J, Pecherkova P, Klamova H, Stastna Markova M, Srbova D, Benesova A, Polivkova V, Jurcek T, Zackova D, Mayer J, Ernst T, Mahon FX, Saussele S, Roeder I, Cross NCP, Hochhaus A. Analysis of chronic myeloid leukaemia during deep molecular response by genomic PCR: a traffic light stratification model with impact on treatment-free remission. Leukemia 2020; 34:2113-2124. [PMID: 32472084 DOI: 10.1038/s41375-020-0882-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022]
Abstract
This work investigated patient-specific genomic BCR-ABL1 fusions as markers of measurable residual disease (MRD) in chronic myeloid leukaemia, with a focus on relevance to treatment-free remission (TFR) after achievement of deep molecular response (DMR) on tyrosine kinase inhibitor (TKI) therapy. DNA and mRNA BCR-ABL1 measurements by qPCR were compared in 2189 samples (129 patients) and by digital PCR in 1279 sample (62 patients). A high correlation was found at levels of disease above MR4, but there was a poor correlation for samples during DMR. A combination of DNA and RNA MRD measurements resulted in a better prediction of molecular relapse-free survival (MRFS) after TKI stop (n = 17) or scheduled interruption (n = 25). At 18 months after treatment cessation, patients with stopped or interrupted TKI therapy who were DNA negative/RNA negative during DMR maintenance (green group) had an MRFS of 80% and 100%, respectively, compared with those who were DNA positive/RNA negative (MRFS = 57% and 67%, respectively; yellow group) or DNA positive/RNA positive (MRFS = 20% for both cohorts; red group). Thus, we propose a "traffic light" stratification as a TFR predictor based on DNA and mRNA BCR-ABL1 measurements during DMR maintenance before TKI cessation.
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MESH Headings
- Adult
- Aged
- Female
- Fusion Proteins, bcr-abl/genetics
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/mortality
- Male
- Middle Aged
- Neoplasm, Residual
- Polymerase Chain Reaction/methods
- Protein Kinase Inhibitors/therapeutic use
- Protein-Tyrosine Kinases/antagonists & inhibitors
- RNA, Messenger/analysis
- Remission Induction
- Withholding Treatment
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Affiliation(s)
- Katerina Machova Polakova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic.
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic.
| | - Hana Zizkova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jan Zuna
- CLIP, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Eliska Motlova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Lenka Hovorkova
- CLIP, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Andrea Gottschalk
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Jitka Koblihova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Pavla Pecherkova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Hana Klamova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
- Institute of Clinical and Experimental Hematology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marketa Stastna Markova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
- Institute of Clinical and Experimental Hematology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Dana Srbova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Adela Benesova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Vaclava Polivkova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Tomas Jurcek
- Center of Molecular Biology and Gene Therapy, Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Daniela Zackova
- Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Mayer
- Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Thomas Ernst
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, University of Jena, Jena, Germany
| | - Francois X Mahon
- BERGONIE Institute BORDEAUX, INSERM U1218 University of Bordeaux, Bordeaux, France
| | - Susanne Saussele
- Department of Haematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - Nicholas C P Cross
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury and Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andreas Hochhaus
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, University of Jena, Jena, Germany
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14
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Lauber C, Correia N, Trumpp A, Rieger MA, Dolnik A, Bullinger L, Roeder I, Seifert M. Survival differences and associated molecular signatures of DNMT3A-mutant acute myeloid leukemia patients. Sci Rep 2020; 10:12761. [PMID: 32728112 PMCID: PMC7391693 DOI: 10.1038/s41598-020-69691-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/13/2020] [Indexed: 12/17/2022] Open
Abstract
Acute myeloid leukemia (AML) is a very heterogeneous and highly malignant blood cancer. Mutations of the DNA methyltransferase DNMT3A are among the most frequent recurrent genetic lesions in AML. The majority of DNMT3A-mutant AML patients shows fast relapse and poor survival, but also patients with long survival or long-term remission have been reported. Underlying molecular signatures and mechanisms that contribute to these survival differences are only poorly understood and have not been studied in detail so far. We applied hierarchical clustering to somatic gene mutation profiles of 51 DNMT3A-mutant patients from The Cancer Genome Atlas (TCGA) AML cohort revealing two robust patient subgroups with profound differences in survival. We further determined molecular signatures that distinguish both subgroups. Our results suggest that FLT3 and/or NPM1 mutations contribute to survival differences of DNMT3A-mutant patients. We observed an upregulation of genes of the p53, VEGF and DNA replication pathway and a downregulation of genes of the PI3K-Akt pathway in short- compared to long-lived patients. We identified that the majority of measured miRNAs was downregulated in the short-lived group and we found differentially expressed microRNAs between both subgroups that have not been reported for AML so far (miR-153-2, miR-3065, miR-95, miR-6718) suggesting that miRNAs could be important for prognosis. In addition, we learned gene regulatory networks to predict potential major regulators and found several genes and miRNAs with known roles in AML pathogenesis, but also interesting novel candidates involved in the regulation of hematopoiesis, cell cycle, cell differentiation, and immunity that may contribute to the observed survival differences of both subgroups and could therefore be important for prognosis. Moreover, the characteristic gene mutation and expression signatures that distinguished short- from long-lived patients were also predictive for independent DNMT3A-mutant AML patients from other cohorts and could also contribute to further improve the European LeukemiaNet (ELN) prognostic scoring system. Our study represents the first in-depth computational approach to identify molecular factors associated with survival differences of DNMT3A-mutant AML patients and could trigger additional studies to develop robust molecular markers for a better stratification of AML patients with DNMT3A mutations.
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Affiliation(s)
- Chris Lauber
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Nádia Correia
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael A Rieger
- Department of Medicine, Hematology/Oncology, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Anna Dolnik
- Department of Hematology, Oncology and Tumorimmunology, Charité University Medicine Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumorimmunology, Charité University Medicine Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany. .,National Center for Tumor Diseases (NCT), Dresden, Germany.
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15
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Kloenne M, Niehaus S, Lampe L, Merola A, Reinelt J, Roeder I, Scherf N. Domain-specific cues improve robustness of deep learning-based segmentation of CT volumes. Sci Rep 2020; 10:10712. [PMID: 32612129 PMCID: PMC7329868 DOI: 10.1038/s41598-020-67544-y] [Citation(s) in RCA: 5] [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: 02/05/2020] [Accepted: 06/04/2020] [Indexed: 11/08/2022] Open
Abstract
Machine learning has considerably improved medical image analysis in the past years. Although data-driven approaches are intrinsically adaptive and thus, generic, they often do not perform the same way on data from different imaging modalities. In particular computed tomography (CT) data poses many challenges to medical image segmentation based on convolutional neural networks (CNNs), mostly due to the broad dynamic range of intensities and the varying number of recorded slices of CT volumes. In this paper, we address these issues with a framework that adds domain-specific data preprocessing and augmentation to state-of-the-art CNN architectures. Our major focus is to stabilise the prediction performance over samples as a mandatory requirement for use in automated and semi-automated workflows in the clinical environment. To validate the architecture-independent effects of our approach we compare a neural architecture based on dilated convolutions for parallel multi-scale processing (a modified Mixed-Scale Dense Network: MS-D Net) to traditional scaling operations (a modified U-Net). Finally, we show that an ensemble model combines the strengths across different individual methods. Our framework is simple to implement into existing deep learning pipelines for CT analysis. It performs well on a range of tasks such as liver and kidney segmentation, without significant differences in prediction performance on strongly differing volume sizes and varying slice thickness. Thus our framework is an essential step towards performing robust segmentation of unknown real-world samples.
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Affiliation(s)
- Marie Kloenne
- AICURA medical, Bessemerstrasse 22, 12103, Berlin, Germany
- Technische Fakultät, Universität Bielefeld, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Sebastian Niehaus
- AICURA medical, Bessemerstrasse 22, 12103, Berlin, Germany
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Leonie Lampe
- AICURA medical, Bessemerstrasse 22, 12103, Berlin, Germany
| | - Alberto Merola
- AICURA medical, Bessemerstrasse 22, 12103, Berlin, Germany
| | - Janis Reinelt
- AICURA medical, Bessemerstrasse 22, 12103, Berlin, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
- National Center of Tumor Diseases (NCT) Partner Site Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Nico Scherf
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany.
- Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstrasse 1a, 04103, Leipzig, Germany.
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16
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Bondarieva A, Raveendran K, Telychko V, Rao HBDP, Ravindranathan R, Zorzompokou C, Finsterbusch F, Dereli I, Papanikos F, Tränkner D, Schleiffer A, Fei JF, Klimova A, Ito M, Kulkarni DS, Roeder I, Hunter N, Tóth A. Proline-rich protein PRR19 functions with cyclin-like CNTD1 to promote meiotic crossing over in mouse. Nat Commun 2020; 11:3101. [PMID: 32555348 PMCID: PMC7303132 DOI: 10.1038/s41467-020-16885-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 05/27/2020] [Indexed: 01/05/2023] Open
Abstract
Orderly chromosome segregation is enabled by crossovers between homologous chromosomes in the first meiotic division. Crossovers arise from recombination-mediated repair of programmed DNA double-strand breaks (DSBs). Multiple DSBs initiate recombination, and most are repaired without crossover formation, although one or more generate crossovers on each chromosome. Although the underlying mechanisms are ill-defined, the differentiation and maturation of crossover-specific recombination intermediates requires the cyclin-like CNTD1. Here, we identify PRR19 as a partner of CNTD1. We find that, like CNTD1, PRR19 is required for timely DSB repair and the formation of crossover-specific recombination complexes. PRR19 and CNTD1 co-localise at crossover sites, physically interact, and are interdependent for accumulation, indicating a PRR19-CNTD1 partnership in crossing over. Further, we show that CNTD1 interacts with a cyclin-dependent kinase, CDK2, which also accumulates in crossover-specific recombination complexes. Thus, the PRR19-CNTD1 complex may enable crossover differentiation by regulating CDK2.
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Affiliation(s)
- Anastasiia Bondarieva
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Kavya Raveendran
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Vladyslav Telychko
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - H B D Prasada Rao
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Ramya Ravindranathan
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Chrysoula Zorzompokou
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Friederike Finsterbusch
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Ihsan Dereli
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Frantzeskos Papanikos
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Daniel Tränkner
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna BioCenter (VBC), 1030, Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Dr. Bohr-Gasse 3, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Ji-Feng Fei
- Institute for Brain Research and Rehabilitation, South China Normal University, 510631, Guangzhou, China
| | - Anna Klimova
- National Center for Tumor Diseases (NCT), Dresden, Germany
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Masaru Ito
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Dhananjaya S Kulkarni
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Ingo Roeder
- National Center for Tumor Diseases (NCT), Dresden, Germany
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
- Department of Molecular & Cellular Biology, University of California Davis, Davis, CA, USA
| | - Attila Tóth
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany.
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17
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Erdmann K, Salomo K, Klimova A, Heberling U, Lohse-Fischer A, Fuehrer R, Thomas C, Roeder I, Froehner M, Wirth MP, Fuessel S. Urinary MicroRNAs as Potential Markers for Non-Invasive Diagnosis of Bladder Cancer. Int J Mol Sci 2020; 21:ijms21113814. [PMID: 32471285 PMCID: PMC7312501 DOI: 10.3390/ijms21113814] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 12/21/2022] Open
Abstract
Currently, voided urine cytology (VUC) serves as the gold standard for the detection of bladder cancer (BCa) in urine. Despite its high specificity, VUC has shortcomings in terms of sensitivity. Therefore, alternative biomarkers are being searched, which might overcome these disadvantages as a useful adjunct to VUC. The aim of this study was to evaluate the diagnostic potential of the urinary levels of selected microRNAs (miRs), which might represent such alternative biomarkers due to their BCa-specific expression. Expression levels of nine BCa-associated microRNAs (miR-21, -96, -125b, -126, -145, -183, -205, -210, -221) were assessed by quantitative PCR in urine sediments from 104 patients with primary BCa and 46 control subjects. Receiver operating characteristic (ROC) curve analyses revealed a diagnostic potential for miR-96, -125b, -126, -145, -183, and -221 with area under the curve (AUC) values between 0.605 and 0.772. The combination of the four best candidates resulted in sensitivity, specificity, positive and negative predictive values (NPV), and accuracy of 73.1%, 95.7%, 97.4%, 61.1%, and 80.0%, respectively. Combined with VUC, sensitivity and NPV could be increased by nearly 8%, each surpassing the performance of VUC alone. The present findings suggested a diagnostic potential of miR-125b, -145, -183, and -221 in combination with VUC for non-invasive detection of BCa in urine.
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Affiliation(s)
- Kati Erdmann
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (K.S.); (U.H.); (A.L.-F.); (R.F.); (C.T.); (M.F.); (M.P.W.)
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany; (A.K.); (I.R.)
| | - Karsten Salomo
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (K.S.); (U.H.); (A.L.-F.); (R.F.); (C.T.); (M.F.); (M.P.W.)
| | - Anna Klimova
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany; (A.K.); (I.R.)
- Institute for Medical Informatics and Biometrics, Technische Universität Dresden, 01307 Dresden, Germany
| | - Ulrike Heberling
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (K.S.); (U.H.); (A.L.-F.); (R.F.); (C.T.); (M.F.); (M.P.W.)
| | - Andrea Lohse-Fischer
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (K.S.); (U.H.); (A.L.-F.); (R.F.); (C.T.); (M.F.); (M.P.W.)
| | - Romy Fuehrer
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (K.S.); (U.H.); (A.L.-F.); (R.F.); (C.T.); (M.F.); (M.P.W.)
| | - Christian Thomas
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (K.S.); (U.H.); (A.L.-F.); (R.F.); (C.T.); (M.F.); (M.P.W.)
| | - Ingo Roeder
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany; (A.K.); (I.R.)
- Institute for Medical Informatics and Biometrics, Technische Universität Dresden, 01307 Dresden, Germany
| | - Michael Froehner
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (K.S.); (U.H.); (A.L.-F.); (R.F.); (C.T.); (M.F.); (M.P.W.)
| | - Manfred P. Wirth
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (K.S.); (U.H.); (A.L.-F.); (R.F.); (C.T.); (M.F.); (M.P.W.)
| | - Susanne Fuessel
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (K.S.); (U.H.); (A.L.-F.); (R.F.); (C.T.); (M.F.); (M.P.W.)
- Correspondence: ; Tel.: +49-351-45814544
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18
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Johansson P, Klein-Hitpass L, Budeus B, Kuhn M, Lauber C, Seifert M, Roeder I, Pförtner R, Stuschke M, Dührsen U, Eckstein A, Dürig J, Küppers R. Identifying Genetic Lesions in Ocular Adnexal Extranodal Marginal Zone Lymphomas of the MALT Subtype by Whole Genome, Whole Exome and Targeted Sequencing. Cancers (Basel) 2020; 12:cancers12040986. [PMID: 32316399 PMCID: PMC7225979 DOI: 10.3390/cancers12040986] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 03/10/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022] Open
Abstract
The pathogenesis of ocular adnexal marginal zone lymphomas of mucosa-associated lymphatic tissue-type (OAML) is not fully understood. We performed whole genome sequencing (WGS) and/or whole exome sequencing (WES) for 13 cases of OAML and sequenced 38 genes selected from this analysis in a large cohort of 82 OAML. Besides confirmation of frequent mutations in the genes transducin beta like 1 X-linked receptor 1 (TBL1XR1) and cAMP response element binding protein (CREBBP), we newly identifed JAK3 as a frequently mutated gene in OAML (11% of cases). In our retrospective cohort, JAK3 mutant cases had a shorter progression-free survival compared with unmutated cases. Other newly identified genes recurrently mutated in 5-10% of cases included members of the collagen family (collagen type XII alpha 1/2 (COL12A1, COL1A2)) and DOCK8. Evaluation of the WGS data of six OAML did not reveal translocations or a current infection of the lymphoma cells by viruses. Evaluation of the WGS data for copy number aberrations confirmed frequent loss of TNFAIP3, and revealed recurrent gains of the NOTCH target HES4, and of members of the CEBP transcription factor family. Overall, we identified several novel genes recurrently affected by point mutations or copy number alterations, but our study also indicated that the landscape of frequently (>10% of cases) mutated protein-coding genes in OAML is now largely known.
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Affiliation(s)
- Patricia Johansson
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (U.D.); (J.D.)
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany; (L.K.-H.); (B.B.); (R.K.)
- Correspondence: ; Tel.: +49-201-723-85845
| | - Ludger Klein-Hitpass
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany; (L.K.-H.); (B.B.); (R.K.)
| | - Bettina Budeus
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany; (L.K.-H.); (B.B.); (R.K.)
| | - Matthias Kuhn
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany; (M.K.); (C.L.); (M.S.); (I.R.)
| | - Chris Lauber
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany; (M.K.); (C.L.); (M.S.); (I.R.)
| | - Michael Seifert
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany; (M.K.); (C.L.); (M.S.); (I.R.)
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany; (M.K.); (C.L.); (M.S.); (I.R.)
| | - Roman Pförtner
- Department of Oral and Cranio-Maxillofacial Surgery, Kliniken Essen-Mitte, Evang. Huyssens-Stiftung/Knappschaft GmbH, University Hospital of Essen, 45136 Essen, Germany;
| | - Martin Stuschke
- Department of Radiotherapy, University Hospital Essen, 45147 Essen, Germany;
| | - Ulrich Dührsen
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (U.D.); (J.D.)
| | - Anja Eckstein
- Department of Ophthalmology, Molecular Ophthalmology Group, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Jan Dürig
- Department of Hematology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (U.D.); (J.D.)
- German Cancer Consortium (DKTK), 45147 Essen, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany; (L.K.-H.); (B.B.); (R.K.)
- German Cancer Consortium (DKTK), 45147 Essen, Germany
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19
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Hoffmann K, Cazemier K, Baldow C, Schuster S, Kheifetz Y, Schirm S, Horn M, Ernst T, Volgmann C, Thiede C, Hochhaus A, Bornhäuser M, Suttorp M, Scholz M, Glauche I, Loeffler M, Roeder I. Integration of mathematical model predictions into routine workflows to support clinical decision making in haematology. BMC Med Inform Decis Mak 2020; 20:28. [PMID: 32041606 PMCID: PMC7011438 DOI: 10.1186/s12911-020-1039-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 11/08/2018] [Accepted: 01/29/2020] [Indexed: 02/05/2023] Open
Abstract
Background Individualization and patient-specific optimization of treatment is a major goal of modern health care. One way to achieve this goal is the application of high-resolution diagnostics together with the application of targeted therapies. However, the rising number of different treatment modalities also induces new challenges: Whereas randomized clinical trials focus on proving average treatment effects in specific groups of patients, direct conclusions at the individual patient level are problematic. Thus, the identification of the best patient-specific treatment options remains an open question. Systems medicine, specifically mechanistic mathematical models, can substantially support individual treatment optimization. In addition to providing a better general understanding of disease mechanisms and treatment effects, these models allow for an identification of patient-specific parameterizations and, therefore, provide individualized predictions for the effect of different treatment modalities. Results In the following we describe a software framework that facilitates the integration of mathematical models and computer simulations into routine clinical processes to support decision-making. This is achieved by combining standard data management and data exploration tools, with the generation and visualization of mathematical model predictions for treatment options at an individual patient level. Conclusions By integrating model results in an audit trail compatible manner into established clinical workflows, our framework has the potential to foster the use of systems-medical approaches in clinical practice. We illustrate the framework application by two use cases from the field of haematological oncology.
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Affiliation(s)
- Katja Hoffmann
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Katja Cazemier
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Christoph Baldow
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Silvio Schuster
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Yuri Kheifetz
- Institute for Medical Informatics, Statistics and Epidemiology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Sibylle Schirm
- Institute for Medical Informatics, Statistics and Epidemiology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Matthias Horn
- Institute for Medical Informatics, Statistics and Epidemiology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Thomas Ernst
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Constanze Volgmann
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Christian Thiede
- Department of Internal Medicine, Medical Clinic I, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Andreas Hochhaus
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Martin Bornhäuser
- Department of Internal Medicine, Medical Clinic I, University Hospital Carl Gustav Carus Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - Meinolf Suttorp
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany. .,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.
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20
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Hähnel T, Baldow C, Guilhot J, Guilhot F, Saussele S, Mustjoki S, Jilg S, Jost PJ, Dulucq S, Mahon FX, Roeder I, Fassoni AC, Glauche I. Model-based inference and classification of immunological control mechanisms from TKI cessation and dose reduction in CML patients. Cancer Res 2020; 80:2394-2406. [DOI: 10.1158/0008-5472.can-19-2175] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/18/2019] [Accepted: 02/05/2020] [Indexed: 11/16/2022]
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21
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Zakrzewski F, de Back W, Weigert M, Wenke T, Zeugner S, Mantey R, Sperling C, Friedrich K, Roeder I, Aust D, Baretton G, Hönscheid P. Automated detection of the HER2 gene amplification status in Fluorescence in situ hybridization images for the diagnostics of cancer tissues. Sci Rep 2019; 9:8231. [PMID: 31160649 PMCID: PMC6546913 DOI: 10.1038/s41598-019-44643-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/21/2019] [Indexed: 01/03/2023] Open
Abstract
The human epidermal growth factor receptor 2 (HER2) gene amplification status is a crucial marker for evaluating clinical therapies of breast or gastric cancer. We propose a deep learning-based pipeline for the detection, localization and classification of interphase nuclei depending on their HER2 gene amplification state in Fluorescence in situ hybridization (FISH) images. Our pipeline combines two RetinaNet-based object localization networks which are trained (1) to detect and classify interphase nuclei into distinct classes normal, low-grade and high-grade and (2) to detect and classify FISH signals into distinct classes HER2 or centromere of chromosome 17 (CEN17). By independently classifying each nucleus twice, the two-step pipeline provides both robustness and interpretability for the automated detection of the HER2 amplification status. The accuracy of our deep learning-based pipeline is on par with that of three pathologists and a set of 57 validation images containing several hundreds of nuclei are accurately classified. The automatic pipeline is a first step towards assisting pathologists in evaluating the HER2 status of tumors using FISH images, for analyzing FISH images in retrospective studies, and for optimizing the documentation of each tumor sample by automatically annotating and reporting of the HER2 gene amplification specificities.
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Affiliation(s)
- Falk Zakrzewski
- Institute of Pathology, University Hospital Carl Gustav Carus (UKD), TU Dresden, Dresden, Germany.
| | - Walter de Back
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany.,Center for Information Services and High Performance Computing (ZIH), TU Dresden, Dresden, Germany
| | - Martin Weigert
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.,Center for Systems Biology Dresden (CSBD), Dresden, Germany
| | | | - Silke Zeugner
- Institute of Pathology, University Hospital Carl Gustav Carus (UKD), TU Dresden, Dresden, Germany
| | - Robert Mantey
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - Christian Sperling
- Institute of Pathology, University Hospital Carl Gustav Carus (UKD), TU Dresden, Dresden, Germany
| | - Katrin Friedrich
- Institute of Pathology, University Hospital Carl Gustav Carus (UKD), TU Dresden, Dresden, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - Daniela Aust
- Institute of Pathology, University Hospital Carl Gustav Carus (UKD), TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - Gustavo Baretton
- Institute of Pathology, University Hospital Carl Gustav Carus (UKD), TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - Pia Hönscheid
- Institute of Pathology, University Hospital Carl Gustav Carus (UKD), TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
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22
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César Fassoni A, Roeder I, Glauche I. To Cure or Not to Cure: Consequences of Immunological Interactions in CML Treatment. Bull Math Biol 2019; 81:2345-2395. [DOI: 10.1007/s11538-019-00608-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/21/2019] [Indexed: 10/26/2022]
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23
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Nieswand V, Richter M, Berner R, von der Hagen M, Klimova A, Roeder I, Koch T, Sabatowski R, Gossrau G. The prevalence of headache in German pupils of different ages and school types. Cephalalgia 2019; 39:1030-1040. [DOI: 10.1177/0333102419837156] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background/objective Headache in pupils is underestimated and has a negative impact on learning and life. The aim of this study was to investigate headache prevalence and its collateral effects, in pupils of different ages and school types in a German city. Methods Anonymized questionnaires were distributed to 5419 pupils attending primary and secondary schools. Demographics, headache frequency, analgesic use, school absence and, for secondary school children, data on lifestyle were collected. Results The questionnaire was returned by 2706 children (49%), 1362 (50.3%) girls, 1344 (49.7%) boys. Of these, 36.6% indicated a frequency of 1, and 31.5% a frequency of ≥ 2 headache days per month within the last 3 months. Headache prevalence increased with school grade, age and secondary school type: 63.6%, 67.2% and 79.5% for primary school children, pupils attending 8-year and pupils attending 6-year secondary schools, respectively. With secondary school level I certificates, pupils are prepared for general professional training in 6 years. Secondary school level II results, after 8 years of training, in university entrance level II certificates, which are the precondition for university studies. Girls reported significantly more headache than boys (73% vs. 63.1%). A significant relationship has been observed between headache frequency and school absence and between headache intensity and headache frequency. Of pupils with headache at least twice a month, 48.1% reported analgesic intake. Ibuprofen (49.1%) and paracetamol (32.8%) were the most frequently used analgesics. Of those pupils with headache ≥ 2 days/month, 68.3% did not have a specific headache diagnosis. Concomitant diseases and regular drug intake, analgesic intake for another reason than headache, caffeine consumption and lack of participation in sports were positively correlated with headache. Conclusions The majority of pupils suffer from headache at least once a month. Since frequent headache results in educational and social limitations, pupils at risk should be identified and referred to headache education programs. Efforts are needed to improve the management of juvenile headache patients.
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Affiliation(s)
- Vera Nieswand
- Pain Center, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Matthias Richter
- Department of Pediatrics, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Reinhard Berner
- Department of Pediatrics, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Maja von der Hagen
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Anna Klimova
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
- Institute for Medical Informatics and Biometrics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Ingo Roeder
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
- Institute for Medical Informatics and Biometrics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Thea Koch
- Department of Anesthesiology and Intensive Care Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Rainer Sabatowski
- Pain Center, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Department of Anesthesiology and Intensive Care Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Gudrun Gossrau
- Pain Center, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
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24
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Gaspari E, Franke A, Robles-Diaz D, Zweigerdt R, Roeder I, Zerjatke T, Kempf H. Paracrine mechanisms in early differentiation of human pluripotent stem cells: Insights from a mathematical model. Stem Cell Res 2018; 32:1-7. [PMID: 30145492 DOI: 10.1016/j.scr.2018.07.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/24/2018] [Indexed: 02/01/2023] Open
Abstract
With their capability to self-renew and differentiate into derivatives of all three germ layers, human pluripotent stem cells (hPSCs) offer a unique model to study aspects of human development in vitro. Directed differentiation towards mesendodermal lineages is a complex process, involving transition through a primitive streak (PS)-like stage. We have recently shown PS-like patterning from hPSCs into definitive endoderm, cardiac as well as presomitic mesoderm by only modulating the bulk cell density and the concentration of the GSK3 inhibitor CHIR99021, a potent activator of the WNT pathway. The patterning process is modulated by a complex paracrine network, whose identity and mechanistic consequences are poorly understood. To study the underlying dynamics, we here applied mathematical modeling based on ordinary differential equations. We compared time-course data of early hPSC differentiation to increasingly complex model structures with incremental numbers of paracrine factors. Model simulations suggest at least three paracrine factors being required to recapitulate the experimentally observed differentiation kinetics. Feedback mechanisms from both undifferentiated and differentiated cells turned out to be crucial. Evidence from double knock-down experiments and secreted protein enrichment allowed us to hypothesize on the identity of two of the three predicted factors. From a practical perspective, the mathematical model predicts optimal settings for directing lineage-specific differentiation. This opens new avenues for rational stem cell bioprocessing in more advanced culture systems, e.g. in perfusion-fed bioreactors enabling cell therapies.
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Affiliation(s)
- Erika Gaspari
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany; Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Annika Franke
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), REBIRTH-Cluster of Excellence, Hannover Medical School, Germany
| | - Diana Robles-Diaz
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), REBIRTH-Cluster of Excellence, Hannover Medical School, Germany
| | - Robert Zweigerdt
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), REBIRTH-Cluster of Excellence, Hannover Medical School, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Thomas Zerjatke
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany.
| | - Henning Kempf
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), REBIRTH-Cluster of Excellence, Hannover Medical School, Germany.
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25
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Fassoni AC, Baldow C, Roeder I, Glauche I. Reduced tyrosine kinase inhibitor dose is predicted to be as effective as standard dose in chronic myeloid leukemia: a simulation study based on phase III trial data. Haematologica 2018; 103:1825-1834. [PMID: 29954936 PMCID: PMC6278983 DOI: 10.3324/haematol.2018.194522] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [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: 03/29/2018] [Accepted: 06/26/2018] [Indexed: 02/05/2023] Open
Abstract
Continuing tyrosine kinase inhibitor (TKI)-mediated targeting of the BCR-ABL1 oncoprotein is the standard therapy for chronic myeloid leukemia (CML) and allows for a sustained disease control in the majority of patients. While therapy cessation for patients appeared as a safe option for about half of those patients with optimal response, no systematic assessment of long-term TKI dose de-escalation has been made. We use a mathematical model to analyze and consistently describe biphasic treatment responses from TKI-treated patients from two independent clinical phase III trials. Scale estimates reveal that drug efficiency determines the initial response while the long-term behavior is limited by the rare activation of leukemic stem cells. We use this mathematical framework to investigate the influence of different dosing regimens on the treatment outcome. We provide strong evidence to suggest that TKI dose de-escalation (at least 50%) does not lead to a reduction of long-term treatment efficiency for most patients, who have already achieved sustained remission, and maintains the secondary decline of BCR-ABL1 levels. We demonstrate that continuous BCR-ABL1 monitoring provides patient-specific predictions of an optimal reduced dose without decreasing the anti-leukemic effect on residual leukemic stem cells. Our results are consistent with the interim results of the DESTINY trial and provide clinically testable predictions. Our results suggest that dose-halving should be considered as a long-term treatment option for CML patients with good response under continuing maintenance therapy with TKIs. We emphasize the clinical potential of this approach to reduce treatment-related side-effects and treatment costs.
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Affiliation(s)
- Artur C Fassoni
- Instituto de Matemática e Computação, Universidade Federal de Itajubá, Brazil.,Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Christoph Baldow
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Germany
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26
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Diebner HH, Zerjatke T, Griehl M, Roeder I. Metabolism is the tie: The Bertalanffy-type cancer growth model as common denominator of various modelling approaches. Biosystems 2018; 167:1-23. [PMID: 29605248 DOI: 10.1016/j.biosystems.2018.03.004] [Citation(s) in RCA: 4] [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: 02/22/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 10/17/2022]
Abstract
Cancer or tumour growth has been addressed from a variety of mathematical modelling perspectives in the past. Examples are single variable growth models, reaction diffusion models, compartment models, individual cell-based models, clonal competition models, to name only a few. In this paper, we show that the so called Bertalanffy-type growth model is a macroscopic model variant that can be conceived as an optimal condensed modelling approach that to a high degree preserves complexity with respect to the aforementioned more complex modelling variants. The derivation of the Bertalanffy-type model is crucially based on features of metabolism. Therefore, this model contains a shape parameter that can be interpreted as a resource utilisation efficiency. This shape parameter reflects features that are usually captured in much more complex models. To be specific, the shape parameter is related to morphological structures of tumours, which in turn depend on metabolic conditions. We, furthermore, show that a single variable variant of the Bertalanffy-type model can straightforwardly be extended to a multiclonal competition model. Since competition is crucially based on available shared or clone-specific resources, the metabolism-based approach is an obvious candidate to capture clonal competition. Depending on the specific context, metabolic reprogramming or other oncogene driven changes either lead to a suppression of cancer cells or to an improved competition resulting in outgrowth of tumours. The parametrisation of the Bertalanffy-type growth model allows to account for this observed variety of cancer characteristics. The shape parameter, conceived as a classifier for healthy and oncogenic phenotypes, supplies a link to survival and evolutionary stability concepts discussed in demographic studies, such as opportunistic versus equilibrium strategies.
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Affiliation(s)
- Hans H Diebner
- Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstrasse 74, D-01307 Dresden, Germany.
| | - Thomas Zerjatke
- Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstrasse 74, D-01307 Dresden, Germany
| | - Max Griehl
- Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstrasse 74, D-01307 Dresden, Germany
| | - Ingo Roeder
- Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstrasse 74, D-01307 Dresden, Germany
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27
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Hohenstein B, Julius U, Lansberg P, Jaeger B, Mellwig KP, Weiss N, Graehlert X, Roeder I, Ramlow W. Rationale and design of MultiSELECt: A European Multi center S tudy on the E ffect of L ipoprotein(a) E limination by lipoprotein apheresis on C ardiovascular ou t comes. ATHEROSCLEROSIS SUPP 2017; 30:180-186. [DOI: 10.1016/j.atherosclerosissup.2017.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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MacLean AL, Smith MA, Liepe J, Sim A, Khorshed R, Rashidi NM, Scherf N, Krinner A, Roeder I, Lo Celso C, Stumpf MPH. Single Cell Phenotyping Reveals Heterogeneity Among Hematopoietic Stem Cells Following Infection. Stem Cells 2017; 35:2292-2304. [DOI: 10.1002/stem.2692] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 04/28/2017] [Accepted: 06/01/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Adam L. MacLean
- Department of Life Sciences; Imperial College London; London United Kingdom
| | - Maia A. Smith
- Department of Life Sciences; Imperial College London; London United Kingdom
| | - Juliane Liepe
- Department of Life Sciences; Imperial College London; London United Kingdom
| | - Aaron Sim
- Department of Life Sciences; Imperial College London; London United Kingdom
| | - Reema Khorshed
- Department of Life Sciences; Imperial College London; London United Kingdom
| | - Narges M. Rashidi
- Department of Life Sciences; Imperial College London; London United Kingdom
| | - Nico Scherf
- Institute for Medical Informatics and Biometry, Technische Universitat Dresden; Dresden Germany
| | - Axel Krinner
- Institute for Medical Informatics and Biometry, Technische Universitat Dresden; Dresden Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Technische Universitat Dresden; Dresden Germany
| | - Cristina Lo Celso
- Department of Life Sciences; Imperial College London; London United Kingdom
| | - Michael P. H. Stumpf
- Department of Life Sciences; Imperial College London; London United Kingdom
- MRC London Institute of Medical Sciences, Imperial College London; London United Kingdom
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29
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Klose M, Florian MC, Geiger H, Roeder I, Glauche I. Mathematical modeling of aging-related changes in the symmetry of hematopoietic stem cell divisions. Exp Hematol 2017. [DOI: 10.1016/j.exphem.2017.06.205] [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: 11/29/2022]
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30
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Bandoła J, Richter C, Ryser M, Jamal A, Ashton MP, von Bonin M, Kuhn M, Dorschner B, Alexopoulou D, Navratiel K, Roeder I, Dahl A, Hedrich CM, Bonifacio E, Brenner S, Thieme S. Neurotrophin Receptor p75NTR Regulates Immune Function of Plasmacytoid Dendritic Cells. Front Immunol 2017; 8:981. [PMID: 28861085 PMCID: PMC5562693 DOI: 10.3389/fimmu.2017.00981] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/31/2017] [Indexed: 11/16/2022] Open
Abstract
Plasmacytoid dendritic cells (pDCs) regulate innate and adaptive immunity. Neurotrophins and their receptors control the function of neuronal tissue. In addition, they have been demonstrated to be part of the immune response but little is known about the effector immune cells involved. We report, for the first time, the expression and immune-regulatory function of the low affinity neurotrophin receptor p75 neurotrophin receptor (p75NTR) by the antigen-presenting pDCs, mediated by toll-like receptor (TLR) 9 activation and differential phosphorylation of interferon regulatory factor 3 and 7. The modulation of p75NTR on pDCs significantly influences disease progression of asthma in an ovalbumin-induced mouse model mediated by the TLR9 signaling pathway. p75NTR activation of pDCs from patients with asthma increased allergen-specific T cell proliferation and cytokine secretion in nerve growth factor concentration-dependent manner. Further, p75NTR activation of pDCs delayed the onset of autoimmune diabetes in RIP-CD80GP mice and aggravated graft-versus-host disease in a xenotransplantation model. Thus, p75NTR signaling on pDCs constitutes a new and critical mechanism connecting neurotrophin signaling and immune response regulation with great therapeutic potential for a variety of immune disorders.
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Affiliation(s)
- Joanna Bandoła
- Department of Pediatrics, University Clinic Dresden, Dresden, Germany
| | - Cornelia Richter
- Department of Pediatrics, University Clinic Dresden, Dresden, Germany
| | - Martin Ryser
- Department of Pediatrics, University Clinic Dresden, Dresden, Germany
| | - Arshad Jamal
- Department of Pediatrics, University Clinic Dresden, Dresden, Germany.,Department of Medical Laboratory Sciences, Imperial College of Business Studies, Lahore, Pakistan
| | - Michelle P Ashton
- DFG-Center for Regenerative Therapies Dresden, Cluster of Excellence, Technische Universitaet Dresden, Dresden, Germany
| | - Malte von Bonin
- Medical Clinic I, University Clinic Dresden, Dresden, Germany.,DKTK-German Cancer Consortium, Partner Site Dresden, University Clinic Dresden, Dresden, Germany.,DKFZ-German Cancer Research Center, Heidelberg, Germany
| | - Matthias Kuhn
- Faculty of Medicine, Institute for Medical Informatics and Biometry, Technische Universitaet Dresden, Dresden, Germany
| | | | - Dimitra Alexopoulou
- BIOTEChnology Center/DFG-Center for Regenerative Therapies Dresden, Cluster of Excellence, Technische Universitaet Dresden, Dresden, Germany
| | - Katrin Navratiel
- Department of Pediatrics, University Clinic Dresden, Dresden, Germany
| | - Ingo Roeder
- Faculty of Medicine, Institute for Medical Informatics and Biometry, Technische Universitaet Dresden, Dresden, Germany
| | - Andreas Dahl
- BIOTEChnology Center/DFG-Center for Regenerative Therapies Dresden, Cluster of Excellence, Technische Universitaet Dresden, Dresden, Germany
| | | | - Ezio Bonifacio
- DFG-Center for Regenerative Therapies Dresden, Cluster of Excellence, Technische Universitaet Dresden, Dresden, Germany
| | - Sebastian Brenner
- Department of Pediatrics, University Clinic Dresden, Dresden, Germany.,DFG-Center for Regenerative Therapies Dresden, Cluster of Excellence, Technische Universitaet Dresden, Dresden, Germany
| | - Sebastian Thieme
- Department of Pediatrics, University Clinic Dresden, Dresden, Germany
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31
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Cornils K, Thielecke L, Winkelmann D, Aranyossy T, Lesche M, Dahl A, Roeder I, Fehse B, Glauche I. Clonal competition in BcrAbl-driven leukemia: how transplantations can accelerate clonal conversion. Mol Cancer 2017; 16:120. [PMID: 28709463 PMCID: PMC5512731 DOI: 10.1186/s12943-017-0668-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 04/25/2017] [Accepted: 05/25/2017] [Indexed: 12/14/2022] Open
Abstract
Background Clonal competition in cancer describes the process in which the progeny of a cell clone supersedes or succumbs to other competing clones due to differences in their functional characteristics, mostly based on subsequently acquired mutations. Even though the patterns of those mutations are well explored in many tumors, the dynamical process of clonal selection is underexposed. Methods We studied the dynamics of clonal competition in a BcrAbl-induced leukemia using a γ-retroviral vector library encoding the oncogene in conjunction with genetic barcodes. To this end, we studied the growth dynamics of transduced cells on the clonal level both in vitro and in vivo in transplanted mice. Results While we detected moderate changes in clonal abundancies in vitro, we observed monoclonal leukemias in 6/30 mice after transplantation, which intriguingly were caused by only two different BcrAbl clones. To analyze the success of these clones, we applied a mathematical model of hematopoietic tissue maintenance, which indicated that a differential engraftment capacity of these two dominant clones provides a possible explanation of our observations. These findings were further supported by additional transplantation experiments and increased BcrAbl transcript levels in both clones. Conclusion Our findings show that clonal competition is not an absolute process based on mutations, but highly dependent on selection mechanisms in a given environmental context. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0668-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kerstin Cornils
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Present Adress: University Medical Center Hamburg-Eppendorf, Pediatric Hematology and Oncology & Research Institute Children's Cancer Center Hamburg, Martinistr. 52, 20246, Hamburg, Germany.
| | - Lars Thielecke
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Doreen Winkelmann
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Aranyossy
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mathias Lesche
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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32
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Herold S, Kuhn M, Bonin MV, Stange T, Platzbecker U, Radke J, Lange T, Sockel K, Gutsche K, Schetelig J, Röllig C, Schuster C, Roeder I, Dahl A, Mohr B, Serve H, Brandts C, Ehninger G, Bornhäuser M, Thiede C. Donor cell leukemia: evidence for multiple preleukemic clones and parallel long term clonal evolution in donor and recipient. Leukemia 2017; 31:1637-1640. [PMID: 28348390 DOI: 10.1038/leu.2017.104] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- S Herold
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - M Kuhn
- Institut für Medizinische Informatik und Biometrie, TU Dresden, Dresden, Germany
| | - M V Bonin
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Dresden, Germany.,Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - T Stange
- Institut für Medizinische Informatik und Biometrie, TU Dresden, Dresden, Germany
| | - U Platzbecker
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - J Radke
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - T Lange
- Abteilung Hämatologie, Universitätsklinikum Leipzig AöR, Leipzig, Germany
| | - K Sockel
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - K Gutsche
- Klinik für Hämatologie und Onkologie, Städtisches Klinikum Görlitz, Görlitz, Germany
| | - J Schetelig
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - C Röllig
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - C Schuster
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - I Roeder
- Institut für Medizinische Informatik und Biometrie, TU Dresden, Dresden, Germany
| | - A Dahl
- Deep Sequencing Core Facility, Center for Regenerative Medicine, TU Dresden, Dresden, Germany
| | - B Mohr
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - H Serve
- Medizinische Klinik II, Klinikum der Johann-Wolfgang-Goethe-Universität, Frankfurt am Main, Germany
| | - C Brandts
- Medizinische Klinik II, Klinikum der Johann-Wolfgang-Goethe-Universität, Frankfurt am Main, Germany
| | - G Ehninger
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - M Bornhäuser
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - C Thiede
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
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33
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Herberg M, Glauche I, Zerjatke T, Winzi M, Buchholz F, Roeder I. Dissecting mechanisms of mouse embryonic stem cells heterogeneity through a model-based analysis of transcription factor dynamics. J R Soc Interface 2016; 13:rsif.2016.0167. [PMID: 27097654 DOI: 10.1098/rsif.2016.0167] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/29/2016] [Indexed: 01/06/2023] Open
Abstract
Pluripotent mouse embryonic stem cells (mESCs) show heterogeneous expression levels of transcription factors (TFs) involved in pluripotency regulation, among them Nanog and Rex1. The expression of both TFs can change dynamically between states of high and low activity, correlating with the cells' capacity for self-renewal. Stochastic fluctuations as well as sustained oscillations in gene expression are possible mechanisms to explain this behaviour, but the lack of suitable data hampered their clear distinction. Here, we present a systems biology approach in which novel experimental data on TF heterogeneity is complemented by an agent-based model of mESC self-renewal. Because the model accounts for intracellular interactions, cell divisions and heredity structures, it allows for evaluating the consistency of the proposed mechanisms with data on population growth and on TF dynamics after cell sorting. Our model-based analysis revealed that a bistable, noise-driven network model fulfils the minimal requirements to consistently explain Nanog and Rex1 expression dynamics in heterogeneous and sorted mESC populations. Moreover, we studied the impact of TF-related proliferation capacities on the frequency of state transitions and demonstrate that cellular genealogies can provide insights into the heredity structures of mESCs.
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Affiliation(s)
- Maria Herberg
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany Interdisciplinary Center for Bioinformatics, Faculty of Medicine, Universität Leipzig, Leipzig, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Thomas Zerjatke
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Maria Winzi
- University Cancer Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Frank Buchholz
- University Cancer Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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34
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Proschmann R, Baldow C, Rothe T, Suttorp M, Thiede C, Tauer JT, Müller MC, Hochhaus A, Roeder I, Glauche I. Response dynamics of pediatric patients with chronic myeloid leukemia on imatinib therapy. Haematologica 2016; 102:e39-e42. [PMID: 27856510 DOI: 10.3324/haematol.2016.154138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Rick Proschmann
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry, Technische Universität Dresden, Mannheim, Germany
| | - Christoph Baldow
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry, Technische Universität Dresden, Mannheim, Germany
| | - Tino Rothe
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry, Technische Universität Dresden, Mannheim, Germany
| | - Meinolf Suttorp
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital "Carl Gustav Carus", Technische Universität Dresden, Mannheim, Germany
| | - Christian Thiede
- Department of Internal Medicine, Medical Clinic I, University Hospital "Carl Gustav Carus", Technische Universität Dresden, Mannheim, Germany
| | - Josephine T Tauer
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital "Carl Gustav Carus", Technische Universität Dresden, Mannheim, Germany
| | - Martin C Müller
- Department of Internal Medicine, Medical Clinic III, Medical Faculty Mannheim, Ruprecht-Karls-University Heidelberg, Mannheim, Germany
| | - Andreas Hochhaus
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Germany
| | - Ingo Roeder
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry, Technische Universität Dresden, Mannheim, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
| | - Ingmar Glauche
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry, Technische Universität Dresden, Mannheim, Germany
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35
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Herling M, Rengstl B, Scholtysik R, Hartmann S, Küppers R, Hansmann ML, Diebner HH, Roeder I, Abken H, Newrzela S, Kirberg J. Concepts in mature T-cell lymphomas - highlights from an international joint symposium on T-cell immunology and oncology<sup/>. Leuk Lymphoma 2016; 58:788-796. [PMID: 27643643 DOI: 10.1080/10428194.2016.1222381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Growing attention in mature T-cell lymphomas/leukemias (MTCL) is committed to more accurate and meaningful classifications, improved pathogenetic concepts and expanded therapeutic options. This requires considerations of the immunologic concepts of T-cell homeostasis and the specifics of T-cell receptor (TCR) affinities and signaling. Scientists from various disciplines established the CONTROL-T research unit and in an international conference on MTCL they brought together experts from T-cell immunity, oncology, immunotherapy and systems biology. We report here meeting highlights on the covered topics of diagnostic pitfalls, implications by the new WHO classification, insights from discovered genomic lesions as well as TCR-centric concepts of cellular dynamics in host defense, auto-immunity and tumorigenic clonal escape, including predictions to be derived from in vivo imaging and mathematical modeling. Presentations on novel treatment approaches were supplemented by strategies of optimizing T-cell immunotherapies. Work packages, that in joint efforts would advance the field of MTCL more efficiently, are identified.
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Affiliation(s)
- Marco Herling
- a Department of Internal Medicine, Center for Integrated Oncology (CIO) Köln-Bonn, Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD) , University of Cologne , Cologne , Germany
| | - Benjamin Rengstl
- b Dr. Senckenberg Institute of Pathology, Goethe-University , Frankfurt/M , Germany
| | - René Scholtysik
- c Institute of Cell Biology (Cancer Research), University of Duisburg-Essen , Essen , Germany
| | - Sylvia Hartmann
- b Dr. Senckenberg Institute of Pathology, Goethe-University , Frankfurt/M , Germany
| | - Ralf Küppers
- c Institute of Cell Biology (Cancer Research), University of Duisburg-Essen , Essen , Germany
| | - Martin-Leo Hansmann
- b Dr. Senckenberg Institute of Pathology, Goethe-University , Frankfurt/M , Germany
| | - Hans H Diebner
- d Faculty of Medicine Carl Gustav Carus , Technische Universität Dresden, Institute for Medical Informatics and Biometry , Dresden , Germany
| | - Ingo Roeder
- d Faculty of Medicine Carl Gustav Carus , Technische Universität Dresden, Institute for Medical Informatics and Biometry , Dresden , Germany
| | - Hinrich Abken
- a Department of Internal Medicine, Center for Integrated Oncology (CIO) Köln-Bonn, Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD) , University of Cologne , Cologne , Germany.,e Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany
| | - Sebastian Newrzela
- b Dr. Senckenberg Institute of Pathology, Goethe-University , Frankfurt/M , Germany
| | - Jörg Kirberg
- f Division of Immunology , Paul-Ehrlich-Institute , Langen , Germany
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Kuhn M, Stange T, Herold S, Thiede C, Roeder I. Finding small somatic structural variants in exome sequencing data: a machine learning approach. Comput Stat 2016. [DOI: 10.1007/s00180-016-0674-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Diebner HH, Marré B, Roeder I, Walter MH. Process-based approach to modeling recurrent-event data explicated on the basis of occurrences of tooth losses in two different prosthetic treatment concepts. Trials 2016; 17:244. [PMID: 27185170 PMCID: PMC4869190 DOI: 10.1186/s13063-016-1360-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 09/30/2015] [Accepted: 04/23/2016] [Indexed: 11/10/2022] Open
Abstract
Background In studies comparing different prosthetic treatment concepts the repeated loss of teeth was chosen as the primary outcome. The resulting data appear to represent a data structure of recurrent events. However, the application of an existing method for recurrent events is far from straightforward. Often only the first event or the final state is analyzed using Kaplan–Meier survival statistics, thereby giving a great deal of information away. Methods The paper presents a strategy for the analysis of recurrent data using a previously published study on the influence of different prosthetic treatment concepts for the shortened dental arch on tooth loss. A method based on cumulative sample history functions of recurrent events was adjusted for tooth loss. The shapes of these cumulative functions suggest a time dependency of the recurrence rate. To keep the model as simple as possible, a tripartite Poisson process (which assumes piecewise time-independent rates) was fitted to the cumulative mean functions stratified by treatment. Results Within the middle interval of the three-phasic process, the treatment effects differ significantly, which is interpreted as a delay of tooth loss due to the use of one type of prosthesis (fixed) compared with the other (removable). Conclusions An analysis based on cumulative history functions is based on process, therefore, temporally changing characteristics are better captured than in methods for survival analyses. The presented approach offers useful new insight into the temporal behavior of ongoing tooth loss after prosthetic treatment. Trial registration The trial has been registered at controlled-trials.com under ISRCTN97265367 (registration date 4 April 2008). Electronic supplementary material The online version of this article (doi:10.1186/s13063-016-1360-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hans H Diebner
- Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstrasse 74, Dresden, D-01307, Germany.
| | - Birgit Marré
- Department of Prosthetic Dentistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dental School, Fetscherstrasse 74, Dresden, D-01307, Germany
| | - Ingo Roeder
- Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstrasse 74, Dresden, D-01307, Germany
| | - Michael H Walter
- Department of Prosthetic Dentistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dental School, Fetscherstrasse 74, Dresden, D-01307, Germany
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Diebner HH, Kirberg J, Roeder I. An evolutionary stability perspective on oncogenesis control in mature T-cell populations. J Theor Biol 2016; 389:88-100. [PMID: 26549469 DOI: 10.1016/j.jtbi.2015.10.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/05/2015] [Accepted: 10/19/2015] [Indexed: 01/29/2023]
Abstract
Here we present a mathematical model for the dynamics of oncogenesis control in mature T-cell populations within the blood and lymphatic system. T-cell homeostasis is maintained by clonal competition for trophic niches (survival signals stimulated through interactions with self-antigens bound to major histocompatibility molecules), where a clone is defined as the set of T cells carrying the same antigen specific T-cell receptor (TCR). We analytically derive fitness functions of healthy and leukemic clone variants, respectively, that capture the dependency of the stability of the healthy T-cell pool against leukemic invaders on clonal diversity and kinetic parameters. Similar to the stability of ecosystems with high biodiversity, leukemic mutants are suppressed within polyclonal T-cell populations, i.e., in the presence of a huge number of different TCRs. To the contrary, for a low clonal diversity the leukemic clone variants are able to invade the healthy T-cell pool. The model, therefore, describes the experimentally observed phenomenon that preleukemic clone variants prevail in quasi-monoclonal experimental settings (in mice), whereas in polyclonal settings the healthy TCR variants are able to suppress the outgrowth of tumours. Between the two extremal situations of mono- and polyclonality there exists a range of coexistence of healthy and oncogenic clone variants with moderate fitness (stability) each. A variation of cell cycle times considerably changes the dynamics within this coexistence region. Faster proliferating variants increase their chance to dominate. Finally, a simplified niche variation scheme illustrates a possible mechanism to increase clonal T-cell diversity given a small niche diversity.
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Affiliation(s)
- Hans H Diebner
- Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstrasse 74, D-01307 Dresden, Germany.
| | - Jörg Kirberg
- Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Ingo Roeder
- Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstrasse 74, D-01307 Dresden, Germany
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Garthe A, Roeder I, Kempermann G. Mice in an enriched environment learn more flexibly because of adult hippocampal neurogenesis. Hippocampus 2015; 26:261-71. [PMID: 26311488 PMCID: PMC5049654 DOI: 10.1002/hipo.22520] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 08/25/2015] [Indexed: 12/21/2022]
Abstract
We here show that living in a stimulus‐rich environment (ENR) improves water maze learning with respect to specific key indicators that in previous loss‐of‐function experiments have been shown to rely on adult hippocampal neurogenesis. Analyzing the strategies employed by mice to locate the hidden platform in the water maze revealed that ENR facilitated task acquisition by increasing the probability to use effective search strategies. ENR also enhanced the animals’ behavioral flexibility, when the escape platform was moved to a new location. Treatment with temozolomide, which is known to reduce adult neurogenesis, abolished the effects of ENR on both acquisition and flexibility, while leaving other aspects of water maze learning untouched. These characteristic effects and interdependencies were not seen in parallel experiments with voluntary wheel running (RUN), a second pro‐neurogenic behavioral stimulus. Since the histological assessment of adult neurogenesis is by necessity an end‐point measure, the levels of neurogenesis over the course of the experiment can only be inferred and the present study focused on behavioral parameters as analytical endpoints. Although the correlation of physical activity with precursor cell proliferation and of learning and the survival of new neurons is well established, how the specific functional effects described here relate to dynamic changes in the stem cell niche remains to be addressed. Nevertheless, our findings support the hypothesis that adult neurogenesis is a critical mechanism underlying the beneficial effects of leading an active live, rich in experiences. © 2015 The Authors Hippocampus Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Alexander Garthe
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Adult Neurogenesis, Dresden, Germany.,CRTD-DFG Research Center for Regenerative Therapies Dresden, Genomics of Regeneration, Technische Universität Dresden, Dresden, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Adult Neurogenesis, Dresden, Germany.,CRTD-DFG Research Center for Regenerative Therapies Dresden, Genomics of Regeneration, Technische Universität Dresden, Dresden, Germany
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Abstract
The maintenance of pluripotency in embryonic stem cells (ESCs), its loss during lineage specification or its re-induction to generate induced pluripotent stem cells are central topics in stem cell biology. To uncover the molecular basis and the design principles of pluripotency control, a multitude of experimental, but also an increasing number of computational, studies have been published. Here, we consider recent reports that apply computational or mathematical modelling approaches to describe the regulatory processes that underlie cell fate decisions in mouse ESCs. We summarise the principles, the strengths and potentials but also the limitations of different computational strategies.
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Affiliation(s)
- Maria Herberg
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden D-01307, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden D-01307, Germany
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41
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Chmelova H, Cohrs CM, Chouinard JA, Petzold C, Kuhn M, Chen C, Roeder I, Kretschmer K, Speier S. Distinct roles of β-cell mass and function during type 1 diabetes onset and remission. Diabetes 2015; 64:2148-60. [PMID: 25605805 DOI: 10.2337/db14-1055] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 01/10/2015] [Indexed: 11/13/2022]
Abstract
Cure of type 1 diabetes (T1D) by immune intervention at disease onset depends on the restoration of insulin secretion by endogenous β-cells. However, little is known about the potential of β-cell mass and function to recover after autoimmune attack ablation. Using a longitudinal in vivo imaging approach, we show how functional status and mass of β-cells adapt in response to the onset and remission of T1D. We demonstrate that infiltration reduces β-cell mass prior to onset and, together with emerging hyperglycemia, affects β-cell function. After immune intervention, persisting hyperglycemia prevents functional recovery but promotes β-cell mass increase in mouse islets. When blood glucose levels return to normoglycemia β-cell mass expansion stops, and subsequently glucose tolerance recovers in combination with β-cell function. Similar to mouse islets, human islets exhibit cell exhaustion and recovery in response to transient hyperglycemia. However, the effect of hyperglycemia on human islet mass increase is minor and transient. Our data demonstrate a major role of functional exhaustion and recovery of β-cells during T1D onset and remission. Therefore, these findings support early intervention therapy for individuals with T1D.
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Affiliation(s)
- Helena Chmelova
- Deutsche Forschungsgemeinschaft (DFG)-Research Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany Paul Langerhans Institute Dresden of Helmholtz Centre Munich, University Clinic Carl Gustav Carus of Technische Universität Dresden, German Centre for Diabetes Research (DZD), Dresden, Germany
| | - Christian M Cohrs
- Deutsche Forschungsgemeinschaft (DFG)-Research Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany Paul Langerhans Institute Dresden of Helmholtz Centre Munich, University Clinic Carl Gustav Carus of Technische Universität Dresden, German Centre for Diabetes Research (DZD), Dresden, Germany
| | - Julie A Chouinard
- Deutsche Forschungsgemeinschaft (DFG)-Research Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany Paul Langerhans Institute Dresden of Helmholtz Centre Munich, University Clinic Carl Gustav Carus of Technische Universität Dresden, German Centre for Diabetes Research (DZD), Dresden, Germany
| | - Cathleen Petzold
- Deutsche Forschungsgemeinschaft (DFG)-Research Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Matthias Kuhn
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Chunguang Chen
- Deutsche Forschungsgemeinschaft (DFG)-Research Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany Paul Langerhans Institute Dresden of Helmholtz Centre Munich, University Clinic Carl Gustav Carus of Technische Universität Dresden, German Centre for Diabetes Research (DZD), Dresden, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karsten Kretschmer
- Deutsche Forschungsgemeinschaft (DFG)-Research Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany Paul Langerhans Institute Dresden of Helmholtz Centre Munich, University Clinic Carl Gustav Carus of Technische Universität Dresden, German Centre for Diabetes Research (DZD), Dresden, Germany
| | - Stephan Speier
- Deutsche Forschungsgemeinschaft (DFG)-Research Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany Paul Langerhans Institute Dresden of Helmholtz Centre Munich, University Clinic Carl Gustav Carus of Technische Universität Dresden, German Centre for Diabetes Research (DZD), Dresden, Germany
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Niederberger T, Failmezger H, Uskat D, Poron D, Glauche I, Scherf N, Roeder I, Schroeder T, Tresch A. Factor graph analysis of live cell–imaging data reveals mechanisms of cell fate decisions. Bioinformatics 2015; 31:1816-23. [DOI: 10.1093/bioinformatics/btv040] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/19/2015] [Indexed: 11/13/2022] Open
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Herberg M, Zerjatke T, de Back W, Glauche I, Roeder I. Image-based quantification and mathematical modeling of spatial heterogeneity in ESC colonies. Cytometry A 2015; 87:481-90. [DOI: 10.1002/cyto.a.22598] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/11/2014] [Accepted: 11/06/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Maria Herberg
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden; Dresden Germany
| | - Thomas Zerjatke
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden; Dresden Germany
| | - Walter de Back
- Center for Information Services and High Performance Computing, Technische Universität Dresden; Dresden Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden; Dresden Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden; Dresden Germany
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Cornils K, Winkelmann D, Thielecke L, Aranyossy T, Dahl A, Kroeger N, Roeder I, Glauche I, Fehse B. Assessment of clonality in BcrAbl-induced leukaemia by genetic barcodes. Exp Hematol 2014. [DOI: 10.1016/j.exphem.2014.07.104] [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: 11/16/2022]
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Glauche I, Cornils K, Thielecke L, Dahl A, Aranyossy T, Roeder I, Fehse B. Improving the design of viral barcodes for optimal bioinformatical analysis. Exp Hematol 2014. [DOI: 10.1016/j.exphem.2014.07.127] [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: 10/25/2022]
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Bach E, Zerjatke T, Herklotz M, Scherf N, Niederwieser D, Roeder I, Pompe T, Cross M, Glauche I. Elucidating functional heterogeneity in hematopoietic progenitor cells: a combined experimental and modeling approach. Exp Hematol 2014; 42:826-37.e1-17. [PMID: 24878352 DOI: 10.1016/j.exphem.2014.05.011] [Citation(s) in RCA: 5] [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] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 04/07/2014] [Accepted: 05/19/2014] [Indexed: 12/28/2022]
Abstract
A detailed understanding of the mechanisms maintaining the hierarchical balance of cell types in hematopoiesis will be important for the therapeutic manipulation of normal and leukemic cells. Mathematical modeling is expected to make an important contribution to this area, but the iterative development of increasingly accurate models will rely on repeated validation using experimental data of sufficient resolution to distinguish between alternative model scenarios. The multipotent hematopoietic progenitor FDCP-Mix cells maintain a hierarchy from self-renewal to post-mitotic differentiation in vitro and are accessible to detailed analysis. Here, we report the development of a combined mathematical modeling and experimental approach to study the principles underlying heterogeneity in FDCP-Mix cultures. We adapt a single-cell based model of hematopoiesis to the conditions of cell culture and describe an association between proliferative history and phenotype of FDCP-Mix cells. While data derived from population studies are incapable of distinguishing between three mechanistically different model scenarios, statistical analysis of single cell tracking data provides a resolution sufficient to select one of them. This scenario favors differences between granulocytic and monocytic lineage with respect to their proliferative behavior and death rates as a mechanistic explanation for the observed heterogeneity. Our results demonstrate the power of a combined experimental/modeling approach in which single cell fate analysis is the key to revealing regulatory principles at the cellular level.
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Affiliation(s)
- Enrica Bach
- Department of Hematology, Oncology and Hemostasiology, Universität Leipzig, Leipzig, Germany
| | - Thomas Zerjatke
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, Dresden, Germany
| | - Manuela Herklotz
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, Dresden, Germany
| | - Nico Scherf
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, Dresden, Germany
| | - Dietger Niederwieser
- Department of Hematology, Oncology and Hemostasiology, Universität Leipzig, Leipzig, Germany
| | - Ingo Roeder
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, Dresden, Germany
| | - Tilo Pompe
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, Dresden, Germany; Institute of Biochemistry, Universität Leipzig, Leipzig, Germany
| | - Michael Cross
- Department of Hematology, Oncology and Hemostasiology, Universität Leipzig, Leipzig, Germany
| | - Ingmar Glauche
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, Dresden, Germany.
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Lützner C, Voigt H, Roeder I, Kirschner S, Lützner J. Placement makes a difference: accuracy of an accelerometer in measuring step number and stair climbing. Gait Posture 2014; 39:1126-32. [PMID: 24629310 DOI: 10.1016/j.gaitpost.2014.01.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/19/2013] [Accepted: 01/26/2014] [Indexed: 02/02/2023]
Abstract
UNLABELLED Accurate and easy-to-use measurement tools are required to evaluate the effect of treatments on patient activity. Comfortable device placement and fixation are important for patient compliance. The aim of this study was the evaluation of the accuracy of an accelerometer at different placements and slow velocities. METHODS A total of 43 healthy volunteers were included for a literature-based treadmill protocol using five accelerometer positions; a subset of 18 volunteers performed an extended treadmill protocol with velocities between 0.1 and 2.6m/s and finally stair climbing. RESULTS An alternative accelerometer position at the anterolateral aspect of the middle shank did measure steps more accurately than at the manufacturer suggested position, especially during slow velocities. Participants preferred the alternative placement at the shank. The accuracy of different accelerometer positions was excellent at velocities between 1.0 and 2.2m/s. During slow velocities below 1.0m/s steps were recorded less accurately. Accepting an error of five percent, the accelerometer recorded steps accurately from 0.5m/s at the alternative placement and from 0.8m/s at the manufacturer suggested placement. Stair climbing was not recorded accurately by any accelerometer position. CONCLUSION For measuring step number during slow velocities, the alternative position should be favoured. Stair climbing was not recorded accurately by any tested placement.
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Affiliation(s)
- Cornelia Lützner
- Department of Orthopaedic Surgery, University Hospital Carl Gustav Carus, TU Dresden, Germany
| | - Heike Voigt
- Department of Orthopaedic Surgery, University Hospital Carl Gustav Carus, TU Dresden, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Medical Faculty Carl Gustav Carus, TU Dresden, Germany
| | - Stephan Kirschner
- Department of Orthopaedic Surgery, University Hospital Carl Gustav Carus, TU Dresden, Germany
| | - Jörg Lützner
- Department of Orthopaedic Surgery, University Hospital Carl Gustav Carus, TU Dresden, Germany.
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Abstract
Mouse embryonic stem cells (mESCs) can be maintained in a proliferative and undifferentiated state over many passages (self-renewal) while retaining the potential to give rise to every cell type of the organism (pluripotency). Autocrine FGF4/Erk signalling has been identified as a major stimulus for fate decisions and lineage commitment in these cells. Recent findings on serum-free culture conditions with specific inhibitors (known as 2i) demonstrate that the inhibition of this pathway reduces transcription factor heterogeneity and is vital to maintain ground state pluripotency of mESCs. We suggest a novel mathematical model to explicitly integrate FGF4/Erk signalling into an interaction network of key pluripotency factors (namely Oct4, Sox2, Nanog and Rex1). The envisaged model allows to explore whether and how proposed mechanisms and feedback regulations can account for different expression patterns in mESC cultures. We demonstrate that an FGF4/Erk-mediated negative feedback is sufficient to induce molecular heterogeneity with respect to Nanog and Rex1 expression and thus critically regulates the propensity for differentiation and the loss of pluripotency. Furthermore, we compare simulation results on the transcription factor dynamics in different self-renewing states and during differentiation with experimental data on a Rex1GFPd2 reporter cell line using flow cytometry and qRT-PCR measurements. Concluding from our results we argue that interaction between FGF4/Erk signalling and Nanog expression qualifies as a key mechanism to manipulate mESC pluripotency. In particular, we infer that ground state pluripotency under 2i is achieved by shifting stable expression pattern of Nanog from a bistable into a monostable regulation impeding stochastic state transitions. Furthermore, we derive testable predictions on altering the degree of Nanog heterogeneity and on the frequency of state transitions in LIF/serum conditions to challenge our model assumptions.
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Affiliation(s)
- Maria Herberg
- Institute for Medical Informatics and Biometry, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- * E-mail:
| | - Tüzer Kalkan
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Austin Smith
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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Schmid B, Shah G, Scherf N, Weber M, Thierbach K, Campos CP, Roeder I, Aanstad P, Huisken J. High-speed panoramic light-sheet microscopy reveals global endodermal cell dynamics. Nat Commun 2014; 4:2207. [PMID: 23884240 PMCID: PMC3731668 DOI: 10.1038/ncomms3207] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 06/28/2013] [Indexed: 01/05/2023] Open
Abstract
The ever-increasing speed and resolution of modern microscopes make the storage and post-processing of images challenging and prevent thorough statistical analyses in developmental biology. Here, instead of deploying massive storage and computing power, we exploit the spherical geometry of zebrafish embryos by computing a radial maximum intensity projection in real time with a 240-fold reduction in data rate. In our four-lens selective plane illumination microscope (SPIM) setup the development of multiple embryos is recorded in parallel and a map of all labelled cells is obtained for each embryo in <10 s. In these panoramic projections, cell segmentation and flow analysis reveal characteristic migration patterns and global tissue remodelling in the early endoderm. Merging data from many samples uncover stereotypic patterns that are fundamental to endoderm development in every embryo. We demonstrate that processing and compressing raw image data in real time is not only efficient but indispensable for image-based systems biology. Systematic large-scale analysis of embryonic development requires the processing of large amounts of microscopy data. Here Schmid et al. solve this problem by developing a high-speed imaging system that projects zebrafish embryos onto a ‘world map’ in real time, revealing characteristic migration patterns in the early endoderm.
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Affiliation(s)
- Benjamin Schmid
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
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Cornils K, Thielecke L, Hüser S, Forgber M, Thomaschewski M, Kleist N, Hussein K, Riecken K, Volz T, Gerdes S, Glauche I, Dahl A, Dandri M, Roeder I, Fehse B. Multiplexing clonality: combining RGB marking and genetic barcoding. Nucleic Acids Res 2014; 42:e56. [PMID: 24476916 PMCID: PMC3985654 DOI: 10.1093/nar/gku081] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
RGB marking and DNA barcoding are two cutting-edge technologies in the field of clonal cell marking. To combine the virtues of both approaches, we equipped LeGO vectors encoding red, green or blue fluorescent proteins with complex DNA barcodes carrying color-specific signatures. For these vectors, we generated highly complex plasmid libraries that were used for the production of barcoded lentiviral vector particles. In proof-of-principle experiments, we used barcoded vectors for RGB marking of cell lines and primary murine hepatocytes. We applied single-cell polymerase chain reaction to decipher barcode signatures of individual RGB-marked cells expressing defined color hues. This enabled us to prove clonal identity of cells with one and the same RGB color. Also, we made use of barcoded vectors to investigate clonal development of leukemia induced by ectopic oncogene expression in murine hematopoietic cells. In conclusion, by combining RGB marking and DNA barcoding, we have established a novel technique for the unambiguous genetic marking of individual cells in the context of normal regeneration as well as malignant outgrowth. Moreover, the introduction of color-specific signatures in barcodes will facilitate studies on the impact of different variables (e.g. vector type, transgenes, culture conditions) in the context of competitive repopulation studies.
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Affiliation(s)
- Kerstin Cornils
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf, Martinistrasse 52, Hamburg 20246, Germany, Institute for Medical Informatics and Biometry, Faculty of Medicine, Technische Universität Dresden, Dresden 01307, Germany, ALS Automated Lab Solutions GmbH, Jena 07747, Germany, Department of Neuropathology, Hannover Medical School, Institute of Pathology, Hannover 30625, Germany, Department of Internal Medicine I, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany, Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, Dresden 01307, Germany
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