1
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Roider T, Baertsch MA, Fitzgerald D, Vöhringer H, Brinkmann BJ, Czernilofsky F, Knoll M, Llaó-Cid L, Mathioudaki A, Faßbender B, Herbon M, Lautwein T, Bruch PM, Liebers N, Schürch CM, Passerini V, Seifert M, Brobeil A, Mechtersheimer G, Müller-Tidow C, Weigert O, Seiffert M, Nolan GP, Huber W, Dietrich S. Multimodal and spatially resolved profiling identifies distinct patterns of T cell infiltration in nodal B cell lymphoma entities. Nat Cell Biol 2024; 26:478-489. [PMID: 38379051 PMCID: PMC10940160 DOI: 10.1038/s41556-024-01358-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 01/15/2024] [Indexed: 02/22/2024]
Abstract
The redirection of T cells has emerged as an attractive therapeutic principle in B cell non-Hodgkin lymphoma (B-NHL). However, a detailed characterization of lymphoma-infiltrating T cells across B-NHL entities is missing. Here we present an in-depth T cell reference map of nodal B-NHL, based on cellular indexing of transcriptomes and epitopes, T cell receptor sequencing, flow cytometry and multiplexed immunofluorescence applied to 101 lymph nodes from patients with diffuse large B cell, mantle cell, follicular or marginal zone lymphoma, and from healthy controls. This multimodal resource revealed quantitative and spatial aberrations of the T cell microenvironment across and within B-NHL entities. Quantitative differences in PD1+ TCF7- cytotoxic T cells, T follicular helper cells or IKZF3+ regulatory T cells were linked to their clonal expansion. The abundance of PD1+ TCF7- cytotoxic T cells was associated with poor survival. Our study portrays lymphoma-infiltrating T cells with unprecedented comprehensiveness and provides a unique resource for the investigation of lymphoma biology and prognosis.
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Affiliation(s)
- Tobias Roider
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc A Baertsch
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Donnacha Fitzgerald
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Harald Vöhringer
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Berit J Brinkmann
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Felix Czernilofsky
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mareike Knoll
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Laura Llaó-Cid
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
- Molecular Pathology of Lymphoid Neoplasms, Fundació de Recerca Clinic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | | | - Bianca Faßbender
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Maxime Herbon
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Tobias Lautwein
- Genomics and Transcriptomics Laboratory, University of Düsseldorf, Düsseldorf, Germany
| | - Peter-Martin Bruch
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Nora Liebers
- European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
- National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Christian M Schürch
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Verena Passerini
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Marc Seifert
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Alexander Brobeil
- Department of Pathology, University of Heidelberg, Heidelberg, Germany
| | | | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Oliver Weigert
- German Cancer Research Center, Heidelberg, Germany
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research, Ludwig-Maximilians-University Hospital, Munich, Germany
- German Cancer Consortium, Munich, Germany
| | - Martina Seiffert
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wolfgang Huber
- Molecular Medicine Partnership Unit, Heidelberg, Germany.
- European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany.
- Molecular Medicine Partnership Unit, Heidelberg, Germany.
- European Molecular Biology Laboratory, Heidelberg, Germany.
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany.
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIO ABCD), Aachen Bonn Cologne Düsseldorf, Germany.
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2
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Liebers N, Bruch PM, Terzer T, Hernandez-Hernandez M, Paramasivam N, Fitzgerald D, Altmann H, Roider T, Kolb C, Knoll M, Lenze A, Platzbecker U, Röllig C, Baldus C, Serve H, Bornhäuser M, Hübschmann D, Müller-Tidow C, Stölzel F, Huber W, Benner A, Zenz T, Lu J, Dietrich S. Ex vivo drug response profiling for response and outcome prediction in hematologic malignancies: the prospective non-interventional SMARTrial. Nat Cancer 2023; 4:1648-1659. [PMID: 37783805 PMCID: PMC10733146 DOI: 10.1038/s43018-023-00645-5] [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] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/31/2023] [Indexed: 10/04/2023]
Abstract
Ex vivo drug response profiling is a powerful tool to study genotype-drug response associations and is being explored as a tool set for precision medicine in cancer. Here we conducted a prospective non-interventional trial to investigate feasibility of ex vivo drug response profiling for treatment guidance in hematologic malignancies (SMARTrial, NCT03488641 ). The primary endpoint to provide drug response profiling reports within 7 d was met in 91% of all study participants (N = 80). Secondary endpoint analysis revealed that ex vivo resistance to chemotherapeutic drugs predicted chemotherapy treatment failure in vivo. We confirmed the predictive value of ex vivo response to chemotherapy in a validation cohort of 95 individuals with acute myeloid leukemia treated with daunorubicin and cytarabine. Ex vivo drug response profiles improved ELN-22 risk stratification in individuals with adverse risk. We conclude that ex vivo drug response profiling is clinically feasible and has the potential to predict chemotherapy response in individuals with hematologic malignancies beyond clinically established genetic markers.
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Affiliation(s)
- Nora Liebers
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIO ABCD), Aachen Bonn Cologne Düsseldorf, Germany
| | - Peter-Martin Bruch
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIO ABCD), Aachen Bonn Cologne Düsseldorf, Germany
| | - Tobias Terzer
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Nagarajan Paramasivam
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Donnacha Fitzgerald
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Tobias Roider
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Carolin Kolb
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Mareike Knoll
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Angela Lenze
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | | | | | - Claudia Baldus
- Department of Internal Medicine II, University Hospital of Kiel, Kiel, Germany
| | - Hubert Serve
- Department of Internal Medicine II, University Hospital of Frankfurt Main, Frankfurt am Main, Germany
| | | | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Friedrich Stölzel
- Department of Internal Medicine II, University Hospital of Kiel, Kiel, Germany
| | - Wolfgang Huber
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, Universitätsspital & Universität Zürich, Zürich, Switzerland
- The LOOP Zürich-Medical Research Center, Zürich, Switzerland
| | - Junyan Lu
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany.
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIO ABCD), Aachen Bonn Cologne Düsseldorf, Germany.
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany.
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3
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Lima FA, Otte F, Vakili M, Ardana-Lamas F, Biednov M, Dall’Antonia F, Frankenberger P, Gawelda W, Gelisio L, Han H, Huang X, Jiang Y, Kloos M, Kluyver T, Knoll M, Kubicek K, Bermudez Macias IJ, Schulz J, Turkot O, Uemura Y, Valerio J, Wang H, Yousef H, Zalden P, Khakhulin D, Bressler C, Milne C. Experimental capabilities for liquid jet samples at sub-MHz rates at the FXE Instrument at European XFEL. J Synchrotron Radiat 2023; 30:1168-1182. [PMID: 37860937 PMCID: PMC10624029 DOI: 10.1107/s1600577523008159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
The Femtosecond X-ray Experiments (FXE) instrument at the European X-ray Free-Electron Laser (EuXFEL) provides an optimized platform for investigations of ultrafast physical, chemical and biological processes. It operates in the energy range 4.7-20 keV accommodating flexible and versatile environments for a wide range of samples using diverse ultrafast X-ray spectroscopic, scattering and diffraction techniques. FXE is particularly suitable for experiments taking advantage of the sub-MHz repetition rates provided by the EuXFEL. In this paper a dedicated setup for studies on ultrafast biological and chemical dynamics in solution phase at sub-MHz rates at FXE is presented. Particular emphasis on the different liquid jet sample delivery options and their performance is given. Our portfolio of high-speed jets compatible with sub-MHz experiments includes cylindrical jets, gas dynamic virtual nozzles and flat jets. The capability to perform multi-color X-ray emission spectroscopy (XES) experiments is illustrated by a set of measurements using the dispersive X-ray spectrometer in von Hamos geometry. Static XES data collected using a multi-crystal scanning Johann-type spectrometer are also presented. A few examples of experimental results on ultrafast time-resolved X-ray emission spectroscopy and wide-angle X-ray scattering at sub-MHz pulse repetition rates are given.
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Affiliation(s)
- F. A. Lima
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - F. Otte
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Fakultät für Physik, Technical University Dortmund, Dortmund, Germany
| | - M. Vakili
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - M. Biednov
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - W. Gawelda
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - L. Gelisio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - X. Huang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Jiang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - T. Kluyver
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Knoll
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - K. Kubicek
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
- Institut für Experimentalphysik, Universität Hamburg, 22607 Hamburg, Germany
| | | | - J. Schulz
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - O. Turkot
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Uemura
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - J. Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Wang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Yousef
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - P. Zalden
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - D. Khakhulin
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - C. Bressler
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
- Institut für Experimentalphysik, Universität Hamburg, 22607 Hamburg, Germany
| | - C. Milne
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
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4
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Herbst SA, Kim V, Roider T, Schitter EC, Bruch PM, Liebers N, Kolb C, Knoll M, Lu J, Dreger P, Müller-Tidow C, Zenz T, Huber W, Dietrich S. Comparing the value of mono- vs coculture for high-throughput compound screening in hematological malignancies. Blood Adv 2023; 7:5925-5936. [PMID: 37352275 PMCID: PMC10558604 DOI: 10.1182/bloodadvances.2022009652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/19/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023] Open
Abstract
Large-scale compound screens are a powerful model system for understanding variability of treatment response and discovering druggable tumor vulnerabilities of hematological malignancies. However, as mostly performed in a monoculture of tumor cells, these assays disregard modulatory effects of the in vivo microenvironment. It is an open question whether and to what extent coculture with bone marrow stromal cells could improve the biological relevance of drug testing assays over monoculture. Here, we established a high-throughput platform to measure ex vivo sensitivity of 108 primary blood cancer samples to 50 drugs in monoculture and coculture with bone marrow stromal cells. Stromal coculture conferred resistance to 52% of compounds in chronic lymphocytic leukemia (CLL) and 36% of compounds in acute myeloid leukemia (AML), including chemotherapeutics, B-cell receptor inhibitors, proteasome inhibitors, and Bromodomain and extraterminal domain inhibitors. Only the JAK inhibitors ruxolitinib and tofacitinib exhibited increased efficacy in AML and CLL stromal coculture. We further confirmed the importance of JAK-STAT signaling for stroma-mediated resistance by showing that stromal cells induce phosphorylation of STAT3 in CLL cells. We genetically characterized the 108 cancer samples and found that drug-gene associations strongly correlated between monoculture and coculture. However, effect sizes were lower in coculture, with more drug-gene associations detected in monoculture than in coculture. Our results justify a 2-step strategy for drug perturbation testing, with large-scale screening performed in monoculture, followed by focused evaluation of potential stroma-mediated resistances in coculture.
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Affiliation(s)
- Sophie A. Herbst
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Vladislav Kim
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Tobias Roider
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Eva C. Schitter
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter-Martin Bruch
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Nora Liebers
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolin Kolb
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Mareike Knoll
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Junyan Lu
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Peter Dreger
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, University Hospital Zürich, Zürich, Switzerland
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
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5
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Roder AE, Johnson KEE, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Chung M, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lässig M, Luksza M, Das S, Gresham D, Ghedin E. Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data. mBio 2023; 14:e0104623. [PMID: 37389439 PMCID: PMC10470513 DOI: 10.1128/mbio.01046-23] [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: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 07/01/2023] Open
Abstract
High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant-calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller and use of replicate sequencing have the most significant impact on single-nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false-negative rates. When replicates are not available, using a combination of multiple callers with more stringent cutoffs is recommended. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intra-host viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intra-host variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host cell, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus nor strongly beneficial can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in the inclusion of false-positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant-calling tools. We used simulated and synthetic data to test their performance against a true set of variants and then used these studies to inform variant identification in data from SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.
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Affiliation(s)
- A. E. Roder
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - K. E. E. Johnson
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - M. Knoll
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - M. Khalfan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - B. Wang
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - S. Schultz-Cherry
- Department of Infectious Diseases, St Jude Children Research Hospital, Memphis, Tennessee, USA
| | - S. Banakis
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - A. Kreitman
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - C. Mederos
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - J.-H. Youn
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - R. Mercado
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - W. Wang
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - M. Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - D. Ruchnewitz
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - M. I. Samanovic
- Department of Medicine, New York University Langone Vaccine Center, New York, New York, USA
| | - M. J. Mulligan
- Department of Medicine, New York University Langone Vaccine Center, New York, New York, USA
| | - M. Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - M. Luksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - S. Das
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - D. Gresham
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - E. Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
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6
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Janssen M, Schmidt C, Bruch PM, Blank MF, Rohde C, Waclawiczek A, Heid D, Renders S, Göllner S, Vierbaum L, Besenbeck B, Herbst SA, Knoll M, Kolb C, Przybylla A, Weidenauer K, Ludwig AK, Fabre M, Gu M, Schlenk RF, Stölzel F, Bornhäuser M, Röllig C, Platzbecker U, Baldus C, Serve H, Sauer T, Raffel S, Pabst C, Vassiliou G, Vick B, Jeremias I, Trumpp A, Krijgsveld J, Müller-Tidow C, Dietrich S. Venetoclax synergizes with gilteritinib in FLT3 wild-type high-risk acute myeloid leukemia by suppressing MCL-1. Blood 2022; 140:2594-2610. [PMID: 35857899 DOI: 10.1182/blood.2021014241] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 11/20/2022] Open
Abstract
BCL-2 inhibition has been shown to be effective in acute myeloid leukemia (AML) in combination with hypomethylating agents or low-dose cytarabine. However, resistance and relapse represent major clinical challenges. Therefore, there is an unmet need to overcome resistance to current venetoclax-based strategies. We performed high-throughput drug screening to identify effective combination partners for venetoclax in AML. Overall, 64 antileukemic drugs were screened in 31 primary high-risk AML samples with or without venetoclax. Gilteritinib exhibited the highest synergy with venetoclax in FLT3 wild-type AML. The combination of gilteritinib and venetoclax increased apoptosis, reduced viability, and was active in venetoclax-azacitidine-resistant cell lines and primary patient samples. Proteomics revealed increased FLT3 wild-type signaling in specimens with low in vitro response to the currently used venetoclax-azacitidine combination. Mechanistically, venetoclax with gilteritinib decreased phosphorylation of ERK and GSK3B via combined AXL and FLT3 inhibition with subsequent suppression of the antiapoptotic protein MCL-1. MCL-1 downregulation was associated with increased MCL-1 phosphorylation of serine 159, decreased phosphorylation of threonine 161, and proteasomal degradation. Gilteritinib and venetoclax were active in an FLT3 wild-type AML patient-derived xenograft model with TP53 mutation and reduced leukemic burden in 4 patients with FLT3 wild-type AML receiving venetoclax-gilteritinib off label after developing refractory disease under venetoclax-azacitidine. In summary, our results suggest that combined inhibition of FLT3/AXL potentiates venetoclax response in FLT3 wild-type AML by inducing MCL-1 degradation. Therefore, the venetoclax-gilteritinib combination merits testing as a potentially active regimen in patients with high-risk FLT3 wild-type AML.
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Affiliation(s)
- Maike Janssen
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christina Schmidt
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter-Martin Bruch
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maximilian F Blank
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Christian Rohde
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alexander Waclawiczek
- Division of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Daniel Heid
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Simon Renders
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Stefanie Göllner
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Lisa Vierbaum
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Birgit Besenbeck
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Sophie A Herbst
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mareike Knoll
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Carolin Kolb
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Adriana Przybylla
- Division of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Katharina Weidenauer
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Anne Kathrin Ludwig
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Margarete Fabre
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Hematology, University of Cambridge, Cambridge, United Kingdom
| | - Muxin Gu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Hematology, University of Cambridge, Cambridge, United Kingdom
| | - Richard F Schlenk
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Friedrich Stölzel
- Department of Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Martin Bornhäuser
- Department of Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Christoph Röllig
- Department of Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Uwe Platzbecker
- Medical Clinic and Policlinic I, Hematology and Cellular Therapy, Leipzig University Hospital, Leipzig, Germany
| | - Claudia Baldus
- Department of Hematology and Oncology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Hubert Serve
- Hematology-Oncology, Department of Medicine II, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Tim Sauer
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Simon Raffel
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Caroline Pabst
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - George Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Hematology, University of Cambridge, Cambridge, United Kingdom
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Cancer Consortium, Partner Site Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Cancer Consortium, Partner Site Munich, Munich, Germany
- Department of Pediatrics, University Hospital, Ludwig Maximilian University, Munich, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany
- Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
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7
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Salome P, Walz D, Sforazzini F, Kudak A, Dostal M, Regnery S, Schlamp K, Thomas M, Herth F, Jäkel O, Heußel C, Hoerner-Rieber J, Debus J, Knoll M, Abdollahi A. Multi-Omics Classifier of Tumor Recurrence vs. Radiation-Induced Lung Fibrosis in NSCLC Patients Treated with SBRT. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1542] [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: 11/30/2022]
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8
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Herbst SA, Vesterlund M, Helmboldt AJ, Jafari R, Siavelis I, Stahl M, Schitter EC, Liebers N, Brinkmann BJ, Czernilofsky F, Roider T, Bruch PM, Iskar M, Kittai A, Huang Y, Lu J, Richter S, Mermelekas G, Umer HM, Knoll M, Kolb C, Lenze A, Cao X, Österholm C, Wahnschaffe L, Herling C, Scheinost S, Ganzinger M, Mansouri L, Kriegsmann K, Kriegsmann M, Anders S, Zapatka M, Del Poeta G, Zucchetto A, Bomben R, Gattei V, Dreger P, Woyach J, Herling M, Müller-Tidow C, Rosenquist R, Stilgenbauer S, Zenz T, Huber W, Tausch E, Lehtiö J, Dietrich S. Proteogenomics refines the molecular classification of chronic lymphocytic leukemia. Nat Commun 2022; 13:6226. [PMID: 36266272 PMCID: PMC9584885 DOI: 10.1038/s41467-022-33385-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/14/2022] [Indexed: 12/24/2022] Open
Abstract
Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic-based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterize the proteome and transcriptome alongside genetic and ex-vivo drug response profiling in a clinically annotated CLL discovery cohort (n = 68). Unsupervised clustering of the proteome data reveals six subgroups. Five of these proteomic groups are associated with genetic features, while one group is only detectable at the proteome level. This new group is characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). Classifiers developed to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n = 165, n = 169) confirm that ASB-CLL comprises about 20% of CLL patients. The inferior overall survival in ASB-CLL is also independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling.
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Affiliation(s)
- Sophie A. Herbst
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Mattias Vesterlund
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Alexander J. Helmboldt
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Rozbeh Jafari
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Ioannis Siavelis
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Matthias Stahl
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Eva C. Schitter
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Nora Liebers
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Berit J. Brinkmann
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Czernilofsky
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Tobias Roider
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Peter-Martin Bruch
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Murat Iskar
- grid.7497.d0000 0004 0492 0584Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Adam Kittai
- grid.261331.40000 0001 2285 7943Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH USA
| | - Ying Huang
- grid.261331.40000 0001 2285 7943Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH USA
| | - Junyan Lu
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Sarah Richter
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Georgios Mermelekas
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Husen Muhammad Umer
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Mareike Knoll
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Carolin Kolb
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Angela Lenze
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Xiaofang Cao
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Cecilia Österholm
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Linus Wahnschaffe
- grid.6190.e0000 0000 8580 3777Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Carmen Herling
- grid.6190.e0000 0000 8580 3777Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Sebastian Scheinost
- grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Ganzinger
- grid.7700.00000 0001 2190 4373Institute of Medical Biometry and Informatics, Heidelberg University, Heidelberg, Germany
| | - Larry Mansouri
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Katharina Kriegsmann
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Mark Kriegsmann
- grid.7700.00000 0001 2190 4373Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Simon Anders
- grid.7700.00000 0001 2190 4373Center for Molecular Biology of the University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Marc Zapatka
- grid.7497.d0000 0004 0492 0584Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Giovanni Del Poeta
- grid.6530.00000 0001 2300 0941Division of Hematology, University of Tor Vergata, Rome, Italy
| | - Antonella Zucchetto
- grid.418321.d0000 0004 1757 9741Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Riccardo Bomben
- grid.418321.d0000 0004 1757 9741Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Valter Gattei
- grid.418321.d0000 0004 1757 9741Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Peter Dreger
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Jennifer Woyach
- grid.261331.40000 0001 2285 7943Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH USA
| | - Marco Herling
- grid.6190.e0000 0000 8580 3777Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD), Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Carsten Müller-Tidow
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Richard Rosenquist
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Stephan Stilgenbauer
- grid.6582.90000 0004 1936 9748Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Thorsten Zenz
- grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.412004.30000 0004 0478 9977Department of Medical Oncology and Hematology, University Hospital Zürich, Zürich, Switzerland
| | - Wolfgang Huber
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Eugen Tausch
- grid.6582.90000 0004 1936 9748Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Janne Lehtiö
- grid.452834.c0000 0004 5911 2402Department of Oncology-Pathology, Karolinska Institute and Science for Life Laboratory, Stockholm, Sweden
| | - Sascha Dietrich
- grid.7700.00000 0001 2190 4373Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory (EMBL), Heidelberg, Germany ,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany ,grid.461742.20000 0000 8855 0365Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.14778.3d0000 0000 8922 7789Department of Hematolgy, Oncology and Immunolgy, University Hospital of Düsseldorf, Düsseldorf, Germany
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9
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Vinci D, Jiang Y, Schubert R, Zalden P, Khakhulin D, Frankenberger P, Alves Lima F, Ardana-Lamas F, Deiter C, Biednov M, Huang X, Knoll M, Jimenez D, Otte F, Paul Dutta S, Wang H, Yousef H, Milne C. Ultrafast X-ray diffraction and scattering on the femtosecond X-ray experiment (FXE) instrument at the European XFEL: present status and future perspectives. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322090039] [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: 03/19/2023]
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10
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Roder AE, Johnson KEE, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lassig M, Łuksza M, Das S, Gresham D, Ghedin E. Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data. bioRxiv 2022:2021.05.05.442873. [PMID: 36656775 PMCID: PMC9836620 DOI: 10.1101/2021.05.05.442873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller, and use of replicate sequencing have the most significant impact on single nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false negative rates. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intrahost viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intrahost variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus, nor strongly beneficial, can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in inclusion of false positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant calling tools. We used simulated and synthetic data to test their performance against a true set of variants, and then used these studies to inform variant identification in data from clinical SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.
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11
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Herbst SA, Stolarczyk M, Becirovic T, Czernilofsky F, Liu Y, Kolb C, Knoll M, Herling M, Müller-Tidow C, Dietrich S. Phagocytosis by stroma confounds coculture studies. iScience 2021; 24:103062. [PMID: 34585113 PMCID: PMC8456054 DOI: 10.1016/j.isci.2021.103062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/20/2021] [Accepted: 08/26/2021] [Indexed: 01/23/2023] Open
Abstract
Signals provided by the microenvironment can modify and circumvent pathway activities that are therapeutically targeted by drugs. Bone marrow stromal cell coculture models are frequently used to study the influence of the bone marrow niche on ex vivo drug response. Here, we show that mesenchymal stromal cells from selected donors and NKTert, a stromal cell line, which is commonly used for coculture studies with primary leukemia cells, extensively phagocytose apoptotic cells. This could lead to misinterpretation of results, especially if viability readouts of the target cells (e.g. leukemic cells) in such coculture models are based on the relative proportions of dead and alive cells. Future coculture studies which aim to investigate the impact of bone marrow stromal cells on drug response should take into account that stromal cells have the capacity to phagocytose apoptotic cells. Some bone marrow stroma cells extensively phagocytose apoptotic cells Disappearance of dead cells from cocultures due to phagocytosis confounds results This needs to be considered in studies using relative viabilities in cocultures Bone marrow stroma cell line NKTert could also phagocytose glass spheres
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Affiliation(s)
- Sophie A. Herbst
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Marta Stolarczyk
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Tina Becirovic
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Felix Czernilofsky
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Yi Liu
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Carolin Kolb
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Mareike Knoll
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Marco Herling
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD), University of Cologne, Cologne, Germany
- Clinic of Hematology, Cellular Therapy and Hemostaseology, University of Leipzig, Leipzig, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Corresponding author
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Knoll M, Gerhardter H, Tomazic P, Hochenauer C. Investigations of lateral particle distribution for spherical and highly non-spherical particles by means of steady-state/transient RANS and LES simulations. POWDER TECHNOL 2021. [DOI: 10.1016/j.powtec.2020.10.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Knoll M, Balermpas P, von der Grün J, Tawk B, Adeberg S, Tinhofer I, Budach V, Linge A, Krause M, Stuschke M, Grosu A, Zips D, Combs S, Belka C, Kriegsmann M, Weichert W, Baumann M, Roedel C, Debus J, Abdollahi A. Superior Prognostic Performance of an Immunohistochemistry Trained DNA-Methylation Based PD-L1 Score in Patients with HNSCC Treated with Radiochemotherapy: A Multicenter Study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG). Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Klein C, Schlegel J, Knoll M, Dokic I, Moustafa M, Mairani A, Brons S, Zimmermann A, Zenke F, Blaukat A, Debus J, Abdollahi A. Trimodal Therapy Consisting of DNA-PK Inhibition, PD-L1 Immune Checkpoint Blockade and Radiotherapy with Carbon Ions. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.916] [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: 11/17/2022]
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Furkel J, Hasheminasab S, Moustafa M, Kriegsmann K, Schlegel J, Zhou C, Kriegsmann M, Debus J, Knoll M, Abdollahi A. Single Cell Transcriptomics Based Deconvolution Of Radiation Induced Lung Fibrosis (RILF) Model. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sforazzini F, Salome P, Kudak A, Ulrich M, Bougatf N, Debus J, Knoll M, Abdollahi A. pyCuRT: An Automated Data Curation Workflow for Radiotherapy Big Data Analysis using Pythons’ NyPipe. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.221] [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: 11/26/2022]
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Breitegger P, Schweighofer B, Wegleiter H, Knoll M, Lang B, Bergmann A. Towards low-cost QEPAS sensors for nitrogen dioxide detection. Photoacoustics 2020; 18:100169. [PMID: 32309133 PMCID: PMC7155225 DOI: 10.1016/j.pacs.2020.100169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 01/07/2020] [Accepted: 01/14/2020] [Indexed: 05/09/2023]
Abstract
Increasing awareness of the adverse health effects of air pollution leads to a demand of low-cost sensors for the measurement of pollutants such as NO2. However, commercially available low-cost sensors lack accuracy and long-term stability, and suffer from cross-sensitivity to other gases. These drawbacks can be overcome by the method of quartz-enhanced photoacoustic spectroscopy (QEPAS). In QEPAS modulated light is absorbed by the NO2 molecules, which results in the production of a sound wave. The sound wave is detected by resonance of a quartz tuning fork, which results in a measurable electric signal. Due to the small size of the tuning forks, the gas sensing element can be smaller than 1 cm3. We present the first bare fork QEPAS setup for the ppb-level detection of NO2, which is ideally suited for environmental trace gas detection without the need of using micro-resonators. Micro-resonators are commonly used to amplify photoacoustic signals. However, micro-resonators have different dependencies on environmental conditions than tuning forks, which makes them difficult to operate in changing conditions. In contrast, our bare fork QEPAS setup is more robust and easily adopted by the use of a low-cost temperature and humidity sensor. By using acoustic filters the integration time could be increased to offer higher sensitivity at a continuous flow rate of 200 std cm3 min-1. The 1σ noise equivalent concentration is determined to 21 ppb NO2 in synthetic air for 120 s measurement time, allowing detection which satisfies international health and safety standards thresholds.
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Affiliation(s)
- P Breitegger
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
| | - B Schweighofer
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
| | - H Wegleiter
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
| | - M Knoll
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
| | - B Lang
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
| | - A Bergmann
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
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Knoll M, Gerhardter H, Prieler R, Mühlböck M, Tomazic P, Hochenauer C. Particle classification and drag coefficients of irregularly-shaped combustion residues with various size and shape. POWDER TECHNOL 2019. [DOI: 10.1016/j.powtec.2019.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gerhardter H, Prieler R, Schluckner C, Knoll M, Hochenauer C, Mühlböck M, Tomazic P, Schroettner H. Modelling convective heat transfer to non-spherical particles. POWDER TECHNOL 2019. [DOI: 10.1016/j.powtec.2018.11.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Gerhardter H, Prieler R, Mayr B, Knoll M, Mühlböck M, Tomazic P, Hochenauer C. Evaluation of drag models for particles and powders with non-uniform size and shape. POWDER TECHNOL 2018. [DOI: 10.1016/j.powtec.2018.02.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nowrouzi A, Sertorio M, Akbarpour M, Kuhar M, Golestaneh AF, Schwager C, Perentesis J, Zheng Y, Debus J, Wells S, Wells J, Abdollahi A, Knoll M. Radiobiological Effects of Photon, Proton and Carbon Ion Irradiation on Human Pluripotent-Stem-Cell-Derived Gastrointestinal Organoids. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.2075] [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: 11/30/2022]
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Li Y, Abeghyan S, Berndgen K, Baha-Shanjani M, Deron G, Englisch U, Karabekyan S, Ketenoglu B, Knoll M, Wolff-Fabris F, Viehweger M, Yakopov M, Pflueger J. Magnetic Measurement Techniques for the Large-Scale Production of Undulator Segments for the European XFEL. ACTA ACUST UNITED AC 2015. [DOI: 10.1080/08940886.2015.1037679] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Potter B, Lob M, Mercaldo R, Hetzler A, Kaistha V, Khan H, Kingston N, Knoll M, Maloy‐Franklin B, Melvin K, Ruiz‐Pelet P, Ozsoy N, Schmitt E, Wheeler L, Potter M, Rutter M, Yahn G, Parente D. A long‐term study examining the antibacterial effectiveness of Agion silver zeolite technology on door handles within a college campus. Lett Appl Microbiol 2014; 60:120-127. [DOI: 10.1111/lam.12356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/02/2014] [Accepted: 10/24/2014] [Indexed: 01/07/2023]
Affiliation(s)
- B.A. Potter
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - M. Lob
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - R. Mercaldo
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - A. Hetzler
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - V. Kaistha
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - H. Khan
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - N. Kingston
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - M. Knoll
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - B. Maloy‐Franklin
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - K. Melvin
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - P. Ruiz‐Pelet
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - N. Ozsoy
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - E. Schmitt
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - L. Wheeler
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | | | - M.A. Rutter
- Department of Mathematics Penn State Erie The Behrend College Erie PA USA
| | - G. Yahn
- Advanced Finishing USA Fairview PA USA
| | - D.H. Parente
- Sam and Irene Black School of Business Penn State Erie The Behrend College Erie PA USA
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Knoll M, Pei X, Zelefsky M. Long-Term Urinary and Rectal Tolerance in Prostate Cancer Survivors Treated With Definitive Conformal Radiation Therapy. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.2092] [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: 10/24/2022]
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Dumane V, Hunt M, Steinberger E, Knoll M, Green S, Bakst R. SU-E-T-342: Use of Patient Geometry Measurements to Predict Dosimetric Gain with VMAT Over 3D for Chestwall and Regional Nodal Radiation. Med Phys 2014. [DOI: 10.1118/1.4888675] [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: 11/07/2022] Open
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Dumane V, Knoll M, Green S, Bakst R. Comparison of VMAT, Partially Wide Tangents, and Photon/Electrons for Treatment of Reconstructed Chest Wall, Supraclavicular, Axillary, and Internal Mammary Nodes. Int J Radiat Oncol Biol Phys 2013. [DOI: 10.1016/j.ijrobp.2013.06.2017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Philippi M, Altenhöner T, Köhler M, Schmidt J, Roth S, Knoll M. Wahrgenommene soziale Unterstützung und subjektive Gesundheit von Krankenhauspatienten. Gesundheitswesen 2013. [DOI: 10.1055/s-0033-1354045] [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: 10/26/2022]
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Soller L, Knoll M, Ben-Shoshan M, Harrington DW, Fragapane J, Joseph L, St Pierre Y, St Pierre Y, La Vieille S, Wilson K, Elliott SJ, Clarke AE. The prevalence of food allergy among Aboriginal people in Canada. Clin Transl Allergy 2013. [PMCID: PMC3723655 DOI: 10.1186/2045-7022-3-s3-p77] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Klenske J, Knoll M, Kornovski Y. [Global ablation of endometrium as a new uterus sparing operative method in uterine dysfunctional bleeding]. Akush Ginekol (Sofiia) 2012; 51:17-20. [PMID: 23610912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A new method of endometrial ablation has been presented. This is the method of bipolar tridimensional device "NOVA SURE". This innovative method enables to destruct the basal and functional layer of the uterus and thus leads to amenorrhea and hypomenorrhea.
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Zurawski V, Driscoll A, Deluca A, Knoll M, Murdoch D, O’Connor O, Dupont-Rouzeyrol M, Missotte I, Moïsi J, Besson-Leaud L, Chevalier C, Debarnot V, Levine O, Mermond S. Lower respiratory infections (LRIs) etiologies in hospitalized children in New Caledonia: a PERCH pilot study. BMC Proc 2011. [DOI: 10.1186/1753-6561-5-s1-p108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Therre P, Riemer-Hommel P, Knoll M. [School meals at secondary schools: an analysis in the district of St. Wendel in the Province Saarland, Germany]. Gesundheitswesen 2011; 74:467-75. [PMID: 21796587 DOI: 10.1055/s-0031-1280848] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
INTRODUCTION This study focuses on the nutrition of young people in schools. The Saarland state government mandates the implementation of the "quality standards for school meals", developed by the Germany Society of Nutrition (Deutschen Gesellschaft für Ernährung, DGE) in schools offering school meals. This research evaluates the state of implementation. METHODS 4-week menu plans were evaluated using a stratified random sample of selected schools (n25%-sample=5, ntotal=23). In addition, all catering services of the district (ncaterer=5) were interviewed by written survey focused on any information on the company, the type of food, the menu design as well as general information. RESULTS None of the analysed menu plans met the DGE standard. The analysis of the menu plans allows for an assessment of the nutritional quality of food. Interviews with caterers provide background information on menu design. DISCUSSION The analysis of a randomised 25%-sample shows that the target specifications of the DGE are only implemented by a small number of schools in the exemplary selected district of St. Wendel, Germany. As the German Child and Youth Health Survey (KiGGS), also this evaluation shows that the quality of school meals deviates significantly from the recommendations of the DGE. There is a clear need for action.
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Affiliation(s)
- P Therre
- HTW des Saarlandes, Fakultät für Sozialwissenschaften, Dept. Gesundheit und Pflege, Saarbrücken
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Zurawski V, Driscoll A, Deluca A, Knoll M, Murdoch D, O’Connor O, Dupont-Rouzeyrol M, Missotte I, Moïsi J, Besson-Leaud L, Chevalier C, Debarnot V, Levine O, Mermond S. Lower respiratory infections (LRIs) etiologies in hospitalized children in New Caledonia: a PERCH pilot study. BMC Proc 2011. [PMCID: PMC3019423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- V Zurawski
- Pasteur Institute of New Caledonia, Noumea, New Caledonia
| | - A Driscoll
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - A Deluca
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - M Knoll
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - D Murdoch
- Department of Microbiology, Canterbury Health Laboratories, Christchurch, New Zealand
| | - O O’Connor
- Pasteur Institute of New Caledonia, Noumea, New Caledonia
| | | | - I Missotte
- Paediatric Ward, Territorial Hospital Center of Magenta, Noumea, New Caledonia
| | - J Moïsi
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - L Besson-Leaud
- Paediatric Ward, Territorial Hospital Center of Magenta, Noumea, New Caledonia
| | - C Chevalier
- Paediatric Emergency Unit, Territorial Hospital Center of Magenta, Noumea, New Caledonia
| | - V Debarnot
- Paediatric Emergency Unit, Territorial Hospital Center of Magenta, Noumea, New Caledonia
| | - O Levine
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - S Mermond
- Pasteur Institute of New Caledonia, Noumea, New Caledonia
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Vering T, Adam S, Berns T, Schäfer R, Schwartenbeck G, Steinkuhl R, Tombach B, Knoll M. Erprobung von VISY-1 im Realtest: Probenahme und Glucosebestimmung. BIOMED ENG-BIOMED TE 2009. [DOI: 10.1515/bmte.1998.43.s1.562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Gocke D, Kolter G, Gauchenova E, Knoll M, Berthold Sjöberg C, Schneider G, Pleiss J, Müller M, Pohl M. Rationales Enzymdesign für die (S)-selektive Benzoinkondensation. CHEM-ING-TECH 2009. [DOI: 10.1002/cite.200950205] [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: 11/05/2022]
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Okpara-Hofmann J, Knoll M, Dürr M, Schmitt B, Borneff-Lipp M. Comparison of low-temperature hydrogen peroxide gas plasma sterilization for endoscopes using various Sterrad models. J Hosp Infect 2005; 59:280-5. [PMID: 15749314 DOI: 10.1016/j.jhin.2004.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2002] [Accepted: 09/09/2004] [Indexed: 11/26/2022]
Abstract
This study compared the effectiveness of sterilizing four types of endoscope using different models of the Sterrad system (Sterrad 50, 100, 100S and 200). Sterilization levels meeting international requirements were attained in all cases with carriers inoculated with Geobacillus stearothermophilus spores. The endoscopes were tested in half cycles ('overkill'). This is the first study to compare the Sterrad models marketed to date in terms of effective sterilization of endoscopes with narrow lumens.
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Affiliation(s)
- J Okpara-Hofmann
- Institute of Hygiene, Medical Faculty, Martin-Luther-University Halle-Wittenberg, Johann-Andreas-Segner-Str. 12, D-06097 Halle/Saale, Germany.
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Pool-Zobel BL, Dornacher I, Lambertz R, Knoll M, Seitz HK. Genetic damage and repair in human rectal cells for biomonitoring: sex differences, effects of alcohol exposure, and susceptibilities in comparison to peripheral blood lymphocytes. Mutat Res 2004; 551:127-34. [PMID: 15225587 DOI: 10.1016/j.mrfmmm.2004.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Revised: 03/16/2004] [Accepted: 03/23/2004] [Indexed: 10/26/2022]
Abstract
INTRODUCTION Cells other than lymphocytes may be preferable as surrogate biomarkers during exposure monitoring. In nutritional toxicology, cells from colorectal tissues are particularly relevant for studying associations between food and cancer. Thus, we have previously shown that colonic cells of males have higher levels of DNA damage than females, which (among other factors) could be due to a higher consumption of alcoholic beverages by males. To test this hypothesis, we have performed a first exploratory study to compare DNA damage in rectal cells from biopsies of male patients with alcohol abuse and of male and female controls. Peripheral blood lymphocytes were additionally monitored to assess systemic exposure loads. METHODS Cells were isolated and subjected to microgelelectrophoresis +/- endonuclease III to measure DNA breaks and oxidized pyrimidine bases ("comet-assay"). Cell aliquots were treated with H(2)O(2) for 5min in suspension culture and processed immediately or after 60min to determine induced damage and its persistence. RESULTS Pooled data from subjects of all groups revealed that oxidative DNA damage in rectal cells directly correlated to damage in lymphocytes. Female controls had lower levels of DNA damage than male controls, confirming the previous studies. An unexpected result was that male alcohol abusers had significantly less genetic damage than male controls. Also, repair was detected in lymphocytes of male alcohol abusers and female controls, but not in male controls. CONCLUSION This is the first time the comet-assay has been used to detect genotoxicity in human rectal cells as a biomonitoring tool. Our pilot study confirms earlier reports on sex differences and indicates a good correlation between damage in rectal cells and damage in lymphocytes and implies that alcohol exposure enhances endogenous defence.
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Affiliation(s)
- B L Pool-Zobel
- Department of Nutritional Toxicology, Director of the Institute for Nutrition, Friedrich-Schiller-University of Jena, Dornburger Str. 25, 07743 Jena, Germany.
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Gorschlüter A, Mak LH, Sundermeier C, Ross B, Knoll M. Electro-magnetic base technology for estremely sensitive immunosensors and DNA-chips. BIOMED ENG-BIOMED TE 2003; 47 Suppl 1 Pt 1:213-6. [PMID: 12451820 DOI: 10.1515/bmte.2002.47.s1a.213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We report on the development of an innovative electro-magnetic base technology for estremely sensitive sensors allowing the electrical detection of biological analytes like antigenes or DNA as well as a simple multiple detection of binding forces occurring at specific bonds between proteins. The technology is based on the strong impact of specifically captured magnetic microbeads on an electrical current generated in a fluid by a small sensor chip with an array of activated microelectrodes. The new technological principle with the on-chip detection of analytes will be suitable for large scale applications due to its mass production compatible technologies and allow an alternative way to monitor relevant substances without the consumption of critical additional solutions and reagents.
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Affiliation(s)
- A Gorschlüter
- Institut für Chemo- und Biosensorik (ICB) e.V., D-48149 Münster, Deutschland.
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Perdomo J, Hinkers H, Sundermeier C, Seifert W, Martínez Morell O, Knoll M. Miniaturized real-time monitoring system for L-lactate and glucose using microfabricated multi-enzyme sensors. Biosens Bioelectron 2001; 15:515-22. [PMID: 11419648 DOI: 10.1016/s0956-5663(00)00087-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A miniaturized on-line monitoring system for the detection of L-lactate and glucose is presented. The system is based on a microfabricated multi-enzyme silicon sensor chip with flow channels integrated on the chip. The sensors were fabricated in containment technology. They were characterized in test solutions. The cross-talking behaviour was investigated and was found to be practically negligible. The linear measurement ranges of both glucose and lactate sensors were large enough for most practical applications. As a result of the miniaturization the analyte consumption could be reduced to a few nmol min(-1). The system was equipped with a microdialysis probe whose recovery was 45% for lactate and 37% for glucose in test solutions using a flow rate of 3 microl min(-1). Lower flow rates of 0.5 microl min(-1) resulted in recoveries of over 90%. The long-term stability of the system was acceptable. Initial measurements have also been performed in vitro using human blood serum.
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Affiliation(s)
- J Perdomo
- Centro de Investigaciones en Microelectrónica, Instituto Superior Politécnico Jose A. Echererria, Havana, Cuba
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40
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Riedl CR, Stephen RL, Daha LK, Knoll M, Plas E, Pflüger H. Electromotive administration of intravesical bethanechol and the clinical impact on acontractile detrusor management: introduction of a new test. J Urol 2000; 164:2108-11. [PMID: 11061937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
PURPOSE It is often difficult to determine the functional status of the detrusor muscle in patients with detrusor areflexia. We performed a clinical study to establish a test defining residual detrusor capacity in such patients. MATERIALS AND METHODS In phase 1, 5 controls with detrusor areflexia were tested with an intravesical instillation of 20 mg. bethanechol in 150 cc of sodium chloride 0.3% with and without 20 mA. of pulsed current applied via an electrode catheter through the saline. Cystometry simultaneously recorded intravesical pressure changes. In phase 2, 45 patients with detrusor areflexia were tested with electromotive administration of intravesical bethanechol. In phase 3, 25 mg. bethanechol given orally once daily were prescribed for 15 patients and voiding control was assessed after 6 weeks of therapy. RESULTS Neither bethanechol without current nor current through saline only led to increased intravesical pressure. However, we noted a mean pressure increase of 34 cm. water during the electromotive administration of bethanechol in 24 of 26 patients with areflexia and neurological disease compared to only 3 cm. water in 3 of 11 with a history of chronic bladder dilatation. Oral bethanechol restored spontaneous voiding in 9 of 11 patients who had had a positive response to the electromotive administration of bethanechol, whereas all 4 without a pressure increase during the electromotive administration of bethanechol did not void spontaneously. CONCLUSIONS Electromotive administration of intravesical bethanechol identifies patients with an atonic bladder and adequate residual detrusor muscle function who are candidates for restorative measures, such as oral bethanechol and intravesical electrostimulation. Those who do not respond to the electromotive administration of bethanechol do not benefit from oral bethanechol and are candidates for catheterization.
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Affiliation(s)
- C R Riedl
- Department of Urology, Municipal Hospital Lainz, Vienna, Austria
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Abstract
A potentiometric disposable enzyme sensor for the direct and fast determination of organophosphorus (OP) insecticides was developed by using an organophosphorus hydrolase (OPH) immobilized on an ion-selective electrode. The disposable screen-printed transducer was based on double matrix membrane technology which allows easy mass production. The potentiometric device consisted of a H(+)-sensitive electrode with integrated Ag/AgCl reference electrode. The electrodes were prepared with N,N-dioctadecylmethylamine as H(+)-sensitive ionophore and pH calibration resulted in slopes of 55 mV decade-1 over a pH range from 11 to 6. OPH was isolated from recombinant Escherichia coli DH5 alpha and immobilized within poly(carbamoyl sulfonate) prepolymer on the surface of the H(+)-sensitive electrode without any further fixation membrane. OPH catalyzes the hydrolytic cleavage of OP compounds which releases protons in a concentration proportional to hydrolyzed substrate. Sensor performance was investigated with regard to enzyme load, concentration, pH and temperature of the measuring buffer using paraoxon as analyte. Best sensitivity and response time were obtained with sensors prepared with 250 U of OPH and measuring at 37 degrees C in 1.0 mM HEPES buffer, pH 9.3, containing 100 mM NaCl. The enzyme sensor exhibited a linear calibration range of 0.01-0.15 mM chlorpyrifos, 0.05-0.35 mM diazinon, 0.05-0.4 mM paraoxon and 0.007-0.05 mM parathion, respectively. For all these analytes response times to reach 95% of maximum change in potential did not exceed 5 min. Sensors stored under dry conditions at 4 degrees C still showed 60% of initial hydrolytic rate after 70 d. The sensors even when stored dry were ready for measurements after 5 min incubation in measuring buffer. A range of putative interfering substances did not influence sensor response, and suitability of measuring OPs in soil extracts was ascertained.
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Affiliation(s)
- S Gäberlein
- Institut für Chemo- und Biosensorik, Mendelstr. 7, 48149 Münster, Germany
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Plegge V, Slama M, Süselbeck B, Wienke D, Spener F, Knoll M, Zaborosch C. Analysis of ternary mixtures with a single dynamic microbial sensor and chemometrics using a nonlinear multivariate calibration. Anal Chem 2000; 72:2937-42. [PMID: 10905331 DOI: 10.1021/ac991034w] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
An amperometric biosensor based on immobilized bacterial cells of Alcaligenes eutrophus KT02 and an oxygen electrode was integrated in a flow-through system. Because microorganisms metabolize various organic analytes in a specific manner, the sensor shows for different pure analytes distinct time-dependent oxygen consumption rates that can be treated as characteristic patterns. This behavior is conserved also when the biosensor is exposed to a mixture of these organic analytes; the sensor with a particular type of microorganisms responds with a total signal. The respiration curves as time-dependent amplitudes were subdivided into several time channels. This procedure creates an additional data dimension and makes the single sensor "dynamic". Using multivariate calibration models with only one single biosensor, simultaneous quantitative analysis of ternary mixtures of acetate, L-lactate, and succinate was realized. A nonlinear algorithm that compensated for conceivable interactions of the analytes was superior to a partial least-squares algorithm. Each analyte was predicted more precisely by the nonlinear approach resulting in root-mean-square errors of prediction of 0.20 mg/L for acetate, 0.43 mg/L for L-lactate, and 0.73 mg/L for succinate.
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Affiliation(s)
- V Plegge
- Institüt für Chemo- und Biosensorik, Münster, Germany
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43
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König A, Reul T, Harmeling C, Spener F, Knoll M, Zaborosch C. Multimicrobial sensor using microstructured three-dimensional electrodes based on silicon technology. Anal Chem 2000; 72:2022-8. [PMID: 10815960 DOI: 10.1021/ac9908391] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two microbial strains with different substrate spectra were immobilized separately within a single biosensor chip featuring four individually addressable platinum electrodes. These were sputtered onto the inner surface of four isolated pyramidal cavities ("containments") micromachined on a silicon wafer. The biosensor chip was integrated into a flow-through system to measure the oxygen consumption of the immobilized microorganisms in the presence of assimilable analytes. As a model system, a yeast for the determination of biochemical oxygen demand (BOD) and a strain capable of degrading polycyclic aromatic hydrocarbons (PAH) were chosen. It was shown that the simple and mass-producible containment sensor exhibits good performance data: lower detection limit 0.1 mg/L naphthalene and 1 mg/L sensor-BOD; calibration range up to 30 mg/L; precision 3-6%; response time 2-3 min; service life up to 40 days; shelf life at 4 degrees C 6 months. The versatility of the multimicrobial sensor was demonstrated by measuring ordinary municipal wastewater samples as well as various aqueous samples contaminated with PAH. The concept of a multimicrobial sensor not only enlarges the substrate spectrum for sum parameters such as BOD but leads to additional information which allows for a more differentiated and immediate knowledge of sample composition. Using chemometrical data analysis, the multimicrobial sensor lays a foundation for developing an "electronic tongue".
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Affiliation(s)
- A König
- Institut für Chemo- und Biosensorik, Münster, Germany
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Lam X, Gieseke C, Knoll M, Talbot P. Assay and importance of adhesive interaction between hamster (Mesocricetus auratus) oocyte-cumulus complexes and the oviductal epithelium. Biol Reprod 2000; 62:579-88. [PMID: 10684798 DOI: 10.1095/biolreprod62.3.579] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Adhesion between the oocyte-cumulus complex and infundibulum plays an important, but poorly understood, role in oocyte pick-up. The purposes of this study were to determine which components of the oocyte-cumulus complex and oviductal epithelium function in adhesion, to measure adhesion under physiological conditions, and to examine the effect of modulation of adhesion on oocyte-cumulus complex pick-up rate. Oocyte-cumulus complexes containing an expanded matrix were readily transported into the oviduct, while unexpanded complexes lacking an extracellular matrix were not picked up, indicating that the matrix is necessary for pick-up. Transmission electron microscopy revealed that during pick-up, adhesion occurred specifically between the ciliary crowns of the oviduct and the granules and filaments of the cumulus matrix. An assay was developed using vacuum from a low-flow peristaltic precision pump, modified for bi-directional flow, to measure the strength of adhesion between the oocyte-cumulus complex and the oviductal epithelium, and adhesion was measured during physiological conditions. The lectin wheat germ agglutinin and the polycation poly-L-lysine were then used to modulate adhesion, and the effects of increasing or decreasing adhesion on oocyte pick-up rate and ciliary beat frequency were examined. The data show that 1) the matrix of the oocyte-cumulus complex and the ciliary crowns of the oviduct function in adhesion during pick-up and that adhesion is necessary for pick-up, 2) adhesion can be assayed quantitatively and is very uniform among control infundibula, and 3) decreasing or increasing adhesion decreases oocyte pick-up rate and in some cases prevents pick-up without affecting ciliary beat frequency.
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Affiliation(s)
- X Lam
- Department of Neuroscience, University of California, Riverside, California 92521, USA
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Riedl C, Knoll M, Plas E, Stephen R, Pfluger H. Intravesical Electromotive Drug Administration for the Treatment of Non-Infectious Chronic Cystitis. J Urol 1999. [DOI: 10.1016/s0022-5347(05)68909-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- C.R. Riedl
- Department of Urology and Ludwig-Boltzmann-Institute for Urology and Andrology, Municipal Hospital Lainz, Vienna, Austria, and University of Salt Lake City, Salt Lake City, Utah
| | - M. Knoll
- Department of Urology and Ludwig-Boltzmann-Institute for Urology and Andrology, Municipal Hospital Lainz, Vienna, Austria, and University of Salt Lake City, Salt Lake City, Utah
| | - E. Plas
- Department of Urology and Ludwig-Boltzmann-Institute for Urology and Andrology, Municipal Hospital Lainz, Vienna, Austria, and University of Salt Lake City, Salt Lake City, Utah
| | - R.L. Stephen
- Department of Urology and Ludwig-Boltzmann-Institute for Urology and Andrology, Municipal Hospital Lainz, Vienna, Austria, and University of Salt Lake City, Salt Lake City, Utah
| | - H. Pfluger
- Department of Urology and Ludwig-Boltzmann-Institute for Urology and Andrology, Municipal Hospital Lainz, Vienna, Austria, and University of Salt Lake City, Salt Lake City, Utah
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Abstract
This paper reports some new results on enzyme based silicon containment sensors. For the first time an L-lactate sensor in containment technology is presented. Through optimization of the buffer system the stability of the lactate sensor was enhanced and the linear response of over 10 mM was achieved. The glucose sensor has also been optimized for a large linear measurement range exceeding 30 mM. A two-enzyme chip with glucose and lactate sensor elements which were integrated on one silicon chip is presented. The response behaviour of the two-enzyme chip was very similar to the single chip behaviour. No cross-talking effects could be observed. A fabrication process for mass-production is described.
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Affiliation(s)
- J Perdomo
- Fachhochschule Muenster, Steinfurt, Germany
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47
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Affiliation(s)
- P Talbot
- Department of Biology, University of California, Riverside, California 92521, USA
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Eggenstein C, Borchardt M, Diekmann C, Gründig B, Dumschat C, Cammann K, Knoll M, Spener F. A disposable biosensor for urea determination in blood based on an ammonium-sensitive transducer. Biosens Bioelectron 1999; 14:33-41. [PMID: 10028647 DOI: 10.1016/s0956-5663(98)00103-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A potentiometric urea-sensitive biosensor using a NH4(+)-sensitive disposable electrode in double matrix membrane (DMM) technology as transducer is described. The ion-sensitive polymer matrix membrane was formed in the presence of an additional electrochemical inert filter paper matrix to improve the reproducibility in sensor production. The electrodes were prepared from one-side silver-coated filter paper, which is encapsulated for insulation by a heat-sealing film. A defined volume of the NH4(+)-sensitive polymer matrix membrane cocktail was deposited on this filter paper. To obtain the urea-biosensor a layer of urease was cast onto the ion-sensitive membrane. Poly (carbamoylsulfonate) hydrogel, produced from a hydrophilic polyurethane prepolymer blocked with bisulfite, served as immobilisation material. The disposable urea sensitive electrode was combined with a disposable Ag/AgCl reference electrode to obtain the disposable urea biosensor. The sensor responded rapidly and in a stable manner to changes in urea concentrations between 7.2 x 10(-5) and 2.1 x 10(-2)mol/l. The detection limit was 2 x 10(-5) mol/l urea and the slope in the linear range 52 mV/decade. By taking into consideration the influence of the interfering K(+)- and Na(+)-ions the sensor can be used for the determination of urea in human blood and serum samples (diluted or undiluted). A good correlation was found with the data obtained by the spectrophotometric routine method.
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Affiliation(s)
- C Eggenstein
- Institut für Chemo- und Biosensorik Münster, Germany
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Vering T, Adam S, Berns T, Schäfer R, Schwartenbeck G, Steinkuhl R, Tombach B, Knoll M. [Evaluation of VISY-1 in an in vivo test: sampling and glucose determination]. BIOMED ENG-BIOMED TE 1998; 43 Suppl:562-3. [PMID: 9859492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- T Vering
- Institut für Chemo- und Biosensorik, ICB, Münster
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Vering T, Adam S, Drewer H, Dumschat C, Steinkuhl R, Schulze A, Siegel EG, Knoll M. Wearable microdialysis system for continuous in vivo monitoring of glucose. Analyst 1998; 123:1605-9. [PMID: 9830173 DOI: 10.1039/a800017d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a new system to monitor glucose continuously in vivo. The miniaturised system is very easy to handle and was optimised to a resource-saving working modus. Sampling was performed by means of a biocompatible microdialysis needle probe inserted into the subcutaneous tissue. During glucose tolerance tests the results of our monitoring system were correlated with the glucose level of the venous blood stream. A comparison according to the procedure known as 'error grid analysis' provided an excellent correlation between the two completely independent analyses systems with the reference determination results. All values obtained with our systems were clinically correct or at least clinically acceptable.
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Affiliation(s)
- T Vering
- Institut für Chemo- und Biosensorik e.V., Münster, Germany
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