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Gomez-Zepeda D, Michna T, Ziesmann T, Distler U, Tenzer S. HowDirty: An R package to evaluate molecular contaminants in LC-MS experiments. Proteomics 2024; 24:e2300134. [PMID: 37679057 DOI: 10.1002/pmic.202300134] [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: 07/24/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
Contaminants derived from consumables, reagents, and sample handling often negatively affect LC-MS data acquisition. In proteomics experiments, they can markedly reduce identification performance, reproducibility, and quantitative robustness. Here, we introduce a data analysis workflow combining MS1 feature extraction in Skyline with HowDirty, an R-markdown-based tool, that automatically generates an interactive report on the molecular contaminant level in LC-MS data sets. To facilitate the interpretation of the results, the HTML report is self-contained and self-explanatory, including plots that can be easily interpreted. The R package HowDirty is available from https://github.com/DavidGZ1/HowDirty. To demonstrate a showcase scenario for the application of HowDirty, we assessed the impact of ultrafiltration units from different providers on sample purity after filter-assisted sample preparation (FASP) digestion. This allowed us to select the filter units with the lowest contamination risk. Notably, the filter units with the lowest contaminant levels showed higher reproducibility regarding the number of peptides and proteins identified. Overall, HowDirty enables the efficient evaluation of sample quality covering a wide range of common contaminant groups that typically impair LC-MS analyses, facilitating corrective or preventive actions to minimize instrument downtime.
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Affiliation(s)
- David Gomez-Zepeda
- Helmholtz-Institute for Translational Oncology Mainz (HI-TRON), Mainz, Rheinland-Pfalz, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
| | - Thomas Michna
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
| | - Tanja Ziesmann
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
| | - Stefan Tenzer
- Helmholtz-Institute for Translational Oncology Mainz (HI-TRON), Mainz, Rheinland-Pfalz, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
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2
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Gomez-Zepeda D, Arnold-Schild D, Beyrle J, Declercq A, Gabriels R, Kumm E, Preikschat A, Łącki MK, Hirschler A, Rijal JB, Carapito C, Martens L, Distler U, Schild H, Tenzer S. Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS 2Rescore with MS 2PIP timsTOF fragmentation prediction model. Nat Commun 2024; 15:2288. [PMID: 38480730 PMCID: PMC10937930 DOI: 10.1038/s41467-024-46380-y] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we develop a highly sensitive method for identifying HLAIps using liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS). In addition, we train a timsTOF-specific peak intensity MS2PIP model for tryptic and non-tryptic peptides and implement it in MS2Rescore (v3) together with the CCS predictor from ionmob. The optimized method, Thunder-DDA-PASEF, semi-selectively fragments singly and multiply charged HLAIps based on their IMS and m/z. Moreover, the method employs the high sensitivity mode and extended IMS resolution with fewer MS/MS frames (300 ms TIMS ramp, 3 MS/MS frames), doubling the coverage of immunopeptidomics analyses, compared to the proteomics-tailored DDA-PASEF (100 ms TIMS ramp, 10 MS/MS frames). Additionally, rescoring boosts the HLAIps identification by 41.7% to 33%, resulting in 5738 HLAIps from as little as one million JY cell equivalents, and 14,516 HLAIps from 20 million. This enables in-depth profiling of HLAIps from diverse human cell lines and human plasma. Finally, profiling JY and Raji cells transfected to express the SARS-CoV-2 spike protein results in 16 spike HLAIps, thirteen of which have been reported to elicit immune responses in human patients.
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Affiliation(s)
- David Gomez-Zepeda
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
- Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, Division 191, Heidelberg, Germany.
| | - Danielle Arnold-Schild
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Julian Beyrle
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
- Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Division 191, Heidelberg, Germany
| | - Arthur Declercq
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Elena Kumm
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Annica Preikschat
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Aurélie Hirschler
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, ProFI - FR2048, Strasbourg, France
| | - Jeewan Babu Rijal
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, ProFI - FR2048, Strasbourg, France
| | - Christine Carapito
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, ProFI - FR2048, Strasbourg, France
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
- Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, Division 191, Heidelberg, Germany.
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
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Farrukh A, Musabyimana JP, Distler U, Mahlich VJ, Mueller J, Bick F, Tenzer S, Pradel G, Ngwa CJ. The Plasmodium falciparum CCCH zinc finger protein MD3 regulates male gametocytogenesis through its interaction with RNA-binding proteins. Mol Microbiol 2024; 121:543-564. [PMID: 38148574 DOI: 10.1111/mmi.15215] [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: 06/29/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/28/2023]
Abstract
The transmission of malaria parasites to mosquitoes is dependent on the formation of gametocytes. Once fully matured, gametocytes are able to transform into gametes in the mosquito's midgut, a process accompanied with their egress from the enveloping erythrocyte. Gametocyte maturation and gametogenesis require a well-coordinated gene expression program that involves a wide spectrum of regulatory proteins, ranging from histone modifiers to transcription factors to RNA-binding proteins. Here, we investigated the role of the CCCH zinc finger protein MD3 in Plasmodium falciparum gametocytogenesis. MD3 was originally identified as an epigenetically regulated protein of immature gametocytes and recently shown to be involved in male development in a barcode-based screen in P. berghei. We report that MD3 is mainly present in the cytoplasm of immature male P. falciparum gametocytes. Parasites deficient of MD3 are impaired in gametocyte maturation and male gametocytogenesis. BioID analysis in combination with co-immunoprecipitation assays unveiled an interaction network of MD3 with RNA-binding proteins like PABP1 and ALBA3, with translational initiators, regulators and repressors like elF4G, PUF1, NOT1 and CITH, and with further regulators of gametocytogenesis, including ZNF4, MD1 and GD1. We conclude that MD3 is part of a regulator complex crucial for post-transcriptional fine-tuning of male gametocytogenesis.
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Affiliation(s)
- Afia Farrukh
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Jean Pierre Musabyimana
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Ute Distler
- Core Facility for Mass Spectrometry, Institute of Immunology, University Medical Centre of the Johannes-Gutenberg University, Mainz, Germany
| | - Vanessa Jil Mahlich
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Julius Mueller
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Fabian Bick
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Stefan Tenzer
- Core Facility for Mass Spectrometry, Institute of Immunology, University Medical Centre of the Johannes-Gutenberg University, Mainz, Germany
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Che Julius Ngwa
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
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4
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Sassmannshausen J, Bennink S, Distler U, Küchenhoff J, Minns AM, Lindner SE, Burda PC, Tenzer S, Gilberger TW, Pradel G. Comparative proteomics of vesicles essential for the egress of Plasmodium falciparum gametocytes from red blood cells. Mol Microbiol 2024; 121:431-452. [PMID: 37492994 DOI: 10.1111/mmi.15125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/27/2023]
Abstract
Transmission of malaria parasites to the mosquito is mediated by sexual precursor cells, the gametocytes. Upon entering the mosquito midgut, the gametocytes egress from the enveloping erythrocyte while passing through gametogenesis. Egress follows an inside-out mode during which the membrane of the parasitophorous vacuole (PV) ruptures prior to the erythrocyte membrane. Membrane rupture requires exocytosis of specialized egress vesicles of the parasites; that is, osmiophilic bodies (OBs) involved in rupturing the PV membrane, and vesicles that harbor the perforin-like protein PPLP2 (here termed P-EVs) required for erythrocyte lysis. While some OB proteins have been identified, like G377 and MDV1/Peg3, the majority of egress vesicle-resident proteins is yet unknown. Here, we used high-resolution imaging and BioID methods to study the two egress vesicle types in Plasmodium falciparum gametocytes. We show that OB exocytosis precedes discharge of the P-EVs and that exocytosis of the P-EVs, but not of the OBs, is calcium sensitive. Both vesicle types exhibit distinct proteomes with the majority of proteins located in the OBs. In addition to known egress-related proteins, we identified novel components of OBs and P-EVs, including vesicle-trafficking proteins. Our data provide insight into the immense molecular machinery required for the inside-out egress of P. falciparum gametocytes.
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Affiliation(s)
- Juliane Sassmannshausen
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Sandra Bennink
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Ute Distler
- Core Facility for Mass Spectrometry, Institute of Immunology, University Medical Centre of the Johannes-Gutenberg University, Mainz, Germany
| | - Juliane Küchenhoff
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Allen M Minns
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Paul-Christian Burda
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Stefan Tenzer
- Core Facility for Mass Spectrometry, Institute of Immunology, University Medical Centre of the Johannes-Gutenberg University, Mainz, Germany
| | - Tim W Gilberger
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
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5
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Felten M, Distler U, von Wiegen N, Łącki M, Behl C, Tenzer S, Stöcker W, Körschgen H. Substrate profiling of the metalloproteinase ovastacin uncovers specific enzyme-substrate interactions and discloses fertilization-relevant substrates. FEBS J 2024; 291:114-131. [PMID: 37690456 DOI: 10.1111/febs.16954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/07/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
The metalloproteinase ovastacin is released by the mammalian egg upon fertilization and cleaves a distinct peptide bond in zona pellucida protein 2 (ZP2), a component of the enveloping extracellular matrix. This limited proteolysis causes zona pellucida hardening, abolishes sperm binding, and thereby regulates fertility. Accordingly, this process is tightly controlled by the plasma protein fetuin-B, an endogenous competitive inhibitor. At present, little is known about how the cleavage characteristics of ovastacin differ from closely related proteases. Physiological implications of ovastacin beyond ZP2 cleavage are still obscure. In this study, we employed N-terminal amine isotopic labeling of substrates (N-TAILS) contained in the secretome of mouse embryonic fibroblasts to elucidate the substrate specificity and the precise cleavage site specificity. Furthermore, we were able to unravel the physicochemical properties governing ovastacin-substrate interactions as well as the individual characteristics that distinguish ovastacin from similar proteases, such as meprins and tolloid. Eventually, we identified several substrates whose cleavage could affect mammalian fertilization. Consequently, these substrates indicate newly identified functions of ovastacin in mammalian fertilization beyond zona pellucida hardening.
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Affiliation(s)
- Matthias Felten
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Nele von Wiegen
- Institute of Pathobiochemistry, The Autophagy Lab, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Mateusz Łącki
- Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Christian Behl
- Institute of Pathobiochemistry, The Autophagy Lab, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Walter Stöcker
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Germany
| | - Hagen Körschgen
- Institute of Pathobiochemistry, The Autophagy Lab, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
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6
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Anyaegbunam UA, More P, Fontaine JF, Cate VT, Bauer K, Distler U, Araldi E, Bindila L, Wild P, Andrade-Navarro MA. A Systematic Review of Lipid-Focused Cardiovascular Disease Research: Trends and Opportunities. Curr Issues Mol Biol 2023; 45:9904-9916. [PMID: 38132464 PMCID: PMC10742042 DOI: 10.3390/cimb45120618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023] Open
Abstract
Lipids are important modifiers of protein function, particularly as parts of lipoproteins, which transport lipophilic substances and mediate cellular uptake of circulating lipids. As such, lipids are of particular interest as blood biological markers for cardiovascular disease (CVD) as well as for conditions linked to CVD such as atherosclerosis, diabetes mellitus, obesity and dietary states. Notably, lipid research is particularly well developed in the context of CVD because of the relevance and multiple causes and risk factors of CVD. The advent of methods for high-throughput screening of biological molecules has recently resulted in the generation of lipidomic profiles that allow monitoring of lipid compositions in biological samples in an untargeted manner. These and other earlier advances in biomedical research have shaped the knowledge we have about lipids in CVD. To evaluate the knowledge acquired on the multiple biological functions of lipids in CVD and the trends in their research, we collected a dataset of references from the PubMed database of biomedical literature focused on plasma lipids and CVD in human and mouse. Using annotations from these records, we were able to categorize significant associations between lipids and particular types of research approaches, distinguish non-biological lipids used as markers, identify differential research between human and mouse models, and detect the increasingly mechanistic nature of the results in this field. Using known associations between lipids and proteins that metabolize or transport them, we constructed a comprehensive lipid-protein network, which we used to highlight proteins strongly connected to lipids found in the CVD-lipid literature. Our approach points to a series of proteins for which lipid-focused research would bring insights into CVD, including Prostaglandin G/H synthase 2 (PTGS2, a.k.a. COX2) and Acylglycerol kinase (AGK). In this review, we summarize our findings, putting them in a historical perspective of the evolution of lipid research in CVD.
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Affiliation(s)
- Uchenna Alex Anyaegbunam
- Computational Biology and Data Mining Group (CBDM), Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, 55122 Mainz, Germany
| | - Piyush More
- Computational Biology and Data Mining Group (CBDM), Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, 55122 Mainz, Germany
- Department of Pharmacology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Jean-Fred Fontaine
- Computational Biology and Data Mining Group (CBDM), Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, 55122 Mainz, Germany
- Central Institute for Decision Support Systems in Crop Protection (ZEPP), 55545 Bad Kreuznach, Germany
| | - Vincent ten Cate
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), University Medical Center, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Katrin Bauer
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Computational Systems Medicine, Center for Thrombosis and Hemostasis (CTH), 55131 Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Research Centre for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Elisa Araldi
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Computational Systems Medicine, Center for Thrombosis and Hemostasis (CTH), 55131 Mainz, Germany
| | - Laura Bindila
- Institute of Physiological Chemistry, University Medical Center, 55131 Mainz, Germany
| | - Philipp Wild
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), University Medical Center, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Miguel A. Andrade-Navarro
- Computational Biology and Data Mining Group (CBDM), Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, 55122 Mainz, Germany
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7
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Clausen BE, Amon L, Backer RA, Berod L, Bopp T, Brand A, Burgdorf S, Chen L, Da M, Distler U, Dress RJ, Dudziak D, Dutertre CA, Eich C, Gabele A, Geiger M, Ginhoux F, Giusiano L, Godoy GJ, Hamouda AEI, Hatscher L, Heger L, Heidkamp GF, Hernandez LC, Jacobi L, Kaszubowski T, Kong WT, Lehmann CHK, López-López T, Mahnke K, Nitsche D, Renkawitz J, Reza RA, Sáez PJ, Schlautmann L, Schmitt MT, Seichter A, Sielaff M, Sparwasser T, Stoitzner P, Tchitashvili G, Tenzer S, Tochoedo NR, Vurnek D, Zink F, Hieronymus T. Guidelines for mouse and human DC functional assays. Eur J Immunol 2023; 53:e2249925. [PMID: 36563126 DOI: 10.1002/eji.202249925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 12/24/2022]
Abstract
This article is part of the Dendritic Cell Guidelines article series, which provides a collection of state-of-the-art protocols for the preparation, phenotype analysis by flow cytometry, generation, fluorescence microscopy, and functional characterization of mouse and human dendritic cells (DC) from lymphoid organs and various non-lymphoid tissues. Recent studies have provided evidence for an increasing number of phenotypically distinct conventional DC (cDC) subsets that on one hand exhibit a certain functional plasticity, but on the other hand are characterized by their tissue- and context-dependent functional specialization. Here, we describe a selection of assays for the functional characterization of mouse and human cDC. The first two protocols illustrate analysis of cDC endocytosis and metabolism, followed by guidelines for transcriptomic and proteomic characterization of cDC populations. Then, a larger group of assays describes the characterization of cDC migration in vitro, ex vivo, and in vivo. The final guidelines measure cDC inflammasome and antigen (cross)-presentation activity. While all protocols were written by experienced scientists who routinely use them in their work, this article was also peer-reviewed by leading experts and approved by all co-authors, making it an essential resource for basic and clinical DC immunologists.
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Affiliation(s)
- Björn E Clausen
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Lukas Amon
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Ronald A Backer
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Luciana Berod
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Tobias Bopp
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Immunology, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Anna Brand
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Sven Burgdorf
- Laboratory of Cellular Immunology, LIMES Institute, University of Bonn, Bonn, Germany
| | - Luxia Chen
- Department of Dermatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Meihong Da
- Department of Dermatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ute Distler
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Immunology, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Regine J Dress
- Institute of Systems Immunology, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
- Medical Immunology Campus Erlangen (MICE), Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Germany
| | - Charles-Antoine Dutertre
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Christina Eich
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Anna Gabele
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Immunology, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Melanie Geiger
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Florent Ginhoux
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Lucila Giusiano
- Institute of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Gloria J Godoy
- Institute of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Ahmed E I Hamouda
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Lukas Hatscher
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Gordon F Heidkamp
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Lola C Hernandez
- Cell Communication and Migration Laboratory, Institute of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lukas Jacobi
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Tomasz Kaszubowski
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Wan Ting Kong
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Christian H K Lehmann
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
- Medical Immunology Campus Erlangen (MICE), Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Germany
| | - Tamara López-López
- Cell Communication and Migration Laboratory, Institute of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Karsten Mahnke
- Department of Dermatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Dominik Nitsche
- Laboratory of Cellular Immunology, LIMES Institute, University of Bonn, Bonn, Germany
| | - Jörg Renkawitz
- Biomedical Center (BMC), Walter Brendel Center of Experimental Medicine, Institute of Cardiovascular Physiology and Pathophysiology, Klinikum der Universität, LMU Munich, Munich, Germany
| | - Rifat A Reza
- Biomedical Center (BMC), Walter Brendel Center of Experimental Medicine, Institute of Cardiovascular Physiology and Pathophysiology, Klinikum der Universität, LMU Munich, Munich, Germany
| | - Pablo J Sáez
- Cell Communication and Migration Laboratory, Institute of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Schlautmann
- Laboratory of Cellular Immunology, LIMES Institute, University of Bonn, Bonn, Germany
| | - Madeleine T Schmitt
- Biomedical Center (BMC), Walter Brendel Center of Experimental Medicine, Institute of Cardiovascular Physiology and Pathophysiology, Klinikum der Universität, LMU Munich, Munich, Germany
| | - Anna Seichter
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Malte Sielaff
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Immunology, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Tim Sparwasser
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Patrizia Stoitzner
- Department of Dermatology, Venerology & Allergology, Medical University Innsbruck, Innsbruck, Austria
| | - Giorgi Tchitashvili
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Stefan Tenzer
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Immunology, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz), Mainz, Germany
| | - Nounagnon R Tochoedo
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Damir Vurnek
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Fabian Zink
- Laboratory of Cellular Immunology, LIMES Institute, University of Bonn, Bonn, Germany
| | - Thomas Hieronymus
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
- Institute of Cell and Tumor Biology, RWTH Aachen University, Medical Faculty, Germany
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8
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Teschner D, Gomez-Zepeda D, Declercq A, Łącki MK, Avci S, Bob K, Distler U, Michna T, Martens L, Tenzer S, Hildebrandt A. Ionmob: a Python package for prediction of peptide collisional cross-section values. Bioinformatics 2023; 39:btad486. [PMID: 37540201 PMCID: PMC10521631 DOI: 10.1093/bioinformatics/btad486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/30/2023] [Accepted: 08/03/2023] [Indexed: 08/05/2023] Open
Abstract
MOTIVATION Including ion mobility separation (IMS) into mass spectrometry proteomics experiments is useful to improve coverage and throughput. Many IMS devices enable linking experimentally derived mobility of an ion to its collisional cross-section (CCS), a highly reproducible physicochemical property dependent on the ion's mass, charge and conformation in the gas phase. Thus, known peptide ion mobilities can be used to tailor acquisition methods or to refine database search results. The large space of potential peptide sequences, driven also by posttranslational modifications of amino acids, motivates an in silico predictor for peptide CCS. Recent studies explored the general performance of varying machine-learning techniques, however, the workflow engineering part was of secondary importance. For the sake of applicability, such a tool should be generic, data driven, and offer the possibility to be easily adapted to individual workflows for experimental design and data processing. RESULTS We created ionmob, a Python-based framework for data preparation, training, and prediction of collisional cross-section values of peptides. It is easily customizable and includes a set of pretrained, ready-to-use models and preprocessing routines for training and inference. Using a set of ≈21 000 unique phosphorylated peptides and ≈17 000 MHC ligand sequences and charge state pairs, we expand upon the space of peptides that can be integrated into CCS prediction. Lastly, we investigate the applicability of in silico predicted CCS to increase confidence in identified peptides by applying methods of re-scoring and demonstrate that predicted CCS values complement existing predictors for that task. AVAILABILITY AND IMPLEMENTATION The Python package is available at github: https://github.com/theGreatHerrLebert/ionmob.
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Affiliation(s)
- David Teschner
- Institute of Computer Science, Johannes Gutenberg University, 55128 Mainz, Germany
| | - David Gomez-Zepeda
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
- Immunoproteomics Unit, Helmholtz-Institute for Translational Oncology (HI-TRON), 55131 Mainz, Germany
| | - Arthur Declercq
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Gent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Mateusz K Łącki
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Seymen Avci
- Institute of Computer Science, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Konstantin Bob
- Institute of Computer Science, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Thomas Michna
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
- Immunoproteomics Unit, Helmholtz-Institute for Translational Oncology (HI-TRON), 55131 Mainz, Germany
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Gent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
- Immunoproteomics Unit, Helmholtz-Institute for Translational Oncology (HI-TRON), 55131 Mainz, Germany
| | - Andreas Hildebrandt
- Institute of Computer Science, Johannes Gutenberg University, 55128 Mainz, Germany
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9
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Kirschner F, Arnold-Schild D, Leps C, Łącki MK, Klein M, Chen Y, Ludt A, Marini F, Kücük C, Stein L, Distler U, Sielaff M, Michna T, Riegel K, Rajalingam K, Bopp T, Tenzer S, Schild H. Modulation of cellular transcriptome and proteome composition by azidohomoalanine-implications on click chemistry-based secretome analysis. J Mol Med (Berl) 2023; 101:855-867. [PMID: 37231147 PMCID: PMC10300158 DOI: 10.1007/s00109-023-02333-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/25/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
The analysis of the secretome provides important information on proteins defining intercellular communication and the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, secretome data can support decisions for diagnosis and therapy. The mass spectrometry-based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro. Metabolic labeling using azide-containing amino acid analogs in combination with click chemistry facilitates this type of analysis in the presence of serum, preventing serum starvation-induced effects. The modified amino acid analogs, however, are less efficiently incorporated into newly synthesized proteins and may perturb protein folding. Combining transcriptome and proteome analysis, we elucidate in detail the effects of metabolic labeling with the methionine analog azidohomoalanine (AHA) on gene and protein expression. Our data reveal that 15-39% of the proteins detected in the secretome displayed changes in transcript and protein expression induced by AHA labeling. Gene Ontology (GO) analyses indicate that metabolic labeling using AHA leads to induction of cellular stress and apoptosis-related pathways and provide first insights on how this affects the composition of the secretome on a global scale. KEY MESSAGES: Azide-containing amino acid analogs affect gene expression profiles. Azide-containing amino acid analogs influence cellular proteome. Azidohomoalanine labeling induces cellular stress and apoptotic pathways. Secretome consists of proteins with dysregulated expression profiles.
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Affiliation(s)
- Friederike Kirschner
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Danielle Arnold-Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Christian Leps
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Matthias Klein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Yannic Chen
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Annekathrin Ludt
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Can Kücük
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Lara Stein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Malte Sielaff
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Thomas Michna
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Kristina Riegel
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tobias Bopp
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
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10
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Nelke C, Schroeter CB, Stascheit F, Huntemann N, Pawlitzki M, Willison AG, Räuber S, Melzer N, Distler U, Tenzer S, Stühler K, Roos A, Meisel A, Meuth SG, Ruck T. Eculizumab treatment alters the proteometabolome beyond the inhibiton of complement. JCI Insight 2023:169135. [PMID: 37227781 PMCID: PMC10371336 DOI: 10.1172/jci.insight.169135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Therapeutic strategies targeting complement have revolutionized the treatment of myasthenia gravis (MG). However, a deeper understanding of complement modulation in the human system is required to improve treatment responses and identify "off-target effects" shaping long-term outcomes. For this purpose, we studied a cohort of MG patients treated with either eculizumab (n = 10) or azathioprine (n = 10) as well as treatment-naïve (n = 10) patients using a combined proteomics and metabolomics approach. This strategy confirmed known effects of eculizumab on the terminal complement cascade. Beyond that, eculizumab modulated the serum proteometabolome as distinct pathways were altered in eculizumab-treated patients including the oxidative stress response, mitogen-activated protein kinase signaling and lipid metabolism with particular emphasis on arachidonic acid signaling. We detected reduced levels of arachidonate 5-lipoxygenase (ALOX5) and leukotriene A4 (LTA4) in eculizumab-treated patients. Mechanistically, ligation of the C5a receptor (C5aR) is needed for ALOX5 metabolism and generation of downstream leukotrienes. As eculizumab prevents cleavage of C5 into C5a, decreased engagement of C5aR may inhibit ALOX5-mediated synthesis of pro-inflammatory leukotrienes. These findings indicate distinct "off-target effects" induced by eculizumab, illuminating potential mechanisms of action that may be harnessed to improve treatment outcomes.
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Affiliation(s)
- Christopher Nelke
- Department of Neurology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Frauke Stascheit
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Niklas Huntemann
- Department of Neurology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marc Pawlitzki
- Department of Neurology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alice G Willison
- Department of Neurology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Saskia Räuber
- Department of Neurology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nico Melzer
- Department of Neurology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ute Distler
- Luxembourg Clinical Proteomics Center, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Luxembourg
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Heinrich Heine University, Düsseldorf, Germany
| | - Andreas Roos
- Department of Neuropediatrics, University of Duisburg-Essen, Essen, Germany
| | - Andreas Meisel
- Neuroscience Clinical Research Center, Charité - Universitätsmedizin Berlin, berlin, Germany
| | - Sven G Meuth
- Department of Neurology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tobias Ruck
- Department of Neurology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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11
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Cox EM, El-Behi M, Ries S, Vogt JF, Kohlhaas V, Michna T, Manfroi B, Al-Maarri M, Wanke F, Tirosh B, Pondarre C, Lezeau H, Yogev N, Mittenzwei R, Descatoire M, Weller S, Weill JC, Reynaud CA, Boudinot P, Jouneau L, Tenzer S, Distler U, Rensing-Ehl A, König C, Staniek J, Rizzi M, Magérus A, Rieux-Laucat F, Wunderlich FT, Hövelmeyer N, Fillatreau S. AKT activity orchestrates marginal zone B cell development in mice and humans. Cell Rep 2023; 42:112378. [PMID: 37060566 DOI: 10.1016/j.celrep.2023.112378] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 12/14/2022] [Accepted: 03/27/2023] [Indexed: 04/16/2023] Open
Abstract
The signals controlling marginal zone (MZ) and follicular (FO) B cell development remain incompletely understood. Here, we show that AKT orchestrates MZ B cell formation in mice and humans. Genetic models that increase AKT signaling in B cells or abolish its impact on FoxO transcription factors highlight the AKT-FoxO axis as an on-off switch for MZ B cell formation in mice. In humans, splenic immunoglobulin (Ig) D+CD27+ B cells, proposed as an MZ B cell equivalent, display higher AKT signaling than naive IgD+CD27- and memory IgD-CD27+ B cells and develop in an AKT-dependent manner from their precursors in vitro, underlining the conservation of this developmental pathway. Consistently, CD148 is identified as a receptor indicative of the level of AKT signaling in B cells, expressed at a higher level in MZ B cells than FO B cells in mice as well as humans.
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Affiliation(s)
- Eva-Maria Cox
- Institute for Molecular Medicine Mainz, University Hospital of Mainz, 55131 Mainz, Germany
| | - Mohamed El-Behi
- Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, 156-160, rue de Vaugirard, 75015 Paris, France
| | - Stefanie Ries
- Deutsches Rheuma-Forschungszentrum, a Leibniz Institute, 10117 Berlin, Germany
| | - Johannes F Vogt
- Institute for Molecular Medicine Mainz, University Hospital of Mainz, 55131 Mainz, Germany
| | - Vivien Kohlhaas
- Max Planck Institute for Metabolism Research Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP) Cologne, 50931 Cologne, Germany
| | - Thomas Michna
- Institute for Immunology, University Medical Centre of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Benoît Manfroi
- Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, 156-160, rue de Vaugirard, 75015 Paris, France
| | - Mona Al-Maarri
- Max Planck Institute for Metabolism Research Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP) Cologne, 50931 Cologne, Germany
| | - Florian Wanke
- Institute for Molecular Medicine Mainz, University Hospital of Mainz, 55131 Mainz, Germany
| | - Boaz Tirosh
- The Hebrew University of Jerusalem, Institute for Drug Research, Jerusalem, Israel
| | - Corinne Pondarre
- Service de Pédiatrie Générale, Centre de Référence de la Drépanocytose, Centre Intercommunal de Créteil, Créteil, France; Inserm U955, Université Paris XII, Créteil, France
| | - Harry Lezeau
- Service de Pédiatrie Générale, Centre de Référence de la Drépanocytose, Centre Intercommunal de Créteil, Créteil, France; Inserm U955, Université Paris XII, Créteil, France
| | - Nir Yogev
- Faculty of Medicine, Department of Dermatology, University of Cologne, 50931 Cologne, Germany
| | - Romy Mittenzwei
- Institute for Molecular Medicine Mainz, University Hospital of Mainz, 55131 Mainz, Germany
| | - Marc Descatoire
- Laboratory of Immune Inherited Disorders, Department of Immunology and Allergology Lausanne Hospital CHUV, Lausanne, Switzerland
| | - Sandra Weller
- Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, 156-160, rue de Vaugirard, 75015 Paris, France
| | - Jean-Claude Weill
- Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, 156-160, rue de Vaugirard, 75015 Paris, France
| | - Claude-Agnès Reynaud
- Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, 156-160, rue de Vaugirard, 75015 Paris, France
| | - Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Stefan Tenzer
- Institute for Immunology, University Medical Centre of the Johannes-Gutenberg University Mainz, Mainz, Germany; Research Centre for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany; Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz), Mainz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Centre of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Anne Rensing-Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph König
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; University of Freiburg, Faculty of Biology, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Julian Staniek
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Aude Magérus
- Université Paris Cité, Institut Imagine, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, 75015 Paris, France
| | - Frederic Rieux-Laucat
- Université Paris Cité, Institut Imagine, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, 75015 Paris, France
| | - F Thomas Wunderlich
- Max Planck Institute for Metabolism Research Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP) Cologne, 50931 Cologne, Germany
| | - Nadine Hövelmeyer
- Institute for Molecular Medicine Mainz, University Hospital of Mainz, 55131 Mainz, Germany; Research Centre for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany.
| | - Simon Fillatreau
- Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, 156-160, rue de Vaugirard, 75015 Paris, France; Université de Paris Cité, Paris Descartes, Faculté de Médecine, Paris, France; AP-HP, Hôpital Necker Enfants Malades, Paris, France.
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12
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Kechagioglou P, Dupont C, Yurugi H, Distler U, Tenzer S, Chernobrovkin A, Riegel K, Mooz J, Lambert M, Dötsch V, Cosenza S, Fruchtman SM, Rajalingam K. Abstract 5987: Differential targets engaged by narazaciclib in comparison to the approved CDK4/6 inhibitors contribute to enhanced inhibition of tumor cell growth. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-5987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
CDK4/6 inhibitors are clinically approved for the treatment of HR+, HER2- metastatic breast cancer by reinstating the G1/S checkpoint in tumor cells. Despite clinical benefit, safety concerns such as neutropenia and diarrhea, and disease progression, raises a critical need to identify novel therapeutic strategies. Narazaciclib (ON123300), novel CDK4/6i, designed to enhance efficacy and safety by its multi-targeted kinase inhibitor activity at low nM concentrations against CDK4/6, ARK5, CSF1R, and c-Kit. Narazaciclib is in Ph I trials; NCT04739293 and CXHL1900340; studying different administration regimens. Since several oncogenic signaling pathways are affected, we examined the efficacy of ON123300 in various breast cancer cell lines, and consolidate its mechanism of action by identifying the other targets engaged by ON123300. To identify direct and secondary targets engaged by narazaciclib and palbociclib, proteome wide Cellular Thermal Shift Assay (CETSA) was performed. To investigate narazaciclib’s effect on signaling pathways, Integrative Inferred Kinase Activity (INKA) was performed. Bioinformatics analysis explored the potential clinical effect of the identified targets. Molecular docking simulations investigated the potential interactions of narazaciclib to engage the new targets compared to other CDK4/6i. Both CETSA and INKA analysis revealed more potential targets engaged by narazaciclib compared to palbociclib in both MDA-MB-231 lysates and intact cells such as BUB1, CHEK1, AURKA, GSK3α and GSK3β. In TNBC patients with BUB1 overexpression bioinformatics analysis indicates a low survival correlation. Docking data showed a higher affinity of narazaciclib with BUB1 compared to palbociclib and abemaciclib. A stronger induction of apoptosis and senescence was detected in narazaciclib treated MMTV-PYMT cells, a murine mammary carcinoma model, compared to the other CDK4/6i, while narazaciclib enhanced CCL5 and CXCL10 mRNA levels. Reduction of PD-L1 protein levels and a promoting effect on the H2D1 and B2M mRNA levels was perceived in narazaciclib treated PYMT cells. Lastly, inhibition of autophagy, both at the early and late stages, may sensitize cancer cells to narazaciclib and induce irreversible cell proliferation inhibition, providing a novel therapeutic approach. Our data unveiled the differential targets engaged by narazaciclib in comparison to palbociblib. Narazaciclib treatment led to BUB1 protein degradation, overexpression of which is associated with poor prognosis in TNBC. Combination of narazaciclib with autophagy inhibitors sensitized several breast cancer cells to cell death. Narazaciclib treatment may promote antitumor immunity by influencing the expression of various immune modulators in the tumor cells which needs to be further validated in preclinical animal models; and ultimately in the clinic.
Citation Format: Petros Kechagioglou, Camille Dupont, Hajime Yurugi, Ute Distler, Stefan Tenzer, Alexey Chernobrovkin, Kristina Riegel, Juliane Mooz, Mahil Lambert, Volker Dötsch, Stephen Cosenza, Steven M. Fruchtman, Krishnaraj Rajalingam. Differential targets engaged by narazaciclib in comparison to the approved CDK4/6 inhibitors contribute to enhanced inhibition of tumor cell growth. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5987.
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Affiliation(s)
- Petros Kechagioglou
- 1University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Camille Dupont
- 1University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hajime Yurugi
- 1University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Ute Distler
- 1University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stefan Tenzer
- 1University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Kristina Riegel
- 1University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Juliane Mooz
- 1University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | | | | | | | - Krishnaraj Rajalingam
- 1University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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Afzal M, Sielaff M, Distler U, Schuppan D, Tenzer S, Longin CFH. Reference proteomes of five wheat species as starting point for future design of cultivars with lower allergenic potential. NPJ Sci Food 2023; 7:9. [PMID: 36966156 PMCID: PMC10039927 DOI: 10.1038/s41538-023-00188-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/06/2023] [Indexed: 03/27/2023] Open
Abstract
Wheat is an important staple food and its processing quality is largely driven by proteins. However, there is a sizable number of people with inflammatory reactions to wheat proteins, namely celiac disease, wheat allergy and the syndrome of non-celiac wheat sensitivity. Thus, proteome profiles should be of high importance for stakeholders along the wheat supply chain. We applied liquid chromatography-tandem mass spectrometry-based proteomics to establish the flour reference proteome for five wheat species, ancient to modern, each based on 10 cultivars grown in three diverse environments. We identified at least 2540 proteins in each species and a cluster analyses clearly separated the species based on their proteome profiles. Even more, >50% of proteins significantly differed between species - many of them implicated in products' quality, grain-starch synthesis, plant stress regulation and proven or potential allergic reactions in humans. Notably, the expression of several important wheat proteins was found to be mainly driven by genetics vs. environmental factors, which enables selection and refinement of improved cultivars for the wheat supply chain as long as rapid test methods will be developed. Especially einkorn expressed 5.4 and 7.2-fold lower quantities of potential allergens and immunogenic amylase trypsin inhibitors, respectively, than common wheat, whereas potential allergen content was intermediate in tetraploid wheat species. This urgently warrants well-targeted clinical studies, where the developed reference proteomes will help to design representative test diets.
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Affiliation(s)
- Muhammad Afzal
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Malte Sielaff
- Institute for Immunology and Research Center for Immune Therapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Ute Distler
- Institute for Immunology and Research Center for Immune Therapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Detlef Schuppan
- Institute of Translational Immunology and Research Center for Immune Therapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA, 02215, USA
| | - Stefan Tenzer
- Institute for Immunology and Research Center for Immune Therapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany.
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Chen K, Huang X, Distler U, Tenzer S, Günay-Esiyok Ö, Gupta N. Apically-located P4-ATPase1-Lem1 complex internalizes phosphatidylserine and regulates motility-dependent invasion and egress in Toxoplasma gondii. Comput Struct Biotechnol J 2023; 21:1893-1906. [PMID: 36936814 PMCID: PMC10015115 DOI: 10.1016/j.csbj.2023.02.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The membrane asymmetry regulated by P4-ATPases is crucial for the functioning of eukaryotic cells. The underlying spatial translocation or flipping of specific lipids is usually assured by respective P4-ATPases coupled to conforming non-catalytic subunits. Our previous work has identified five P4-ATPases (TgP4-ATPase1-5) and three non-catalytic partner proteins (TgLem1-3) in the intracellular protozoan pathogen, Toxoplasma gondii. However, their flipping activity, physiological relevance and functional coupling remain unknown. Herein, we demonstrate that TgP4-ATPase1 and TgLem1 work together to translocate phosphatidylserine (PtdSer) during the lytic cycle of T. gondii. Both proteins localize in the plasma membrane at the invasive (apical) end of its acutely-infectious tachyzoite stage. The genetic knockout of P4-ATPase1 and conditional depletion of Lem1 in tachyzoites severely disrupt the asexual reproduction and translocation of PtdSer across the plasma membrane. Moreover, the phenotypic analysis of individual mutants revealed a requirement of lipid flipping for the motility, egress and invasion of tachyzoites. Not least, the proximity-dependent biotinylation and reciprocal immunoprecipitation assays demonstrated the physical interaction of P4-ATPase1 and Lem1. Our findings disclose the mechanism and significance of PtdSer flipping during the lytic cycle and identify the P4-ATPase1-Lem1 heterocomplex as a potential drug target in T. gondii.
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Key Words
- BSA, bovine serum albumin
- CDC50, Cell Division Control 50
- COS, crossover sequence
- Cdc50
- DAPI, 4′,6-diamidino-2-phenylindole
- DHFR-TS, dihydrofolate reductase – thymidylate synthase
- HFF, human foreskin fibroblast
- HXGPRT, hypoxanthine-xanthine-guanine phosphoribosyltransferase
- IAA, indole-3-acetic acid
- LEM, Ligand Effector Module
- Lem1
- NBD, nitrobenzoxadiazole
- NBD-lipid
- P4-ATPase1
- PBS, phosphate-buffered saline
- Phosphatidylserine
- Phospholipid flipping
- PtdCho, phosphatidylcholine
- PtdEtn, phosphatidylethanolamine
- PtdSer, phosphatidylserine
- PtdThr, phosphatidylthreonine
- UTR, untranslated region
- cGMP, cyclic Guanosine Monophosphate
- mAID, (mini) auxin-inducible degron
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Affiliation(s)
- Kai Chen
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Xiyu Huang
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Özlem Günay-Esiyok
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Nishith Gupta
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
- Intracellular Parasite Education and Research Labs (iPEARL), Department of Biological Sciences, Birla Institute of Technology and Science, Pilani (BITS-P), Hyderabad, India
- Corresponding author at: Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany.
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Renaud E, Riegel K, Romero R, Suryamohan K, Distler U, Tenzer S, Schad A, Musholt TJ, Rajalingam K. Multiomic analysis of papillary thyroid cancers identifies BAIAP2L1-BRAF fusion and requirement of TRIM25, PDE5A and PKCδ for tumorigenesis. Mol Cancer 2022; 21:195. [PMID: 36217175 PMCID: PMC9549631 DOI: 10.1186/s12943-022-01665-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/22/2022] [Indexed: 11/21/2022] Open
Abstract
Background Papillary thyroid carcinoma (PTC) is one of the most common forms of thyroid cancer with a cure rate of over 90% after surgery. However, aggressive forms may still occur, and personalized therapeutic strategies are increasingly required. Methods We performed integrated genomic and proteomic analysis of PTC tumor samples from patients who did not harbor BRAF or RAS mutations. We validate the analysis and present in-depth molecular analysis of the identified genetic rearrangement by employing biochemical and cell biological assays. Finally, we employ 3D spheroid models, loss of function studies and chemical inhibitors to target the hitherto upregulated factors. The data are analysed with appropriate statistical tests which are mentioned in the legends section. Results In a 23-year-old patient with thyroiditis, we identified a novel rearrangement leading to a BAIAP2L1-BRAF fusion that transforms immortalized human thyroid cells in a kinase and CC-domain dependent manner. Moreover, quantitative proteomic analysis of the same patient samples revealed the upregulation of several proteins including the Ubiquitin E3 ligase TRIM25, PDE5A, and PKCδ. Further, in a cohort of PTC patients, we observed higher expression of TRIM25 and PKCδ in the tumor and metastatic lesions, when compared to the matched normal tissue. Inhibition of TRIM25, PDE5A and PKCδ with small molecules or RNA interference affected not only viability and proliferation of BAIAP2L1-BRAF transformed cells, but also the viability, growth and invasion of corresponding 3D spheroid cultures. Conclusions Apart from unveiling a novel oncogenic BRAF fusion in PTCs, our data may open a novel avenue of therapeutic targeting in human PTCs. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01665-y.
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Affiliation(s)
- Emilie Renaud
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany
| | - Kristina Riegel
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany
| | - Rossana Romero
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany
| | | | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany
| | - Arno Schad
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany
| | - Thomas J Musholt
- Endocrine Surgery Section, Department of General, Visceral and Transplantation Surgery, University Medicine, 55131, Mainz, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany.
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Vo KC, Ruga L, Psathaki OE, Franzkoch R, Distler U, Tenzer S, Hensel M, Hegemann P, Gupta N. Plasticity and therapeutic potential of cAMP and cGMP-specific phosphodiesterases in Toxoplasma gondii. Comput Struct Biotechnol J 2022; 20:5775-5789. [PMID: 36382189 PMCID: PMC9619220 DOI: 10.1016/j.csbj.2022.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/03/2022] Open
Abstract
Toxoplasma gondii is a common zoonotic protozoan pathogen adapted to intracellular parasitism in many host cells of diverse organisms. Our previous work has identified 18 cyclic nucleotide phosphodiesterase (PDE) proteins encoded by the parasite genome, of which 11 are expressed during the lytic cycle of its acutely-infectious tachyzoite stage in human cells. Here, we show that ten of these enzymes are promiscuous dual-specific phosphodiesterases, hydrolyzing cAMP and cGMP. TgPDE1 and TgPDE9, with a Km of 18 μM and 31 μM, respectively, are primed to hydrolyze cGMP, whereas TgPDE2 is highly specific to cAMP (Km, 14 μM). Immuno-electron microscopy revealed various subcellular distributions of TgPDE1, 2, and 9, including in the inner membrane complex, apical pole, plasma membrane, cytosol, dense granule, and rhoptry, indicating spatial control of signaling within tachyzoites. Notably, despite shared apical location and dual-catalysis, TgPDE8 and TgPDE9 are fully dispensable for the lytic cycle and show no functional redundancy. In contrast, TgPDE1 and TgPDE2 are individually required for optimal growth, and their collective loss is lethal to the parasite. In vitro phenotyping of these mutants revealed the roles of TgPDE1 and TgPDE2 in proliferation, gliding motility, invasion and egress of tachyzoites. Moreover, our enzyme inhibition assays in conjunction with chemogenetic phenotyping underpin TgPDE1 as a target of commonly-used PDE inhibitors, BIPPO and zaprinast. Finally, we identified a retinue of TgPDE1 and TgPDE2-interacting kinases and phosphatases, possibly regulating the enzymatic activity. In conclusion, our datasets on the catalytic function, physiological relevance, subcellular localization and drug inhibition of key phosphodiesterases highlight the previously-unanticipated plasticity and therapeutic potential of cyclic nucleotide signaling in T. gondii.
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Key Words
- 3′IT, 3′-insertional tagging
- Apicomplexa
- COS, crossover sequence
- CRISPR, clustered regularly interspaced short palindromic repeats
- DHFR-TS, dihydrofolate reductase – thymidylate synthase
- HFF, human foreskin fibroblast
- HXGPRT, hypoxanthine-xanthine-guanine phosphoribosyl transferase
- IMC, inner membrane complex
- Lytic cycle
- MoI, multiplicity of infection
- PDE, phosphodiesterase
- PKA, protein kinase A
- PKG, protein kinase G
- PM, plasma membrane
- Phosphodiesterase
- S. C., selection cassette
- TEM, transmission electron microscopy
- Tachyzoite
- cAMP & cGMP signaling
- sgRNA, single guide RNA
- smHA, spaghetti monster-HA
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Affiliation(s)
- Kim Chi Vo
- Department of Molecular Parasitology, Institute of Biology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Liberta Ruga
- Department of Molecular Parasitology, Institute of Biology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Olympia Ekaterini Psathaki
- University of Osnabrück, Center of Cellular Nanoanalytics (CellNanOs), Integrated Bioimaging Faciltiy (iBiOs), Germany
| | - Rico Franzkoch
- University of Osnabrück, Center of Cellular Nanoanalytics (CellNanOs), Integrated Bioimaging Faciltiy (iBiOs), Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Michael Hensel
- University of Osnabrück, Center of Cellular Nanoanalytics (CellNanOs), Integrated Bioimaging Faciltiy (iBiOs), Germany
| | - Peter Hegemann
- Department of Molecular Parasitology, Institute of Biology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Nishith Gupta
- Department of Molecular Parasitology, Institute of Biology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani (BITS-P), Hyderabad, India
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Bensaoud C, Tenzer S, Poplawski A, Medina JM, Jmel MA, Voet H, Mekki I, Aparicio-Puerta E, Cuveele B, Distler U, Marini F, Hackenberg M, Kotsyfakis M. Quantitative proteomics analysis reveals core and variable tick salivary proteins at the tick-vertebrate host interface. Mol Ecol 2022; 31:4162-4175. [PMID: 35661311 DOI: 10.1111/mec.16561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/30/2022] [Accepted: 04/04/2022] [Indexed: 11/28/2022]
Abstract
Few studies have examined tick proteomes, how they adapt to their environment, and their roles in the parasite-host interactions that drive tick infestation and pathogen transmission. Here we used a proteomics approach to screen for biologically and immunologically relevant proteins acting at the tick-host interface during tick feeding and, as proof of principle, measured host antibody responses to some of the discovered candidates. We used a label-free quantitative proteomic workflow to study salivary proteomes of (i) wild Ixodes ricinus ticks fed on different hosts; (ii) wild or laboratory ticks fed on the same host; and (iii) adult ticks co-fed with nymphs. Our results reveal high and stable expression of several protease inhibitors and other tick-specific proteins under different feeding conditions. Most pathways functionally enriched in sialoproteomes were related to proteolysis, endopeptidase, and amine-binding activities. The generated catalog of tick salivary proteins enabled the selection of six candidate secreted immunogenic peptides for rabbit immunizations, three of which induced strong and durable antigen-specific antibody responses in rabbits. Furthermore, rabbits exposed to ticks mounted immune responses against the candidate peptides/proteins, confirming their expression at the tick-vertebrate interface. Our approach provides insights into tick adaptation strategies to different feeding conditions and promising candidates for developing anti-tick vaccines or markers of exposure of vertebrate hosts to tick bites.
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Affiliation(s)
- Chaima Bensaoud
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Budweis, Czechia
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Alicia Poplawski
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - José María Medina
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, Granada, Spain.,Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento s/n, Granada, Spain
| | - Mohamed Amine Jmel
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Budweis, Czechia
| | - Hanne Voet
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Budweis, Czechia.,University of Antwerp, Wilrijk, Belgium
| | - Imen Mekki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Budweis, Czechia.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Ernesto Aparicio-Puerta
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, Granada, Spain.,Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento s/n, Granada, Spain
| | - Brent Cuveele
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Budweis, Czechia.,University of Antwerp, Wilrijk, Belgium
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Michael Hackenberg
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, Granada, Spain.,Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento s/n, Granada, Spain
| | - Michalis Kotsyfakis
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Budweis, Czechia
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Kechagioglou P, Dupont C, Yurugi H, Distler U, Tenzer S, Chernobrovkin A, Riegel K, Cosenza S, Fruchtman SM, Rajalingam K. Narazaciclib’s kinase inhibitory activity is differentiated from approved CDK4/6 inhibitors in preclinical models. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e15096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e15096 Background: Despite clinical benefit of CDK4/6 inhibitors in HR+Her2-mBC, patients progress. Neutropenia and diarrhea are safety concerns. Narazaciclib (ON 123300) is a multi-targeted kinase inhibitor of CDK4/6, ARK5 (NUAK1), CSF1R, and c-Kit at low nM concentrations designed to enhance efficacy and safety. Narazaciclib is in Ph I trials; NCT04739293 and CXHL1900340; in different regimens. Treatment of tumor cell lines with narazaciclib induces G1; G2 arrest and apoptosis. Mouse models suggest narazaciclib causes less neutropenia than palbociclib (palbo). Since signaling pathways are affected, we explored the activity of narazaciclib in direct comparisons with abemaciclib (abe), palbo and ribociclib (ribo) using in vitro and cell based assays. Methods: Comparison of narazaciclib’s in vitro IC50 profile to abe, palbo and ribo was studied against a panel of 370 kinases (HotSpot). Kd values were determined by KINOMEscan. Intracellular IC50 kinase values were determined by NanoBret technology. Protein specific binding of narazaciclib and palbo was investigated by Cellular Thermal Shift Assay (CETSA). To investigate narazaciclib’s effect on signaling pathways, integrative Inferred Kinase Activity (INKA) analysis was performed. Results: Narazaciclib and abe were found to be the most promiscuous in vitro kinase inhibitors and ribo the most specific. Abe and narazaciclib had similar profiles against the CDK family members. Kd values of CDK4/cyclinD1 binding show similar trends; abe (0.08 nM), narazaciclib (0.18 nM), palbo (0.75 nM) and ribo (1.3 nM). Narazaciclib and abe displayed nM activity against CDK2/cyclinA. The IC50 values against GSK3β, whose inhibition putatively causes diarrhea, was 374 nM for narazaciclib and 13 nM for abe. Although narazaciclib displayed nM IC50 values in the in vitro assays against many CDKs, narazaciclib was very specific in cellular kinase assays with highest activity against CDK4/6, CSF1R and NUAK1. CETSA-MS revealed more potential targets engaged by narazaciclib compared to palbo in both lysates and intact cells such as CHEK1, AAK1, BMP2K, GSK3α and GSK3β, but did not identify binding to NUAK1 or CSF1R. INKA analysis demonstrated that narazaciclib induced unique deregulated phosphorylation compared to palbo, including BUB1 (highly expressed in TNBC), NUAK1, CAMK2D, CDK16 and ULK1. Inhibition of autophagy, both at early and late stages, may sensitize cancer cells to narazaciclib and induce irreversible cell proliferation inhibition, providing a novel therapeutic approach. Conclusions: These studies identify important differences generated from assay models studying kinase inhibition, binding and pathway engagement and will guide future studies with narazaciclib targeting specific kinase driven tumors with the potential for improved safety. These preclinical data await confirmation from current and future clinical trials.
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Affiliation(s)
| | - Camille Dupont
- Johannes Gutenberg University Medical Centre Mainz, Mainz, Germany
| | - Hajime Yurugi
- Johannes Gutenberg University Medical Centre Mainz, Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
| | | | - Kristina Riegel
- Johannes Gutenberg University Medical Centre Mainz, Mainz, Germany
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Bittel M, Reichert P, Sarfati I, Dressel A, Leikam S, Uderhardt S, Stolzer I, Phu TA, Ng M, Vu NK, Tenzer S, Distler U, Wirtz S, Rothhammer V, Neurath MF, Raffai RL, Günther C, Momma S. Visualizing transfer of microbial biomolecules by outer membrane vesicles in microbe-host-communication in vivo. J Extracell Vesicles 2021; 10:e12159. [PMID: 34664784 PMCID: PMC8524437 DOI: 10.1002/jev2.12159] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 12/29/2022] Open
Abstract
The intestinal microbiota influences mammalian host physiology in health and disease locally in the gut but also in organs devoid of direct contact with bacteria such as the liver and brain. Extracellular vesicles (EVs) or outer membrane vesicles (OMVs) released by microbes are increasingly recognized for their potential role as biological shuttle systems for inter-kingdom communication. However, physiologically relevant evidence for the transfer of functional biomolecules from the intestinal microbiota to individual host cells by OMVs in vivo is scarce. By introducing Escherichia coli engineered to express Cre-recombinase (E. coliCre ) into mice with a Rosa26.tdTomato-reporter background, we leveraged the Cre-LoxP system to report the transfer of bacterial OMVs to recipient cells in vivo. Colonizing the intestine of these mice with E. coliCre , resulted in Cre-recombinase induced fluorescent reporter gene-expression in cells along the intestinal epithelium, including intestinal stem cells as well as mucosal immune cells such as macrophages. Furthermore, even far beyond the gut, bacterial-derived Cre induced extended marker gene expression in a wide range of host tissues, including the heart, liver, kidney, spleen, and brain. Together, our findings provide a method and proof of principle that OMVs can serve as a biological shuttle system for the horizontal transfer of functional biomolecules between bacteria and mammalian host cells.
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Affiliation(s)
- Miriam Bittel
- Department of Medicine 1Friedrich‐Alexander‐University Erlangen‐NürnbergErlangenGermany
| | - Patrick Reichert
- Department of Medicine 1Friedrich‐Alexander‐University Erlangen‐NürnbergErlangenGermany
| | - Ilann Sarfati
- Department of Medicine 1Friedrich‐Alexander‐University Erlangen‐NürnbergErlangenGermany
- Deutsches Zentrum ImmuntherapieFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Anja Dressel
- Department of Medicine 1Friedrich‐Alexander‐University Erlangen‐NürnbergErlangenGermany
- Deutsches Zentrum ImmuntherapieFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Stefanie Leikam
- Department of Medicine 1Friedrich‐Alexander‐University Erlangen‐NürnbergErlangenGermany
| | - Stefan Uderhardt
- Department of Internal Medicine 3University Hospital Erlangen and Friedrich‐Alexander‐University Erlangen‐Nürnberg (FAU)ErlangenGermany
- Exploratory Research UnitOptical Imaging Centre ErlangenFriedrich‐Alexander‐University Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Iris Stolzer
- Department of Medicine 1Friedrich‐Alexander‐University Erlangen‐NürnbergErlangenGermany
- Deutsches Zentrum ImmuntherapieFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Tuan Anh Phu
- Northern California Institute for Research and EducationSan FranciscoCaliforniaUSA
| | - Martin Ng
- Northern California Institute for Research and EducationSan FranciscoCaliforniaUSA
| | - Ngan K. Vu
- Northern California Institute for Research and EducationSan FranciscoCaliforniaUSA
| | - Stefan Tenzer
- Institute of ImmunologyUniversity Medical Centre of the Johannes‐Gutenberg University MainzMainzGermany
- Research Centre for Immunotherapy (FZI)University Medical Center of the Johannes‐Gutenberg University MainzMainzGermany
| | - Ute Distler
- Institute of ImmunologyUniversity Medical Centre of the Johannes‐Gutenberg University MainzMainzGermany
- Research Centre for Immunotherapy (FZI)University Medical Center of the Johannes‐Gutenberg University MainzMainzGermany
| | - Stefan Wirtz
- Department of Medicine 1Friedrich‐Alexander‐University Erlangen‐NürnbergErlangenGermany
- Deutsches Zentrum ImmuntherapieFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Veit Rothhammer
- Neurology Department (Experimental Glia Biology)University Hospital Erlangen and Friedrich‐Alexander‐University Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Markus F. Neurath
- Department of Medicine 1Friedrich‐Alexander‐University Erlangen‐NürnbergErlangenGermany
- Deutsches Zentrum ImmuntherapieFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Robert L. Raffai
- Department of SurgeryDivision of Vascular and Endovascular SurgeryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Department of Veterans AffairsSurgical Service (112G)San Francisco VA Medical CentreSan FranciscoCaliforniaUSA
| | - Claudia Günther
- Department of Medicine 1Friedrich‐Alexander‐University Erlangen‐NürnbergErlangenGermany
- Deutsches Zentrum ImmuntherapieFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Stefan Momma
- Institute of Neurology (Edinger Institute)Goethe UniversityFrankfurt am MainGermany
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20
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Ihbe N, Le Prieult F, Wang Q, Distler U, Sielaff M, Tenzer S, Thal SC, Mittmann T. Adaptive Mechanisms of Somatostatin-Positive Interneurons after Traumatic Brain Injury through a Switch of α Subunits in L-Type Voltage-Gated Calcium Channels. Cereb Cortex 2021; 32:1093-1109. [PMID: 34411234 DOI: 10.1093/cercor/bhab268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/28/2022] Open
Abstract
Unilateral traumatic brain injury (TBI) causes cortical dysfunctions spreading to the primarily undamaged hemisphere. This phenomenon, called transhemispheric diaschisis, is mediated by an imbalance of glutamatergic versus GABAergic neurotransmission. This study investigated the role of GABAergic, somatostatin-positive (SST) interneurons in the contralateral hemisphere 72 h after unilateral TBI. The brain injury was induced to the primary motor/somatosensory cortex of glutamate decarboxylase 67-green fluorescent protein (GAD67-GFP) knock-in mice at postnatal days 19-21 under anesthesia in vivo. Single GFP+ interneurons of the undamaged, contralateral cortex were isolated by fluorescence-activated cell sorting and analyzed by mass spectrometry. TBI caused a switch of 2 α subunits of pore-forming L-type voltage-gated calcium channels (VGCC) in GABAergic interneurons, an increased expression of CaV1.3, and simultaneous ablation of CaV1.2. This switch was associated with 1) increased excitability of single SST interneurons in patch-clamp recordings and (2) a recovery from early network hyperactivity in the contralateral hemisphere in microelectrode array recordings of acute slices. The electrophysiological changes were sensitive to pharmacological blockade of CaV1.3 (isradipine, 100 nM). These data identify a switch of 2 α subunits of VGCCs in SST interneurons early after TBI as a mechanism to counterbalance post-traumatic hyperexcitability.
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Affiliation(s)
- Natascha Ihbe
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Florie Le Prieult
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Qi Wang
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Malte Sielaff
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Serge C Thal
- Clinic for Anesthesiology, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Thomas Mittmann
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
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21
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Jung S, Fuchs N, Johe P, Wagner A, Diehl E, Yuliani T, Zimmer C, Barthels F, Zimmermann RA, Klein P, Waigel W, Meyr J, Opatz T, Tenzer S, Distler U, Räder HJ, Kersten C, Engels B, Hellmich UA, Klein J, Schirmeister T. Fluorovinylsulfones and -Sulfonates as Potent Covalent Reversible Inhibitors of the Trypanosomal Cysteine Protease Rhodesain: Structure-Activity Relationship, Inhibition Mechanism, Metabolism, and In Vivo Studies. J Med Chem 2021; 64:12322-12358. [PMID: 34378914 DOI: 10.1021/acs.jmedchem.1c01002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Rhodesain is a major cysteine protease of Trypanosoma brucei rhodesiense, a pathogen causing Human African Trypanosomiasis, and a validated drug target. Recently, we reported the development of α-halovinylsulfones as a new class of covalent reversible cysteine protease inhibitors. Here, α-fluorovinylsulfones/-sulfonates were optimized for rhodesain based on molecular modeling approaches. 2d, the most potent and selective inhibitor in the series, shows a single-digit nanomolar affinity and high selectivity toward mammalian cathepsins B and L. Enzymatic dilution assays and MS experiments indicate that 2d is a slow-tight binder (Ki = 3 nM). Furthermore, the nonfluorinated 2d-(H) shows favorable metabolism and biodistribution by accumulation in mice brain tissue after intraperitoneal and oral administration. The highest antitrypanosomal activity was observed for inhibitors with an N-terminal 2,3-dihydrobenzo[b][1,4]dioxine group and a 4-Me-Phe residue in P2 (2e/4e) with nanomolar EC50 values (0.14/0.80 μM). The different mechanisms of reversible and irreversible inhibitors were explained using QM/MM calculations and MD simulations.
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Affiliation(s)
- Sascha Jung
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Natalie Fuchs
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Patrick Johe
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Annika Wagner
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Erika Diehl
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Tri Yuliani
- Institute for Pharmacology and Clinical Pharmacy, Goethe University, Max-von-Laue-Str. 9, 60439 Frankfurt, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Philipp Klein
- Department of Chemistry, Organic Chemistry Section, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Waldemar Waigel
- Department of Physical and Theoretical Chemistry, Julius-Maximilians-University, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Jessica Meyr
- Department of Physical and Theoretical Chemistry, Julius-Maximilians-University, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Till Opatz
- Department of Chemistry, Organic Chemistry Section, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center, Johannes Gutenberg University, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center, Johannes Gutenberg University, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Hans-Joachim Räder
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Bernd Engels
- Department of Physical and Theoretical Chemistry, Julius-Maximilians-University, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Ute A Hellmich
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jochen Klein
- Institute for Pharmacology and Clinical Pharmacy, Goethe University, Max-von-Laue-Str. 9, 60439 Frankfurt, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
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22
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Abstract
The Bruker timsTOF Pro is an instrument that couples trapped ion mobility spectrometry (TIMS) to high-resolution time-of-flight (TOF) mass spectrometry (MS). For proteomics, lipidomics, and metabolomics applications, the instrument is typically interfaced with a liquid chromatography (LC) system. The resulting LC-TIMS-MS data sets are, in general, several gigabytes in size and are stored in the proprietary Bruker Tims data format (TDF). The raw data can be accessed using proprietary binaries in C, C++, and Python on Windows and Linux operating systems. Here we introduce a suite of computer programs for data accession, including OpenTIMS, TimsR, and TimsPy. OpenTIMS is a C++ library capable of reading Bruker TDF files. It opens up Bruker's proprietary codebase. TimsPy and TimsR build on top of OpenTIMS, enabling swift and user-friendly data access to the raw data with Python and R. Both programs are available under a GPL3 license on all major platforms, extending the possibility to interact with timsTOF data to macOS. Additionally, OpenTIMS is capable of translating Bruker data into HDF5 files that can be easily analyzed from Python with the vaex module. OpenTIMS and TimsPy therefore provide easy and quick access to Bruker timsTOF raw data.
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Affiliation(s)
- Mateusz K Łącki
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, 55131 Mainz, Germany
| | - Michał P Startek
- Department of Mathematics, Informatics, and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
| | | | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, 55131 Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, 55131 Mainz, Germany
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23
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Sielaff M, Curella V, Neerukonda M, Afzal M, El Hassouni K, Distler U, Schuppan D, Longin CFH, Tenzer S. Hybrid QconCAT-Based Targeted Absolute and Data-Independent Acquisition-Based Label-Free Quantification Enables In-Depth Proteomic Characterization of Wheat Amylase/Trypsin Inhibitor Extracts. J Proteome Res 2021; 20:1544-1557. [PMID: 33507751 DOI: 10.1021/acs.jproteome.0c00752] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Wheat amylase/trypsin inhibitors (ATIs) have gained significant relevance as inducers of intestinal and extra-intestinal inflammation. In this study, we present a novel hybrid data-independent acquisition (DIA) liquid chromatography-mass spectrometry (LC-MS) approach, combining QconCAT technology with short microflow LC gradients and DIA and apply the method toward the quantitative proteome analysis of ATI extracts. The presented method is fast, robust, and reproducible and provides precise QconCAT-based absolute quantification of major ATI proteins while simultaneously quantifying the proteome by label-free quantification (LFQ). We analyzed extracts of 60 varieties of common wheat grown in replication and evaluated the reproducibility and precision of the workflow for the quantification of ATIs. Applying the method to analyze different wheat species (i.e., common wheat, spelt, durum wheat, emmer, and einkorn) and comparing the results to published data, we validated inter-laboratory and cross-methodology reproducibility of ATI quantification, which is essential in the context of large-scale breeding projects. Additionally, we applied our workflow to assess environmental effects on ATI expression, analyzing ATI content and proteome of same varieties grown at different locations. Finally, we explored the potential of combining QconCAT-based absolute quantification with DIA-based LFQ proteome analysis for the generation of new hypotheses or assay development.
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Affiliation(s)
- Malte Sielaff
- Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Valentina Curella
- Institute of Translational Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Manjusha Neerukonda
- Institute of Translational Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Muhammad Afzal
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany
| | - Khaoula El Hassouni
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Detlef Schuppan
- Institute of Translational Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany.,Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
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24
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Sinitcyn P, Hamzeiy H, Salinas Soto F, Itzhak D, McCarthy F, Wichmann C, Steger M, Ohmayer U, Distler U, Kaspar-Schoenefeld S, Prianichnikov N, Yılmaz Ş, Rudolph JD, Tenzer S, Perez-Riverol Y, Nagaraj N, Humphrey SJ, Cox J. MaxDIA enables library-based and library-free data-independent acquisition proteomics. Nat Biotechnol 2021; 39:1563-1573. [PMID: 34239088 PMCID: PMC8668435 DOI: 10.1038/s41587-021-00968-7] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA-hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA's bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies-BoxCar acquisition and trapped ion mobility spectrometry-both lead to deep and accurate proteome quantification.
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Affiliation(s)
- Pavel Sinitcyn
- grid.418615.f0000 0004 0491 845XComputational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Hamid Hamzeiy
- grid.418615.f0000 0004 0491 845XComputational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Favio Salinas Soto
- grid.418615.f0000 0004 0491 845XComputational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel Itzhak
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA
| | - Frank McCarthy
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA
| | - Christoph Wichmann
- grid.418615.f0000 0004 0491 845XComputational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | - Ute Distler
- grid.5802.f0000 0001 1941 7111Institute for Immunology, Johannes Gutenberg University, Mainz, Germany
| | | | - Nikita Prianichnikov
- grid.418615.f0000 0004 0491 845XComputational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Şule Yılmaz
- grid.418615.f0000 0004 0491 845XComputational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Jan Daniel Rudolph
- grid.418615.f0000 0004 0491 845XComputational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany ,grid.6584.f0000 0004 0553 2276Bosch Center for Artificial Intelligence, Renningen, Germany
| | - Stefan Tenzer
- grid.5802.f0000 0001 1941 7111Institute for Immunology, Johannes Gutenberg University, Mainz, Germany
| | - Yasset Perez-Riverol
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Sean J. Humphrey
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, New South Wales Australia
| | - Jürgen Cox
- grid.418615.f0000 0004 0491 845XComputational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany ,grid.7914.b0000 0004 1936 7443Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway
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25
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Barthels F, Marincola G, Marciniak T, Konhäuser M, Hammerschmidt S, Bierlmeier J, Distler U, Wich PR, Tenzer S, Schwarzer D, Ziebuhr W, Schirmeister T. Asymmetric Disulfanylbenzamides as Irreversible and Selective Inhibitors of Staphylococcus aureus Sortase A. ChemMedChem 2020; 15:839-850. [PMID: 32118357 PMCID: PMC7318353 DOI: 10.1002/cmdc.201900687] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/07/2020] [Indexed: 12/19/2022]
Abstract
Staphylococcus aureus is one of the most frequent causes of nosocomial and community-acquired infections, with drug-resistant strains being responsible for tens of thousands of deaths per year. S. aureus sortase A inhibitors are designed to interfere with virulence determinants. We have identified disulfanylbenzamides as a new class of potent inhibitors against sortase A that act by covalent modification of the active-site cysteine. A broad series of derivatives were synthesized to derive structure-activity relationships (SAR). In vitro and in silico methods allowed the experimentally observed binding affinities and selectivities to be rationalized. The most active compounds were found to have single-digit micromolar Ki values and caused up to a 66 % reduction of S. aureus fibrinogen attachment at an effective inhibitor concentration of 10 μM. This new molecule class exhibited minimal cytotoxicity, low bacterial growth inhibition and impaired sortase-mediated adherence of S. aureus cells.
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Affiliation(s)
- Fabian Barthels
- Institute for Pharmacy and BiochemistryJohannes-Gutenberg-University of MainzStaudinger Weg 555128MainzGermany
| | - Gabriella Marincola
- Institute for Molecular Infection BiologyJulius-Maximilians-University of WürzburgJosef-Schneider-Strasse 297080WürzburgGermany
| | - Tessa Marciniak
- Institute for Molecular Infection BiologyJulius-Maximilians-University of WürzburgJosef-Schneider-Strasse 297080WürzburgGermany
| | - Matthias Konhäuser
- Institute for Pharmacy and BiochemistryJohannes-Gutenberg-University of MainzStaudinger Weg 555128MainzGermany
| | - Stefan Hammerschmidt
- Institute for Pharmacy and BiochemistryJohannes-Gutenberg-University of MainzStaudinger Weg 555128MainzGermany
| | - Jan Bierlmeier
- Interfaculty Institute of BiochemistryEberhard-Karls-University of TübingenHoppe-Seyler-Strasse 472076TübingenGermany
| | - Ute Distler
- Institute for ImmunologyUniversity Medical CenterJohannes-Gutenberg-University of MainzLangenbeckstr. 155131MainzGermany
- Focus Program Translational Neuroscience (FTN)University Medical CenterLangenbeckstr. 155131MainzGermany
| | - Peter R. Wich
- Institute for Pharmacy and BiochemistryJohannes-Gutenberg-University of MainzStaudinger Weg 555128MainzGermany
- School of Chemical EngineeringUniversity of New South WalesScience and Engineering BuildingSydneyNSW 2052Australia
| | - Stefan Tenzer
- Institute for ImmunologyUniversity Medical CenterJohannes-Gutenberg-University of MainzLangenbeckstr. 155131MainzGermany
| | - Dirk Schwarzer
- Interfaculty Institute of BiochemistryEberhard-Karls-University of TübingenHoppe-Seyler-Strasse 472076TübingenGermany
| | - Wilma Ziebuhr
- Institute for Molecular Infection BiologyJulius-Maximilians-University of WürzburgJosef-Schneider-Strasse 297080WürzburgGermany
| | - Tanja Schirmeister
- Institute for Pharmacy and BiochemistryJohannes-Gutenberg-University of MainzStaudinger Weg 555128MainzGermany
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26
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Klein P, Barthels F, Johe P, Wagner A, Tenzer S, Distler U, Le TA, Schmid P, Engel V, Engels B, Hellmich UA, Opatz T, Schirmeister T. Naphthoquinones as Covalent Reversible Inhibitors of Cysteine Proteases-Studies on Inhibition Mechanism and Kinetics. Molecules 2020; 25:molecules25092064. [PMID: 32354191 PMCID: PMC7248907 DOI: 10.3390/molecules25092064] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
The facile synthesis and detailed investigation of a class of highly potent protease inhibitors based on 1,4-naphthoquinones with a dipeptidic recognition motif (HN-l-Phe-l-Leu-OR) in the 2-position and an electron-withdrawing group (EWG) in the 3-position is presented. One of the compound representatives, namely the acid with EWG = CN and with R = H proved to be a highly potent rhodesain inhibitor with nanomolar affinity. The respective benzyl ester (R = Bn) was found to be hydrolyzed by the target enzyme itself yielding the free acid. Detailed kinetic and mass spectrometry studies revealed a reversible covalent binding mode. Theoretical calculations with different density functionals (DFT) as well as wavefunction-based approaches were performed to elucidate the mode of action.
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Affiliation(s)
- Philipp Klein
- Department of Chemistry, Organic Chemistry Section, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany;
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, 55128 Mainz, Germany; (F.B.); (P.J.)
| | - Patrick Johe
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, 55128 Mainz, Germany; (F.B.); (P.J.)
| | - Annika Wagner
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg-Universität, Johann-Joachim Becherweg 30, 55128 Mainz, Germany; (A.W.); (U.A.H.)
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center, Johannes Gutenberg-Universität Mainz, Langenbeckstr. 1, 55131 Mainz, Germany; (S.T.); (U.D.)
| | - Ute Distler
- Institute of Immunology, University Medical Center, Johannes Gutenberg-Universität Mainz, Langenbeckstr. 1, 55131 Mainz, Germany; (S.T.); (U.D.)
| | - Thien Anh Le
- Institute of Physical and Theoretical Chemistry, Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany; (T.A.L.); (P.S.); (V.E.); (B.E.)
| | - Paul Schmid
- Institute of Physical and Theoretical Chemistry, Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany; (T.A.L.); (P.S.); (V.E.); (B.E.)
| | - Volker Engel
- Institute of Physical and Theoretical Chemistry, Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany; (T.A.L.); (P.S.); (V.E.); (B.E.)
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany; (T.A.L.); (P.S.); (V.E.); (B.E.)
| | - Ute A. Hellmich
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg-Universität, Johann-Joachim Becherweg 30, 55128 Mainz, Germany; (A.W.); (U.A.H.)
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60323 Frankfurt, Germany
| | - Till Opatz
- Department of Chemistry, Organic Chemistry Section, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany;
- Correspondence: (T.O.); (T.S.); Tel.: +49-(0)6131-39-22272 (T.O.); +49-(0)6131-39-25742 (T.S.)
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, 55128 Mainz, Germany; (F.B.); (P.J.)
- Correspondence: (T.O.); (T.S.); Tel.: +49-(0)6131-39-22272 (T.O.); +49-(0)6131-39-25742 (T.S.)
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27
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Kehl T, Schneider L, Kattler K, Stöckel D, Wegert J, Gerstner N, Ludwig N, Distler U, Schick M, Keller U, Tenzer S, Gessler M, Walter J, Keller A, Graf N, Meese E, Lenhof HP. REGGAE: a novel approach for the identification of key transcriptional regulators. Bioinformatics 2019; 34:3503-3510. [PMID: 29741575 PMCID: PMC6184769 DOI: 10.1093/bioinformatics/bty372] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/03/2018] [Indexed: 12/13/2022] Open
Abstract
Motivation Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes. Results Here, we present REGulator-Gene Association Enrichment (REGGAE), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov-Smirnov-like test statistic that implicitly combines associations between regulators and their target genes with an enrichment approach to prioritize the influence of transcriptional regulators. We evaluated our method in two different application scenarios, which demonstrate that REGGAE is well suited for uncovering the influence of transcriptional regulators and is a valuable tool for the elucidation of complex regulatory mechanisms. Availability and implementation REGGAE is freely available at https://regulatortrail.bioinf.uni-sb.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken D-66041, Germany
| | - Lara Schneider
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken D-66041, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, Saarbrücken D-66041, Germany
| | - Daniel Stöckel
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken D-66041, Germany
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Würzburg University, Würzburg, Germany
| | - Nico Gerstner
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken D-66041, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
| | - Ute Distler
- Institute for Immunology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Markus Schick
- Department of Internal Medicine III, School of Medicine, Technische Universität München, Munich, Germany
| | - Ulrich Keller
- Department of Internal Medicine III, School of Medicine, Technische Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Tenzer
- Institute for Immunology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Würzburg University, Würzburg, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, Saarbrücken D-66041, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken D-66041, Germany
| | - Norbert Graf
- Department of Pediatric Oncology and Hematology, Medical School, Saarland University, Homburg, Germany
| | - Eckart Meese
- Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken D-66041, Germany
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28
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Garg A, Orru R, Ye W, Distler U, Chojnacki JE, Köhn M, Tenzer S, Sönnichsen C, Wolf E. Structural and mechanistic insights into the interaction of the circadian transcription factor BMAL1 with the KIX domain of the CREB-binding protein. J Biol Chem 2019; 294:16604-16619. [PMID: 31515273 DOI: 10.1074/jbc.ra119.009845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
The mammalian CLOCK:BMAL1 transcription factor complex and its coactivators CREB-binding protein (CBP)/p300 and mixed-lineage leukemia 1 (MLL1) critically regulate circadian transcription and chromatin modification. Circadian oscillations are regulated by interactions of BMAL1's C-terminal transactivation domain (TAD) with the KIX domain of CBP/p300 (activating) and with the clock protein CRY1 (repressing) as well as by the BMAL1 G-region preceding the TAD. Circadian acetylation of Lys537 within the G-region enhances repressive BMAL1-TAD-CRY1 interactions. Here, we characterized the interaction of the CBP-KIX domain with BMAL1 proteins, including the BMAL1-TAD, parts of the G-region, and Lys537 Tethering the small compound 1-10 in the MLL-binding pocket of the CBP-KIX domain weakened BMAL1 binding, and MLL1-bound KIX did not form a ternary complex with BMAL1, indicating that the MLL-binding pocket is important for KIX-BMAL1 interactions. Small-angle X-ray scattering (SAXS) models of BMAL1 and BMAL1:KIX complexes revealed that the N-terminal BMAL1 G-region including Lys537 forms elongated extensions emerging from the bulkier BMAL1-TAD:KIX core complex. Fitting high-resolution KIX domain structures into the SAXS-derived envelopes suggested that the G-region emerges near the MLL-binding pocket, further supporting a role of this pocket in BMAL1 binding. Additionally, mutations in the second CREB-pKID/c-Myb-binding pocket of the KIX domain moderately impacted BMAL1 binding. The BMAL1(K537Q) mutation mimicking Lys537 acetylation, however, did not affect the KIX-binding affinity, in contrast to its enhancing effect on CRY1 binding. Our results significantly advance the mechanistic understanding of the protein interaction networks controlling CLOCK:BMAL1- and CBP-dependent gene regulation in the mammalian circadian clock.
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Affiliation(s)
- Archit Garg
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany.,Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, 55128 Mainz, Germany
| | - Roberto Orru
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, 55128 Mainz, Germany
| | - Weixiang Ye
- Institute of Physical Chemistry, Johannes Gutenberg-University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, 55131 Mainz, Germany
| | | | - Maja Köhn
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, 55131 Mainz, Germany
| | - Carsten Sönnichsen
- Institute of Physical Chemistry, Johannes Gutenberg-University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Eva Wolf
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany .,Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, 55128 Mainz, Germany
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29
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Distler U, Łącki MK, Schumann S, Wanninger M, Tenzer S. Enhancing Sensitivity of Microflow-Based Bottom-Up Proteomics through Postcolumn Solvent Addition. Anal Chem 2019; 91:7510-7515. [PMID: 31117400 DOI: 10.1021/acs.analchem.9b00118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The introduction of more sensitive mass spectrometers allows researchers to adapt front-end liquid chromatography (LC) to individual needs for the analysis of complex proteomes. Where absolute sensitivity is not paramount, it is advantageous to switch from a highly sensitive nanoflow-LC setup, the de facto standard platform in mass-spectrometry (MS)-based discovery proteomics, to a more robust, high-throughput-compatible microflow or conventional-flow setup. To enhance the microflow-LC-MS electrospray process of complex proteomic samples, we tested the effects of different solvents, including 2-propanol, methanol, and acetonitrile, pure or as mixture with dimethyl sulfoxide, which were added postcolumn to the eluting sample. Postcolumn addition of organic solvents strongly enhanced the electrospray efficiency in microflow-LC-MS experiments and improved the sensitivity across the entire gradient and for early eluting peptides by up to 10-fold. Postcolumn solvent addition did not negatively affect chromatographic performance and resulted in an overall 28-36% increase in identifications at both the protein and peptide levels. The presented microflow-LC-MS workflow, including postcolumn solvent addition, can be easily adopted on any LC-MS/MS platform.
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Affiliation(s)
- Ute Distler
- Institute of Immunology , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany.,Focus Program Translational Neuroscience (FTN) , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany
| | - Sven Schumann
- Institute of Anatomy , Otto von Guericke University Magdeburg , Magdeburg 39120 , Germany
| | - Markus Wanninger
- Waters Corporation , Milford , Massachusetts 01757 , United States
| | - Stefan Tenzer
- Institute of Immunology , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany
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30
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Bohnert S, Heck L, Gruber C, Neumann H, Distler U, Tenzer S, Yemelin A, Thines E, Jacob S. Fungicide resistance towards fludioxonil conferred by overexpression of the phosphatase gene
Mo
PTP
2
in
Magnaporthe oryzae. Mol Microbiol 2018; 111:662-677. [DOI: 10.1111/mmi.14179] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Stefan Bohnert
- Institut für Biotechnologie und Wirkstoff‐Forschung gGmbH (IBWF) Erwin‐Schrödinger‐Str. 56 D‐67663 Kaiserslautern
| | - Larissa Heck
- Johannes Gutenberg‐University Mainz Mikrobiologie und Weinforschung am Institut für Molekulare Physiologie Johann‐Joachim‐Becherweg 15 D‐55128 Mainz
| | - Christoph Gruber
- Institut für Biotechnologie und Wirkstoff‐Forschung gGmbH (IBWF) Erwin‐Schrödinger‐Str. 56 D‐67663 Kaiserslautern
| | - Hendrik Neumann
- Johannes Gutenberg‐University Mainz Mikrobiologie und Weinforschung am Institut für Molekulare Physiologie Johann‐Joachim‐Becherweg 15 D‐55128 Mainz
| | - Ute Distler
- Institute for Immunology University Medical Center of Mainz Langenbeck‐Str. 1 D‐55101 Mainz
| | - Stefan Tenzer
- Institute for Immunology University Medical Center of Mainz Langenbeck‐Str. 1 D‐55101 Mainz
| | - Alexander Yemelin
- Institut für Biotechnologie und Wirkstoff‐Forschung gGmbH (IBWF) Erwin‐Schrödinger‐Str. 56 D‐67663 Kaiserslautern
| | - Eckhard Thines
- Institut für Biotechnologie und Wirkstoff‐Forschung gGmbH (IBWF) Erwin‐Schrödinger‐Str. 56 D‐67663 Kaiserslautern
- Johannes Gutenberg‐University Mainz Mikrobiologie und Weinforschung am Institut für Molekulare Physiologie Johann‐Joachim‐Becherweg 15 D‐55128 Mainz
| | - Stefan Jacob
- Institut für Biotechnologie und Wirkstoff‐Forschung gGmbH (IBWF) Erwin‐Schrödinger‐Str. 56 D‐67663 Kaiserslautern
- Johannes Gutenberg‐University Mainz Mikrobiologie und Weinforschung am Institut für Molekulare Physiologie Johann‐Joachim‐Becherweg 15 D‐55128 Mainz
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31
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Kehl T, Schneider L, Kattler K, Stöckel D, Wegert J, Gerstner N, Ludwig N, Distler U, Tenzer S, Gessler M, Walter J, Keller A, Graf N, Meese E, Lenhof HP. The role of TCF3 as potential master regulator in blastemal Wilms tumors. Int J Cancer 2018; 144:1432-1443. [PMID: 30155889 DOI: 10.1002/ijc.31834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/05/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022]
Abstract
Wilms tumors are the most common type of pediatric kidney tumors. While the overall prognosis for patients is favorable, especially tumors that exhibit a blastemal subtype after preoperative chemotherapy have a poor prognosis. For an improved risk assessment and therapy stratification, it is essential to identify the driving factors that are distinctive for this aggressive subtype. In our study, we compared gene expression profiles of 33 tumor biopsies (17 blastemal and 16 other tumors) after neoadjuvant chemotherapy. The analysis of this dataset using the Regulator Gene Association Enrichment algorithm successfully identified several biomarkers and associated molecular mechanisms that distinguish between blastemal and nonblastemal Wilms tumors. Specifically, regulators involved in embryonic development and epigenetic processes like chromatin remodeling and histone modification play an essential role in blastemal tumors. In this context, we especially identified TCF3 as the central regulatory element. Furthermore, the comparison of ChIP-Seq data of Wilms tumor cell cultures from a blastemal mouse xenograft and a stromal tumor provided further evidence that the chromatin states of blastemal cells share characteristics with embryonic stem cells that are not present in the stromal tumor cell line. These stem-cell like characteristics could potentially add to the increased malignancy and chemoresistance of the blastemal subtype. Along with TCF3, we detected several additional biomarkers that are distinctive for blastemal Wilms tumors after neoadjuvant chemotherapy and that may provide leads for new therapeutic regimens.
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Affiliation(s)
- Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Lara Schneider
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | - Daniel Stöckel
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Würzburg University, Würzburg, Germany
| | - Nico Gerstner
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Nicole Ludwig
- Human Genetics, Saarland University, Homburg, Germany
| | - Ute Distler
- Institute for Immunology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Würzburg University, Würzburg, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Norbert Graf
- Department of Pediatric Oncology and Hematology, Medical School, Saarland University, Homburg, Germany
| | - Eckart Meese
- Human Genetics, Saarland University, Homburg, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
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32
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Ruder B, Murtadak V, Stürzl M, Wirtz S, Distler U, Tenzer S, Mahapatro M, Greten FR, Hu Y, Neurath MF, Cesarman E, Ballon G, Günther C, Becker C. Chronic intestinal inflammation in mice expressing viral Flip in epithelial cells. Mucosal Immunol 2018; 11:1621-1629. [PMID: 30104627 PMCID: PMC8063487 DOI: 10.1038/s41385-018-0068-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/04/2018] [Accepted: 07/10/2018] [Indexed: 02/04/2023]
Abstract
Viruses are present in the intestinal microflora and are currently discussed as a potential causative mechanism for the development of inflammatory bowel disease. A number of viruses, such as Human Herpesvirus-8, express homologs to cellular FLIPs, which are major contributors for the regulation of epithelial cell death. In this study we analyzed the consequences of constitutive expression of HHV8-viral FLIP in intestinal epithelial cells (IECs) in mice. Surprisingly, expression of vFlip disrupts tissue homeostasis and induces severe intestinal inflammation. Moreover vFlipIEC-tg mice showed reduced Paneth cell numbers, associated with excessive necrotic cell death. On a molecular level vFlip expression altered classical and alternative NFκB activation. Blocking of alternative NFκB signaling by deletion of Ikka in vivo largely protected mice from inflammation and Paneth cell loss induced by vFLIP. Collectively, our data provide functional evidence that expression of a single viral protein in IECs can be sufficient to disrupt epithelial homeostasis and to initiate chronic intestinal inflammation.
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Affiliation(s)
- Barbara Ruder
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Vinay Murtadak
- Division of Molecular and Experimental Surgery, Department of Surgery, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Department of Surgery, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Stefan Wirtz
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Mousumi Mahapatro
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Florian R. Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Yinling Hu
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Markus F. Neurath
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, USA
| | - Gianna Ballon
- Department of Pathology and Laboratory Medicine, Northwell Health, Lake Success, NY, USA
| | - Claudia Günther
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Christoph Becker
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
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33
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Lacher SM, Thurm C, Distler U, Mohebiany AN, Israel N, Kitic M, Ebering A, Tang Y, Klein M, Wabnitz GH, Wanke F, Samstag Y, Bopp T, Kurschus FC, Simeoni L, Tenzer S, Waisman A. NF-κB inducing kinase (NIK) is an essential post-transcriptional regulator of T-cell activation affecting F-actin dynamics and TCR signaling. J Autoimmun 2018; 94:110-121. [PMID: 30061013 DOI: 10.1016/j.jaut.2018.07.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/20/2018] [Accepted: 07/25/2018] [Indexed: 11/16/2022]
Abstract
NF-κB inducing kinase (NIK) is the key protein of the non-canonical NF-κB pathway and is important for the development of lymph nodes and other secondary immune organs. We elucidated the specific role of NIK in T cells using T-cell specific NIK-deficient (NIKΔT) mice. Despite showing normal development of lymphoid organs, NIKΔT mice were resistant to induction of CNS autoimmunity. T cells from NIKΔT mice were deficient in late priming, failed to up-regulate T-bet and to transmigrate into the CNS. Proteomic analysis of activated NIK-/- T cells showed de-regulated expression of proteins involved in the formation of the immunological synapse: in particular, proteins involved in cytoskeleton dynamics. In line with this we found that NIK-deficient T cells were hampered in phosphorylation of Zap70, LAT, AKT, ERK1/2 and PLCγ upon TCR engagement. Hence, our data disclose a hitherto unknown function of NIK in T-cell priming and differentiation.
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MESH Headings
- Actins/genetics
- Actins/immunology
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/immunology
- Animals
- Central Nervous System/immunology
- Central Nervous System/pathology
- Encephalomyelitis, Autoimmune, Experimental/chemically induced
- Encephalomyelitis, Autoimmune, Experimental/genetics
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Encephalomyelitis, Autoimmune, Experimental/pathology
- Gene Expression Profiling
- Gene Expression Regulation
- Lymph Nodes/immunology
- Lymph Nodes/pathology
- Lymphocyte Activation
- Membrane Proteins/genetics
- Membrane Proteins/immunology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mitogen-Activated Protein Kinase 1/genetics
- Mitogen-Activated Protein Kinase 1/immunology
- Mitogen-Activated Protein Kinase 3/genetics
- Mitogen-Activated Protein Kinase 3/immunology
- Myelin-Oligodendrocyte Glycoprotein/administration & dosage
- Peptide Fragments/administration & dosage
- Phospholipase C gamma/genetics
- Phospholipase C gamma/immunology
- Phosphoproteins/genetics
- Phosphoproteins/immunology
- Primary Cell Culture
- Protein Serine-Threonine Kinases/deficiency
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/immunology
- Proto-Oncogene Proteins c-akt/genetics
- Proto-Oncogene Proteins c-akt/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Signal Transduction
- Spleen/immunology
- Spleen/pathology
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/immunology
- T-Lymphocytes/immunology
- T-Lymphocytes/pathology
- ZAP-70 Protein-Tyrosine Kinase/genetics
- ZAP-70 Protein-Tyrosine Kinase/immunology
- NF-kappaB-Inducing Kinase
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Affiliation(s)
- Sonja M Lacher
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Christoph Thurm
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology, and Inflammation, Otto von Guericke University, Magdeburg, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Alma N Mohebiany
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Nicole Israel
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Maja Kitic
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Anna Ebering
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Yilang Tang
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Matthias Klein
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Guido H Wabnitz
- Institute of Immunology, Section Molecular Immunology, Ruprecht-Karls-University, Heidelberg, Germany
| | - Florian Wanke
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Yvonne Samstag
- Institute of Immunology, Section Molecular Immunology, Ruprecht-Karls-University, Heidelberg, Germany
| | - Tobias Bopp
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Florian C Kurschus
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Luca Simeoni
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology, and Inflammation, Otto von Guericke University, Magdeburg, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.
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34
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Shen L, Tenzer S, Hess M, Distler U, Tubbe I, Montermann E, Schimmer S, Dittmer U, Grabbe S, Bros M. Friend virus limits adaptive cellular immune responses by imprinting a maturation-resistant and T helper type 2-biased immunophenotype in dendritic cells. PLoS One 2018; 13:e0192541. [PMID: 29425215 PMCID: PMC5806892 DOI: 10.1371/journal.pone.0192541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/25/2018] [Indexed: 12/28/2022] Open
Abstract
The murine Friend virus (FV) retrovirus model has been widely used to study anti-viral immune responses, and virus-induced cancer. Here we analyzed FV immune evasion mechanisms on the level of dendritic cells (DC) essential for the induction of primary adaptive immune responses. Comparative quantitative proteome analysis of FV-infected DC (FV-DC) of different genotypes (BALB/c, C57BL/6) and non-infected DC revealed numerous genotype-independently regulated proteins rergulating metabolic activity, cytoskeletal rearrangements, and antigen processing/presentation. These alterations may promote virion production in FV-DC. Stimulation of FV-DC with LPS resulted in strongly enhanced IL-10 production which was partially responsible for their attenuated T cell (CD4+, CD8+) stimulatory capacity. Stimulated FV-DC induced less IFN-γ production in T cells required for cellular anti-viral responses, but more T helper cell type 2 (Th2)-associated cytokines (IL-4, IL-5, IL-13). We conclude that FV reprograms DC to promote viral spreading and immune deviation by imprinting a largely maturation-resistant, Th2-biased immunophenotype.
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Affiliation(s)
- Limei Shen
- Department of Dermatology, University Medical Center, Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center, Mainz, Germany
| | - Moritz Hess
- Institute for Medical Biometry, Epidemiology and Informatics, University Medical Center, Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center, Mainz, Germany
| | - Ingrid Tubbe
- Department of Dermatology, University Medical Center, Mainz, Germany
| | - Evelyn Montermann
- Department of Dermatology, University Medical Center, Mainz, Germany
| | - Simone Schimmer
- Institute for Virology of the University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology of the University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Stephan Grabbe
- Department of Dermatology, University Medical Center, Mainz, Germany
- * E-mail:
| | - Matthias Bros
- Department of Dermatology, University Medical Center, Mainz, Germany
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Abstract
The identification of the major virulence factors that drive pathogenicity is critical for gaining insight into the underlying molecular mechanisms of diseases. Although genetic approaches combined with functional analyses have markedly increased the rate of virulence factor discovery, the divergence between genome and proteome can impair the identification of important markers, in particular, of those that act in concert or depend on specific environmental factors. Recently, membrane-coated nanomaterials mimicking source cells of interest have emerged as powerful tools that can be used for improved tumor targeting and as "nanotraps" to capture chemokines and bacterial toxins. In this issue of ACS Nano, Lapek et al. demonstrate that membrane-coated nanosponges in combination with quantitative proteomics can also be used as efficient "fishing devices" for the identification of cell-type-specific virulence factors.
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Affiliation(s)
- Ute Distler
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz , Langenbeckstr. 1, 55131 Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz , Langenbeckstr. 1, 55131 Mainz, Germany
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Sielaff M, Kuharev J, Bohn T, Hahlbrock J, Bopp T, Tenzer S, Distler U. Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range. J Proteome Res 2017; 16:4060-4072. [DOI: 10.1021/acs.jproteome.7b00433] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Malte Sielaff
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Jörg Kuharev
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Toszka Bohn
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Jennifer Hahlbrock
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Tobias Bopp
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Stefan Tenzer
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Ute Distler
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
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Riebel M, Fronk P, Distler U, Tenzer S, Decker H. Proteomic profiling of German Dornfelder grape berries using data-independent acquisition. Plant Physiol Biochem 2017; 118:64-70. [PMID: 28618374 DOI: 10.1016/j.plaphy.2017.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/29/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
Grapevine is one of the most important fruit plants throughout the world. Sequencing of the grape genome in 2007 enabled in-depth analyses of the grape proteome. Whereas many studies addressed changes in proteomic composition of grapes during ripening, we focused on the proteome of mature grape berries from Dornfelder, a characteristic red wine grape for Germany. Current data-independent acquisition proteomics technology enables the analysis of proteomic compositions in a degree of accuracy that was unreachable only a few years ago. Using a label-free proteomics approach, we quantified 712 proteins in mature Dornfelder grape berries, of which 650 could be annotated by the Blast2GO software. Besides identification of proteins, our analysis provides protein amounts using the TOP3 absolute quantification approach. Most of the proteins (200) in mature Dornfelder grape berries are involved in stress response. In addition, all glycolytic key enzymes were detected in mature grape berries suggesting that glycolysis is still active, whereas sugar accumulation through gluconeogenesis utilizing malate as substrate seems to play a minor role.
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Affiliation(s)
- Matthias Riebel
- Institute for Molecular Physiology, Molecular Biophysics, Johannes Gutenberg University Mainz, Jakob-Welder-Weg, 26, D-55128 Mainz, Germany.
| | - Petra Fronk
- Institute for Molecular Physiology, Molecular Biophysics, Johannes Gutenberg University Mainz, Jakob-Welder-Weg, 26, D-55128 Mainz, Germany.
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, D-55131 Mainz, Germany.
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, D-55131 Mainz, Germany.
| | - Heinz Decker
- Institute for Molecular Physiology, Molecular Biophysics, Johannes Gutenberg University Mainz, Jakob-Welder-Weg, 26, D-55128 Mainz, Germany.
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38
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Reim D, Distler U, Halbedl S, Verpelli C, Sala C, Bockmann J, Tenzer S, Boeckers TM, Schmeisser MJ. Proteomic Analysis of Post-synaptic Density Fractions from Shank3 Mutant Mice Reveals Brain Region Specific Changes Relevant to Autism Spectrum Disorder. Front Mol Neurosci 2017; 10:26. [PMID: 28261056 PMCID: PMC5306440 DOI: 10.3389/fnmol.2017.00026] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/23/2017] [Indexed: 12/03/2022] Open
Abstract
Disruption of the human SHANK3 gene can cause several neuropsychiatric disease entities including Phelan-McDermid syndrome, autism spectrum disorder (ASD), and intellectual disability. Although, a wide array of neurobiological studies strongly supports a major role for SHANK3 in organizing the post-synaptic protein scaffold, the molecular processes at synapses of individuals harboring SHANK3 mutations are still far from being understood. In this study, we biochemically isolated the post-synaptic density (PSD) fraction from striatum and hippocampus of adult Shank3Δ11-/- mutant mice and performed ion-mobility enhanced data-independent label-free LC–MS/MS to obtain the corresponding PSD proteomes (Data are available via ProteomeXchange with identifier PXD005192). This unbiased approach to identify molecular disturbances at Shank3 mutant PSDs revealed hitherto unknown brain region specific alterations including a striatal decrease of several molecules encoded by ASD susceptibility genes such as the serine/threonine kinase Cdkl5 and the potassium channel KCa1.1. Being the first comprehensive analysis of brain region specific PSD proteomes from a Shank3 mutant line, our study provides crucial information on molecular alterations that could foster translational treatment studies for SHANK3 mutation-associated synaptopathies and possibly also ASD in general.
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Affiliation(s)
- Dominik Reim
- Institute for Anatomy and Cell Biology, Ulm UniversityUlm, Germany; International Graduate School in Molecular Medicine, Ulm UniversityUlm, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University MainzMainz, Germany; Focus Program Translational Neurosciences, University Medical Center of the Johannes-Gutenberg University MainzMainz, Germany
| | - Sonja Halbedl
- Institute for Anatomy and Cell Biology, Ulm UniversityUlm, Germany; International Graduate School in Molecular Medicine, Ulm UniversityUlm, Germany
| | - Chiara Verpelli
- CNR Neuroscience InstituteMilan, Italy; BIOMETRA, University of MilanMilan, Italy
| | - Carlo Sala
- CNR Neuroscience InstituteMilan, Italy; BIOMETRA, University of MilanMilan, Italy
| | - Juergen Bockmann
- Institute for Anatomy and Cell Biology, Ulm University Ulm, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz Mainz, Germany
| | | | - Michael J Schmeisser
- Institute for Anatomy and Cell Biology, Ulm UniversityUlm, Germany; Division of Neuroanatomy, Institute of Anatomy, Otto-von-Guericke UniversityMagdeburg, Germany; Leibniz Institute for NeurobiologyMagdeburg, Germany
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Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S. A multicenter study benchmarks software tools for label-free proteome quantification. Nat Biotechnol 2016; 34:1130-1136. [PMID: 27701404 PMCID: PMC5120688 DOI: 10.1038/nbt.3685] [Citation(s) in RCA: 227] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/26/2016] [Indexed: 12/12/2022]
Abstract
Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test data sets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation-window setups. For consistent evaluation, we developed LFQbench, an R package, to calculate metrics of precision and accuracy in label-free quantitative MS and report the identification performance, robustness and specificity of each software tool. Our reference data sets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.
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Affiliation(s)
- Pedro Navarro
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Jörg Kuharev
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Ludovic C Gillet
- Department of Biology, Institute of Molecular Systems Biology, Eidgenoessische Technische Hochschule (IMSB-ETH) Zurich, Zurich, Switzerland
| | | | - Brendan MacLean
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Hannes L. Röst
- Department of Biology, Institute of Molecular Systems Biology, Eidgenoessische Technische Hochschule (IMSB-ETH) Zurich, Zurich, Switzerland
| | | | - Chih-Chiang Tsou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology, Eidgenoessische Technische Hochschule (IMSB-ETH) Zurich, Zurich, Switzerland
- PhD Program in Systems Biology, University of Zurich and Eidgenoessische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Alexey I. Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenoessische Technische Hochschule (IMSB-ETH) Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
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40
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Vogt J, Yang JW, Mobascher A, Cheng J, Li Y, Liu X, Baumgart J, Thalman C, Kirischuk S, Unichenko P, Horta G, Radyushkin K, Stroh A, Richers S, Sahragard N, Distler U, Tenzer S, Qiao L, Lieb K, Tüscher O, Binder H, Ferreiros N, Tegeder I, Morris AJ, Gropa S, Nürnberg P, Toliat MR, Winterer G, Luhmann HJ, Huai J, Nitsch R. Molecular cause and functional impact of altered synaptic lipid signaling due to a prg-1 gene SNP. EMBO Mol Med 2016; 8:25-38. [PMID: 26671989 PMCID: PMC4718157 DOI: 10.15252/emmm.201505677] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Loss of plasticity‐related gene 1 (PRG‐1), which regulates synaptic phospholipid signaling, leads to hyperexcitability via increased glutamate release altering excitation/inhibition (E/I) balance in cortical networks. A recently reported SNP in prg‐1 (R345T/mutPRG‐1) affects ~5 million European and US citizens in a monoallelic variant. Our studies show that this mutation leads to a loss‐of‐PRG‐1 function at the synapse due to its inability to control lysophosphatidic acid (LPA) levels via a cellular uptake mechanism which appears to depend on proper glycosylation altered by this SNP. PRG‐1+/− mice, which are animal correlates of human PRG‐1+/mut carriers, showed an altered cortical network function and stress‐related behavioral changes indicating altered resilience against psychiatric disorders. These could be reversed by modulation of phospholipid signaling via pharmacological inhibition of the LPA‐synthesizing molecule autotaxin. In line, EEG recordings in a human population‐based cohort revealed an E/I balance shift in monoallelic mutPRG‐1 carriers and an impaired sensory gating, which is regarded as an endophenotype of stress‐related mental disorders. Intervention into bioactive lipid signaling is thus a promising strategy to interfere with glutamate‐dependent symptoms in psychiatric diseases.
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Affiliation(s)
- Johannes Vogt
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Jenq-Wei Yang
- Institute for Physiology and Pathophysiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Arian Mobascher
- Department of Psychiatry and Psychotherapy, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Jin Cheng
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Yunbo Li
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Xingfeng Liu
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Jan Baumgart
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Carine Thalman
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Sergei Kirischuk
- Institute for Physiology and Pathophysiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Petr Unichenko
- Institute for Physiology and Pathophysiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Guilherme Horta
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Konstantin Radyushkin
- Focus Program Translational Neuroscience (FTN), University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Albrecht Stroh
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Sebastian Richers
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Nassim Sahragard
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Ute Distler
- Focus Program Translational Neuroscience (FTN), University Medical Center, Johannes Gutenberg-University, Mainz, Germany Institute for Immunology, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Lianyong Qiao
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Klaus Lieb
- Department of Psychiatry and Psychotherapy, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Oliver Tüscher
- Department of Psychiatry and Psychotherapy, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Harald Binder
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Nerea Ferreiros
- Institute of Clinical Pharmacology Goethe-University Hospital, Frankfurt am Main, Germany
| | - Irmgard Tegeder
- Institute of Clinical Pharmacology Goethe-University Hospital, Frankfurt am Main, Germany
| | - Andrew J Morris
- Division of Cardiovascular Medicine, Gill Heart Institute, University of Kentucky, Lexington, KY, USA
| | - Sergiu Gropa
- Department of Neurology, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Mohammad R Toliat
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Georg Winterer
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Heiko J Luhmann
- Institute for Physiology and Pathophysiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Jisen Huai
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Robert Nitsch
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
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41
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Schirmeister T, Kesselring J, Jung S, Schneider TH, Weickert A, Becker J, Lee W, Bamberger D, Wich PR, Distler U, Tenzer S, Johé P, Hellmich UA, Engels B. Quantum Chemical-Based Protocol for the Rational Design of Covalent Inhibitors. J Am Chem Soc 2016; 138:8332-5. [DOI: 10.1021/jacs.6b03052] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Tanja Schirmeister
- Institut
für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Jochen Kesselring
- Institut
für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Sascha Jung
- Institut
für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Thomas H. Schneider
- Institut
für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Anastasia Weickert
- Institut
für Phys. und Theor. Chemie, Universität Würzburg, Emil-Fischer-Straße
42, 97074 Würzburg, Germany
| | - Johannes Becker
- Institut
für Phys. und Theor. Chemie, Universität Würzburg, Emil-Fischer-Straße
42, 97074 Würzburg, Germany
| | - Wook Lee
- Institut
für Phys. und Theor. Chemie, Universität Würzburg, Emil-Fischer-Straße
42, 97074 Würzburg, Germany
| | - Denise Bamberger
- Institut
für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Peter R. Wich
- Institut
für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Ute Distler
- Institut
für Immunologie, Universitätsmedizin der Johannes-Gutenberg Universität Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Stefan Tenzer
- Institut
für Immunologie, Universitätsmedizin der Johannes-Gutenberg Universität Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Patrick Johé
- Institut
für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Ute A. Hellmich
- Institut
für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, J.-J. Becherweg 30, 55128 Mainz, Germany
- Center
for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Theodor-W.-Adorno-Platz
1, 60323 Frankfurt, Germany
| | - Bernd Engels
- Institut
für Phys. und Theor. Chemie, Universität Würzburg, Emil-Fischer-Straße
42, 97074 Würzburg, Germany
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42
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Distler U, Kuharev J, Navarro P, Tenzer S. Label-free quantification in ion mobility–enhanced data-independent acquisition proteomics. Nat Protoc 2016; 11:795-812. [DOI: 10.1038/nprot.2016.042] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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43
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Kuharev J, Navarro P, Distler U, Jahn O, Tenzer S. In-depth evaluation of software tools for data-independent acquisition based label-free quantification. Proteomics 2015; 15:3140-51. [PMID: 25545627 DOI: 10.1002/pmic.201400396] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/22/2014] [Accepted: 12/17/2014] [Indexed: 12/21/2022]
Abstract
Label-free quantification (LFQ) based on data-independent acquisition workflows currently experiences increasing popularity. Several software tools have been recently published or are commercially available. The present study focuses on the evaluation of three different software packages (Progenesis, synapter, and ISOQuant) supporting ion mobility enhanced data-independent acquisition data. In order to benchmark the LFQ performance of the different tools, we generated two hybrid proteome samples of defined quantitative composition containing tryptically digested proteomes of three different species (mouse, yeast, Escherichia coli). This model dataset simulates complex biological samples containing large numbers of both unregulated (background) proteins as well as up- and downregulated proteins with exactly known ratios between samples. We determined the number and dynamic range of quantifiable proteins and analyzed the influence of applied algorithms (retention time alignment, clustering, normalization, etc.) on quantification results. Analysis of technical reproducibility revealed median coefficients of variation of reported protein abundances below 5% for MS(E) data for Progenesis and ISOQuant. Regarding accuracy of LFQ, evaluation with synapter and ISOQuant yielded superior results compared to Progenesis. In addition, we discuss reporting formats and user friendliness of the software packages. The data generated in this study have been deposited to the ProteomeXchange Consortium with identifier PXD001240 (http://proteomecentral.proteomexchange.org/dataset/PXD001240).
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Affiliation(s)
- Jörg Kuharev
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Pedro Navarro
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
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44
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Distler U, Kuharev J, Tenzer S. Biomedical applications of ion mobility-enhanced data-independent acquisition-based label-free quantitative proteomics. Expert Rev Proteomics 2014; 11:675-84. [DOI: 10.1586/14789450.2014.971114] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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45
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Distler U, Schmeisser MJ, Pelosi A, Reim D, Kuharev J, Weiczner R, Baumgart J, Boeckers TM, Nitsch R, Vogt J, Tenzer S. In‐depth protein profiling of the postsynaptic density from mouse hippocampus using data‐independent acquisition proteomics. Proteomics 2014; 14:2607-13. [DOI: 10.1002/pmic.201300520] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 08/04/2014] [Accepted: 09/08/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Ute Distler
- Focus Program Translational Neuroscience (FTN) University Medical Center of the Johannes‐Gutenberg University Mainz Mainz Germany
- Institute for Immunology University Medical Center of the Johannes‐Gutenberg University Mainz Mainz Germany
| | | | - Assunta Pelosi
- Institute of Microscopic Anatomy and Neurobiology University Medical Center of the Johannes‐Gutenberg University Mainz Germany
| | - Dominik Reim
- Institute for Anatomy and Cell Biology Ulm University Ulm Germany
| | - Jörg Kuharev
- Institute for Immunology University Medical Center of the Johannes‐Gutenberg University Mainz Mainz Germany
| | - Roland Weiczner
- Institute of Microscopic Anatomy and Neurobiology University Medical Center of the Johannes‐Gutenberg University Mainz Germany
| | - Jan Baumgart
- Institute of Microscopic Anatomy and Neurobiology University Medical Center of the Johannes‐Gutenberg University Mainz Germany
| | | | - Robert Nitsch
- Focus Program Translational Neuroscience (FTN) University Medical Center of the Johannes‐Gutenberg University Mainz Mainz Germany
- Institute of Microscopic Anatomy and Neurobiology University Medical Center of the Johannes‐Gutenberg University Mainz Germany
| | - Johannes Vogt
- Focus Program Translational Neuroscience (FTN) University Medical Center of the Johannes‐Gutenberg University Mainz Mainz Germany
- Institute of Microscopic Anatomy and Neurobiology University Medical Center of the Johannes‐Gutenberg University Mainz Germany
| | - Stefan Tenzer
- Institute for Immunology University Medical Center of the Johannes‐Gutenberg University Mainz Mainz Germany
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Docter D, Distler U, Storck W, Kuharev J, Wünsch D, Hahlbrock A, Knauer SK, Tenzer S, Stauber RH. Quantitative profiling of the protein coronas that form around nanoparticles. Nat Protoc 2014; 9:2030-44. [DOI: 10.1038/nprot.2014.139] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Michel A, Schüler A, Friedrich P, Döner F, Bopp T, Radsak M, Hoffmann M, Relle M, Distler U, Kuharev J, Tenzer S, Feyerabend TB, Rodewald HR, Schild H, Schmitt E, Becker M, Stassen M. Mast cell-deficient Kit(W-sh) "Sash" mutant mice display aberrant myelopoiesis leading to the accumulation of splenocytes that act as myeloid-derived suppressor cells. J Immunol 2013; 190:5534-44. [PMID: 23636054 DOI: 10.4049/jimmunol.1203355] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mast cell-deficient Kit(W-sh) "sash" mice are widely used to investigate mast cell functions. However, mutations of c-Kit also affect additional cells of hematopoietic and nonimmune origin. In this study, we demonstrate that Kit(W-sh) causes aberrant extramedullary myelopoiesis characterized by the expansion of immature lineage-negative cells, common myeloid progenitors, and granulocyte/macrophage progenitors in the spleen. A consistent feature shared by these cell types is the reduced expression of c-Kit. Populations expressing intermediate and high levels of Ly6G, a component of the myeloid differentiation Ag Gr-1, are also highly expanded in the spleen of sash mice. These cells are able to suppress T cell responses in vitro and phenotypically and functionally resemble myeloid-derived suppressor cells (MDSC). MDSC typically accumulate in tumor-bearing hosts and are able to dampen immune responses. Consequently, transfer of MDSC from naive sash mice into line 1 alveolar cell carcinoma tumor-bearing wild-type littermates leads to enhanced tumor progression. However, although it can also be observed in sash mice, accelerated growth of transplanted line 1 alveolar cell carcinoma tumors is a mast cell-independent phenomenon. Thus, the Kit(W-sh) mutation broadly affects key steps in myelopoiesis that may have an impact on mast cell research.
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Affiliation(s)
- Anastasija Michel
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
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Müthing J, Distler U. Advances on the compositional analysis of glycosphingolipids combining thin-layer chromatography with mass spectrometry. Mass Spectrom Rev 2010; 29:425-479. [PMID: 19609886 DOI: 10.1002/mas.20253] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Glycosphingolipids (GSLs), composed of a hydrophilic carbohydrate chain and a lipophilic ceramide anchor, play pivotal roles in countless biological processes, including infectious diseases and the development of cancer. Knowledge of the number and sequence of monosaccharides and their anomeric configuration and linkage type, which make up the principal items of the glyco code of biologically active carbohydrate chains, is essential for exploring the function of GSLs. As part of the investigation of the vertebrate glycome, GSL analysis is undergoing rapid expansion owing to the application of novel biochemical and biophysical technologies. Mass spectrometry (MS) takes part in the network of collaborations to further unravel structural and functional aspects within the fascinating world of GSLs with the ultimate aim to better define their role in human health and disease. However, a single-method analytical MS technique without supporting tools is limited yielding only partial structural information. Because of its superior resolving power, robustness, and easy handling, high-performance thin-layer chromatography (TLC) is widely used as an invaluable tool in GSL analysis. The intention of this review is to give an insight into current advances obtained by coupling supplementary techniques such as TLC and mass spectrometry. A retrospective view of the development of this concept and the recent improvements by merging (1) TLC separation of GSLs, (2) their detection with oligosaccharide-specific proteins, and (3) in situ MS analysis of protein-detected GSLs directly on the TLC plate, are provided. The procedure works on a nanogram scale and was successfully applied to the identification of cancer-associated GSLs in several types of human tumors. The combination of these two supplementary techniques opens new doors by delivering specific structural information of trace quantities of GSLs with only limited investment in sample preparation.
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Affiliation(s)
- Johannes Müthing
- Institute for Hygiene, University of Münster, Robert-Koch-Str. 41, D-48149 Münster, Germany.
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Müsken A, Souady J, Dreisewerd K, Zhang W, Distler U, Peter-Katalinić J, Miller-Podraza H, Karch H, Müthing J. Application of thin-layer chromatography/infrared matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometry to structural analysis of bacteria-binding glycosphingolipids selected by affinity detection. Rapid Commun Mass Spectrom 2010; 24:1032-1038. [PMID: 20213676 DOI: 10.1002/rcm.4480] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Glycosphingolipids (GSLs) play key roles in the manifestation of infectious diseases as attachment sites for pathogens. The thin-layer chromatography (TLC) overlay assay represents one of the most powerful approaches for the detection of GSL receptors of microorganisms. Here we report on the direct structural characterization of microbial GSL receptors by employment of the TLC overlay assay combined with infrared matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometry (IR-MALDI-o-TOF-MS). The procedure includes TLC separation of GSL mixtures, overlay of the chromatogram with GSL-specific bacteria, detection of bound microbes with primary antibodies against bacterial surface proteins and appropriate alkaline phosphatase labeled secondary antibodies, and in situ MS analysis of bacteria-specific GSL receptors. The combined method works on microgram scale of GSL mixtures and is advantageous in that it omits laborious and time-consuming GSL extraction from the silica gel layer. This technique was successfully applied to the compositional analysis of globo-series neutral GSLs recognized by P-fimbriated Escherichia coli bacteria, which were used as model microorganisms for infection of the human urinary tract. Thus, direct TLC/IR-MALDI-o-TOF-MS adds a novel facet to this fast and sensitive method offering a wide range of applications for the investigation of carbohydrate-specific pathogens involved in human infectious diseases.
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Affiliation(s)
- Anne Müsken
- Institute for Hygiene, University of Münster, D-48149 Münster, Germany
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Distler U, Souady J, Hülsewig M, Drmić-Hofman I, Haier J, Friedrich AW, Karch H, Senninger N, Dreisewerd K, Berkenkamp S, Schmidt MA, Peter-Katalinić J, Müthing J. Shiga toxin receptor Gb3Cer/CD77: tumor-association and promising therapeutic target in pancreas and colon cancer. PLoS One 2009; 4:e6813. [PMID: 19714252 PMCID: PMC2730034 DOI: 10.1371/journal.pone.0006813] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 06/22/2009] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Despite progress in adjuvant chemotherapy in the recent decades, pancreatic and colon cancers remain common causes of death worldwide. Bacterial toxins, which specifically bind to cell surface-exposed glycosphingolipids, are a potential novel therapy. We determined the expression of globotriaosylceramide (Gb3Cer/CD77), the Shiga toxin receptor, in human pancreatic and colon adenocarcinomas. METHODOLOGY/PRINCIPAL FINDINGS Tissue lipid extracts of matched pairs of cancerous and adjacent normal tissue from 21 pancreatic and 16 colon cancer patients were investigated with thin-layer chromatography overlay assay combined with a novel mass spectrometry approach. Gb3Cer/CD77 was localized by immunofluorescence microscopy of cryosections from malignant and corresponding healthy tissue samples. 62% of pancreatic and 81% of colon adenocarcinomas showed increased Gb3Cer/CD77 expression, whereas 38% and 19% of malignant pancreas and colon tissue, respectively, did not, indicating an association of this marker with neoplastic transformation. Also, Gb3Cer/CD77 was associated with poor differentiation (G>2) in pancreatic cancer (P = 0.039). Mass spectrometric analysis evidenced enhanced expression of Gb3Cer/CD77 with long (C24) and short chain fatty acids (C16) in malignant tissues and pointed to the presence of hydroxylated fatty acid lipoforms, which are proposed to be important for receptor targeting. They could be detected in 86% of pancreatic and about 19% of colon adenocarcinomas. Immunohistology of tissue cryosections indicated tumor-association of these receptors. CONCLUSIONS/SIGNIFICANCE Enhanced expression of Gb3Cer/CD77 in most pancreatic and colon adenocarcinomas prompts consideration of Shiga toxin, its B-subunit or B-subunit-derivatives as novel therapeutic strategies for the treatment of these challenging malignancies.
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Affiliation(s)
- Ute Distler
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Jamal Souady
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Marcel Hülsewig
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Irena Drmić-Hofman
- Department of Pathology, Laboratory for Clinical and Forensic Genetics, University Hospital and Medical School Split, Split, Croatia
| | - Jörg Haier
- Department of General Surgery, University Hospital Münster, Münster, Germany
| | | | - Helge Karch
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Norbert Senninger
- Department of General Surgery, University Hospital Münster, Münster, Germany
| | - Klaus Dreisewerd
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | | | | | - Jasna Peter-Katalinić
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
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