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Gheitasi R, Röll D, Müller MM, Naseri M, König R, Slevogt H, Pletz MW, Makarewicz O. Exploring secretory proteome and cytokine kinetic of human peripheral blood mononuclear cells exposed to methicillin-resistant Staphylococcus aureus biofilms and planktonic bacteria. Front Immunol 2024; 15:1334616. [PMID: 38571946 PMCID: PMC10989517 DOI: 10.3389/fimmu.2024.1334616] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/26/2024] [Indexed: 04/05/2024] Open
Abstract
Staphylococcus aureus is a highly successful pathogen infecting various body parts and forming biofilms on natural and artificial surfaces resulting in difficult-to-treat and chronic infections. We investigated the secreted cytokines and proteomes of isolated peripheral blood mononuclear cells (PBMCs) from healthy volunteers exposed to methicillin-resistant S. aureus (MRSA) biofilms or planktonic bacteria. Additionally, the cytokine profiles in sera from patients with community-acquired pneumonia (CAP) caused by S. aureus were investigated. The aim was to gain insights into the immune response involved and differentiate between the planktonic and sessile MRSA forms. We identified 321 and 298 targets that were significantly differently expressed in PBMCs when exposed to planktonic or biofilm-embedded bacteria, respectively. PBMCs exposed to planktonic MRSA cells secreted increased levels of TNF-α, while IL-18 was elevated when exposed to the biofilm. The machine-learning analyses of the cytokine profiles obtained for the in vitro PBMCs and CAP sera distinguished between the two types of bacteria forms based on cytokines IL-18, IL12, and IL-17, and with a lower importance IL-6. Particularly, IL-18 which has not been correlated with S. aureus biofilms so far might represent a suitable marker for monitoring chronification during MRSA infection to individualize the therapy, but this hypothesis must be proved in clinical trials.
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Affiliation(s)
- Reza Gheitasi
- Institute of Infectious Diseases and Infection Control, Jena University Hospital/Friedrich Schiller University, Jena, Germany
| | - Daniela Röll
- Institute of Infectious Diseases and Infection Control, Jena University Hospital/Friedrich Schiller University, Jena, Germany
| | - Mario M Müller
- Septomics Research Center, Jena University Hospital, Jena, Germany
- Integrated Research and Treatment Center - Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Mohadeseh Naseri
- Institute of Infectious Diseases and Infection Control, Jena University Hospital/Friedrich Schiller University, Jena, Germany
| | - Rainer König
- Institute of Infectious Diseases and Infection Control, Jena University Hospital/Friedrich Schiller University, Jena, Germany
- Integrated Research and Treatment Center - Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Hortense Slevogt
- Respiratory Infection Dynamics, Helmholtz Centre for Infection Research-HZI Braunschweig, Braunschweig, Germany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, German Center for Lung Research (DZL), Biomedical Research in Endstage & Obstructive Lung Disease (BREATH), Hannover, Germany
| | - Mathias W Pletz
- Institute of Infectious Diseases and Infection Control, Jena University Hospital/Friedrich Schiller University, Jena, Germany
- Integrated Research and Treatment Center - Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
- CAPNETZ STIFTUNG, Hannover, Germany
| | - Oliwia Makarewicz
- Institute of Infectious Diseases and Infection Control, Jena University Hospital/Friedrich Schiller University, Jena, Germany
- Integrated Research and Treatment Center - Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
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Mahajan UM, Erber J, Shamsrizi P, Voit F, Vielhauer J, Johlke AL, Benesch C, Khaled NB, Reinecke F, Rudi WS, Klein M, Jakob C, Oswald M, König R, Schulz C, Mayerle J, Stubbe HC. Validation of the SACOV-19 score for identifying patients at risk of complicated or more severe COVID-19: a prospective study. Infection 2023; 51:1669-1678. [PMID: 37166617 PMCID: PMC10173210 DOI: 10.1007/s15010-023-02041-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/20/2023] [Indexed: 05/12/2023]
Abstract
PURPOSE Identification of patients at risk of complicated or more severe COVID-19 is of pivotal importance, since these patients might require monitoring, antiviral treatment, and hospitalization. In this study, we prospectively evaluated the SACOV-19 score for its ability to predict complicated or more severe COVID-19. METHODS In this prospective multicenter study, we included 124 adult patients with acute COVID-19 in three German hospitals, who were diagnosed in an early, uncomplicated stage of COVID-19 within 72 h of inclusion. We determined the SACOV-19 score at baseline and performed a follow-up at 30 days. RESULTS The SACOV-19 score's AUC was 0.816. At a cutoff of > 3, it predicted deterioration to complicated or more severe COVID-19 with a sensitivity of 94% and a specificity of 55%. It performed significantly better in predicting complicated COVID-19 than the random tree-based SACOV-19 predictive model, the CURB-65, 4C mortality, or qCSI scores. CONCLUSION The SACOV-19 score is a feasible tool to aid decision making in acute COVID-19.
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Affiliation(s)
- Ujjwal Mukund Mahajan
- Department of Medicine II, Medizinische Klinik und Poliklinik II, Hospital of the LMU Munich, LMU Klinikum, Campus Großhadern, Marchioninistr. 15, 81377, Munich, Germany
- German Center for Infection Research, Partner Site Munich, Munich, Germany
| | - Johanna Erber
- Department of Internal Medicine II, Technical University of Munich, School of Medicine, University Hospital Rechts Der Isar, Munich, Germany
| | - Parichehr Shamsrizi
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Florian Voit
- Department of Internal Medicine II, Technical University of Munich, School of Medicine, University Hospital Rechts Der Isar, Munich, Germany
| | - Jakob Vielhauer
- Department of Medicine II, Medizinische Klinik und Poliklinik II, Hospital of the LMU Munich, LMU Klinikum, Campus Großhadern, Marchioninistr. 15, 81377, Munich, Germany
- German Center for Infection Research, Partner Site Munich, Munich, Germany
| | - Anna-Lena Johlke
- Department of Medicine II, Medizinische Klinik und Poliklinik II, Hospital of the LMU Munich, LMU Klinikum, Campus Großhadern, Marchioninistr. 15, 81377, Munich, Germany
- German Center for Infection Research, Partner Site Munich, Munich, Germany
| | - Christopher Benesch
- Department of Medicine II, Medizinische Klinik und Poliklinik II, Hospital of the LMU Munich, LMU Klinikum, Campus Großhadern, Marchioninistr. 15, 81377, Munich, Germany
- German Center for Infection Research, Partner Site Munich, Munich, Germany
| | - Najib Ben Khaled
- Department of Medicine II, Medizinische Klinik und Poliklinik II, Hospital of the LMU Munich, LMU Klinikum, Campus Großhadern, Marchioninistr. 15, 81377, Munich, Germany
- German Center for Infection Research, Partner Site Munich, Munich, Germany
| | - Felix Reinecke
- Department of Anesthesiology, Hospital of the LMU Munich, Munich, Germany
| | - Wolf-Stephan Rudi
- Department of Medicine I, Hospital of the LMU Munich, Munich, Germany
| | - Matthias Klein
- Department of Neurology, Hospital of the LMU Munich, Munich, Germany
| | - Carolin Jakob
- Department I of Internal Medicine, University Hospital of Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Marcus Oswald
- Institute for Infectious Diseases and Infection Control, RG Systemsbiology, Jena University Hospital, Jena, Germany
| | - Rainer König
- Institute for Infectious Diseases and Infection Control, RG Systemsbiology, Jena University Hospital, Jena, Germany
| | - Christian Schulz
- Department of Medicine II, Medizinische Klinik und Poliklinik II, Hospital of the LMU Munich, LMU Klinikum, Campus Großhadern, Marchioninistr. 15, 81377, Munich, Germany
- German Center for Infection Research, Partner Site Munich, Munich, Germany
| | - Julia Mayerle
- Department of Medicine II, Medizinische Klinik und Poliklinik II, Hospital of the LMU Munich, LMU Klinikum, Campus Großhadern, Marchioninistr. 15, 81377, Munich, Germany
| | - Hans Christian Stubbe
- Department of Medicine II, Medizinische Klinik und Poliklinik II, Hospital of the LMU Munich, LMU Klinikum, Campus Großhadern, Marchioninistr. 15, 81377, Munich, Germany.
- German Center for Infection Research, Partner Site Munich, Munich, Germany.
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3
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Krychowiak M, König R, Barbui T, Brezinsek S, Brunner J, Effenberg F, Endler M, Feng Y, Flom E, Gao Y, Gradic D, Hacker P, Harris J, Hirsch M, Höfel U, Jakubowski M, Kornejew P, Otte M, Pandey A, Pedersen T, Puig A, Reimold F, Schmitz O, Schröder T, Winters V, Zhang D. First feedback-controlled divertor detachment in W7-X: Experience from TDU operation and prospects for operation with actively cooled divertor. Nuclear Materials and Energy 2023. [DOI: 10.1016/j.nme.2023.101363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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4
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Chung H, Wickel J, Oswald M, Dargvainiene J, Rupp J, Rohde G, Witzenrath M, Leypoldt F, König R, Pletz MW, Geis C. Neurofilament light chain levels predict encephalopathy and outcome in community-acquired pneumonia. Ann Clin Transl Neurol 2022; 10:204-212. [PMID: 36479924 PMCID: PMC9930427 DOI: 10.1002/acn3.51711] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE Serum neurofilament light chain (sNfL) is a biomarker for neuroaxonal damage and has been found to be elevated in several neurological diseases with neuronal destruction. New onset of confusion is a hallmark of severity in infections. The objective of this study was to determine whether sNfL levels are increased in patients with community-acquired pneumonia (CAP) and if increased sNfL levels are associated with disease-associated confusion or disease severity. METHODS In this observational study, sNfL levels were determined with single-molecule array technology in CAP patients of the CAPNETZ cohort with validated CRB (confusion, respiratory rate, and blood pressure)-65 score. We determined associations between log-transformed sNfL concentrations, well-defined clinical characteristics, and unfavorable outcome in multivariable analyses. Receiver operating characteristic (ROC) analysis was performed to assess the prediction accuracy of sNfL levels for confusion in CAP patients. RESULTS sNfL concentrations were evaluated in 150 CAP patients. Patients with confusion had higher sNfL levels as compared to non-confusion patients of comparable overall disease severity. ROC analysis of sNfL and confusion provided an area under the curve (AUC) of 0.73 (95% CI 0.62-0.82). Log-transformed sNfL levels were not associated with general disease severity. In a logistic regression analysis, log2-sNfL was identified as a strong predictor for an unfavorable outcome. INTERPRETATION sNfL levels are specifically associated with confusion and not with pneumonia disease severity, thus reflecting a potential objective marker for encephalopathy in these patients. Furthermore, sNfL levels are also associated with unfavorable outcome in these patients and might help clinicians to identify patients at risk.
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Affiliation(s)
- Ha‐Yeun Chung
- Section of Translational Neuroimmunology, Department of NeurologyJena University HospitalJenaGermany,Center for Sepsis Control and CareJena University HospitalJenaGermany
| | - Jonathan Wickel
- Section of Translational Neuroimmunology, Department of NeurologyJena University HospitalJenaGermany,Center for Sepsis Control and CareJena University HospitalJenaGermany
| | - Marcus Oswald
- Systems Biology Research Group, Institute for Infectious Diseases and Infection Control (IIMK)Jena University HospitalJenaGermany
| | - Justina Dargvainiene
- Neuroimmunology, Institute of Clinical Chemistry and Department of Neurology, UKSH Kiel/LübeckKiel UniversityKielGermany
| | - Jan Rupp
- Department of Infectious Diseases and MicrobiologyUniversity Hospital Schleswig‐HolsteinLübeckGermany,CAPNETZ STIFTUNGHannoverGermany
| | - Gernot Rohde
- CAPNETZ STIFTUNGHannoverGermany,Biomedical Research in Endstage in Obstructive Lung Disease Hannover (BREATH)German Center for Lung Research (DZL)HannoverGermany,Department of Respiratory Medicine, Medical Clinic IFrankfurt University Hospital, Goethe University FrankfurtFrankfurt/MainGermany
| | - Martin Witzenrath
- CAPNETZ STIFTUNGHannoverGermany,Department of Infectious Diseases and Respiratory MedicineCharité – Universitätsmedizin BerlinBerlinGermany
| | - Frank Leypoldt
- Neuroimmunology, Institute of Clinical Chemistry and Department of Neurology, UKSH Kiel/LübeckKiel UniversityKielGermany
| | - Rainer König
- Systems Biology Research Group, Institute for Infectious Diseases and Infection Control (IIMK)Jena University HospitalJenaGermany
| | - Mathias W. Pletz
- Center for Sepsis Control and CareJena University HospitalJenaGermany,CAPNETZ STIFTUNGHannoverGermany,Institute of Infectious Diseases and Infection ControlJena University HospitalJenaGermany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of NeurologyJena University HospitalJenaGermany,Center for Sepsis Control and CareJena University HospitalJenaGermany
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5
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Wang E, König R, Krychowiak M, Brezinsek S, Drews P, Gradic D, Jakubowski M, Kornejew P, Kremeyer T, Killer C, Liang Y, Neubauer O, Pandey A, Rudischhauser L, Sereda S, Schlisio G, Xu S. Radiation characteristics of detached divertor plasmas in W7-X. Nuclear Materials and Energy 2022. [DOI: 10.1016/j.nme.2022.101283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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6
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Flom E, Krychowiak M, Schmitz O, König R, Barbui T, Henke F, Jakubowski M, Kwak S, Loch S, Muñoz Burgos J, Svensson J. Bayesian modeling of collisional-radiative models applicable to thermal helium beam plasma diagnostics. Nuclear Materials and Energy 2022. [DOI: 10.1016/j.nme.2022.101269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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7
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Muley VY, König R. Human transcriptional gene regulatory network compiled from 14 data resources. Biochimie 2021; 193:115-125. [PMID: 34740743 DOI: 10.1016/j.biochi.2021.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 11/02/2022]
Abstract
The transcriptional regulatory network (TRN) in a cell orchestrates spatio-temporal expression of genes to generate cellular responses for maintenance, reproduction, development and survival of the cell and its hosting organism. Transcription factors (TF) regulate the expression of their target genes (TG) and are the fundamental units of TRN. Several databases have been developed to catalogue human TRN based on low- and high-throughput experimental and computational studies considering their importance in understanding cellular physiology. However, literature lacks their comparative assessment on the strengths and weaknesses. We compared over 2.2 million regulatory pairs between 1379 TF and 22,518 TG from 14 resources. Our study reveals that the TF and TG were common across data resources but not their regulatory pairs. TF and TG of the regulatory pairs showed weak expression correlation, significant gene ontology overlap, co-citations in PubMed and low numbers of TF-TG pairs representing transcriptional repression relationships. We assigned each TF-TG regulatory pair a combined confidence score reflecting its reliability based on its presence in multiple databases. The assembled TRN contains 2,246,598 TF-TG pairs, of which, 44,284 with information on TF's activating or repressing effects on their TG and is available upon request. This study brings the information about transcriptional regulation scattered over the literature and databases at one place in the form of one of the most comprehensive and complete human TRN assembled to date. It will be a valuable resource for benchmarking TRN prediction tools, and to the scientific community working in functional genomics, gene expression and regulation analysis.
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Affiliation(s)
| | - Rainer König
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany.
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8
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Meyer S, Meyberg-Solomayer G, König R, Geuer S, Geipel M, Nourkami-Tutdibi N, Oehl-Jaschkowitz B, Lindner U, Marquardt T. Exome Analysis of a New Disease-causing Mutation in a Preterm Neonate with NP-C Disease. Klin Padiatr 2021; 233:252-253. [PMID: 34102701 DOI: 10.1055/a-1481-9016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Sascha Meyer
- Department of Pediatrics and Neonatology, Saarland University Hospital and Saarland University Faculty of Medicine, Homburg, Germany
| | | | - Rainer König
- Department of Genetics, Bioscientia Institut fur Medizinische Diagnostik GmbH, Ingelheim, Germany
| | - Sinje Geuer
- Department of Genetics, Bioscientia Institut fur Medizinische Diagnostik GmbH, Ingelheim, Germany
| | - Martina Geipel
- Department of Pediatrics and Neonatology, Saarland University Hospital and Saarland University Faculty of Medicine, Homburg, Germany
| | - Nasesien Nourkami-Tutdibi
- Department of Pediatrics and Neonatology, Saarland University Hospital and Saarland University Faculty of Medicine, Homburg, Germany
| | | | - Ulrike Lindner
- Department of Pediatrics and Neonatology, Saarland University Hospital and Saarland University Faculty of Medicine, Homburg, Germany
| | - Thorsten Marquardt
- Westfälische Wilhelms University Münster, Department of Pediatrics, Münster, Germany
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9
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Endler M, Baldzuhn J, Beidler C, Bosch HS, Bozhenkov S, Buttenschön B, Dinklage A, Fellinger J, Feng Y, Fuchert G, Gao Y, Geiger J, Grulke O, Hartmann D, Jakubowski M, König R, Laqua H, Lazerson S, McNeely P, Naujoks D, Neuner U, Otte M, Pasch E, Sunn Pedersen T, Perseo V, Puig Sitjes A, Rahbarnia K, Rust N, Schmitz O, Spring A, Stange T, von Stechow A, Turkin Y, Wang E, Wolf R. Wendelstein 7-X on the path to long-pulse high-performance operation. Fusion Engineering and Design 2021. [DOI: 10.1016/j.fusengdes.2021.112381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Hubeny M, Höschen D, Neubauer O, Hoek R, Czymek G, Naujoks D, Hathiramani D, Bardawil D, Unterberg B, König R, Brezinsek S, Linsmeier C. Progress on MATEO probe heads and observation system. Fusion Engineering and Design 2021. [DOI: 10.1016/j.fusengdes.2021.112297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kwak S, Hergenhahn U, Höfel U, Krychowiak M, Pavone A, Svensson J, Ford O, König R, Bozhenkov S, Fuchert G, Pasch E, Brunner KJ, Knauer J, Kornejew P, Trimiño Mora H, Pedersen TS. Bayesian inference of spatially resolved Z eff profiles from line integrated bremsstrahlung spectra. Rev Sci Instrum 2021; 92:043505. [PMID: 34243367 DOI: 10.1063/5.0043777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/12/2021] [Indexed: 06/13/2023]
Abstract
In nuclear fusion research, the effective ion charge Zeff, which characterizes the overall content of impurities, can be experimentally derived from the plasma electron-ion bremsstrahlung, given the electron density ne and temperature Te. At Wendelstein 7-X, a multichannel near-infrared spectrometer is installed to collect the plasma bremsstrahlung along 27 lines of sight covering more than half the plasma cross section, which provides information on Zeff over the entire plasma radius. To infer spatially resolved Zeff profiles, a Bayesian model is developed in the Minerva framework. Zeff, ne, and Te profiles are modeled as Gaussian processes, whose smoothness is determined by hyperparameters. These profiles are transformed to fields in Cartesian coordinates, given the poloidal magnetic flux surfaces calculated by the variational moments equilibrium code. Given all these physical quantities, the model predicts line-of-sight integrals of near-infrared bremsstrahlung spectra. The model includes the predictive (forward) models of the interferometer, Thomson scattering system, and visible and near-infrared spectrometers. Given the observations of all these diagnostics, the posterior probability distribution of Zeff profiles is calculated and shown as an inference solution. The smoothness (gradient) of the profiles is optimally chosen by Bayesian Occam's razor. Furthermore, wall reflections can significantly pollute the measurements of the plasma bremsstrahlung, which leads to over-estimation of Zeff values in the edge region. In the first results presented in this work, this problem does not appear, and the posterior samples of Zeff profiles are overall plausible and consistent with Zeff values inferred, given the data from the single-channel visible spectrometer.
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Affiliation(s)
- Sehyun Kwak
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - U Hergenhahn
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - U Höfel
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - M Krychowiak
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - A Pavone
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - J Svensson
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - O Ford
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - R König
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - S Bozhenkov
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - G Fuchert
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - E Pasch
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - K J Brunner
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - J Knauer
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - P Kornejew
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | | | - T S Pedersen
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
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12
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König R, Kolte A, Ahlers O, Oswald M, Krauss V, Roell D, Sommerfeld O, Dimopoulos G, Tsangaris I, Antoniadou E, Jaishankar N, Bogatsch H, Löffler M, Rödel M, Garcia-Moreno M, Tuchscherr L, Sprung CL, Singer M, Brunkhorst F, Oppert M, Gerlach H, Claus RA, Coldewey SM, Briegel J, Giamarellos-Bourboulis EJ, Keh D, Bauer M. Use of IFNγ/IL10 Ratio for Stratification of Hydrocortisone Therapy in Patients With Septic Shock. Front Immunol 2021; 12:607217. [PMID: 33767693 PMCID: PMC7985546 DOI: 10.3389/fimmu.2021.607217] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 09/16/2020] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Large clinical trials testing hydrocortisone therapy in septic shock have produced conflicting results. Subgroups may benefit of hydrocortisone treatment depending on their individual immune response. We performed an exploratory analysis of the database from the international randomized controlled clinical trial Corticosteroid Therapy of Septic Shock (CORTICUS) employing machine learning to a panel of 137 variables collected from the Berlin subcohort comprising 83 patients including demographic and clinical measures, organ failure scores, leukocyte counts and levels of circulating cytokines. The identified theranostic marker was validated against data from a cohort of the Hellenic Sepsis Study Group (HSSG) (n = 246), patients enrolled in the clinical trial of Sodium Selenite and Procalcitonin Guided Antimicrobial Therapy in Severe Sepsis (SISPCT, n = 118), and another, smaller clinical trial (Crossover study, n = 20). In addition, in vitro blood culture experiments and in vivo experiments in mouse models were performed to assess biological plausibility. A low serum IFNγ/IL10 ratio predicted increased survival in the hydrocortisone group whereas a high ratio predicted better survival in the placebo group. Using this marker for a decision rule, we applied it to three validation sets and observed the same trend. Experimental studies in vitro revealed that IFNγ/IL10 was negatively associated with the load of (heat inactivated) pathogens in spiked human blood and in septic mouse models. Accordingly, an in silico analysis of published IFNγ and IL10 values in bacteremic and non-bacteremic patients with the Systemic Inflammatory Response Syndrome supported this association between the ratio and pathogen burden. We propose IFNγ/IL10 as a molecular marker supporting the decision to administer hydrocortisone to patients in septic shock. Prospective clinical studies are necessary and standard operating procedures need to be implemented, particularly to define a generic threshold. If confirmed, IFNγ/IL10 may become a suitable theranostic marker for an urging clinical need.
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Affiliation(s)
- Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Amol Kolte
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Olaf Ahlers
- Department of Anesthesiology and Operative Intensive Care Medicine (CCM, CVK), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Veiko Krauss
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Daniela Roell
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Oliver Sommerfeld
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - George Dimopoulos
- 2nd Department of Critical Care Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Iraklis Tsangaris
- 2nd Department of Critical Care Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Eleni Antoniadou
- Intensive Care Unit, “George Gennimatas” Thessaloniki General Hospital, Thessaloniki, Greece
| | - Neeraja Jaishankar
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | | | - Markus Löffler
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Markus Rödel
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | | | - Lorena Tuchscherr
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Charles L. Sprung
- Department of Anesthesiology and Critical Care Medicine, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Mervyn Singer
- Division of Medicine, Bloomsbury Institute of Intensive Care Medicine, University College London, London, United Kingdom
| | - Frank Brunkhorst
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Michael Oppert
- Department of Emergency and Intensive Care Medicine, Klinikum Ernst von Bergmann, Potsdam, Germany
| | - Herwig Gerlach
- Department of Anesthesia, Operative Intensive Care Medicine, and Pain Management, Vivantes Neukölln Hospital, Berlin, Germany
| | - Ralf A. Claus
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
| | - Sina M. Coldewey
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
- Septomics Research Center, Jena University Hospital, Jena, Germany
| | - Josef Briegel
- Department of Anesthesiology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Evangelos J. Giamarellos-Bourboulis
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Didier Keh
- Department of Anesthesiology and Operative Intensive Care Medicine (CCM, CVK), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Bauer
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
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13
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Sommerfeld O, Medyukhina A, Neugebauer S, Ghait M, Ulferts S, Lupp A, König R, Wetzker R, Schulz S, Figge MT, Bauer M, Press AT. Targeting Complement C5a Receptor 1 for the Treatment of Immunosuppression in Sepsis. Mol Ther 2021; 29:338-346. [PMID: 32966769 PMCID: PMC7791006 DOI: 10.1016/j.ymthe.2020.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/25/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Complement factor C5a was originally identified as a powerful promoter of inflammation through activation of the C5a receptor 1 (C5ar1). Recent evidence suggests involvement of C5a not only in pro- but also in anti-inflammatory signaling. The present study aims to unveil the role of C5ar1 as potential therapeutic target in a murine sepsis model. Our study discloses a significantly increased survival in models of mild to moderate but not severe sepsis of C5ar1-deficient mice. The decreased mortality of C5ar1-deficient mice is accompanied by improved pathogen clearance and largely preserved liver function. C5ar1-deficient mice exhibited a significantly increased production of the pro-inflammatory mediator interferon-γ (IFN-γ) and a decreased production of the anti-inflammatory cytokine interleukin-10 (IL-10). Together, these data uncover C5a signaling as a mediator of immunosuppressive processes during sepsis and describe the C5ar1 and related changes of the IFN-γ to IL-10 ratio as markers for the immunological (dys)function accompanying sepsis.
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Affiliation(s)
- Oliver Sommerfeld
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Anna Medyukhina
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Sophie Neugebauer
- Institute of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany
| | - Mohamed Ghait
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Svenja Ulferts
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Amelie Lupp
- Institute of Pharmacology and Toxicology, Jena University Hospital, Jena, Germany
| | - Rainer König
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, Jena, Germany
| | - Reinhard Wetzker
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
| | - Stefan Schulz
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Institute of Pharmacology and Toxicology, Jena University Hospital, Jena, Germany
| | - Marc Thilo Figge
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany; Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Michael Bauer
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Adrian T Press
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.
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14
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Bär I, Ast V, Meyer D, König R, Rauner M, Hofbauer LC, Müller JP. Aberrant Bone Homeostasis in AML Is Associated with Activated Oncogenic FLT3-Dependent Cytokine Networks. Cells 2020; 9:cells9112443. [PMID: 33182501 PMCID: PMC7697865 DOI: 10.3390/cells9112443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 01/02/2023] Open
Abstract
Acute myeloid leukaemia (AML) is a haematopoietic malignancy caused by a combination of genetic and epigenetic lesions. Activation of the oncoprotein FLT3 ITD (Fms-like tyrosine kinase with internal tandem duplications) represents a key driver mutation in 25–30% of AML patients. FLT3 is a class III receptor tyrosine kinase, which plays a role in cell survival, proliferation, and differentiation of haematopoietic progenitors of lymphoid and myeloid lineages. Mutant FLT3 ITD results in an altered signalling quality, which causes cell transformation. Recent evidence indicates an effect of FLT3 ITD on bone homeostasis in addition to haematological aberrations. Using gene expression data repositories of FLT3 ITD-positive AML patients, we identified activated cytokine networks that affect the formation of the haematopoietic niche by controlling osteoclastogenesis and osteoblast functions. In addition, aberrant oncogenic FLT3 signalling of osteogenesis-specific cytokines affects survival of AML patients and may be used for prognosis. Thus, these data highlight the intimate crosstalk between leukaemic and osteogenic cells within the osteohaematopoietic niche.
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Affiliation(s)
- Isabel Bär
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany;
| | - Volker Ast
- Institute for Clinical Chemistry, Medical Faculty Mannheim, Heidelberg University, 69117 Heidelberg, Germany;
| | - Daria Meyer
- Center for Infectious Diseases and Infection Control, Jena University Hospital, 07745 Jena, Germany; (D.M.); (R.K.)
| | - Rainer König
- Center for Infectious Diseases and Infection Control, Jena University Hospital, 07745 Jena, Germany; (D.M.); (R.K.)
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), 07745 Jena, Germany
| | - Martina Rauner
- Department of Medicine III & Center for Healthy Aging, Technical University Dresden, 01069 Dresden, Germany;
| | - Lorenz C. Hofbauer
- Department of Medicine III & Center for Healthy Aging, Technical University Dresden, 01069 Dresden, Germany;
- Correspondence: (L.C.H.); (J.P.M.); Tel.: +49-351-458-3173 (L.C.H.); +49-364-1939-5634 (J.P.M.)
| | - Jörg P. Müller
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany;
- Correspondence: (L.C.H.); (J.P.M.); Tel.: +49-351-458-3173 (L.C.H.); +49-364-1939-5634 (J.P.M.)
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15
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Hassan MIA, Kruse JM, Krüger T, Dahse HM, Cseresnyés Z, Blango MG, Slevogt H, Hörhold F, Ast V, König R, Figge MT, Kniemeyer O, Brakhage AA, Voigt K. Functional surface proteomic profiling reveals the host heat-shock protein A8 as a mediator of Lichtheimia corymbifera recognition by murine alveolar macrophages. Environ Microbiol 2020; 22:3722-3740. [PMID: 32583550 DOI: 10.1111/1462-2920.15140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/11/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]
Abstract
Mucormycosis is an emergent, fatal fungal infection of humans and warm-blooded animals caused by species of the order Mucorales. Immune cells of the innate immune system serve as the first line of defence against inhaled spores. Alveolar macrophages were challenged with the mucoralean fungus Lichtheimia corymbifera and subjected to biotinylation and streptavidin enrichment procedures followed by LC-MS/MS analyses. A total of 28 host proteins enriched for binding to macrophage-L. corymbifera interaction. Among those, the HSP70-family protein Hspa8 was found to be predominantly responsive to living and heat-killed spores of a virulent and an attenuated strain of L. corymbifera. Confocal scanning laser microscopy of infected macrophages revealed colocalization of Hspa8 with phagocytosed spores of L. corymbifera. The amount of detectable Hspa8 was dependent on the multiplicity of infection. Incubation of alveolar macrophages with an anti-Hspa8 antibody prior to infection reduced their capability to phagocytose spores of L. corymbifera. In contrast, anti-Hspa8 antibodies did not abrogate the phagocytosis of Aspergillus fumigatus conidia by macrophages. These results suggest an important contribution of the heat-shock family protein Hspa8 in the recognition of spores of the mucoralean fungus L. corymbifera by host alveolar macrophages and define a potential immunomodulatory therapeutic target.
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Affiliation(s)
- Mohamed I Abdelwahab Hassan
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Pests and Plant Protection Department, National Research Centre, 33rd El Buhouth St., Dokki, Giza, 12622, Egypt
| | - Janis M Kruse
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Zoltán Cseresnyés
- Department of Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Matthew G Blango
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Hortense Slevogt
- Host Septomics Group, Centre for Innovation Competence (ZIK) Septomics, University Hospital Jena, Jena, Germany
| | - Franziska Hörhold
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Volker Ast
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Marc Thilo Figge
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Department of Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Axel A Brakhage
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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16
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Hörhold F, Eisel D, Oswald M, Kolte A, Röll D, Osen W, Eichmüller SB, König R. Reprogramming of macrophages employing gene regulatory and metabolic network models. PLoS Comput Biol 2020; 16:e1007657. [PMID: 32097424 PMCID: PMC7059956 DOI: 10.1371/journal.pcbi.1007657] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 07/16/2019] [Revised: 03/06/2020] [Accepted: 01/14/2020] [Indexed: 12/20/2022] Open
Abstract
Upon exposure to different stimuli, resting macrophages undergo classical or alternative polarization into distinct phenotypes that can cause fatal dysfunction in a large range of diseases, such as systemic infection leading to sepsis or the generation of an immunosuppressive tumor microenvironment. Investigating gene regulatory and metabolic networks, we observed two metabolic switches during polarization. Most prominently, anaerobic glycolysis was utilized by M1-polarized macrophages, while the biosynthesis of inosine monophosphate was upregulated in M2-polarized macrophages. Moreover, we observed a switch in the urea cycle. Gene regulatory network models revealed E2F1, MYC, PPARγ and STAT6 to be the major players in the distinct signatures of these polarization events. Employing functional assays targeting these regulators, we observed the repolarization of M2-like cells into M1-like cells, as evidenced by their specific gene expression signatures and cytokine secretion profiles. The predicted regulators are essential to maintaining the M2-like phenotype and function and thus represent potential targets for the therapeutic reprogramming of immunosuppressive M2-like macrophages.
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Affiliation(s)
- Franziska Hörhold
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - David Eisel
- Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz, Germany
| | - Marcus Oswald
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - Amol Kolte
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - Daniela Röll
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - Wolfram Osen
- Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan B. Eichmüller
- Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rainer König
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
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17
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Michaely L, Gregor K, Keller M, Rissmann M, König R, Gutjahr B, Dornbusch S, Schön K, Puff C, Ulrich R, Becker S, Groschup M, Baumgärtner W, Eiden M, Spitzbarth I. Characterization of Different Monoclonal and Polyclonal Antibodies for Immunohistological Detection of Rift Valley Fever Virus Antigens. J Comp Pathol 2020. [DOI: 10.1016/j.jcpa.2019.10.141] [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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18
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Poos AM, Kordaß T, Kolte A, Ast V, Oswald M, Rippe K, König R. Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. BMC Bioinformatics 2019; 20:737. [PMID: 31888467 PMCID: PMC6937852 DOI: 10.1186/s12859-019-3323-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 11/12/2019] [Accepted: 12/16/2019] [Indexed: 01/15/2023] Open
Abstract
Background Reactivation of the telomerase reverse transcriptase gene TERT is a central feature for unlimited proliferation of the majority of cancers. However, the underlying regulatory processes are only partly understood. Results We assembled regulator binding information from serveral sources to construct a generic human and mouse gene regulatory network. Advancing our “Mixed Integer linear Programming based Regulatory Interaction Predictor” (MIPRIP) approach, we identified the most common and cancer-type specific regulators of TERT across 19 different human cancers. The results were validated by using the well-known TERT regulation by the ETS1 transcription factor in a subset of melanomas with mutations in the TERT promoter. Our improved MIPRIP2 R-package and the associated generic regulatory networks are freely available at https://github.com/KoenigLabNM/MIPRIP. Conclusion MIPRIP 2.0 identified common as well as tumor type specific regulators of TERT. The software can be easily applied to transcriptome datasets to predict gene regulation for any gene and disease/condition under investigation.
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Affiliation(s)
- Alexandra M Poos
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.,Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Theresa Kordaß
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Amol Kolte
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Volker Ast
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.
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19
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König R, Cao X, Oswald M, Forstner C, Rohde G, Rupp J, Witzenrath M, Welte T, Kolditz M, Pletz M. Macrolide combination therapy for patients hospitalised with community-acquired pneumonia? An individualised approach supported by machine learning. Eur Respir J 2019; 54:13993003.00824-2019. [PMID: 31537702 DOI: 10.1183/13993003.00824-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 09/05/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND The role of macrolide/β-lactam combination therapy in community-acquired pneumonia (CAP) of moderate severity is a matter of debate. Macrolides expand the coverage to atypical pathogens and attenuate pulmonary inflammation, but have been associated with cardiovascular toxicity and drug interactions. We developed a decision tree based on aetiological and clinical parameters, which are available ex ante to support a personalised decision for or against macrolides for the best clinical outcome of the individual patient. METHODS We employed machine learning in a cross-validation scheme based on a well-balanced selection of 4898 patients after propensity score matching to data available on admission of 6440 hospitalised patients with moderate severity (non-intensive care unit patients) from the observational, prospective, multinational CAPNETZ study. We aimed to improve the primary outcome of 180-day survival. RESULTS We found a simple decision tree of patient characteristics comprising chronic cardiovascular and chronic respiratory comorbidities as well as leukocyte counts in the respiratory secretion at enrolment. Specifically, we found that patients without cardiovascular or patients with respiratory comorbidities and high leukocyte counts in the respiratory secretion benefit from macrolide treatment. Patients identified to be treated in compliance with our treatment suggestion had a lower mortality of 27% (OR 1.83, 95% CI 1.48-2.27; p<0.001) compared to the observed standard of care. CONCLUSION Stratifying macrolide treatment in patients following a simple treatment rule may lead to considerably reduced mortality in CAP. A future randomised controlled trial confirming our result is necessary before implementing this rule into the clinical routine.
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Affiliation(s)
- Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Network Modelling, Hans Knöll Institut Jena, Jena, Germany.,These authors contributed equally
| | - Xueqi Cao
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Network Modelling, Hans Knöll Institut Jena, Jena, Germany.,These authors contributed equally
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Network Modelling, Hans Knöll Institut Jena, Jena, Germany.,These authors contributed equally
| | - Christina Forstner
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.,Dept of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Gernot Rohde
- Dept of Respiratory Medicine, Medical Clinic I, Goethe University Hospital, Frankfurt/Main, Germany.,CAPNETZ STIFTUNG, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL)
| | - Jan Rupp
- CAPNETZ STIFTUNG, Hannover Medical School, Hannover, Germany.,Dept of Infectious Diseases and Microbiology, University-Hospital Schleswig-Holstein/Campus Lübeck, University of Lübeck, Lübeck, Germany
| | - Martin Witzenrath
- CAPNETZ STIFTUNG, Hannover Medical School, Hannover, Germany.,Division of Pulmonary Inflammation, and Dept of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Tobias Welte
- CAPNETZ STIFTUNG, Hannover Medical School, Hannover, Germany.,Dept of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Martin Kolditz
- Division of Pulmonology, Medical Dept I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Mathias Pletz
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany .,CAPNETZ STIFTUNG, Hannover Medical School, Hannover, Germany
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20
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Höflmayer D, Steinhoff A, Hube-Magg C, Kluth M, Simon R, Burandt E, Tsourlakis MC, Minner S, Sauter G, Büscheck F, Wilczak W, Steurer S, Huland H, Graefen M, Haese A, Heinzer H, Schlomm T, Jacobsen F, Hinsch A, Poos AM, Oswald M, Rippe K, König R, Schroeder C. Expression of CCCTC-binding factor (CTCF) is linked to poor prognosis in prostate cancer. Mol Oncol 2019; 14:129-138. [PMID: 31736271 DOI: 10.1002/1878-0261.12597] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 10/22/2019] [Accepted: 11/12/2019] [Indexed: 01/06/2023] Open
Abstract
The chromatin-organizing factor CCCTC-binding factor (CTCF) is involved in transcriptional regulation, DNA-loop formation, and telomere maintenance. To evaluate the clinical impact of CTCF in prostate cancer, we analyzed CTCF expression by immunohistochemistry on a tissue microarray containing 17 747 prostate cancers. Normal prostate tissue showed negative to low CTCF expression, while in prostate cancers, CTCF expression was seen in 7726 of our 12 555 (61.5%) tumors and was considered low in 44.6% and high in 17% of cancers. Particularly, high CTCF expression was significantly associated with the presence of the transmembrane protease, serine 2:ETS-related gene fusion: Only 10% of ERG-negative cancers, but 30% of ERG-positive cancers had high-level CTCF expression (P < 0.0001). CTCF expression was significantly associated with advanced pathological tumor stage, high Gleason grade (P < 0.0001 each), nodal metastasis (P = 0.0122), and early biochemical recurrence (P < 0.0001). Multivariable modeling revealed that the prognostic impact of CTCF was independent from established presurgical parameters such as clinical stage and Gleason grade of the biopsy. Comparison with key molecular alterations showed strong associations with the expression of the Ki-67 proliferation marker and presence of phosphatase and tensin homolog deletions (P < 0.0001 each). The results of our study identify CTCF expression as a candidate biomarker for prognosis assessment in prostate cancer.
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Affiliation(s)
- Doris Höflmayer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Amélie Steinhoff
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Eike Burandt
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | | | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Franziska Büscheck
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Waldemar Wilczak
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Hartwig Huland
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Alexander Haese
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Hans Heinzer
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Thorsten Schlomm
- Department of Urology, Charité - Universitätsmedizin Berlin, Germany
| | - Frank Jacobsen
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Andrea Hinsch
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Alexandra M Poos
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Faculty of Biosciences, Heidelberg University, Germany.,Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Cornelia Schroeder
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Center Hamburg-Eppendorf, Germany
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21
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Brand C, Pala A, Scheuerle A, Scheglmann K, König R, Kratzer W, Wirtz CR, Antoniadis G, Pedro MT. [Neurolymphomatosis : Two case reports]. Nervenarzt 2019; 89:701-704. [PMID: 29181546 DOI: 10.1007/s00115-017-0460-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- C Brand
- Klinik für Neurochirurgie, Universitätsklinikum Ulm, Ludwig-Heilmeyer-Str. 2, 89312, Günzburg, Deutschland.
| | - A Pala
- Klinik für Neurochirurgie, Universitätsklinikum Ulm, Ludwig-Heilmeyer-Str. 2, 89312, Günzburg, Deutschland
| | - A Scheuerle
- Abteilung Neuropathologie am BKH Günzburg, Universitätsklinikum Ulm, Günzburg, Deutschland
| | | | - R König
- Klinik für Neurochirurgie, Universitätsklinikum Ulm, Ludwig-Heilmeyer-Str. 2, 89312, Günzburg, Deutschland
| | - W Kratzer
- Innere Medizin, Universitätsklinikum Ulm, Ulm, Deutschland
| | - C R Wirtz
- Klinik für Neurochirurgie, Universitätsklinikum Ulm, Ludwig-Heilmeyer-Str. 2, 89312, Günzburg, Deutschland
| | - G Antoniadis
- Klinik für Neurochirurgie, Universitätsklinikum Ulm, Ludwig-Heilmeyer-Str. 2, 89312, Günzburg, Deutschland
| | - M T Pedro
- Klinik für Neurochirurgie, Universitätsklinikum Ulm, Ludwig-Heilmeyer-Str. 2, 89312, Günzburg, Deutschland
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22
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Zhang D, König R, Feng Y, Burhenn R, Brezinsek S, Jakubowski M, Buttenschön B, Niemann H, Pavone A, Krychowiak M, Kwak S, Svensson J, Gao Y, Pedersen TS, Alonso A, Baldzuhn J, Beidler CD, Biedermann C, Bozhenkov S, Brunner KJ, Damm H, Hirsch M, Giannone L, Drewelow P, Effenberg F, Fuchert G, Hammond KC, Höfel U, Killer C, Knauer J, Laqua HP, Laube R, Pablant N, Pasch E, Penzel F, Rahbarnia K, Reimold F, Thomsen H, Winters V, Wagner F, Klinger T. First Observation of a Stable Highly Dissipative Divertor Plasma Regime on the Wendelstein 7-X Stellarator. Phys Rev Lett 2019; 123:025002. [PMID: 31386539 DOI: 10.1103/physrevlett.123.025002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Indexed: 06/10/2023]
Abstract
For the first time, the optimized stellarator Wendelstein 7-X has operated with an island divertor. An operation regime in hydrogen was found in which the total plasma radiation approached the absorbed heating power without noticeable loss of stored energy. The divertor thermography recorded simultaneously a strong reduction of the heat load on all divertor targets, indicating almost complete power detachment. This operation regime was stably sustained over several energy confinement times until the preprogrammed end of the discharge. The plasma radiation is mainly due to oxygen and is located at the plasma edge. This plasma scenario is reproducible and robust at various heating powers, plasma densities, and gas fueling locations. These experimental results show that the island divertor concept actually works and displays good power dissipation potential, producing a promising exhaust concept for the stellarator reactor line.
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Affiliation(s)
- D Zhang
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - R König
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - Y Feng
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - R Burhenn
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - S Brezinsek
- Forschungszentrum Jülich GmbH, IEK-4 52425 Jülich, Germany
| | - M Jakubowski
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - B Buttenschön
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - H Niemann
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - A Pavone
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - M Krychowiak
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - S Kwak
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - J Svensson
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - Y Gao
- Forschungszentrum Jülich GmbH, IEK-4 52425 Jülich, Germany
| | - T S Pedersen
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - A Alonso
- Laboratorio Nacional de Fusion CIEMAT, 28040 Madrid, Spain
| | - J Baldzuhn
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - C D Beidler
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - C Biedermann
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - S Bozhenkov
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - K J Brunner
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - H Damm
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - M Hirsch
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - L Giannone
- Max-Planck-Institut für Plasmaphysik, 85748 Garching, Germany
| | - P Drewelow
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - F Effenberg
- University of Wisconsin, Madison, Wisconsin 53706, USA
| | - G Fuchert
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - K C Hammond
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - U Höfel
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - C Killer
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - J Knauer
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - H P Laqua
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - R Laube
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - N Pablant
- Princeton Plasma Physics Laboratory, Princeton, New Jersey 08540, USA
| | - E Pasch
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - F Penzel
- Max-Planck-Institut für Plasmaphysik, 85748 Garching, Germany
| | - K Rahbarnia
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - F Reimold
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - H Thomsen
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - V Winters
- University of Wisconsin, Madison, Wisconsin 53706, USA
| | - F Wagner
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - T Klinger
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
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23
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Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D, Rippe K. Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Mol Syst Biol 2019; 15:e8339. [PMID: 31118277 PMCID: PMC6529931 DOI: 10.15252/msb.20188339] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In chronic lymphocytic leukemia (CLL), a diverse set of genetic mutations is embedded in a deregulated epigenetic landscape that drives cancerogenesis. To elucidate the role of aberrant chromatin features, we mapped DNA methylation, seven histone modifications, nucleosome positions, chromatin accessibility, binding of EBF1 and CTCF, as well as the transcriptome of B cells from CLL patients and healthy donors. A globally increased histone deacetylase activity was detected and half of the genome comprised transcriptionally downregulated partially DNA methylated domains demarcated by CTCF. CLL samples displayed a H3K4me3 redistribution and nucleosome gain at promoters as well as changes of enhancer activity and enhancer linkage to target genes. A DNA binding motif analysis identified transcription factors that gained or lost binding in CLL at sites with aberrant chromatin features. These findings were integrated into a gene regulatory enhancer containing network enriched for B‐cell receptor signaling pathway components. Our study predicts novel molecular links to targets of CLL therapies and provides a valuable resource for further studies on the epigenetic contribution to the disease.
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Affiliation(s)
- Jan-Philipp Mallm
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Murat Iskar
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics and Heidelberg Center for Personalized Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lara C Klett
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sabrina J Kugler
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Jose M Muino
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Vladimir B Teif
- School of Biological Sciences, University of Essex, Colchester, UK
| | - Alexandra M Poos
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute Jena, Jena, Germany
| | - Sebastian Großmann
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Fabian Erdel
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.,Centre de Biologie Intégrative (CBI), CNRS, UPS, Toulouse, France
| | - Daniele Tavernari
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Sandra D Koser
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sabrina Schumacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute Jena, Jena, Germany
| | - Daniel Remondini
- Department of Physics and Astronomy, Bologna University, Bologna, Italy
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Mertens
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany .,Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
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24
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Kolte A, König R. Temporal progression of gene regulation of peripheral white blood cells explains gender dimorphism of critically ill patients after trauma. Mol Med 2019; 25:19. [PMID: 31096912 PMCID: PMC6521436 DOI: 10.1186/s10020-019-0087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The immune response of the critically ill after severe trauma is sex-specific and may explain the different progression of the disease. This may be explained by a different gene regulatory program of their peripheral immune cells. We investigated the progression of the transcription profiles of peripheral immune cells of the patients to elucidate their distinct physiological response and clinical course. METHODS We compared transcription profiles of whole blood of male and female patients from a larger longitudinal study of critically ill patients after trauma. We developed a statistical analysis pipeline that synchronized the time lapse of the profiles based on the temporal severity score of each patient. RESULTS This enabled to categorize the temporal progression of the disease into two pre-acute, an acute and two post-acute phases. Comparing gene regulation of male and female patients at each phase, we identified distinctively regulated molecular processes mainly in the immune response, but also in the regulation of metabolism allowing to cluster these discriminative gene sets into sets of highly related cellular processes. Compared to male patients and healthy controls, female patients showed upregulation of gene sets of innate immunity in the early phase, upregulation of wound healing processes during the acute phase and upregulation of adaptive immunity in the late phase indicating early recovery. In turn, during the pre-acute and acute phase, male patients showed less suppression of gene sets coding for enzymes of energy metabolism and anabolism, most prominently the tricarboxylic acid cycle and β-oxidation, and cellular maintenance, such as cell cycle, DNA replication and damage response, and RNA metabolism. CONCLUSIONS A stronger innate immune response at the very early phase of the disease may support early clearance of the pathogen and its associated molecular patterns. Upregulation of wound healing processes may explain reduced multiple organ failure during the acute phase. Down regulated energy metabolism during the acute phase may make female patients less susceptible to oxidative stress, the upregulated adaptive immune system reflects an earlier recovery and rebuilding of the adaptive immune system that may protect them from secondary infections. Follow up studies need to be performed confirming these observations experimentally.
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Affiliation(s)
- Amol Kolte
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute Jena, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute Jena, Beutenbergstrasse 11a, 07745 Jena, Germany
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25
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Drews P, Killer C, Cosfeld J, Knieps A, Brezinsek S, Jakubowski M, Brandt C, Bozhenkov S, Dinklage A, Cai J, Endler M, Hammond K, Henkel M, Gao Y, Geiger J, Grulke O, Höschen D, König R, Krämer-Flecken A, Liang Y, Li Y, Liu S, Niemann H, Nicolai D, Neubauer O, Neuner U, Rack M, Rahbarnia K, Rudischhauser L, Sandri N, Satheeswaran G, Schilling S, Thomsen H, Windisch T, Sereda S. Edge plasma measurements on the OP 1.2a divertor plasmas at W7-X using the combined probe. Nuclear Materials and Energy 2019. [DOI: 10.1016/j.nme.2019.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Meinel C, Spartà G, Dahse HM, Hörhold F, König R, Westermann M, Coldewey SM, Cseresnyés Z, Figge MT, Hammerschmidt S, Skerka C, Zipfel PF. Streptococcus pneumoniae From Patients With Hemolytic Uremic Syndrome Binds Human Plasminogen via the Surface Protein PspC and Uses Plasmin to Damage Human Endothelial Cells. J Infect Dis 2019; 217:358-370. [PMID: 28968817 DOI: 10.1093/infdis/jix305] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Pneumococcal hemolytic uremic syndrome (HUS) in children is caused by infections with Streptococcus pneumoniae. Because endothelial cell damage is a hallmark of HUS, we studied how HUS-inducing pneumococci derived from infant HUS patients during the acute phase disrupt the endothelial layer. HUS pneumococci efficiently bound human plasminogen. These clinical isolates of HUS pneumococci efficiently bound human plasminogen via the bacterial surface proteins Tuf and PspC. When activated to plasmin at the bacterial surface, the active protease degraded fibrinogen and cleaved C3b. Here, we show that PspC is a pneumococcal plasminogen receptor and that plasmin generated on the surface of HUS pneumococci damages endothelial cells, causing endothelial retraction and exposure of the underlying matrix. Thus, HUS pneumococci damage endothelial cells in the blood vessels and disturb local complement homeostasis. Thereby, HUS pneumococci promote a thrombogenic state that drives HUS pathology.
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Affiliation(s)
- Christian Meinel
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Giuseppina Spartà
- Klinik für Kinder- und Jugendmedizin, Kantonsspital Winterthur, Switzerland
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Franziska Hörhold
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany.,Associated Group of Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute.,Center for Sepsis Control and Care
| | - Rainer König
- Associated Group of Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute.,Center for Sepsis Control and Care
| | | | - Sina M Coldewey
- Center for Sepsis Control and Care.,Department of Anesthesiology and Intensive Care Medicine.,Septomics Research Center.,Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena
| | - Zoltán Cseresnyés
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena.,Friedrich Schiller University, Jena, Germany
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena.,Friedrich Schiller University, Jena, Germany
| | - Sven Hammerschmidt
- Department Genetics of Microorganisms, Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University, Greifswald
| | - Christine Skerka
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Peter F Zipfel
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany.,Center for Sepsis Control and Care.,Friedrich Schiller University, Jena, Germany
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27
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Eisel D, Das K, Dickes E, König R, Osen W, Eichmüller SB. Cognate Interaction With CD4 + T Cells Instructs Tumor-Associated Macrophages to Acquire M1-Like Phenotype. Front Immunol 2019; 10:219. [PMID: 30853959 PMCID: PMC6395406 DOI: 10.3389/fimmu.2019.00219] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 11/16/2018] [Accepted: 01/25/2019] [Indexed: 12/14/2022] Open
Abstract
The immunosuppressive tumor microenvironment (TME) established by tumor cells, stromal cells and inhibitory immune cells counteracts the function of tumor reactive T cells. Tumor associated macrophages (TAMs) showing functional plasticity contribute to this process as so called M2-like macrophages can suppress the function of effector T cells and promote their differentiation into regulatory T cells (Tregs). Furthermore, tumor antigen specific CD4+ T effector cells can essentially sustain anti-tumoral immune responses as shown for various tumor entities, thus suggesting that cognate interaction between tumor antigen-specific CD4+ Th1 cells and TAMs might shift the intra-tumoral M1/M2 ratio toward M1. This study demonstrates repolarization of M2-like PECs upon MHC II-restricted interaction with tumor specific CD4+ Th1 cells in vitro as shown by extensive gene and protein expression analyses. Moreover, adoptive transfer of OVA-specific OT-II cells into C57BL/6 mice bearing OVA expressing IAb−/− tumors resulted in increased accumulation of M1-like TAMs with enhanced M1 associated gene and protein expression profiles. Thus, this paper highlights a so far underestimated function of the CD4+ Th1/TAM axis in re-conditioning the immunosuppressive tumor microenvironment.
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Affiliation(s)
- David Eisel
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Biosciences Faculty, University of Heidelberg, Heidelberg, Germany.,Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz, Germany
| | - Krishna Das
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Biosciences Faculty, University of Heidelberg, Heidelberg, Germany.,Division of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Elke Dickes
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Wolfram Osen
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan B Eichmüller
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
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28
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Eisel D, Osen W, Das K, Hoerhold FMC, König R, Eichmüller SB. Abstract A067: Cognate interaction with CD4+ T-cells instructs M2-like macrophages to acquire M1-like phenotype. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-a067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Current tumor immunotherapy approaches are based on application of checkpoint inhibitors, such as monoclonal antibodies against PD-1/PD-L1 and CTLA-4 or adoptive T-cell therapy using ex vivo expanded TILs or genetically modified autologous T-cells expressing recombinant T-cell receptors (TCRs) or chimeric antigen receptors (CARs). However, the success of these therapeutic strategies is often limited by various inhibitory immune cell types accumulating in the tumor. In particular, tumor-associated macrophages (TAMs) contribute to the immune suppressive tumor micro-milieu, since so-called M2-like macrophages suppress the function of T effector cells and promote the differentiation of regulatory T-cells (Treg) through secretion of inhibitory cytokines such as TGF-β and IL10. Tumor antigen-specific CD4+ T effector cells, on the other hand, can essentially sustain antitumoral immune responses as shown for various tumor entities. In fact, using peritoneal exudate cells (PECs) as source for macrophages we demonstrate that MHC II restricted interaction between ovalbumin (OVA) specific CD4+ T-cells and M2-like macrophages drives M1 polarization. This was confirmed by detailed gene and protein expression analyses as well as functional assays testing phagocytic and pinocytic activities of repolarized macrophages. Moreover, in a set of preclinical experiments, adoptive transfer of CD4+, OVA-specific OT-II cells into C57BL/6 mice bearing OVA expressing IAb-/- tumors resulted in increased intratumoral number of M1-like TAMs as determined by gene expression analysis and flow cytometry. Furthermore, we observed a significant survival benefit of mice treated with a combination of OVA-specific CD4+ (OT-II) and CD8+ (OT-I) cells after transplantation of B16F10-Ova tumors and a complete response in some mice that rejected the tumor cells also upon a later re-challenge. While the antitumoral effect of this adoptive transfer experiment has been already described, we now offer a possible explanation for the supportive effect of specific CD4+ cells on co-transferred CD8+ cells. Taken together, the instructive impact of CD4+ T-cells on M2-like macrophages described in this presentation points towards a so far underestimated function of the CD4+ T-cell / TAM axis in reconditioning the immunosuppressive tumor micro-milieu.
Citation Format: David Eisel, Wolfram Osen, Krishna Das, Franziska Marie-Claire Hoerhold, Rainer König, Stefan B. Eichmüller. Cognate interaction with CD4+ T-cells instructs M2-like macrophages to acquire M1-like phenotype [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A067.
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Affiliation(s)
- David Eisel
- German Cancer Research Center, Heidelberg, Germany; Innsbruck Medical University, Innsbruck, Austria; Center for Sepsis Control and Care, Jena, Germany
| | - Wolfram Osen
- German Cancer Research Center, Heidelberg, Germany; Innsbruck Medical University, Innsbruck, Austria; Center for Sepsis Control and Care, Jena, Germany
| | - Krishna Das
- German Cancer Research Center, Heidelberg, Germany; Innsbruck Medical University, Innsbruck, Austria; Center for Sepsis Control and Care, Jena, Germany
| | - Franziska Marie-Claire Hoerhold
- German Cancer Research Center, Heidelberg, Germany; Innsbruck Medical University, Innsbruck, Austria; Center for Sepsis Control and Care, Jena, Germany
| | - Rainer König
- German Cancer Research Center, Heidelberg, Germany; Innsbruck Medical University, Innsbruck, Austria; Center for Sepsis Control and Care, Jena, Germany
| | - Stefan B. Eichmüller
- German Cancer Research Center, Heidelberg, Germany; Innsbruck Medical University, Innsbruck, Austria; Center for Sepsis Control and Care, Jena, Germany
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29
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Minner S, Lutz J, Hube-Magg C, Kluth M, Simon R, Höflmayer D, Burandt E, Tsourlakis MC, Sauter G, Büscheck F, Wilczak W, Steurer S, Schlomm T, Huland H, Graefen M, Haese A, Heinzer H, Jacobsen F, Hinsch A, Poos A, Oswald M, Rippe K, König R, Schroeder C. Loss of CCAAT-enhancer-binding protein alpha (CEBPA) is linked to poor prognosis in PTEN deleted and TMPRSS2:ERG fusion type prostate cancers. Prostate 2019; 79:302-311. [PMID: 30430607 DOI: 10.1002/pros.23736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 08/15/2018] [Accepted: 10/17/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND The transcription factor CCAAT-enhancer-binding protein alpha (CEBPA) is a crucial regulator of cell proliferation and differentiation. Expression levels of CEBPA have been suggested to be prognostic in various tumor types. METHODS Here, we analyzed the immunohistochemical expression of CEBPA in a tissue microarray containing more than 17 000 prostate cancer specimens with annotated clinical and molecular data including for example TMPRSS2:ERG fusion and PTEN deletion status. RESULTS Normal prostate glands showed moderate to strong CEBPA staining, while CEBPA expression was frequently reduced (40%) or lost (30%) in prostate cancers. Absence of detectable CEBPA expression was markedly more frequent in ERG negative (45%) as compared to ERG positive cancers (20%, P < 0.0001). Reduced CEBPA expression was linked to unfavorable phenotype (P < 0.0001) and poor prognosis (P = 0.0008). Subgroup analyses revealed, that the prognostic value of CEBPA loss was entirely driven by tumors carrying both TMPRSS2:ERG fusions and PTEN deletions. In this subgroup, CEBPA loss was tightly linked to advanced tumor stage (P < 0.0001), high Gleason grade (P < 0.0001), positive nodal stage (0.0003), and early biochemical recurrence (P = 0.0007), while these associations were absent or markedly diminished in tumors with normal PTEN copy numbers and/or absence of ERG fusion. CONCLUSIONS CEBPA is down regulated in about one third of prostate cancers, but the clinical impact of CEBPA loss is strictly limited to the subset of about 10% prostate cancers carrying both ERG fusion and deletions of the PTEN tumor suppressor. Our findings challenge the concept that prognostic molecular markers may be generally applicable to all prostate cancers.
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Affiliation(s)
- Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Jannes Lutz
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Doris Höflmayer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Eike Burandt
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | | | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Franziska Büscheck
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Waldemar Wilczak
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Thorsten Schlomm
- Department of Urology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Hartwig Huland
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Alexander Haese
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Hans Heinzer
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Frank Jacobsen
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Andrea Hinsch
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Alexandra Poos
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany and Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Jena, Germany
- Faculty of Biosciences, Heidelberg University, Germany
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany and Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Jena, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany and Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Jena, Germany
| | - Cornelia Schroeder
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Center Hamburg-Eppendorf, Germany
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30
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Hubeny M, Höschen D, Rack M, Neubauer O, Bozhenkov S, Czymek G, Unterberg B, König R, Hathiramani D, Brezinsek S, Linsmeier C. Diagnostic setup for the divertor manipulator at wendelstein 7-X. Nuclear Materials and Energy 2019. [DOI: 10.1016/j.nme.2018.11.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Hathiramani D, Ali A, Anda G, Barbui T, Biedermann C, Charl A, Chauvin D, Czymek G, Dhard C, Drewelow P, Dudek A, Effenberg F, Ehrke G, Endler M, Ennis D, Fellinger J, Ford O, Freundt S, Gradic D, Grosser K, Harris J, Hölbe H, Jakubowski M, Knaup M, Kocsis G, König R, Krause M, Kremeyer T, Kornejew P, Krychowiak M, Lambertz H, Jenzsch H, Mayer M, Mohr S, Neubauer O, Otte M, Perseo V, Pilopp D, Rudischhauser L, Schmitz O, Schweer B, Schülke M, Stephey L, Szepesi T, Terra A, Toth M, Wenzel U, Wurden G, Zoletnik S, Pedersen TS. Upgrades of edge, divertor and scrape-off layer diagnostics of W7‐X for OP1.2. Fusion Engineering and Design 2018. [DOI: 10.1016/j.fusengdes.2018.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Ast V, Kordaß T, Oswald M, Kolte A, Eisel D, Osen W, Eichmüller SB, Berndt A, König R. MiR-192, miR-200c and miR-17 are fibroblast-mediated inhibitors of colorectal cancer invasion. Oncotarget 2018; 9:35559-35580. [PMID: 30473751 PMCID: PMC6238973 DOI: 10.18632/oncotarget.26263] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/06/2018] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer remains a leading cause of cancer-related death worldwide. A previous transcriptomics based study characterized molecular subgroups of which the stromal subgroup was associated with the worst clinical outcome. Micro-RNAs (miRNAs) are well-known regulators of gene expression and can follow a non-linear repression mechanism. We set up a model combining piecewise linear and linear regression and applied this combined regression model to a comprehensive colon adenocarcinoma dataset. We identified miRNAs involved in regulating characteristic gene sets, particularly extracellular matrix remodeling in the stromal subgroup. Comparison of expression data from separated (epithelial) cancer cells and stroma cells or fibroblasts associate these regulatory interactions with infiltrating stromal or tumor-associated fibroblasts. MiR-200c, miR-17 and miR-192 were identified as the most promising candidates regulating genes crucial for extracellular matrix remodeling. We validated our computational findings by in vitro assays. Enforced expression of either miR-200c, miR-17 or miR-192 in untransformed human colon fibroblasts down-regulated 85% of all predicted target genes. Expressing these miRNAs singly or in combination in human colon fibroblasts co-cultured with colon cancer cells considerably reduced cancer cell invasion validating these miRNAs as cancer cell infiltration suppressors in tumor associated fibroblasts.
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Affiliation(s)
- Volker Ast
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, 07745 Jena, Germany
| | - Theresa Kordaß
- GMP & T Cell Therapy Unit, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, 07745 Jena, Germany
| | - Amol Kolte
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, 07745 Jena, Germany
| | - David Eisel
- GMP & T Cell Therapy Unit, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Wolfram Osen
- GMP & T Cell Therapy Unit, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Stefan B. Eichmüller
- GMP & T Cell Therapy Unit, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Alexander Berndt
- Institute of Forensic Medicine, Section Pathology, Jena University Hospital, 07747 Jena, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, 07745 Jena, Germany
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33
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Kresinsky A, Bauer R, Schnöder TM, Berg T, Meyer D, Ast V, König R, Serve H, Heidel FH, Böhmer FD, Müller JP. Loss of DEP-1 (Ptprj) promotes myeloproliferative disease in FLT3-ITD acute myeloid leukemia. Haematologica 2018; 103:e505-e509. [PMID: 29880609 DOI: 10.3324/haematol.2017.185306] [Citation(s) in RCA: 8] [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] [Indexed: 02/02/2023] Open
Affiliation(s)
- Anne Kresinsky
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital
| | - Reinhard Bauer
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital
| | - Tina M Schnöder
- Innere Medizin II, Hämatologie und Onkologie, Jena University Hospital.,Leibniz Institute on Aging, Fritz-Lipmann-Institute (FLI), Jena
| | - Tobias Berg
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt
| | - Daria Meyer
- Network modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Volker Ast
- Network modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Rainer König
- Network modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Hubert Serve
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt
| | - Florian H Heidel
- Innere Medizin II, Hämatologie und Onkologie, Jena University Hospital.,Leibniz Institute on Aging, Fritz-Lipmann-Institute (FLI), Jena
| | - Frank-D Böhmer
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital
| | - Jörg P Müller
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital
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34
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Mürtz P, Sprinkart AM, Reick M, Pieper CC, Schievelkamp AH, König R, Schild HH, Willinek WA, Kukuk GM. Accurate IVIM model-based liver lesion characterisation can be achieved with only three b-value DWI. Eur Radiol 2018; 28:4418-4428. [PMID: 29671057 DOI: 10.1007/s00330-018-5401-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The objective of this study was to evaluate a simplified intravoxel incoherent motion (IVIM) approach of diffusion-weighted imaging (DWI) with four b-values for liver lesion characterisation at 1.5 T. METHODS DWI data from a respiratory-gated MRI sequence with b = 0, 50, 250, 800 s/mm2 were retrospectively analysed in 173 lesions and 40 healthy livers. The apparent diffusion coefficient ADC = ADC(0,800) and IVIM-based parameters D1' = ADC(50,800), D2' =ADC(250,800), f1', f2', D*', ADClow = ADC(0,50), and ADCdiff=ADClow-D2' were calculated voxel-wise without fitting procedures. Differences between lesion groups were investigated. RESULTS Focal nodular hyperplasias were best discriminated from all other lesions by f1' with an area under the curve (AUC) of 0.989. Haemangiomas were best discriminated by D1' (AUC of 0.994). For discrimination between malignant and benign lesions, ADC(0,800) and D1' were best suited (AUC of 0.915 and 0.858, respectively). Discriminatory power was further increased by using a combination of D1' and f1'. CONCLUSION IVIM parameters D and f approximated from three b-values provided more discriminatory power between liver lesions than ADC determined from two b-values. The use of b = 0, 50, 800 s/mm2 was superior to that of b = 0, 250, 800 s/mm2. The acquisition of four instead of three b-values has no further benefit for lesion characterisation. KEY POINTS • Diffusion and perfusion characteristics are assessable with only three b-values. • Association of b = 0, 50, 800 s/mm2is superior to b = 0, 250, 800 s/mm2. • A fourth acquired b-value has no benefit for differential diagnosis. • For liver lesion characterisation, simplified IVIM analysis is superior to ADC determination. • Simplified IVIM approach guarantees numerically stable, voxel-wise results and short acquisition times.
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Affiliation(s)
- P Mürtz
- Department of Radiology, University of Bonn, Bonn, Germany.
- Radiologische Klinik der Universität Bonn, Sigmund-Freud-Straße 25, 53105, Bonn, Germany.
| | - A M Sprinkart
- Department of Radiology, University of Bonn, Bonn, Germany
| | - M Reick
- Department of Radiology, University of Bonn, Bonn, Germany
| | - C C Pieper
- Department of Radiology, University of Bonn, Bonn, Germany
| | | | - R König
- Department of Radiology, University of Bonn, Bonn, Germany
| | - H H Schild
- Department of Radiology, University of Bonn, Bonn, Germany
| | - W A Willinek
- Department of Radiology, University of Bonn, Bonn, Germany
| | - G M Kukuk
- Department of Radiology, University of Bonn, Bonn, Germany
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35
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Aramillo Irizar P, Schäuble S, Esser D, Groth M, Frahm C, Priebe S, Baumgart M, Hartmann N, Marthandan S, Menzel U, Müller J, Schmidt S, Ast V, Caliebe A, König R, Krawczak M, Ristow M, Schuster S, Cellerino A, Diekmann S, Englert C, Hemmerich P, Sühnel J, Guthke R, Witte OW, Platzer M, Ruppin E, Kaleta C. Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly. Nat Commun 2018; 9:327. [PMID: 29382830 PMCID: PMC5790807 DOI: 10.1038/s41467-017-02395-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023] Open
Abstract
Disease epidemiology during ageing shows a transition from cancer to degenerative chronic disorders as dominant contributors to mortality in the old. Nevertheless, it has remained unclear to what extent molecular signatures of ageing reflect this phenomenon. Here we report on the identification of a conserved transcriptomic signature of ageing based on gene expression data from four vertebrate species across four tissues. We find that ageing-associated transcriptomic changes follow trajectories similar to the transcriptional alterations observed in degenerative ageing diseases but are in opposite direction to the transcriptomic alterations observed in cancer. We confirm the existence of a similar antagonism on the genomic level, where a majority of shared risk alleles which increase the risk of cancer decrease the risk of chronic degenerative disorders and vice versa. These results reveal a fundamental trade-off between cancer and degenerative ageing diseases that sheds light on the pronounced shift in their epidemiology during ageing. Ageing is associated with a pronounced shift in mortality from cancer to degenerative diseases. Here, the authors show that in concordance with this shift, conserved transcriptional alterations during ageing across four vertebrates align with degenerative diseases but are opposite to those in cancer.
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Affiliation(s)
- Peer Aramillo Irizar
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Sascha Schäuble
- Jena University Language and Information Engineering Lab, Friedrich-Schiller-University Jena, D-07743, Jena, Germany.,GerontoSys JenAge Consortium, D-07745, Jena, Germany
| | - Daniela Esser
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Marco Groth
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Genome Analysis Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Christiane Frahm
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Steffen Priebe
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, D-07745, Jena, Germany
| | - Mario Baumgart
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Biology of Ageing Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Nils Hartmann
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Molecular Genetics Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Shiva Marthandan
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Imageing Facility, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Uwe Menzel
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, D-07745, Jena, Germany
| | - Jule Müller
- Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Silvio Schmidt
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Volker Ast
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, D-07747, Jena, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, D-07745, Jena, Germany
| | - Amke Caliebe
- Institute for Medical Informatics and Statistics, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, D-07747, Jena, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, D-07745, Jena, Germany
| | - Michael Krawczak
- Institute for Medical Informatics and Statistics, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Michael Ristow
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Energy Metabolism Laboratory, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach/Zürich, CH-8603, Switzerland
| | - Stefan Schuster
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Department of Bioinformatics, Friedrich-Schiller-University Jena, D-07743, Jena, Germany
| | - Alessandro Cellerino
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Biology of Ageing Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany.,Laboratory of Neurobiology, Scuola Normale Superiore, University of Pisa, I-56100, Pisa, Italy
| | - Stephan Diekmann
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Molecular Biology Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Christoph Englert
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Molecular Genetics Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany.,Faculty of Biology and Pharmacy, Friedrich-Schiller-University Jena, D-07743, Jena, Germany
| | - Peter Hemmerich
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Imageing Facility, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Jürgen Sühnel
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Biocomputing Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Reinhard Guthke
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, D-07745, Jena, Germany
| | - Otto W Witte
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Matthias Platzer
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Genome Analysis Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Eytan Ruppin
- Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany. .,GerontoSys JenAge Consortium, D-07745, Jena, Germany.
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Zoletnik S, Biedermann C, Cseh G, Kocsis G, König R, Szabolics T, Szepesi T. First results of the multi-purpose real-time processing video camera system on the Wendelstein 7-X stellarator and implications for future devices. Rev Sci Instrum 2018; 89:013502. [PMID: 29390718 DOI: 10.1063/1.4995947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A special video camera has been developed for the 10-camera overview video system of the Wendelstein 7-X (W7-X) stellarator considering multiple application needs and limitations resulting from this complex long-pulse superconducting stellarator experiment. The event detection intelligent camera (EDICAM) uses a special 1.3 Mpixel CMOS sensor with non-destructive read capability which enables fast monitoring of smaller Regions of Interest (ROIs) even during long exposures. The camera can perform simple data evaluation algorithms (minimum/maximum, mean comparison to levels) on the ROI data which can dynamically change the readout process and generate output signals. Multiple EDICAM cameras were operated in the first campaign of W7-X and capabilities were explored in the real environment. Data prove that the camera can be used for taking long exposure (10-100 ms) overview images of the plasma while sub-ms monitoring and even multi-camera correlated edge plasma turbulence measurements of smaller areas can be done in parallel. These latter revealed that filamentary turbulence structures extend between neighboring modules of the stellarator. Considerations emerging for future upgrades of this system and similar setups on future long-pulse fusion experiments such as ITER are discussed.
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Affiliation(s)
- S Zoletnik
- Wigner Research Centre for Physics, P.O. Box 49, H-1525 Budapest, Hungary
| | - C Biedermann
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - G Cseh
- Wigner Research Centre for Physics, P.O. Box 49, H-1525 Budapest, Hungary
| | - G Kocsis
- Wigner Research Centre for Physics, P.O. Box 49, H-1525 Budapest, Hungary
| | - R König
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - T Szabolics
- Wigner Research Centre for Physics, P.O. Box 49, H-1525 Budapest, Hungary
| | - T Szepesi
- Wigner Research Centre for Physics, P.O. Box 49, H-1525 Budapest, Hungary
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Ansari SS, Sharma AK, Zepp M, Ivanova E, Bergmann F, König R, Berger MR. Upregulation of cell cycle genes in head and neck cancer patients may be antagonized by erufosine's down regulation of cell cycle processes in OSCC cells. Oncotarget 2017; 9:5797-5810. [PMID: 29464035 PMCID: PMC5814175 DOI: 10.18632/oncotarget.23537] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/01/2017] [Indexed: 02/06/2023] Open
Abstract
The TCGA database was analyzed to identify deregulation of cell cycle genes across 24 cancer types and ensuing effects on patient survival. Pan-cancer analysis showed that head and neck squamous cell carcinoma (HNSCC) ranks amongst the top four cancers showing deregulated cell cycle genes. Also, the median gene expression of all CDKs and cyclins in HNSCC patient samples was higher than that of the global gene expression. This was verified by IHC staining of CCND1 from HNSCC patients. When evaluating the quartiles with highest and lowest expression, increased CCND1/CDK6 levels had negative implication on patient survival. In search for a drug, which may antagonize this tumor profile, the potential of the alkylphosphocholine erufosine was evaluated against cell lines of the HNSCC subtype, oral squamous cell carcinoma (OSCC) using in-vitro and in-vivo assays. Erufosine inhibited growth of OSCC cell lines concentration dependently. Initial microarray findings revealed that cyclins and CDKs were down-regulated concentration dependently upon exposure to erufosine and participated in negative enrichment of cell cycle processes. These findings, indicating a pan-cdk/cyclin inhibition by erufosine, were verified at both, mRNA and protein levels. Erufosine caused a G2/M block and inhibition of colony formation. Significant tumor growth retardation was seen upon treatment with erufosine in a xenograft model. For the decreased cyclin D1 and CDK 4/6 levels found in tumor tissue, these proteins can serve as biomarker for erufosine intervention. The findings demonstrate the potential of erufosine as cell cycle inhibitor in HNSCC treatment, alone or in combination with current therapeutic agents.
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Affiliation(s)
- Shariq S Ansari
- Toxicology and Chemotherapy Unit, German Cancer Research Center, Heidelberg, Germany
| | - Ashwini K Sharma
- Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.,Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Zepp
- Toxicology and Chemotherapy Unit, German Cancer Research Center, Heidelberg, Germany
| | - Elizabet Ivanova
- Laboratory for Experimental Chemotherapy, Department of Pharmacology, Pharmacotherapy and Toxicology, Faculty of Pharmacy, Medical University of Sofia, Bulgaria
| | - Frank Bergmann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Network Modeling, Leibniz Institute for Natural Products Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
| | - Martin R Berger
- Toxicology and Chemotherapy Unit, German Cancer Research Center, Heidelberg, Germany
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Leonor Fernandes Saraiva JP, Zubiria-Barrera C, Klassert TE, Lautenbach MJ, Blaess M, Claus RA, Slevogt H, König R. Combination of Classifiers Identifies Fungal-Specific Activation of Lysosome Genes in Human Monocytes. Front Microbiol 2017; 8:2366. [PMID: 29238336 PMCID: PMC5712586 DOI: 10.3389/fmicb.2017.02366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 07/07/2017] [Accepted: 11/16/2017] [Indexed: 12/31/2022] Open
Abstract
Blood stream infections can be caused by several pathogens such as viruses, fungi and bacteria and can cause severe clinical complications including sepsis. Delivery of appropriate and quick treatment is mandatory. However, it requires a rapid identification of the invading pathogen. The current gold standard for pathogen identification relies on blood cultures and these methods require a long time to gain the needed diagnosis. The use of in situ experiments attempts to identify pathogen specific immune responses but these often lead to heterogeneous biomarkers due to the high variability in methods and materials used. Using gene expression profiles for machine learning is a developing approach to discriminate between types of infection, but also shows a high degree of inconsistency. To produce consistent gene signatures, capable of discriminating fungal from bacterial infection, we have employed Support Vector Machines (SVMs) based on Mixed Integer Linear Programming (MILP). Combining classifiers by joint optimization constraining them to the same set of discriminating features increased the consistency of our biomarker list independently of leukocyte-type or experimental setup. Our gene signature showed an enrichment of genes of the lysosome pathway which was not uncovered by the use of independent classifiers. Moreover, our results suggest that the lysosome genes are specifically induced in monocytes. Real time qPCR of the identified lysosome-related genes confirmed the distinct gene expression increase in monocytes during fungal infections. Concluding, our combined classifier approach presented increased consistency and was able to "unmask" signaling pathways of less-present immune cells in the used datasets.
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Affiliation(s)
- João P Leonor Fernandes Saraiva
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany.,Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | | | | | | | - Markus Blaess
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Ralf A Claus
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Hortense Slevogt
- Septomics Research Centre, Jena University Hospital, Jena, Germany
| | - Rainer König
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany.,Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
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39
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Abstract
Patient history taking and semiology provide seminal clues to the diagnosis of dissociative seizures. Openness and alertness of the treating physician are essential. Video-electroencephalogram(EEG)-based analyses of the events are crucial to establish the correct diagnosis, particularly in complex cases. The patient-doctor relationship is of particular importance in order to successfully motivate the patient for psychotherapeutic treatment. Coexisting psychiatric morbidity as well as other functional somatic symptoms must be actively explored. Current changes in the established diagnostic manuals, including ICD-11, reflect the ongoing vivid interest and controversial discussions in the field of dissociative disorders.
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Affiliation(s)
- A Joos
- Zentrum für Psychische Erkrankungen, Klinik für Psychosomatische Medizin und Psychotherapie, Universitätsklinikum Freiburg, Medizinische Fakultät, Universität Freiburg, Hauptstraße 8, 79104, Freiburg, Deutschland.
- Kliniken Schmieder, Psychotherapeutische Neurologie, Gailingen, Deutschland.
| | - K Baumann
- Zentrum für Psychische Erkrankungen, Klinik für Psychosomatische Medizin und Psychotherapie, Universitätsklinikum Freiburg, Medizinische Fakultät, Universität Freiburg, Hauptstraße 8, 79104, Freiburg, Deutschland
| | - C E Scheidt
- Zentrum für Psychische Erkrankungen, Klinik für Psychosomatische Medizin und Psychotherapie, Universitätsklinikum Freiburg, Medizinische Fakultät, Universität Freiburg, Hauptstraße 8, 79104, Freiburg, Deutschland
| | - C Lahmann
- Zentrum für Psychische Erkrankungen, Klinik für Psychosomatische Medizin und Psychotherapie, Universitätsklinikum Freiburg, Medizinische Fakultät, Universität Freiburg, Hauptstraße 8, 79104, Freiburg, Deutschland
| | - R König
- Zentrum für Psychische Erkrankungen, Klinik für Psychosomatische Medizin und Psychotherapie, Universitätsklinikum Freiburg, Medizinische Fakultät, Universität Freiburg, Hauptstraße 8, 79104, Freiburg, Deutschland
| | - H-J Busch
- Universitäts-Notfallzentrum, Universitätsklinikum Freiburg, Medizinische Fakultät, Universität Freiburg, Freiburg, Deutschland
| | - A Schulze-Bonhage
- Epilepsiezentrum, Universitätsklinikum Freiburg, Medizinische Fakultät, Universität Freiburg, Freiburg, Deutschland
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40
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Saraiva JP, Oswald M, Biering A, Röll D, Assmann C, Klassert T, Blaess M, Czakai K, Claus R, Löffler J, Slevogt H, König R. Fungal biomarker discovery by integration of classifiers. BMC Genomics 2017; 18:601. [PMID: 28797245 PMCID: PMC5553868 DOI: 10.1186/s12864-017-4006-x] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 08/02/2017] [Indexed: 02/01/2023] Open
Abstract
Background The human immune system is responsible for protecting the host from infection. However, in immunocompromised individuals the risk of infection increases substantially with possible drastic consequences. In extreme, systemic infection can lead to sepsis which is responsible for innumerous deaths worldwide. Amongst its causes are infections by bacteria and fungi. To increase survival, it is mandatory to identify the type of infection rapidly. Discriminating between fungal and bacterial pathogens is key to determine if antifungals or antibiotics should be administered, respectively. For this, in situ experiments have been performed to determine regulation mechanisms of the human immune system to identify biomarkers. However, these studies led to heterogeneous results either due different laboratory settings, pathogen strains, cell types and tissues, as well as the time of sample extraction, to name a few. Methods To generate a gene signature capable of discriminating between fungal and bacterial infected samples, we employed Mixed Integer Linear Programming (MILP) based classifiers on several datasets comprised of the above mentioned pathogens. Results When combining the classifiers by a joint optimization we could increase the consistency of the biomarker gene list independently of the experimental setup. An increase in pairwise overlap (the number of genes that overlap in each cross-validation) of 43% was obtained by this approach when compared to that of single classifiers. The refined gene list was composed of 19 genes and ranked according to consistency in expression (up- or down-regulated) and most of them were linked either directly or indirectly to the ERK-MAPK signalling pathway, which has been shown to play a key role in the immune response to infection. Testing of the identified 12 genes on an unseen dataset yielded an average accuracy of 83%. Conclusions In conclusion, our method allowed the combination of independent classifiers and increased consistency and reliability of the generated gene signatures. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4006-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- João Pedro Saraiva
- Network Modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Marcus Oswald
- Network Modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Antje Biering
- Network Modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Daniela Röll
- Network Modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Cora Assmann
- Septomics Research Centre, Jena University Hospital, Jena, Germany
| | - Tilman Klassert
- Septomics Research Centre, Jena University Hospital, Jena, Germany
| | - Markus Blaess
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | | | - Ralf Claus
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | | | - Hortense Slevogt
- Septomics Research Centre, Jena University Hospital, Jena, Germany
| | - Rainer König
- Network Modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, Germany. .,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.
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Seifert A, König R, Doh M. INTERNET DIFFUSION AMONG OLDER PERSONS IN EUROPE—A STATISTICAL ANALYSIS OF SHARE DATA. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.2747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- A. Seifert
- Center Center of Competence for Gerontology, University of Zurich, Zurich, Switzerland,
- URPP Dynamics of Healthy Aging / University of Zurich, Zurich, Switzerland,
| | - R. König
- Institute of Sociology, University of Zurich, Zurich, Switzerland,
| | - M. Doh
- Department of Psychological Ageing Research, Institute of Psychology, Heidelberg University, Heidelberg, Switzerland
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König R, Grigull P, McCormick K, Feng Y, Ehmler H, Gadelmeier F, Giannone L, Hildebrandt D, Kisslinger J, Klinger T, Naujoks D, Ramasubramanian N, Renner H, Sardei F, Thomsen H, Wagner F, Wenzel U, Werner A, Komori A, Masuzaki S, Matsuoka K, Mioduszewski P, Morisaki T, Obiki T, Ohyabu N. Divertors for Helical Devices: Concepts, Plans, Results, and Problems. Fusion Science and Technology 2017. [DOI: 10.13182/fst04-a551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- R. König
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - P. Grigull
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - K. McCormick
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - Y. Feng
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - H. Ehmler
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - F. Gadelmeier
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - L. Giannone
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - D. Hildebrandt
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - J. Kisslinger
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - T. Klinger
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - D. Naujoks
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - N. Ramasubramanian
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - H. Renner
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - F. Sardei
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - H. Thomsen
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - F. Wagner
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - U. Wenzel
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - A. Werner
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - A. Komori
- National Institute for Fusion Science Toki-shi, Gifu-ken 509-5292, Japan
| | - S. Masuzaki
- National Institute for Fusion Science Toki-shi, Gifu-ken 509-5292, Japan
| | - K. Matsuoka
- National Institute for Fusion Science Toki-shi, Gifu-ken 509-5292, Japan
| | - P. Mioduszewski
- Oak Ridge National Laboratory, P.O. Box 2008, M.S. 6169, Oak Ridge, Tennessee 37831
| | - T. Morisaki
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
| | - T. Obiki
- Kyoto University, Institute of Advanced Energy, Gakasho, Uji, Japan
| | - N. Ohyabu
- Max-Planck-Institut für Plasmaphysik EURATOM Association, D-17491 Greifswald, Germany
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43
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Krychowiak M, Adnan A, Alonso A, Andreeva T, Baldzuhn J, Barbui T, Beurskens M, Biel W, Biedermann C, Blackwell BD, Bosch HS, Bozhenkov S, Brakel R, Bräuer T, Brotas de Carvalho B, Burhenn R, Buttenschön B, Cappa A, Cseh G, Czarnecka A, Dinklage A, Drews P, Dzikowicka A, Effenberg F, Endler M, Erckmann V, Estrada T, Ford O, Fornal T, Frerichs H, Fuchert G, Geiger J, Grulke O, Harris JH, Hartfuß HJ, Hartmann D, Hathiramani D, Hirsch M, Höfel U, Jabłoński S, Jakubowski MW, Kaczmarczyk J, Klinger T, Klose S, Knauer J, Kocsis G, König R, Kornejew P, Krämer-Flecken A, Krawczyk N, Kremeyer T, Książek I, Kubkowska M, Langenberg A, Laqua HP, Laux M, Lazerson S, Liang Y, Liu SC, Lorenz A, Marchuk AO, Marsen S, Moncada V, Naujoks D, Neilson H, Neubauer O, Neuner U, Niemann H, Oosterbeek JW, Otte M, Pablant N, Pasch E, Sunn Pedersen T, Pisano F, Rahbarnia K, Ryć L, Schmitz O, Schmuck S, Schneider W, Schröder T, Schuhmacher H, Schweer B, Standley B, Stange T, Stephey L, Svensson J, Szabolics T, Szepesi T, Thomsen H, Travere JM, Trimino Mora H, Tsuchiya H, Weir GM, Wenzel U, Werner A, Wiegel B, Windisch T, Wolf R, Wurden GA, Zhang D, Zimbal A, Zoletnik S. Overview of diagnostic performance and results for the first operation phase in Wendelstein 7-X (invited). Rev Sci Instrum 2016; 87:11D304. [PMID: 27910389 DOI: 10.1063/1.4964376] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Wendelstein 7-X, a superconducting optimized stellarator built in Greifswald/Germany, started its first plasmas with the last closed flux surface (LCFS) defined by 5 uncooled graphite limiters in December 2015. At the end of the 10 weeks long experimental campaign (OP1.1) more than 20 independent diagnostic systems were in operation, allowing detailed studies of many interesting plasma phenomena. For example, fast neutral gas manometers supported by video cameras (including one fast-frame camera with frame rates of tens of kHz) as well as visible cameras with different interference filters, with field of views covering all ten half-modules of the stellarator, discovered a MARFE-like radiation zone on the inboard side of machine module 4. This structure is presumably triggered by an inadvertent plasma-wall interaction in module 4 resulting in a high impurity influx that terminates some discharges by radiation cooling. The main plasma parameters achieved in OP1.1 exceeded predicted values in discharges of a length reaching 6 s. Although OP1.1 is characterized by short pulses, many of the diagnostics are already designed for quasi-steady state operation of 30 min discharges heated at 10 MW of ECRH. An overview of diagnostic performance for OP1.1 is given, including some highlights from the physics campaigns.
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Affiliation(s)
- M Krychowiak
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - A Adnan
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - A Alonso
- Laboratorio Nacional de Fusión, CIEMAT, Avenida Complutense, Madrid, Spain
| | - T Andreeva
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - J Baldzuhn
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - T Barbui
- University of Wisconsin, Engineering Drive, Madison, Wisconsin 53706, USA
| | - M Beurskens
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - W Biel
- Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung - Plasmaphysik, Partner of the Trilateral Euregio Cluster (TEC), 52425 Jülich, Germany
| | - C Biedermann
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - B D Blackwell
- Australian National University, Acton ACT, 2601 Canberra, Australia
| | - H S Bosch
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - S Bozhenkov
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - R Brakel
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - T Bräuer
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - B Brotas de Carvalho
- Instituto de Plasmas e Fusao Nuclear, Avenue Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - R Burhenn
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - B Buttenschön
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - A Cappa
- Laboratorio Nacional de Fusión, CIEMAT, Avenida Complutense, Madrid, Spain
| | - G Cseh
- Wigner Research Centre for Physics, Konkoly Thege 29-33, H-1121 Budapest, Hungary
| | - A Czarnecka
- Institute of Plasma Physics and Laser Microfusion, Hery Street 23, 01-497 Warsaw, Poland
| | - A Dinklage
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - P Drews
- Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung - Plasmaphysik, Partner of the Trilateral Euregio Cluster (TEC), 52425 Jülich, Germany
| | - A Dzikowicka
- University of Szczecin, al. Papieża Jana Pawła II 22A, Szczecin, Poland
| | - F Effenberg
- University of Wisconsin, Engineering Drive, Madison, Wisconsin 53706, USA
| | - M Endler
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - V Erckmann
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - T Estrada
- Laboratorio Nacional de Fusión, CIEMAT, Avenida Complutense, Madrid, Spain
| | - O Ford
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - T Fornal
- Institute of Plasma Physics and Laser Microfusion, Hery Street 23, 01-497 Warsaw, Poland
| | - H Frerichs
- University of Wisconsin, Engineering Drive, Madison, Wisconsin 53706, USA
| | - G Fuchert
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - J Geiger
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - O Grulke
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - J H Harris
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - H J Hartfuß
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - D Hartmann
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - D Hathiramani
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - M Hirsch
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - U Höfel
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - S Jabłoński
- Institute of Plasma Physics and Laser Microfusion, Hery Street 23, 01-497 Warsaw, Poland
| | - M W Jakubowski
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - J Kaczmarczyk
- Institute of Plasma Physics and Laser Microfusion, Hery Street 23, 01-497 Warsaw, Poland
| | - T Klinger
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - S Klose
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - J Knauer
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - G Kocsis
- Wigner Research Centre for Physics, Konkoly Thege 29-33, H-1121 Budapest, Hungary
| | - R König
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - P Kornejew
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - A Krämer-Flecken
- Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung - Plasmaphysik, Partner of the Trilateral Euregio Cluster (TEC), 52425 Jülich, Germany
| | - N Krawczyk
- Institute of Plasma Physics and Laser Microfusion, Hery Street 23, 01-497 Warsaw, Poland
| | - T Kremeyer
- University of Wisconsin, Engineering Drive, Madison, Wisconsin 53706, USA
| | - I Książek
- Opole University, pl. Kopernika 11a, 45-040 Opole, Poland
| | - M Kubkowska
- Institute of Plasma Physics and Laser Microfusion, Hery Street 23, 01-497 Warsaw, Poland
| | - A Langenberg
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - H P Laqua
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - M Laux
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - S Lazerson
- Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543, USA
| | - Y Liang
- Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung - Plasmaphysik, Partner of the Trilateral Euregio Cluster (TEC), 52425 Jülich, Germany
| | - S C Liu
- Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung - Plasmaphysik, Partner of the Trilateral Euregio Cluster (TEC), 52425 Jülich, Germany
| | - A Lorenz
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - A O Marchuk
- Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung - Plasmaphysik, Partner of the Trilateral Euregio Cluster (TEC), 52425 Jülich, Germany
| | - S Marsen
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - V Moncada
- CEA, IRFM, F-13108 Saint-Paul-lez-Durance, France
| | - D Naujoks
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - H Neilson
- Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543, USA
| | - O Neubauer
- Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung - Plasmaphysik, Partner of the Trilateral Euregio Cluster (TEC), 52425 Jülich, Germany
| | - U Neuner
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - H Niemann
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - J W Oosterbeek
- Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - M Otte
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - N Pablant
- Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543, USA
| | - E Pasch
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - T Sunn Pedersen
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - F Pisano
- University of Cagliari, Via Università, 40, 09124 Cagliari, Italy
| | - K Rahbarnia
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - L Ryć
- Institute of Plasma Physics and Laser Microfusion, Hery Street 23, 01-497 Warsaw, Poland
| | - O Schmitz
- University of Wisconsin, Engineering Drive, Madison, Wisconsin 53706, USA
| | - S Schmuck
- Culham Science Centre, Abingdon OX14 3DB, United Kingdom
| | - W Schneider
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - T Schröder
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - H Schuhmacher
- Physikalisch-Technische Bundesanstalt, Bundesallee 100, 38116 Braunschweig, Germany
| | - B Schweer
- Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung - Plasmaphysik, Partner of the Trilateral Euregio Cluster (TEC), 52425 Jülich, Germany
| | - B Standley
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - T Stange
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - L Stephey
- University of Wisconsin, Engineering Drive, Madison, Wisconsin 53706, USA
| | - J Svensson
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - T Szabolics
- Wigner Research Centre for Physics, Konkoly Thege 29-33, H-1121 Budapest, Hungary
| | - T Szepesi
- Wigner Research Centre for Physics, Konkoly Thege 29-33, H-1121 Budapest, Hungary
| | - H Thomsen
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - J-M Travere
- CEA, IRFM, F-13108 Saint-Paul-lez-Durance, France
| | - H Trimino Mora
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - H Tsuchiya
- NIFS National Institute for Fusion Science, 322-6 Oroshi-cho, Toki 509-5292, Japan
| | - G M Weir
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - U Wenzel
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - A Werner
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - B Wiegel
- Physikalisch-Technische Bundesanstalt, Bundesallee 100, 38116 Braunschweig, Germany
| | - T Windisch
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - R Wolf
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - G A Wurden
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - D Zhang
- Max Planck Institute for Plasma Physics, 17491 Greifswald, Germany
| | - A Zimbal
- Physikalisch-Technische Bundesanstalt, Bundesallee 100, 38116 Braunschweig, Germany
| | - S Zoletnik
- Wigner Research Centre for Physics, Konkoly Thege 29-33, H-1121 Budapest, Hungary
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44
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Barbui T, Krychowiak M, König R, Schmitz O, Muñoz Burgos JM, Schweer B, Terra A. Feasibility of line-ratio spectroscopy on helium and neon as edge diagnostic tool for Wendelstein 7-X. Rev Sci Instrum 2016; 87:11E554. [PMID: 27910613 DOI: 10.1063/1.4962989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A beam emission spectroscopy system on thermal helium (He) and neon (Ne) has been set up at Wendelstein 7-X to measure edge electron temperature and density profiles utilizing the line-ratio technique or its extension by the analysis of absolutely calibrated line emissions. The setup for a first systematic test of these techniques of quantitative atomic spectroscopy in the limiter startup phase (OP1.1) is reported together with first measured profiles. This setup and the first results are an important test for developing the technique for the upcoming high density, low temperature island divertor regime.
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Affiliation(s)
- T Barbui
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - M Krychowiak
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - R König
- Max-Planck-Institut für Plasmaphysik, 17491 Greifswald, Germany
| | - O Schmitz
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - J M Muñoz Burgos
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - B Schweer
- Laboratory for Plasma Physics, Ecole Royale Militaire - Koninklijke Militaire School, 1000 Brussels, Belgium
| | - A Terra
- Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung-Plasmaphysik, Partner of the Trilateral Euregio Cluster (TEC), 52425 Jülich, Germany
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45
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Stephey L, Wurden GA, Schmitz O, Frerichs H, Effenberg F, Biedermann C, Harris J, König R, Kornejew P, Krychowiak M, Unterberg EA. Spectroscopic imaging of limiter heat and particle fluxes and the resulting impurity sources during Wendelstein 7-X startup plasmas. Rev Sci Instrum 2016; 87:11D606. [PMID: 27910364 DOI: 10.1063/1.4959274] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A combined IR and visible camera system [G. A. Wurden et al., "A high resolution IR/visible imaging system for the W7-X limiter," Rev. Sci. Instrum. (these proceedings)] and a filterscope system [R. J. Colchin et al., Rev. Sci. Instrum. 74, 2068 (2003)] were implemented together to obtain spectroscopic data of limiter and first wall recycling and impurity sources during Wendelstein 7-X startup plasmas. Both systems together provided excellent temporal and spatial spectroscopic resolution of limiter 3. Narrowband interference filters in front of the camera yielded C-III and Hα photon flux, and the filterscope system provided Hα, Hβ, He-I, He-II, C-II, and visible bremsstrahlung data. The filterscopes made additional measurements of several points on the W7-X vacuum vessel to yield wall recycling fluxes. The resulting photon flux from both the visible camera and filterscopes can then be compared to an EMC3-EIRENE synthetic diagnostic [H. Frerichs et al., "Synthetic plasma edge diagnostics for EMC3-EIRENE, highlighted for Wendelstein 7-X," Rev. Sci. Instrum. (these proceedings)] to infer both a limiter particle flux and wall particle flux, both of which will ultimately be used to infer the complete particle balance and particle confinement time τP.
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Affiliation(s)
- L Stephey
- University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - G A Wurden
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - O Schmitz
- University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - H Frerichs
- University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - F Effenberg
- University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - C Biedermann
- Max-Planck-Institut für Plasma Physik, Wendelsteinstrasse 1, 17491 Greifswald, Germany
| | - J Harris
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - R König
- Max-Planck-Institut für Plasma Physik, Wendelsteinstrasse 1, 17491 Greifswald, Germany
| | - P Kornejew
- Max-Planck-Institut für Plasma Physik, Wendelsteinstrasse 1, 17491 Greifswald, Germany
| | - M Krychowiak
- Max-Planck-Institut für Plasma Physik, Wendelsteinstrasse 1, 17491 Greifswald, Germany
| | - E A Unterberg
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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46
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Frerichs H, Effenberg F, Schmitz O, Biedermann C, Feng Y, Jakubowski M, König R, Krychowiak M, Lore J, Niemann H, Pedersen TS, Stephey L, Wurden GA. Synthetic plasma edge diagnostics for EMC3-EIRENE, highlighted for Wendelstein 7-X. Rev Sci Instrum 2016; 87:11D441. [PMID: 27910599 DOI: 10.1063/1.4959910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Interpretation of spectroscopic measurements in the edge region of high-temperature plasmas can be a challenge since line of sight integration effects make direct interpretation in terms of quantitative, local emission strengths often impossible. The EMC3-EIRENE code-a 3D fluid edge plasma and kinetic neutral gas transport code-is a suitable tool for full 3D reconstruction of such signals. A versatile synthetic diagnostic module has been developed recently which allows the realistic 3D setup of various plasma edge diagnostics to be captured. We highlight these capabilities with two examples for Wendelstein 7-X (W7-X): a visible camera for the analysis of recycling, and a coherent-imaging system for velocity measurements.
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Affiliation(s)
- H Frerichs
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - F Effenberg
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - O Schmitz
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - C Biedermann
- Max-Planck-Institut für Plasma Physik, 17491 Greifswald, Germany
| | - Y Feng
- Max-Planck-Institut für Plasma Physik, 17491 Greifswald, Germany
| | - M Jakubowski
- Max-Planck-Institut für Plasma Physik, 17491 Greifswald, Germany
| | - R König
- Max-Planck-Institut für Plasma Physik, 17491 Greifswald, Germany
| | - M Krychowiak
- Max-Planck-Institut für Plasma Physik, 17491 Greifswald, Germany
| | - J Lore
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - H Niemann
- Max-Planck-Institut für Plasma Physik, 17491 Greifswald, Germany
| | - T S Pedersen
- Max-Planck-Institut für Plasma Physik, 17491 Greifswald, Germany
| | - L Stephey
- HSX Plasma Laboratory, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - G A Wurden
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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47
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Jacobsen C, Leipold T, Klaus P, Höhne-Zimmer V, Braun T, Köhler V, Tenckhoff B, König R, Karberg K, Krüger K, Wendler J, Wollenhaupt J, Burmester G, Detert J. THU0075 Efficient Screening System for Early Arthritis – A Project of The T2T Initiative in Germany. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.5695] [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: 11/04/2022]
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48
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Sharma AK, Eils R, König R. Copy Number Alterations in Enzyme-Coding and Cancer-Causing Genes Reprogram Tumor Metabolism. Cancer Res 2016; 76:4058-67. [PMID: 27216182 DOI: 10.1158/0008-5472.can-15-2350] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 05/11/2016] [Indexed: 11/16/2022]
Abstract
Somatic copy number alterations frequently occur in the cancer genome affecting not only oncogenic or tumor suppressive genes, but also passenger and potential codriver genes. An intrinsic feature resulting from such genomic perturbations is the deregulation in the metabolism of tumor cells. In this study, we have shown that metabolic and cancer-causing genes are unexpectedly often proximally positioned in the chromosome and share loci with coaltered copy numbers across multiple cancers (19 cancer types from The Cancer Genome Atlas). We have developed an analysis pipeline, Identification of Metabolic Cancer Genes (iMetCG), to infer the functional impact on metabolic remodeling from such coamplifications and codeletions and delineate genes driving cancer metabolism from those that are neutral. Using our identified metabolic genes, we were able to classify tumors based on their tissue and developmental origins. These metabolic genes were similar to known cancer genes in terms of their network connectivity, isoform frequency, and evolutionary features. We further validated these identified metabolic genes by (i) using gene essentiality data from several tumor cell lines, (ii) showing that these identified metabolic genes are strong indicators for patient survival, and (iii) observing a significant overlap between our identified metabolic genes and known cancer-metabolic genes. Our analyses revealed a hitherto unknown generic mechanism for large-scale metabolic reprogramming in cancer cells based on linear gene proximities between cancer-causing and -metabolic genes. We have identified 119 new metabolic cancer genes likely to be involved in rewiring cancer cell metabolism. Cancer Res; 76(14); 4058-67. ©2016 AACR.
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Affiliation(s)
- Ashwini Kumar Sharma
- Network Modeling, Leibniz Institute for Natural Products Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany. Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany. Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Rainer König
- Network Modeling, Leibniz Institute for Natural Products Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany. Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany. Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.
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49
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Salah FS, Ebbinghaus M, Muley VY, Zhou Z, Al-Saadi KRD, Pacyna-Gengelbach M, O'Sullivan GA, Betz H, König R, Wang ZQ, Bräuer R, Petersen I. Tumor suppression in mice lacking GABARAP, an Atg8/LC3 family member implicated in autophagy, is associated with alterations in cytokine secretion and cell death. Cell Death Dis 2016; 7:e2205. [PMID: 27124579 PMCID: PMC4855672 DOI: 10.1038/cddis.2016.93] [Citation(s) in RCA: 29] [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: 08/09/2015] [Revised: 03/11/2016] [Accepted: 03/15/2016] [Indexed: 01/04/2023]
Abstract
GABARAP belongs to an evolutionary highly conserved gene family that has a fundamental role in autophagy. There is ample evidence for a crosstalk between autophagy and apoptosis as well as the immune response. However, the molecular details for these interactions are not fully characterized. Here, we report that the ablation of murine GABARAP, a member of the Atg8/LC3 family that is central to autophagosome formation, suppresses the incidence of tumor formation mediated by the carcinogen DMBA and results in an enhancement of the immune response through increased secretion of IL-1β, IL-6, IL-2 and IFN-γ from stimulated macrophages and lymphocytes. In contrast, TGF-β1 was significantly reduced in the serum of these knockout mice. Further, DMBA treatment of these GABARAP knockout mice reduced the cellularity of the spleen and the growth of mammary glands through the induction of apoptosis. Gene expression profiling of mammary glands revealed significantly elevated levels of Xaf1, an apoptotic inducer and tumor-suppressor gene, in knockout mice. Furthermore, DMBA treatment triggered the upregulation of pro-apoptotic (Bid, Apaf1, Bax), cell death (Tnfrsf10b, Ripk1) and cell cycle inhibitor (Cdkn1a, Cdkn2c) genes in the mammary glands. Finally, tumor growth of B16 melanoma cells after subcutaneous inoculation was inhibited in GABARAP-deficient mice. Together, these data provide strong evidence for the involvement of GABARAP in tumorigenesis in vivo by delaying cell death and its associated immune-related response.
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Affiliation(s)
- F S Salah
- Institute of Pathology, University Hospital - Friedrich Schiller University Jena, Ziegelmühlenweg 1, Jena D-07743, Germany.,Iraqi Centre for Cancer and Medical Genetics Research, Al-Mustansiriya University, Baghdad, Iraq
| | - M Ebbinghaus
- Institute of Physiology 1, University Hospital - Friedrich Schiller University Jena, Teichgraben 8, Jena D-07743, Germany
| | - V Y Muley
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11, Jena D-07745, Germany.,Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Erlanger Allee 101, Jena D-07747, Germany
| | - Z Zhou
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, Jena D-07745, Germany
| | - K R D Al-Saadi
- Iraqi Centre for Cancer and Medical Genetics Research, Al-Mustansiriya University, Baghdad, Iraq
| | - M Pacyna-Gengelbach
- Institute of Pathology, University Medicine Berlin, Campus Charité Mitte, Berlin D-10098, Germany
| | - G A O'Sullivan
- Department of Neurochemistry, Max-Planck Institute for Brain Research, Deutschordenstrasse 46, Frankfurt D-60528, Germany
| | - H Betz
- Department of Neurochemistry, Max-Planck Institute for Brain Research, Deutschordenstrasse 46, Frankfurt D-60528, Germany.,Max-Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg D-69120, Germany
| | - R König
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstrasse 11, Jena D-07745, Germany.,Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Erlanger Allee 101, Jena D-07747, Germany
| | - Z-Q Wang
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, Jena D-07745, Germany.,Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, Bachstrasse 18k, Jena D-07743, Germany
| | - R Bräuer
- Institute of Pathology, University Hospital - Friedrich Schiller University Jena, Ziegelmühlenweg 1, Jena D-07743, Germany
| | - I Petersen
- Institute of Pathology, University Hospital - Friedrich Schiller University Jena, Ziegelmühlenweg 1, Jena D-07743, Germany
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50
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Kordaß T, Weber CEM, Oswald M, Ast V, Bernhardt M, Novak D, Utikal J, Eichmüller SB, König R. SOX5 is involved in balanced MITF regulation in human melanoma cells. BMC Med Genomics 2016; 9:10. [PMID: 26927636 PMCID: PMC4772287 DOI: 10.1186/s12920-016-0170-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 08/07/2015] [Accepted: 02/21/2016] [Indexed: 02/07/2023] Open
Abstract
Background Melanoma is a cancer with rising incidence and new therapeutics are needed. For this, it is necessary to understand the molecular mechanisms of melanoma development and progression. Melanoma differs from other cancers by its ability to produce the pigment melanin via melanogenesis; this biosynthesis is essentially regulated by microphthalmia-associated transcription factor (MITF). MITF regulates various processes such as cell cycling and differentiation. MITF shows an ambivalent role, since high levels inhibit cell proliferation and low levels promote invasion. Hence, well-balanced MITF homeostasis is important for the progression and spread of melanoma. Therefore, it is difficult to use MITF itself for targeted therapy, but elucidating its complex regulation may lead to a promising melanoma-cell specific therapy. Method We systematically analyzed the regulation of MITF with a novel established transcription factor based gene regulatory network model. Starting from comparative transcriptomics analysis using data from cells originating from nine different tumors and a melanoma cell dataset, we predicted the transcriptional regulators of MITF employing ChIP binding information from a comprehensive set of databases. The most striking regulators were experimentally validated by functional assays and an MITF-promoter reporter assay. Finally, we analyzed the impact of the expression of the identified regulators on clinically relevant parameters of melanoma, i.e. the thickness of primary tumors and patient overall survival. Results Our model predictions identified SOX10 and SOX5 as regulators of MITF. We experimentally confirmed the role of the already well-known regulator SOX10. Additionally, we found that SOX5 knockdown led to MITF up-regulation in melanoma cells, while double knockdown with SOX10 showed a rescue effect; both effects were validated by reporter assays. Regarding clinical samples, SOX5 expression was distinctively up-regulated in metastatic compared to primary melanoma. In contrast, survival analysis of melanoma patients with predominantly metastatic disease revealed that low SOX5 levels were associated with a poor prognosis. Conclusion MITF regulation by SOX5 has been shown only in murine cells, but not yet in human melanoma cells. SOX5 has a strong inhibitory effect on MITF expression and seems to have a decisive clinical impact on melanoma during tumor progression. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0170-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Theresa Kordaß
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany. .,Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Erlanger Allee 101, D-07747, Jena, Germany.
| | - Claudia E M Weber
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany.
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Erlanger Allee 101, D-07747, Jena, Germany. .,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Beutenbergstrasse 11a, 07745, Jena, Germany.
| | - Volker Ast
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Erlanger Allee 101, D-07747, Jena, Germany. .,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Beutenbergstrasse 11a, 07745, Jena, Germany.
| | - Mathias Bernhardt
- Skin Cancer Unit, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany. .,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany.
| | - Daniel Novak
- Skin Cancer Unit, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany. .,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany.
| | - Jochen Utikal
- Skin Cancer Unit, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany. .,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany.
| | - Stefan B Eichmüller
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany.
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Erlanger Allee 101, D-07747, Jena, Germany. .,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Beutenbergstrasse 11a, 07745, Jena, Germany. .,Theoretical Bioinformatics, German Cancer Research Center, INF 580, 69121, Heidelberg, Germany.
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