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Glover HL, Mendes M, Gomes-Neto J, Rusilowicz-Jones EV, Rigden DJ, Dittmar G, Urbé S, Clague MJ. Microtubule association of TRIM3 revealed by differential extraction proteomics. J Cell Sci 2024; 137:jcs261522. [PMID: 38149663 PMCID: PMC10917062 DOI: 10.1242/jcs.261522] [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: 08/01/2023] [Accepted: 12/15/2023] [Indexed: 12/28/2023] Open
Abstract
The microtubule network is formed from polymerised tubulin subunits and associating proteins, which govern microtubule dynamics and a diverse array of functions. To identify novel microtubule-binding proteins, we have developed an unbiased biochemical assay, which relies on the selective extraction of cytosolic proteins from U2OS cells, while leaving behind the microtubule network. Candidate proteins are linked to microtubules by their sensitivities to the depolymerising drug nocodazole or the microtubule-stabilising drug taxol, which is quantitated by mass spectrometry. Our approach is benchmarked by co-segregation of tubulin and previously established microtubule-binding proteins. We then identify several novel candidate microtubule-binding proteins, from which we have selected the ubiquitin E3 ligase tripartite motif-containing protein 3 (TRIM3) for further characterisation. We map TRIM3 microtubule binding to its C-terminal NHL-repeat region. We show that TRIM3 is required for the accumulation of acetylated tubulin, following treatment with taxol. Furthermore, loss of TRIM3 partially recapitulates the reduction in nocodazole-resistant microtubules characteristic of α-tubulin acetyltransferase 1 (ATAT1) depletion. These results can be explained by a decrease in ATAT1 following depletion of TRIM3 that is independent of transcription.
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Affiliation(s)
- Hannah L. Glover
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
| | - Marta Mendes
- Proteomics of Cellular Signalling, Department of Infection and Immunity,Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Joana Gomes-Neto
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
| | - Emma V. Rusilowicz-Jones
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
| | - Daniel J. Rigden
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
| | - Gunnar Dittmar
- Proteomics of Cellular Signalling, Department of Infection and Immunity,Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, 2 Avenue de l'Université, Campus Belval, L-4365 Esch-sur-Alzette, Luxembourg
| | - Sylvie Urbé
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
| | - Michael J. Clague
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 3BX, UK
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Schmidt A, Zhang H, Schmitt S, Rausch C, Popp O, Chen J, Cmarko D, Butter F, Dittmar G, Lermyte F, Cardoso MC. The Proteomic Composition and Organization of Constitutive Heterochromatin in Mouse Tissues. Cells 2024; 13:139. [PMID: 38247831 PMCID: PMC10814525 DOI: 10.3390/cells13020139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Pericentric heterochromatin (PCH) forms spatio-temporarily distinct compartments and affects chromosome organization and stability. Albeit some of its components are known, an elucidation of its proteome and how it differs between tissues in vivo is lacking. Here, we find that PCH compartments are dynamically organized in a tissue-specific manner, possibly reflecting compositional differences. As the mouse brain and liver exhibit very different PCH architecture, we isolated native PCH fractions from these tissues, analyzed their protein compositions using quantitative mass spectrometry, and compared them to identify common and tissue-specific PCH proteins. In addition to heterochromatin-enriched proteins, the PCH proteome includes RNA/transcription and membrane-related proteins, which showed lower abundance than PCH-enriched proteins. Thus, we applied a cut-off of PCH-unspecific candidates based on their abundance and validated PCH-enriched proteins. Amongst the hits, MeCP2 was classified into brain PCH-enriched proteins, while linker histone H1 was not. We found that H1 and MeCP2 compete to bind to PCH and regulate PCH organization in opposite ways. Altogether, our workflow of unbiased PCH isolation, quantitative mass spectrometry, and validation-based analysis allowed the identification of proteins that are common and tissue-specifically enriched at PCH. Further investigation of selected hits revealed their opposing role in heterochromatin higher-order architecture in vivo.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Stephanie Schmitt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Oliver Popp
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Jiaxuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Dusan Cmarko
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Gunnar Dittmar
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Frederik Lermyte
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
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Perez-Hernandez D, Suarez-Artiles L, Jones MSO, Dittmar G. Using PrISMa to reveal the interactome of the human claudins family. STAR Protoc 2023; 4:102549. [PMID: 37756153 PMCID: PMC10542633 DOI: 10.1016/j.xpro.2023.102549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/26/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
Here, we provide a protocol for the systematic screening of protein-protein interactions mediated by short linear motifs using the Protein Interaction Screen on a peptide Matrix (PrISMa) technique. We describe how to pull down interacting proteins in a parallelized manner and identify them by mass spectrometry. Finally, we describe a bioinformatic workflow necessary to identify highly probable interaction partners in the large-scale dataset. We describe the application of this method for the transient interactome of the claudin protein family. For complete details on the use and execution of this protocol, please refer to Suarez-Artiles et al.1.
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Affiliation(s)
- Daniel Perez-Hernandez
- Department of Infection and Immunity, Luxembourg Institute of Health, 1A Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Lorena Suarez-Artiles
- Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle Str. 10, 13125 Berlin, Germany
| | - Mattson S O Jones
- Department of Infection and Immunity, Luxembourg Institute of Health, 1A Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Gunnar Dittmar
- Department of Infection and Immunity, Luxembourg Institute of Health, 1A Rue Thomas Edison, 1445 Strassen, Luxembourg; Department of Life Sciences and Medicine, University of Luxembourg, 2 avenue de l'Université, Campus Belval, 4365 Esch-sur-Alzette, Luxembourg.
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Siegel F, Schmidt H, Juneja M, Smith J, Herrmann P, Kobelt D, Sharma K, Fichtner I, Walther W, Dittmar G, Volkmer R, Rathjen FG, Schlag PM, Stein U. GIPC1 regulates MACC1-driven metastasis. Front Oncol 2023; 13:1280977. [PMID: 38144523 PMCID: PMC10748395 DOI: 10.3389/fonc.2023.1280977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
Background Identification of cancer metastasis-relevant molecular networks is desired to provide the basis for understanding and developing intervention strategies. Here we address the role of GIPC1 in the process of MACC1-driven metastasis. MACC1 is a prognostic indicator for patient metastasis formation and metastasis-free survival. MACC1 controls gene transcription, promotes motility, invasion and proliferation of colon cancer cells in vitro, and causes tumor growth and metastasis in mice. Methods By using yeast-two-hybrid assay, mass spectrometry, co-immunoprecipitation and peptide array we analyzed GIPC1 protein binding partners, by using the MACC1 gene promoter and chromatin immunoprecipitation and electrophoretic mobility shift assay we probed for GIPC1 as transcription factor. We employed GIPC1/MACC1-manipulated cell lines for in vitro and in vivo analyses, and we probed the GIPC1/MACC1 impact using human primary colorectal cancer (CRC) tissue. Results We identified MACC1 and its paralogue SH3BP4 as protein binding partners of the protein GIPC1, and we also demonstrated the binding of GIPC1 as transcription factor to the MACC1 promoter (TSS to -60 bp). GIPC1 knockdown reduced endogenous, but not CMV promoter-driven MACC1 expression, and diminished MACC1-induced cell migration and invasion. GIPC1 suppression reduced tumor growth and metastasis in mice intrasplenically transplanted with MACC1-overexpressing CRC cells. In human primary CRC specimens, GIPC1 correlates with MACC1 expression and is of prognostic value for metastasis formation and metastasis-free survival. Combination of MACC1 and GIPC1 expression improved patient survival prognosis, whereas SH3BP4 expression did not show any prognostic value. Conclusions We identified an important, dual function of GIPC1 - as protein interaction partner and as transcription factor of MACC1 - for tumor progression and cancer metastasis.
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Affiliation(s)
- Franziska Siegel
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Hannes Schmidt
- Department Developmental Neurobiology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Manisha Juneja
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Janice Smith
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Pia Herrmann
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Dennis Kobelt
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium, Heidelberg, Germany
| | - Kamal Sharma
- Department Developmental Neurobiology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Iduna Fichtner
- Experimental Pharmacology and Oncology, GmbH, Berlin, Germany
| | - Wolfgang Walther
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Gunnar Dittmar
- Department Mass Spectrometry, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Rudolf Volkmer
- Institute for Medicinal Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Fritz G. Rathjen
- Department Developmental Neurobiology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | | | - Ulrike Stein
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium, Heidelberg, Germany
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Mosel P, Düsing J, Johannesmeier S, Patzlaff-Günther M, Fröhlich S, Mapa J, Kalies S, Bahlmann J, Püster T, Vahlbruch J, Dittmar G, Merdji H, Fajardo M, Trabattoni A, Heisterkamp A, Morgner U, Kovacev M. X-ray generation by fs-laser processing of biological material. Biomed Opt Express 2023; 14:5656-5669. [PMID: 38021146 PMCID: PMC10659813 DOI: 10.1364/boe.499170] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 12/01/2023]
Abstract
The use of ultrashort pulse lasers in medical treatments is increasing and is already an essential tool, particularly in the treatment of eyes, bones and skin. One of the main advantages of laser treatment is that it is fast and minimally invasive. Due to the interaction of ultrashort laser pulses with matter, X-rays can be generated during the laser ablation process. This is important not only for the safety of the patient, but also for the practitioner to ensure that the legally permissible dose is not exceeded. Although our results do not raise safety concerns for existing clinical applications, they might impact future developments at higher peak powers. In order to provide guidance to laser users in the medical field, this paper examines the X-ray emission spectra and dose of several biological materials and describes their dependence on the laser pulse energy.
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Affiliation(s)
- P. Mosel
- Leibniz University Hannover, Welfengarten 1, Hannover 30167, Germany
| | - J. Düsing
- Laser Zentrum Hannover e.V., Hannover 30419, Germany
| | | | | | - S. Fröhlich
- Leibniz University Hannover, Welfengarten 1, Hannover 30167, Germany
| | - J. Mapa
- Leibniz University Hannover, Welfengarten 1, Hannover 30167, Germany
| | - S. Kalies
- Leibniz University Hannover, Welfengarten 1, Hannover 30167, Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany
| | - J. Bahlmann
- Leibniz University Hannover, Welfengarten 1, Hannover 30167, Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany
| | - T. Püster
- Laser Zentrum Hannover e.V., Hannover 30419, Germany
| | - J. Vahlbruch
- Institute of Radioecology and Radiation Protection, Leibniz University Hannover, Hannover 30419, Germany
| | - G. Dittmar
- Ingenieur-Büro Prof. Dr.-Ing. G. Dittmar, Aalen 73433, Germany
| | - H. Merdji
- LOA, ENSTA ParisTech, CNRS, Ecole Polytechnique, Université Paris-Saclay 828 Boulevard des Maréchaux, 91120, Palaiseau, France
| | - M. Fajardo
- GoLP, Instituto de Plasmas e Fusão Nuclear, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - A. Trabattoni
- Leibniz University Hannover, Welfengarten 1, Hannover 30167, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - A. Heisterkamp
- Leibniz University Hannover, Welfengarten 1, Hannover 30167, Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany
| | - U. Morgner
- Leibniz University Hannover, Welfengarten 1, Hannover 30167, Germany
| | - M. Kovacev
- Leibniz University Hannover, Welfengarten 1, Hannover 30167, Germany
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Zhang J, Keibler MA, Dong W, Ghelfi J, Cordes T, Kanashova T, Pailot A, Linster CL, Dittmar G, Metallo CM, Lautenschlaeger T, Hiller K, Stephanopoulos G. Stable Isotope-Assisted Untargeted Metabolomics Identifies ALDH1A1-Driven Erythronate Accumulation in Lung Cancer Cells. Biomedicines 2023; 11:2842. [PMID: 37893215 PMCID: PMC10604529 DOI: 10.3390/biomedicines11102842] [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: 08/07/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Using an untargeted stable isotope-assisted metabolomics approach, we identify erythronate as a metabolite that accumulates in several human cancer cell lines. Erythronate has been reported to be a detoxification product derived from off-target glycolytic metabolism. We use chemical inhibitors and genetic silencing to define the pentose phosphate pathway intermediate erythrose 4-phosphate (E4P) as the starting substrate for erythronate production. However, following enzyme assay-coupled protein fractionation and subsequent proteomics analysis, we identify aldehyde dehydrogenase 1A1 (ALDH1A1) as the predominant contributor to erythrose oxidation to erythronate in cell extracts. Through modulating ALDH1A1 expression in cancer cell lines, we provide additional support. We hence describe a possible alternative route to erythronate production involving the dephosphorylation of E4P to form erythrose, followed by its oxidation by ALDH1A1. Finally, we measure increased erythronate concentrations in tumors relative to adjacent normal tissues from lung cancer patients. These findings suggest the accumulation of erythronate to be an example of metabolic reprogramming in cancer cells, raising the possibility that elevated levels of erythronate may serve as a biomarker of certain types of cancer.
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Affiliation(s)
- Jie Zhang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.Z.); (M.A.K.); (W.D.)
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4367 Belvaux, Luxembourg (A.P.)
- Biomia Aps, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Mark A. Keibler
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.Z.); (M.A.K.); (W.D.)
- Alnylam Pharmaceuticals, Cambridge, MA 02139, USA
| | - Wentao Dong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.Z.); (M.A.K.); (W.D.)
- Department of Chemical Engineering, Department of Genetics, Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA 94305, USA
| | - Jenny Ghelfi
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4367 Belvaux, Luxembourg (A.P.)
| | - Thekla Cordes
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4367 Belvaux, Luxembourg (A.P.)
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Tamara Kanashova
- Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Arnaud Pailot
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4367 Belvaux, Luxembourg (A.P.)
| | - Carole L. Linster
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4367 Belvaux, Luxembourg (A.P.)
| | - Gunnar Dittmar
- Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Christian M. Metallo
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.Z.); (M.A.K.); (W.D.)
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tim Lautenschlaeger
- Department of Radiation Oncology, Wexner Medical Center, Ohio State University, Columbus, OH 43221, USA
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Karsten Hiller
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4367 Belvaux, Luxembourg (A.P.)
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.Z.); (M.A.K.); (W.D.)
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7
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Cirzi C, Dyckow J, Legrand C, Schott J, Guo W, Perez Hernandez D, Hisaoka M, Parlato R, Pitzer C, van der Hoeven F, Dittmar G, Helm M, Stoecklin G, Schirmer L, Lyko F, Tuorto F. Queuosine-tRNA promotes sex-dependent learning and memory formation by maintaining codon-biased translation elongation speed. EMBO J 2023; 42:e112507. [PMID: 37609797 PMCID: PMC10548180 DOI: 10.15252/embj.2022112507] [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: 08/31/2022] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/24/2023] Open
Abstract
Queuosine (Q) is a modified nucleoside at the wobble position of specific tRNAs. In mammals, queuosinylation is facilitated by queuine uptake from the gut microbiota and is introduced into tRNA by the QTRT1-QTRT2 enzyme complex. By establishing a Qtrt1 knockout mouse model, we discovered that the loss of Q-tRNA leads to learning and memory deficits. Ribo-Seq analysis in the hippocampus of Qtrt1-deficient mice revealed not only stalling of ribosomes on Q-decoded codons, but also a global imbalance in translation elongation speed between codons that engage in weak and strong interactions with their cognate anticodons. While Q-dependent molecular and behavioral phenotypes were identified in both sexes, female mice were affected more severely than males. Proteomics analysis confirmed deregulation of synaptogenesis and neuronal morphology. Together, our findings provide a link between tRNA modification and brain functions and reveal an unexpected role of protein synthesis in sex-dependent cognitive performance.
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Affiliation(s)
- Cansu Cirzi
- Division of Epigenetics, DKFZ‐ZMBH AllianceGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Julia Dyckow
- Department of Neurology, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
- Interdisciplinary Center for NeurosciencesHeidelberg UniversityHeidelbergGermany
| | - Carine Legrand
- Division of Epigenetics, DKFZ‐ZMBH AllianceGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Université Paris Cité, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRSParisFrance
| | - Johanna Schott
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Wei Guo
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | | | - Miharu Hisaoka
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Rosanna Parlato
- Division of Neurodegenerative Disorders, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational NeurosciencesHeidelberg UniversityMannheimGermany
| | - Claudia Pitzer
- Interdisciplinary Neurobehavioral Core (INBC), Medical Faculty HeidelbergHeidelberg UniversityHeidelbergGermany
| | | | - Gunnar Dittmar
- Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
- Department of Life Sciences and MedicineUniversity of LuxembourgLuxembourg
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Science (IPBS)Johannes Gutenberg‐University MainzMainzGermany
| | - Georg Stoecklin
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Lucas Schirmer
- Department of Neurology, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
- Interdisciplinary Center for NeurosciencesHeidelberg UniversityHeidelbergGermany
- Mannheim Center for Translational Neuroscience and Institute for Innate Immunoscience, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Frank Lyko
- Division of Epigenetics, DKFZ‐ZMBH AllianceGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Francesca Tuorto
- Division of Epigenetics, DKFZ‐ZMBH AllianceGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty MannheimHeidelberg UniversityMannheimGermany
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8
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Buntenbroich I, Anton V, Perez-Hernandez D, Simões T, Gaedke F, Schauss A, Dittmar G, Riemer J, Escobar-Henriques M. Docking and stability defects in mitofusin highlight the proteasome as a potential therapeutic target. iScience 2023; 26:107014. [PMID: 37416455 PMCID: PMC10320088 DOI: 10.1016/j.isci.2023.107014] [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: 04/27/2022] [Revised: 04/23/2023] [Accepted: 05/29/2023] [Indexed: 07/08/2023] Open
Abstract
Defects in mitochondrial fusion are at the base of many diseases. Mitofusins power membrane-remodeling events via self-interaction and GTP hydrolysis. However, how exactly mitofusins mediate fusion of the outer membrane is still unclear. Structural studies enable tailored design of mitofusin variants, providing valuable tools to dissect this stepwise process. Here, we found that the two cysteines conserved between yeast and mammals are required for mitochondrial fusion, revealing two novel steps of the fusion cycle. C381 is dominantly required for the formation of the trans-tethering complex, before GTP hydrolysis. C805 allows stabilizing the Fzo1 protein and the trans-tethering complex, just prior to membrane fusion. Moreover, proteasomal inhibition rescued Fzo1 C805S levels and membrane fusion, suggesting a possible application for clinically approved drugs. Together, our study provides insights into how assembly or stability defects in mitofusins might cause mitofusin-associated diseases and uncovers potential therapeutic intervention by proteasomal inhibition.
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Affiliation(s)
- Ira Buntenbroich
- Institute for Genetics,University of Cologne, Cologne 50931, Germany
| | - Vincent Anton
- Institute for Genetics,University of Cologne, Cologne 50931, Germany
| | - Daniel Perez-Hernandez
- Proteomics of Cellular Signaling, Luxembourg Institute of Health, Strassen 1445, Luxembourg
| | - Tânia Simões
- Institute for Genetics,University of Cologne, Cologne 50931, Germany
| | - Felix Gaedke
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Astrid Schauss
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Luxembourg Institute of Health, Strassen 1445, Luxembourg
| | - Jan Riemer
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
- Institute for Biochemistry, University of Cologne, Cologne 50931, Germany
| | - Mafalda Escobar-Henriques
- Institute for Genetics,University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany
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9
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Boeddrich A, Haenig C, Neuendorf N, Blanc E, Ivanov A, Kirchner M, Schleumann P, Bayraktaroğlu I, Richter M, Molenda CM, Sporbert A, Zenkner M, Schnoegl S, Suenkel C, Schneider LS, Rybak-Wolf A, Kochnowsky B, Byrne LM, Wild EJ, Nielsen JE, Dittmar G, Peters O, Beule D, Wanker EE. A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease. Genome Med 2023; 15:50. [PMID: 37468900 PMCID: PMC10357615 DOI: 10.1186/s13073-023-01206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/22/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is characterized by the intra- and extracellular accumulation of amyloid-β (Aβ) peptides. How Aβ aggregates perturb the proteome in brains of patients and AD transgenic mouse models, remains largely unclear. State-of-the-art mass spectrometry (MS) methods can comprehensively detect proteomic alterations, providing relevant insights unobtainable with transcriptomics investigations. Analyses of the relationship between progressive Aβ aggregation and protein abundance changes in brains of 5xFAD transgenic mice have not been reported previously. METHODS We quantified progressive Aβ aggregation in hippocampus and cortex of 5xFAD mice and controls with immunohistochemistry and membrane filter assays. Protein changes in different mouse tissues were analyzed by MS-based proteomics using label-free quantification; resulting MS data were processed using an established pipeline. Results were contrasted with existing proteomic data sets from postmortem AD patient brains. Finally, abundance changes in the candidate marker Arl8b were validated in cerebrospinal fluid (CSF) from AD patients and controls using ELISAs. RESULTS Experiments revealed faster accumulation of Aβ42 peptides in hippocampus than in cortex of 5xFAD mice, with more protein abundance changes in hippocampus, indicating that Aβ42 aggregate deposition is associated with brain region-specific proteome perturbations. Generating time-resolved data sets, we defined Aβ aggregate-correlated and anticorrelated proteome changes, a fraction of which was conserved in postmortem AD patient brain tissue, suggesting that proteome changes in 5xFAD mice mimic disease-relevant changes in human AD. We detected a positive correlation between Aβ42 aggregate deposition in the hippocampus of 5xFAD mice and the abundance of the lysosome-associated small GTPase Arl8b, which accumulated together with axonal lysosomal membranes in close proximity of extracellular Aβ plaques in 5xFAD brains. Abnormal aggregation of Arl8b was observed in human AD brain tissue. Arl8b protein levels were significantly increased in CSF of AD patients. CONCLUSIONS We report a comprehensive biochemical and proteomic investigation of hippocampal and cortical brain tissue derived from 5xFAD transgenic mice, providing a valuable resource to the neuroscientific community. We identified Arl8b, with significant abundance changes in 5xFAD and AD patient brains. Arl8b might enable the measurement of progressive lysosome accumulation in AD patients and have clinical utility as a candidate biomarker.
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Affiliation(s)
- Annett Boeddrich
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Christian Haenig
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Nancy Neuendorf
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Andranik Ivanov
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Marieluise Kirchner
- Core Unit Proteomics, Berlin Institute of Health at Charité - University Medicine Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
| | - Philipp Schleumann
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Irem Bayraktaroğlu
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Matthias Richter
- Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Christine Mirjam Molenda
- Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Anje Sporbert
- Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Martina Zenkner
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Sigrid Schnoegl
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Christin Suenkel
- Systems Biology of Gene Regulatory Elements, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Luisa-Sophie Schneider
- Department of Psychiatry, Charité - University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Agnieszka Rybak-Wolf
- Systems Biology of Gene Regulatory Elements, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Bianca Kochnowsky
- Department of Psychiatry, Charité - University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Lauren M Byrne
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Edward J Wild
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- National Hospital for Neurology & Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Jørgen E Nielsen
- Neurogenetics Clinic & Research Lab, Danish Dementia Research Centre, Rigshospitalet, University of Copenhagen, Section 8008, Inge Lehmanns Vej 8, 2100, Copenhagen, Denmark
| | - Gunnar Dittmar
- Core Unit Proteomics, Berlin Institute of Health at Charité - University Medicine Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Proteomics of Cellular Signalling, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Oliver Peters
- Department of Psychiatry, Charité - University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany.
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10
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Largeot A, Klapp V, Viry E, Gonder S, Fernandez Botana I, Blomme A, Benzarti M, Pierson S, Duculty C, Marttila P, Wierz M, Gargiulo E, Pagano G, An N, El Hachem N, Perez Hernandez D, Chakraborty S, Ysebaert L, François JH, Cortez Clemente S, Berchem G, Efremov DG, Dittmar G, Szpakowska M, Chevigné A, Nazarov PV, Helleday T, Close P, Meiser J, Stamatopoulos B, Désaubry L, Paggetti J, Moussay E. Inhibition of MYC translation through targeting of the newly identified PHB-eIF4F complex as a therapeutic strategy in CLL. Blood 2023; 141:3166-3183. [PMID: 37084385 PMCID: PMC10646824 DOI: 10.1182/blood.2022017839] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/08/2023] [Accepted: 03/05/2023] [Indexed: 04/23/2023] Open
Abstract
Dysregulation of messenger RNA (mRNA) translation, including preferential translation of mRNA with complex 5' untranslated regions such as the MYC oncogene, is recognized as an important mechanism in cancer. Here, we show that both human and murine chronic lymphocytic leukemia (CLL) cells display a high translation rate, which is inhibited by the synthetic flavagline FL3, a prohibitin (PHB)-binding drug. A multiomics analysis performed in samples from patients with CLL and cell lines treated with FL3 revealed the decreased translation of the MYC oncogene and of proteins involved in cell cycle and metabolism. Furthermore, inhibiting translation induced a proliferation arrest and a rewiring of MYC-driven metabolism. Interestingly, contrary to other models, the RAS-RAF-(PHBs)-MAPK pathway is neither impaired by FL3 nor implicated in translation regulation in CLL cells. Here, we rather show that PHBs are directly associated with the eukaryotic initiation factor (eIF)4F translation complex and are targeted by FL3. Knockdown of PHBs resembled FL3 treatment. Importantly, inhibition of translation controlled CLL development in vivo, either alone or combined with immunotherapy. Finally, high expression of translation initiation-related genes and PHBs genes correlated with poor survival and unfavorable clinical parameters in patients with CLL. Overall, we demonstrated that translation inhibition is a valuable strategy to control CLL development by blocking the translation of several oncogenic pathways including MYC. We also unraveled a new and direct role of PHBs in translation initiation, thus creating new therapeutic opportunities for patients with CLL.
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MESH Headings
- Humans
- Mice
- Animals
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Eukaryotic Initiation Factor-4F/genetics
- Prohibitins
- Genes, myc
- RNA, Messenger/genetics
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Affiliation(s)
- Anne Largeot
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Vanessa Klapp
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Elodie Viry
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Susanne Gonder
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Iria Fernandez Botana
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Arnaud Blomme
- Laboratory of Cancer Signaling, GIGA Stem Cells, University of Liège, Liège, Belgium
| | - Mohaned Benzarti
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Cancer Research, Cancer Metabolism Group, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Sandrine Pierson
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Chloé Duculty
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Petra Marttila
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Marina Wierz
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Ernesto Gargiulo
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Giulia Pagano
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ning An
- Laboratory of Cancer Signaling, GIGA Stem Cells, University of Liège, Liège, Belgium
| | - Najla El Hachem
- Laboratory of Cancer Signaling, GIGA Stem Cells, University of Liège, Liège, Belgium
| | - Daniel Perez Hernandez
- Department of Infection and Immunity, Proteomics of Cellular Signaling, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Supriya Chakraborty
- Molecular Hematology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Loïc Ysebaert
- Haematology Department, Institut Universitaire du Cancer Toulouse Oncopole, Toulouse, France
| | - Jean-Hugues François
- Laboratoire d’hématologie, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Susan Cortez Clemente
- Département d’hémato-oncologie, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Guy Berchem
- Département d’hémato-oncologie, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
- Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Dimitar G. Efremov
- Molecular Hematology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Gunnar Dittmar
- Department of Infection and Immunity, Proteomics of Cellular Signaling, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Martyna Szpakowska
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Andy Chevigné
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Petr V. Nazarov
- Department of Cancer Research, Multiomics Data Science, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Thomas Helleday
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
- Department of Oncology and Metabolism, Weston Park Cancer Centre, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Pierre Close
- Laboratory of Cancer Signaling, GIGA Stem Cells, University of Liège, Liège, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Johannes Meiser
- Department of Cancer Research, Cancer Metabolism Group, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Basile Stamatopoulos
- Laboratory of Clinical Cell Therapy, ULB-Research Cancer Center, Jules Bordet Institute, Université Libre de Bruxelles, Brussels, Belgium
| | - Laurent Désaubry
- Regenerative Nanomedicine Laboratory (UMR1260), Faculty of Medicine, Fédération de Médecine Translationnelle de Strasbourg, INSERM-University of Strasbourg, Strasbourg, France
| | - Jérôme Paggetti
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Etienne Moussay
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
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11
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Lesur A, Bernardin F, Koncina E, Letellier E, Kruppa G, Schmit PO, Dittmar G. Quantification of 782 Plasma Peptides by Multiplexed Targeted Proteomics. J Proteome Res 2023. [PMID: 37011904 DOI: 10.1021/acs.jproteome.2c00575] [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] [Indexed: 04/05/2023]
Abstract
Blood analysis is one of the foundations of clinical diagnostics. In recent years, the analysis of proteins in blood samples by mass spectrometry has taken a jump forward in terms of sensitivity and the number of identified proteins. The recent development of parallel reaction monitoring with parallel accumulation and serial fragmentation (prm-PASEF) combines ion mobility as an additional separation dimension. This increases the proteome coverage while allowing the use of shorter chromatographic gradients. To demonstrate the method's full potential, we used an isotope-labeled synthetic peptide mix of 782 peptides, derived from 579 plasma proteins, spiked into blood plasma samples with a prm-PASEF measurement allowing the quantification of 565 plasma proteins by targeted proteomics. As a less time-consuming alternative to the prm-PASEF method, we describe guided data independent acquisition (dia)-PASEF (g-dia-PASEF) and compare its application to prm-PASEF for measuring blood plasma. To demonstrate both methods' performance in clinical samples, 20 patient plasma samples from a colorectal cancer (CRC) cohort were analyzed. The analysis identified 14 differentially regulated proteins between the CRC patient and control individual plasma samples. This shows the technique's potential for the rapid and unbiased screening of blood proteins, abolishing the need for the preselection of potential biomarker proteins.
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Affiliation(s)
- Antoine Lesur
- Luxembourg Institute of Health, Strassen L-1445, Luxembourg
| | | | - Eric Koncina
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
| | - Elisabeth Letellier
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
| | - Gary Kruppa
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | | | - Gunnar Dittmar
- Luxembourg Institute of Health, Strassen L-1445, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
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12
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Perez-Hernandez D, Filali L, Thomas C, Dittmar G. An integrated workflow for phosphopeptide identification in natural killer cells (NK-92MI) and their targets (MDA-MB-231) during immunological synapse formation. STAR Protoc 2023; 4:102104. [PMID: 36853697 PMCID: PMC9944981 DOI: 10.1016/j.xpro.2023.102104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/05/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Here, we present a protocol to identify and quantify phosphopeptides during the dynamic formation of an immunological synapse. We describe steps for mixing isotope-labeled immune and target cells, the stabilization of cell-to-cell conjugates by cross-linking, and their isolation by fluorescence-activated cell sorting. We detail the isolation of phosphopeptides by phosphopeptide enrichment and their subsequent measurement by mass spectrometry. Finally, we describe the analysis of the resulting data to separate cell-specific phosphopeptides using the isotope label and label-free quantification.
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Affiliation(s)
- Daniel Perez-Hernandez
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg.
| | - Liza Filali
- Department of Cancer Research, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Clement Thomas
- Department of Cancer Research, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Gunnar Dittmar
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg; Department of Life Sciences and Medicine, University of Luxembourg, Belval, Luxembourg.
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13
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Nordmeyer S, Kraus M, Ziehm M, Kirchner M, Schafstedde M, Kelm M, Niquet S, Stephen MM, Baczko I, Knosalla C, Schapranow MP, Dittmar G, Gotthardt M, Falcke M, Regitz-Zagrosek V, Kuehne T, Mertins P. Disease- and sex-specific differences in patients with heart valve disease: a proteome study. Life Sci Alliance 2023; 6:e202201411. [PMID: 36627164 PMCID: PMC9834574 DOI: 10.26508/lsa.202201411] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Pressure overload in patients with aortic valve stenosis and volume overload in mitral valve regurgitation trigger specific forms of cardiac remodeling; however, little is known about similarities and differences in myocardial proteome regulation. We performed proteome profiling of 75 human left ventricular myocardial biopsies (aortic stenosis = 41, mitral regurgitation = 17, and controls = 17) using high-resolution tandem mass spectrometry next to clinical and hemodynamic parameter acquisition. In patients of both disease groups, proteins related to ECM and cytoskeleton were more abundant, whereas those related to energy metabolism and proteostasis were less abundant compared with controls. In addition, disease group-specific and sex-specific differences have been observed. Male patients with aortic stenosis showed more proteins related to fibrosis and less to energy metabolism, whereas female patients showed strong reduction in proteostasis-related proteins. Clinical imaging was in line with proteomic findings, showing elevation of fibrosis in both patient groups and sex differences. Disease- and sex-specific proteomic profiles provide insight into cardiac remodeling in patients with heart valve disease and might help improve the understanding of molecular mechanisms and the development of individualized treatment strategies.
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Affiliation(s)
- Sarah Nordmeyer
- Deutsches Herzzentrum der Charité - Medical Heart Center of Charité and German Heart Institute Berlin, Institute for Cardiovascular Computer-Assisted Medicine, Berlin, Germany
- Deutsches Herzzentrum der Charité - Medical Heart Center of Charité and German Heart Institute Berlin, Department of Congenital Heart Disease - Pediatric Cardiology, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Milena Kraus
- Hasso Plattner Institute for Digital Engineering, Digital Health Center, University of Potsdam, Potsdam, Germany
| | - Matthias Ziehm
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Proteomics Platform, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Marieluise Kirchner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Proteomics Platform, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Marie Schafstedde
- Deutsches Herzzentrum der Charité - Medical Heart Center of Charité and German Heart Institute Berlin, Institute for Cardiovascular Computer-Assisted Medicine, Berlin, Germany
- Deutsches Herzzentrum der Charité - Medical Heart Center of Charité and German Heart Institute Berlin, Department of Congenital Heart Disease - Pediatric Cardiology, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Marcus Kelm
- Deutsches Herzzentrum der Charité - Medical Heart Center of Charité and German Heart Institute Berlin, Institute for Cardiovascular Computer-Assisted Medicine, Berlin, Germany
- Deutsches Herzzentrum der Charité - Medical Heart Center of Charité and German Heart Institute Berlin, Department of Congenital Heart Disease - Pediatric Cardiology, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sylvia Niquet
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Proteomics Platform, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mariet Mathew Stephen
- Hasso Plattner Institute for Digital Engineering, Digital Health Center, University of Potsdam, Potsdam, Germany
| | - Istvan Baczko
- Department of Pharmacology and Pharmacotherapy, Interdisciplinary Excellence Centre, University of Szeged, Szeged, Hungary
| | - Christoph Knosalla
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Deutsches Herzzentrum der Charité - Medical Heart Center of Charité and German Heart, Department of Cardiothoracic and Vascular Surgery, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Matthieu-P Schapranow
- Hasso Plattner Institute for Digital Engineering, Digital Health Center, University of Potsdam, Potsdam, Germany
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Michael Gotthardt
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Neuromuscular and Cardiovascular Cell Biology, Berlin, Germany
| | - Martin Falcke
- Max Delbrück Center for Molecular Medicine, Mathematical Cell Physiology, Berlin, Germany
| | - Vera Regitz-Zagrosek
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Cardiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Titus Kuehne
- Deutsches Herzzentrum der Charité - Medical Heart Center of Charité and German Heart Institute Berlin, Institute for Cardiovascular Computer-Assisted Medicine, Berlin, Germany
- Deutsches Herzzentrum der Charité - Medical Heart Center of Charité and German Heart Institute Berlin, Department of Congenital Heart Disease - Pediatric Cardiology, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Philipp Mertins
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Proteomics Platform, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
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14
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Poli A, Oudin A, Muller A, Salvato I, Scafidi A, Hunewald O, Domingues O, Nazarov PV, Puard V, Baus V, Azuaje F, Dittmar G, Zimmer J, Michel T, Michelucci A, Niclou SP, Ollert M. Allergic airway inflammation delays glioblastoma progression and reinvigorates systemic and local immunity in mice. Allergy 2023; 78:682-696. [PMID: 36210648 DOI: 10.1111/all.15545] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Numerous patient-based studies have highlighted the protective role of immunoglobulin E-mediated allergic diseases on glioblastoma (GBM) susceptibility and prognosis. However, the mechanisms behind this observation remain elusive. Our objective was to establish a preclinical model able to recapitulate this phenomenon and investigate the role of immunity underlying such protection. METHODS An immunocompetent mouse model of allergic airway inflammation (AAI) was initiated before intracranial implantation of mouse GBM cells (GL261). RAG1-KO mice served to assess tumor growth in a model deficient for adaptive immunity. Tumor development was monitored by MRI. Microglia were isolated for functional analyses and RNA-sequencing. Peripheral as well as tumor-associated immune cells were characterized by flow cytometry. The impact of allergy-related microglial genes on patient survival was analyzed by Cox regression using publicly available datasets. RESULTS We found that allergy establishment in mice delayed tumor engraftment in the brain and reduced tumor growth resulting in increased mouse survival. AAI induced a transcriptional reprogramming of microglia towards a pro-inflammatory-like state, uncovering a microglia gene signature, which correlated with limited local immunosuppression in glioma patients. AAI increased effector memory T-cells in the circulation as well as tumor-infiltrating CD4+ T-cells. The survival benefit conferred by AAI was lost in mice devoid of adaptive immunity. CONCLUSION Our results demonstrate that AAI limits both tumor take and progression in mice, providing a preclinical model to study the impact of allergy on GBM susceptibility and prognosis, respectively. We identify a potentiation of local and adaptive systemic immunity, suggesting a reciprocal crosstalk that orchestrates allergy-induced immune protection against GBM.
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Affiliation(s)
- Aurélie Poli
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.,Department of Cancer Research, Luxembourg Institute of Health, Neuro-Immunology Group, Luxembourg, Luxembourg
| | - Anaïs Oudin
- Department of Cancer Research, NORLUX Neuro-Oncology Laboratory, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Arnaud Muller
- Luxembourg Institute of Health, Bioinformatics Platform, Strassen, Luxembourg
| | - Ilaria Salvato
- Department of Cancer Research, NORLUX Neuro-Oncology Laboratory, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Andrea Scafidi
- Department of Cancer Research, Luxembourg Institute of Health, Neuro-Immunology Group, Luxembourg, Luxembourg
| | - Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Olivia Domingues
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Petr V Nazarov
- Luxembourg Institute of Health, Bioinformatics Platform, Strassen, Luxembourg
| | - Vincent Puard
- Institut Curie Centre de Recherche, PSL Research University, RPPA platform, Paris, France
| | - Virginie Baus
- Department of Cancer Research, NORLUX Neuro-Oncology Laboratory, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Francisco Azuaje
- Luxembourg Institute of Health, Bioinformatics Platform, Strassen, Luxembourg
| | - Gunnar Dittmar
- Luxembourg Institute of Health, Bioinformatics Platform, Strassen, Luxembourg
| | - Jacques Zimmer
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Tatiana Michel
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Alessandro Michelucci
- Department of Cancer Research, Luxembourg Institute of Health, Neuro-Immunology Group, Luxembourg, Luxembourg
| | - Simone P Niclou
- Department of Cancer Research, NORLUX Neuro-Oncology Laboratory, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.,Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, Odense, Denmark
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15
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Gargiulo E, Viry E, Morande PE, Largeot A, Gonder S, Xian F, Ioannou N, Benzarti M, Kleine Borgmann FB, Mittelbronn M, Dittmar G, Nazarov PV, Meiser J, Stamatopoulos B, Ramsay AG, Moussay E, Paggetti J. Extracellular Vesicle Secretion by Leukemia Cells In Vivo Promotes CLL Progression by Hampering Antitumor T-cell Responses. Blood Cancer Discov 2023; 4:54-77. [PMID: 36108149 PMCID: PMC9816815 DOI: 10.1158/2643-3230.bcd-22-0029] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/04/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023] Open
Abstract
Small extracellular vesicle (sEV, or exosome) communication among cells in the tumor microenvironment has been modeled mainly in cell culture, whereas their relevance in cancer pathogenesis and progression in vivo is less characterized. Here we investigated cancer-microenvironment interactions in vivo using mouse models of chronic lymphocytic leukemia (CLL). sEVs isolated directly from CLL tissue were enriched in specific miRNA and immune-checkpoint ligands. Distinct molecular components of tumor-derived sEVs altered CD8+ T-cell transcriptome, proteome, and metabolome, leading to decreased functions and cell exhaustion ex vivo and in vivo. Using antagomiRs and blocking antibodies, we defined specific cargo-mediated alterations on CD8+ T cells. Abrogating sEV biogenesis by Rab27a/b knockout dramatically delayed CLL pathogenesis. This phenotype was rescued by exogenous leukemic sEV or CD8+ T-cell depletion. Finally, high expression of sEV-related genes correlated with poor outcomes in CLL patients, suggesting sEV profiling as a prognostic tool. In conclusion, sEVs shape the immune microenvironment during CLL progression. SIGNIFICANCE sEVs produced in the leukemia microenvironment impair CD8+ T-cell mediated antitumor immune response and are indispensable for leukemia progression in vivo in murine preclinical models. In addition, high expression of sEV-related genes correlated with poor survival and unfavorable clinical parameters in CLL patients. See related commentary by Zhong and Guo, p. 5. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Ernesto Gargiulo
- Tumor–Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Elodie Viry
- Tumor–Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Pablo Elías Morande
- Tumor–Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg.,Instituto de Medicina Experimental (IMEX)-CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Anne Largeot
- Tumor–Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Susanne Gonder
- Tumor–Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg.,Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Feng Xian
- Proteomics of Cellular Signaling, Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Nikolaos Ioannou
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Mohaned Benzarti
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Felix Bruno Kleine Borgmann
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Department of Neurosurgery, Centre Hospitalier de Luxembourg, Luxembourg City, Luxembourg.,Luxembourg Centre of Neuropathology, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Michel Mittelbronn
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Luxembourg Centre of Neuropathology, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg.,Luxembourg Centre of Neuropathology, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,National Center of Pathology, Laboratoire national de santé (LNS), Dudelange, Luxembourg.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Gunnar Dittmar
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Proteomics of Cellular Signaling, Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Petr V. Nazarov
- Multiomics Data Science Group, Department of Cancer Research, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Johannes Meiser
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Basile Stamatopoulos
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, Université Libre de Bruxelles, Brussels, Belgium
| | - Alan G. Ramsay
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Etienne Moussay
- Tumor–Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg.,Corresponding Authors: Jérôme Paggetti, Department of Cancer Research, Luxembourg Institute of Health, 6, Rue Nicolas-Ernest Barblé, Luxembourg, L-1210, Luxembourg. Phone: 352-26970-344; E-mail: ; and Etienne Moussay. Phone: 352-26970-232; E-mail:
| | - Jérôme Paggetti
- Tumor–Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg.,Corresponding Authors: Jérôme Paggetti, Department of Cancer Research, Luxembourg Institute of Health, 6, Rue Nicolas-Ernest Barblé, Luxembourg, L-1210, Luxembourg. Phone: 352-26970-344; E-mail: ; and Etienne Moussay. Phone: 352-26970-232; E-mail:
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16
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Perez-Hernandez D, Jones M, Dittmar G. Protein Interaction Screen on a Peptide Matrix (PrISMa). Methods Mol Biol 2023; 2690:269-280. [PMID: 37450154 DOI: 10.1007/978-1-0716-3327-4_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Protein-protein interactions (PPI) are essential to understanding the cellular function and key mechanisms necessary for life. Although understanding of the interactome and proteome has exploded due to high-throughput methods in the past decade, often limitations in technical methods result in a partial understanding of all PPI. Here we present a protocol dedicated to the Protein Interaction Screen on a peptide Matrix (PrISMa). PrISMa functions as a high-throughput screen unique to targeting weak and transient interactions often missed in other PPI methods. In addition, PrISMa also excels at the mapping of interactions across linear sequences of proteins that are commonly enriched in intrinsically disordered regions (IDRs) which cover 35-40% of the mammalian proteome. This protocol aims to expand the understanding of the targeted proteins by identifying transient interactors.
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Affiliation(s)
- Daniel Perez-Hernandez
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Mattson Jones
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Gunnar Dittmar
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg.
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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17
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Wu Z, Berlemann LA, Bader V, Sehr DA, Dawin E, Covallero A, Meschede J, Angersbach L, Showkat C, Michaelis JB, Münch C, Rieger B, Namgaladze D, Herrera MG, Fiesel FC, Springer W, Mendes M, Stepien J, Barkovits K, Marcus K, Sickmann A, Dittmar G, Busch KB, Riedel D, Brini M, Tatzelt J, Cali T, Winklhofer KF. LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus. EMBO J 2022; 41:e112006. [PMID: 36398858 PMCID: PMC9753471 DOI: 10.15252/embj.2022112006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling; however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here, we show that the NF-κB pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-κB to the nucleus. TNF treatment induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-κB is locally activated and transported to the nucleus by mitochondria, leading to an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 furthermore contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN. Overall, our study reveals a role for mitochondria in amplifying TNF-mediated NF-κB activation, both serving as a signaling platform, as well as a transport mode for activated NF-κB to the nuclear.
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Affiliation(s)
- Zhixiao Wu
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena A Berlemann
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Dominik A Sehr
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Eva Dawin
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | | | - Jens Meschede
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena Angersbach
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Cathrin Showkat
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Jonas B Michaelis
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Christian Münch
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Bettina Rieger
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dmitry Namgaladze
- Institute of Biochemistry I, Faculty of MedicineGoethe‐University FrankfurtFrankfurtGermany
| | - Maria Georgina Herrera
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Fabienne C Fiesel
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Wolfdieter Springer
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Marta Mendes
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
| | - Jennifer Stepien
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katalin Barkovits
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katrin Marcus
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Albert Sickmann
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
- Department of Life Sciences and MedicineUniversity of LuxembourgBelvauxLuxembourg
| | - Karin B Busch
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dietmar Riedel
- Laboratory for Electron MicroscopyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Marisa Brini
- Department of BiologyUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
| | - Tito Cali
- Department of Biomedical SciencesUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
- Padua Neuroscience Center (PNC)University of PaduaPaduaItaly
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
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18
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Müller H, Lesur A, Dittmar G, Gentzel M, Kettner K. Proteomic consequences of TDA1 deficiency in Saccharomyces cerevisiae: Protein kinase Tda1 is essential for Hxk1 and Hxk2 serine 15 phosphorylation. Sci Rep 2022; 12:18084. [PMID: 36302925 PMCID: PMC9613766 DOI: 10.1038/s41598-022-21414-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 09/27/2022] [Indexed: 02/05/2023] Open
Abstract
Hexokinase 2 (Hxk2) of Saccharomyces cerevisiae is a dual function hexokinase, acting as a glycolytic enzyme and being involved in the transcriptional regulation of glucose-repressible genes. Relief from glucose repression is accompanied by phosphorylation of Hxk2 at serine 15, which has been attributed to the protein kinase Tda1. To explore the role of Tda1 beyond Hxk2 phosphorylation, the proteomic consequences of TDA1 deficiency were investigated by difference gel electrophoresis (2D-DIGE) comparing a wild type and a Δtda1 deletion mutant. To additionally address possible consequences of glucose repression/derepression, both were grown at 2% and 0.1% (w/v) glucose. A total of eight protein spots exhibiting a minimum twofold enhanced or reduced fluorescence upon TDA1 deficiency was detected and identified by mass spectrometry. Among the spot identities are-besides the expected Hxk2-two proteoforms of hexokinase 1 (Hxk1). Targeted proteomics analyses in conjunction with 2D-DIGE demonstrated that TDA1 is indispensable for Hxk2 and Hxk1 phosphorylation at serine 15. Thirty-six glucose-concentration-dependent protein spots were identified. A simple method to improve spot quantification, approximating spots as rotationally symmetric solids, is presented along with new data on the quantities of Hxk1 and Hxk2 and their serine 15 phosphorylated forms at high and low glucose growth conditions. The Δtda1 deletion mutant exhibited no altered growth under high or low glucose conditions or on alternative carbon sources. Also, invertase activity, serving as a reporter for glucose derepression, was not significantly altered. Instead, an involvement of Tda1 in oxidative stress response is suggested.
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Affiliation(s)
- Henry Müller
- grid.4488.00000 0001 2111 7257Institute of Physiological Chemistry, Technische Universität Dresden, Medizinische Fakultät Carl Gustav Carus, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Antoine Lesur
- grid.451012.30000 0004 0621 531XLuxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Gunnar Dittmar
- grid.451012.30000 0004 0621 531XLuxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg ,grid.16008.3f0000 0001 2295 9843Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue de Swing, 4367 Belvaux, Luxembourg
| | - Marc Gentzel
- grid.4488.00000 0001 2111 7257Center for Molecular and Cellular Bioengineering (CMCB), TP Molecular Analysis / Mass Spectrometry, Technische Universität Dresden, Tatzberg 46/47, 01307 Dresden, Germany
| | - Karina Kettner
- grid.4488.00000 0001 2111 7257Institute of Physiological Chemistry, Technische Universität Dresden, Medizinische Fakultät Carl Gustav Carus, Fetscherstrasse 74, 01307 Dresden, Germany
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19
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Kortüm B, Radhakrishnan H, Zincke F, Sachse C, Burock S, Keilholz U, Dahlmann M, Walther W, Dittmar G, Kobelt D, Stein U. Combinatorial treatment with statins and niclosamide prevents CRC dissemination by unhinging the MACC1-β-catenin-S100A4 axis of metastasis. Oncogene 2022; 41:4446-4458. [PMID: 36008464 PMCID: PMC9507965 DOI: 10.1038/s41388-022-02407-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/29/2022]
Abstract
Colorectal cancer (CRC) is the second-most common malignant disease worldwide, and metastasis is the main culprit of CRC-related death. Metachronous metastases remain to be an unpredictable, unpreventable, and fatal complication, and tracing the molecular chain of events that lead to metastasis would provide mechanistically linked biomarkers for the maintenance of remission in CRC patients after curative treatment. We hypothesized, that Metastasis-associated in colorectal cancer-1 (MACC1) induces a secretory phenotype to enforce metastasis in a paracrine manner, and found, that the cell-free culture medium of MACC1-expressing CRC cells induces migration. Stable isotope labeling by amino acids in cell culture mass spectrometry (SILAC-MS) of the medium revealed, that S100A4 is significantly enriched in the MACC1-specific secretome. Remarkably, both biomarkers correlate in expression data of independent cohorts as well as within CRC tumor sections. Furthermore, combined elevated transcript levels of the metastasis genes MACC1 and S100A4 in primary tumors and in blood plasma robustly identifies CRC patients at high risk for poor metastasis-free (MFS) and overall survival (OS). Mechanistically, MACC1 strengthens the interaction of β-catenin with TCF4, thus inducing S100A4 synthesis transcriptionally, resulting in elevated secretion to enforce cell motility and metastasis. In cell motility assays, S100A4 was indispensable for MACC1-induced migration, as shown via knock-out and pharmacological inhibition of S100A4. The direct transcriptional and functional relationship of MACC1 and S100A4 was probed by combined targeting with repositioned drugs. In fact, the MACC1-β-catenin-S100A4 axis by statins (MACC1) and niclosamide (S100A4) synergized in inhibiting cancer cell motility in vitro and metastasis in vivo. The MACC1-β-catenin-S100A4 signaling axis is causal for CRC metastasis. Selectively repositioned drugs synergize in restricting MACC1/S100A4-driven metastasis with cross-entity potential.
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Affiliation(s)
- Benedikt Kortüm
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Harikrishnan Radhakrishnan
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Fabian Zincke
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | - Susen Burock
- Charité University Hospital Berlin Centre 10 Charite Comprehensive Cancer Center, Berlin, Germany
| | - Ulrich Keilholz
- Charité University Hospital Berlin Centre 10 Charite Comprehensive Cancer Center, Berlin, Germany
| | - Mathias Dahlmann
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Wolfgang Walther
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Gunnar Dittmar
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Dennis Kobelt
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ulrike Stein
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.
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20
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Abstract
For a long time, targeted and discovery proteomics covered different corners of the detection spectrum, with targeted proteomics focused on small target sets. This changed with the recent advances in highly multiplexed analysis. While discovery proteomics still pushes higher numbers of identified and quantified proteins, the advances in targeted proteomics rose to cover large parts of less complex proteomes or proteomes with low protein detection counts due to dynamic range restrictions, like the blood proteome. These new developments will impact, especially on the field of biomarker discovery and the possibility of using targeted proteomics for diagnostic purposes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marta L Mendes
- Proteomics of cellular signalling, Department of Infection and Immunity, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Gunnar Dittmar
- Proteomics of cellular signalling, Department of Infection and Immunity, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg.,Department of Life Sciences and Medicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
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21
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Günes Günsel G, Conlon TM, Jeridi A, Kim R, Ertüz Z, Lang NJ, Ansari M, Novikova M, Jiang D, Strunz M, Gaianova M, Hollauer C, Gabriel C, Angelidis I, Doll S, Pestoni JC, Edelmann SL, Kohlhepp MS, Guillot A, Bassler K, Van Eeckhoutte HP, Kayalar Ö, Konyalilar N, Kanashova T, Rodius S, Ballester-López C, Genes Robles CM, Smirnova N, Rehberg M, Agarwal C, Krikki I, Piavaux B, Verleden SE, Vanaudenaerde B, Königshoff M, Dittmar G, Bracke KR, Schultze JL, Watz H, Eickelberg O, Stoeger T, Burgstaller G, Tacke F, Heissmeyer V, Rinkevich Y, Bayram H, Schiller HB, Conrad M, Schneider R, Yildirim AÖ. The arginine methyltransferase PRMT7 promotes extravasation of monocytes resulting in tissue injury in COPD. Nat Commun 2022; 13:1303. [PMID: 35288557 PMCID: PMC8921220 DOI: 10.1038/s41467-022-28809-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
Extravasation of monocytes into tissue and to the site of injury is a fundamental immunological process, which requires rapid responses via post translational modifications (PTM) of proteins. Protein arginine methyltransferase 7 (PRMT7) is an epigenetic factor that has the capacity to mono-methylate histones on arginine residues. Here we show that in chronic obstructive pulmonary disease (COPD) patients, PRMT7 expression is elevated in the lung tissue and localized to the macrophages. In mouse models of COPD, lung fibrosis and skin injury, reduced expression of PRMT7 associates with decreased recruitment of monocytes to the site of injury and hence less severe symptoms. Mechanistically, activation of NF-κB/RelA in monocytes induces PRMT7 transcription and consequential mono-methylation of histones at the regulatory elements of RAP1A, which leads to increased transcription of this gene that is responsible for adhesion and migration of monocytes. Persistent monocyte-derived macrophage accumulation leads to ALOX5 over-expression and accumulation of its metabolite LTB4, which triggers expression of ACSL4 a ferroptosis promoting gene in lung epithelial cells. Conclusively, inhibition of arginine mono-methylation might offer targeted intervention in monocyte-driven inflammatory conditions that lead to extensive tissue damage if left untreated. Chronic obstructive pulmonary disease is a progressive and incurable chronic condition that involves accumulation of inflammatory macrophages in the lung tissue. Authors here show in mouse models of lung disease that PRMT7, a protein arginine methyltransferase, is an important regulator of recruitment and the pro-inflammatory phenotype of macrophages.
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22
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Ilina EI, Cialini C, Gerloff DL, Garcia-Escudero MD, Janty C, Thézénas ML, Lesur A, Puard V, Bernardin F, Moter A, Schuster A, Dieterle M, Golebiewska A, Gérardy JJ, Dittmar G, Niclou SP, Müller T, Mittelbronn M. Enzymatic activity of glycosyltransferase GLT8D1 promotes human glioblastoma cell migration. iScience 2022; 25:103842. [PMID: 35198895 PMCID: PMC8850796 DOI: 10.1016/j.isci.2022.103842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/27/2021] [Accepted: 01/27/2022] [Indexed: 11/15/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive primary brain tumor characterized by infiltrative growth of malignant glioma cells into the surrounding brain parenchyma. In this study, our analysis of GBM patient cohorts revealed a significantly higher expression of Glycosyltransferase 8 domain containing 1 (GLT8D1) compared to normal brain tissue and could be associated with impaired patient survival. Increased in vitro expression of GLT8D1 significantly enhanced migration of two different sphere-forming GBM cell lines. By in silico analysis we predicted the 3D-structure as well as the active site residues of GLT8D1. The introduction of point mutations in the predicted active site reduced its glycosyltransferase activity in vitro and consequently impaired GBM tumor cell migration. Examination of GLT8D1 interaction partners by LC-MS/MS implied proteins associated with cytoskeleton and intracellular transport as potential substrates. In conclusion, we demonstrated that the enzymatic activity of glycosyltransferase GLT8D1 promotes GBM cell migration. The glycosyltransferase GLT8D1 is enriched in GBM tissue and cells In silico analysis predicts the 3D structure and the active site of GLT8D1 Enzymatically active GLT8D1 promotes GBM migration Manipulation of GLT8D1 enzymatic activity decreases GBM migration
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Novak G, Kyriakis D, Grzyb K, Bernini M, Rodius S, Dittmar G, Finkbeiner S, Skupin A. Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson's disease. Commun Biol 2022; 5:49. [PMID: 35027645 PMCID: PMC8758783 DOI: 10.1038/s42003-021-02973-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/14/2021] [Indexed: 01/02/2023] Open
Abstract
Parkinson's disease (PD) is the second-most prevalent neurodegenerative disorder, characterized by the loss of dopaminergic neurons (mDA) in the midbrain. The underlying mechanisms are only partly understood and there is no treatment to reverse PD progression. Here, we investigated the disease mechanism using mDA neurons differentiated from human induced pluripotent stem cells (hiPSCs) carrying the ILE368ASN mutation within the PINK1 gene, which is strongly associated with PD. Single-cell RNA sequencing (RNAseq) and gene expression analysis of a PINK1-ILE368ASN and a control cell line identified genes differentially expressed during mDA neuron differentiation. Network analysis revealed that these genes form a core network, members of which interact with all known 19 protein-coding Parkinson's disease-associated genes. This core network encompasses key PD-associated pathways, including ubiquitination, mitochondrial function, protein processing, RNA metabolism, and vesicular transport. Proteomics analysis showed a consistent alteration in proteins of dopamine metabolism, indicating a defect of dopaminergic metabolism in PINK1-ILE368ASN neurons. Our findings suggest the existence of a network onto which pathways associated with PD pathology converge, and offers an inclusive interpretation of the phenotypic heterogeneity of PD.
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Affiliation(s)
- Gabriela Novak
- The Integrative Cell Signalling Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg.
- Center for Systems and Therapeutics, the Gladstone Institutes and Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Dimitrios Kyriakis
- The Integrative Cell Signalling Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Kamil Grzyb
- The Integrative Cell Signalling Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Michela Bernini
- The Integrative Cell Signalling Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sophie Rodius
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Gunnar Dittmar
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, the Gladstone Institutes and Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Alexander Skupin
- The Integrative Cell Signalling Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- University of California San Diego, La Jolla, CA, 92093, USA.
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Hau AC, Mommaerts E, Laub V, Müller T, Dittmar G, Schulte D. Transcriptional cooperation of PBX1 and PAX6 in adult neural progenitor cells. Sci Rep 2021; 11:21013. [PMID: 34697387 PMCID: PMC8545929 DOI: 10.1038/s41598-021-99968-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
PAX6 is a highly conserved transcription factor and key regulator of several neurogenic processes, including the continuous generation of dopaminergic/GABAergic interneurons in the adult ventricular-subventricular (V-SVZ) neurogenic system in mice. Here we report that PAX6 cooperates with the TALE-homeodomain transcription factor PBX1 in this context. Chromatin-immunoprecipitation showed that PBX1 and PAX6 co-occupy shared genomic binding sites in adult V-SVZ stem- and progenitor cell cultures and mouse embryonic stem cells, while depletion of Pbx1 revealed that association of PAX6 with these sites requires the presence of PBX1. Expression profiling together with viral overexpression or knockdown of Pax6 or Pbx1 identified novel PBX1-PAX6 co-regulated genes, including several transcription factors. Computational modeling of genome wide expression identified novel cross-regulatory networks among these very transcription factors. Taken together, the results presented here highlight the intimate link that exists between PAX6 and TALE-HD family proteins and contribute novel insights into how the orchestrated activity of transcription factors shapes adult V-SVZ neurogenesis.
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Affiliation(s)
- Ann-Christin Hau
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany. .,NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Strassen, Luxembourg. .,National Center of Pathology, Laboratoire National de Santé, 1 rue Louis Rech, 3555, Dudelange, Luxembourg.
| | - Elise Mommaerts
- Quantitative Biology Unit, LUXGEN, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Vera Laub
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany
| | - Tamara Müller
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany
| | - Gunnar Dittmar
- Quantitative Biology Unit, LUXGEN, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Dorothea Schulte
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany.
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Coll-de la Rubia E, Martinez-Garcia E, Dittmar G, Nazarov PV, Bebia V, Cabrera S, Gil-Moreno A, Colás E. In silico Approach for Validating and Unveiling New Applications for Prognostic Biomarkers of Endometrial Cancer. Cancers (Basel) 2021; 13:5052. [PMID: 34680205 PMCID: PMC8534093 DOI: 10.3390/cancers13205052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/29/2021] [Accepted: 10/02/2021] [Indexed: 12/20/2022] Open
Abstract
Endometrial cancer (EC) mortality is directly associated with the presence of prognostic factors. Current stratification systems are not accurate enough to predict the outcome of patients. Therefore, identifying more accurate prognostic EC biomarkers is crucial. We aimed to validate 255 prognostic biomarkers identified in multiple studies and explore their prognostic application by analyzing them in TCGA and CPTAC datasets. We analyzed the mRNA and proteomic expression data to assess the statistical prognostic performance of the 255 proteins. Significant biomarkers related to overall survival (OS) and recurrence-free survival (RFS) were combined and signatures generated. A total of 30 biomarkers were associated either to one or more of the following prognostic factors: histological type (n = 15), histological grade (n = 6), FIGO stage (n = 1), molecular classification (n = 16), or they were associated to OS (n = 11), and RFS (n = 5). A prognostic signature composed of 11 proteins increased the accuracy to predict OS (AUC = 0.827). The study validates and identifies new potential applications of 30 proteins as prognostic biomarkers and suggests to further study under-studied biomarkers such as TPX2, and confirms already used biomarkers such as MSH6, MSH2, or L1CAM. These results are expected to advance the quest for biomarkers to accurately assess the risk of EC patients.
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Affiliation(s)
- Eva Coll-de la Rubia
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain; (S.C.); (A.G.-M.)
| | - Elena Martinez-Garcia
- Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (E.M.-G.); (G.D.); (P.V.N.)
| | - Gunnar Dittmar
- Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (E.M.-G.); (G.D.); (P.V.N.)
| | - Petr V. Nazarov
- Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (E.M.-G.); (G.D.); (P.V.N.)
| | - Vicente Bebia
- Gynaecological Department, Vall Hebron University Hospital, CIBERONC, 08035 Barcelona, Spain;
| | - Silvia Cabrera
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain; (S.C.); (A.G.-M.)
- Gynaecological Department, Vall Hebron University Hospital, CIBERONC, 08035 Barcelona, Spain;
| | - Antonio Gil-Moreno
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain; (S.C.); (A.G.-M.)
- Gynaecological Department, Vall Hebron University Hospital, CIBERONC, 08035 Barcelona, Spain;
| | - Eva Colás
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain; (S.C.); (A.G.-M.)
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Cabrera S, Coll-de la Rubia E, Martínez Garcia E, Lesur A, Reques A, Casares de Cal MA, Gomez Tato A, Sabidó E, Borrás E, Peiró R, Dittmar G, Gil-Moreno A, Colas E. 873 Pap-smears allow the identification of protein biomarkers to diagnose endometrial cancer. Diagnostics (Basel) 2021. [DOI: 10.1136/ijgc-2021-esgo.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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27
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Gallet P, Oussalah A, Pouget C, Dittmar G, Chery C, Gauchotte G, Jankowski R, Gueant JL, Houlgatte R. Integrative genomics analysis of nasal intestinal-type adenocarcinomas demonstrates the major role of CACNA1C and paves the way for a simple diagnostic tool in male woodworkers. Clin Epigenetics 2021; 13:179. [PMID: 34563241 PMCID: PMC8467244 DOI: 10.1186/s13148-021-01122-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 06/27/2021] [Indexed: 11/23/2022] Open
Abstract
Background Nasal intestinal-type adenocarcinomas (ITAC) are strongly related to chronic wood dust exposure: The intestinal phenotype relies on CDX2 overexpression but underlying molecular mechanisms remain unknown. Our objectives were to investigate transcriptomic and methylation differences between healthy non-exposed and tumor olfactory cleft mucosae and to compare transcriptomic profiles between non-exposed, wood dust-exposed and ITAC mucosa cells.
Methods We conducted a prospective monocentric study (NCT0281823) including 16 woodworkers with ITAC, 16 healthy exposed woodworkers and 13 healthy, non-exposed, controls. We compared tumor samples with healthy non-exposed samples, both in transcriptome and in methylome analyses. We also investigated wood dust-induced transcriptome modifications of exposed (without tumor) male woodworkers’ samples and of contralateral sides of woodworkers with tumors. We conducted in parallel transcriptome and methylome analysis, and then, the transcriptome analysis was focused on the genes highlighted in methylome analysis. We replicated our results on dataset GSE17433. Results Several clusters of genes enabled the distinction between healthy and ITAC samples. Transcriptomic and IHC analysis confirmed a constant overexpression of CDX2 in ITAC samples, without any specific DNA methylation profile regarding the CDX2 locus. ITAC woodworkers also exhibited a specific transcriptomic profile in their contralateral (non-tumor) olfactory cleft, different from that of other exposed woodworkers, suggesting that they had a different exposure or a different susceptibility. Two top-loci (CACNA1C/CACNA1C-AS1 and SLC26A10) were identified with a hemimethylated profile, but only CACNA1C appeared to be overexpressed both in transcriptomic analysis and in immunohistochemistry. Conclusions Several clusters of genes enable the distinction between healthy mucosa and ITAC samples even in contralateral nasal fossa thus paving the way for a simple diagnostic tool for ITAC in male woodworkers. CACNA1C might be considered as a master gene of ITAC and should be further investigated. Trial registration: NIH ClinicalTrials, NCT0281823, registered May 23d 2016, https://www.clinicaltrials.gov/NCT0281823. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01122-5.
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Affiliation(s)
- Patrice Gallet
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France. .,ENT Department, CHRU NANCY, 54511, Vandoeuvre-lès-Nancy, France.
| | - Abderrahim Oussalah
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France
| | - Celso Pouget
- Pathology Department, CHRU NANCY, 54511, Vandoeuvre-lès-Nancy, France
| | - Gunnar Dittmar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Celine Chery
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France
| | - Guillaume Gauchotte
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France
| | - Roger Jankowski
- ENT Department, CHRU NANCY, 54511, Vandoeuvre-lès-Nancy, France
| | - Jean Louis Gueant
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France
| | - Rémi Houlgatte
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France
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28
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Poli A, Oudin A, Muller A, Hunewald O, Domingues O, Nazarov PV, Puard V, Baus V, Azuaje F, Dittmar G, Zimmer J, Michel T, Niclou SP, Ollert M. KS01.5.A Allergic airway inflammation impacts tumor take and delays experimental glioblastoma progression. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab180.009] [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: 11/12/2022] Open
Abstract
Abstract
BACKGROUND
Numerous epidemiological studies have highlighted the protective role of immunoglobulin E-mediated allergic diseases on glioblastoma (GBM) susceptibility and prognosis. However, the mechanistic explanations behind these phenomena remain unexplored. Our objective was to set up a preclinical model and investigate the mechanisms underlying such protection to improve our understanding of the crosstalk between immune system and brain tumor development.
MATERIAL AND METHODS
A mouse model of allergic airway inflammation (AAI) induced by repeated nasal instillation of House Dust Mite extract was initiated before intracranial implantation of GL261 glioma cells, in both immunocompetent (C57BL/6) and immunodeficient (RAG-KO) mice. Tumor take and tumor growth were monitored by MRI. Central (microglia) and peripheral (spleen, bone marrow) immune cells were characterized by flow cytometry. The response of microglia was further assessed by RNA sequencing. Impact of candidate genes on patient survival was characterized by Cox regression analysis using data from TCGA and CGGA.
RESULTS
Following AAI induction in C57BL/6 mice, engraftment of GL261 cells in the brain was delayed and tumor growth rate was reduced. This correlated with an increase in survival of the mice and was accompanied by increased effector memory T-cells in the circulation. Of note, the survival benefit was lost in RAG-KO mice devoid of adaptive immunity. At the level of the brain, we observed enhanced secretion of TNFα and IL6 in microglia ex vivo. AAI induced a transcriptional reprogramming of microglia towards a pro-inflammatory-like state. We identified an allergy-related microglia gene signature that is associated with improved prognosis of glioma patients.
CONCLUSION
Our results demonstrate that AAI limits both tumor take and GBM progression in mice, providing a preclinical model to study the role of allergic inflammation in GBM susceptibility and prognosis, respectively. At the functional level, we identify a potentiation of microglial and adaptive anti-tumoral immunity. Further investigations are warranted to shed light on the reciprocal crosstalk between microglial reprogramming and peripheral immunity in the context of allergies and brain tumors.
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Affiliation(s)
- A Poli
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - A Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - A Muller
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - O Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - O Domingues
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - P V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - V Puard
- Institut Curie Centre de Recherche, PSL Research University, RPPA platform, Paris, France
| | - V Baus
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - F Azuaje
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - G Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - J Zimmer
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - T Michel
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - S P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - M Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, University of Southern Denmark, Odense, Denmark
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29
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Ramberger E, Suarez-Artiles L, Perez-Hernandez D, Haji M, Popp O, Reimer U, Leutz A, Dittmar G, Mertins P. A universal peptide matrix interactomics approach to disclose motif dependent protein binding. Mol Cell Proteomics 2021; 20:100135. [PMID: 34391889 PMCID: PMC8453223 DOI: 10.1016/j.mcpro.2021.100135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/22/2021] [Accepted: 08/10/2021] [Indexed: 12/02/2022] Open
Abstract
Protein–protein interactions mediated by intrinsically disordered regions are often based on short linear motifs (SLiMs). SLiMs are implicated in signal transduction and gene regulation yet remain technically laborious and notoriously challenging to study. Here, we present an optimized method for a protein interaction screen on a peptide matrix (PRISMA) in combination with quantitative MS. The protocol was benchmarked with previously described SLiM-based protein–protein interactions using peptides derived from EGFR, SOS1, GLUT1, and CEBPB and extended to map binding partners of kinase activation loops. The detailed protocol provides practical considerations for setting up a PRISMA screen and subsequently implementing PRISMA on a liquid-handling robotic platform as a cost-effective high-throughput method. Optimized PRISMA can be universally applied to systematically study SLiM-based interactions and associated post-translational modifications or mutations to advance our understanding of the largely uncharacterized interactomes of intrinsically disordered protein regions. Optimized protocol for analysis of peptide–protein interactions with peptide arrays. Detection of interactions affected by mutations or post-translational modifications. Mapping of interaction sites with overlapping peptide sequences. Implementation on a liquid-handling robotic platform.
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Affiliation(s)
- Evelyn Ramberger
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Lorena Suarez-Artiles
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | | | - Mohamad Haji
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Berlin, Germany
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Institute of Biology, Humboldt University of Berlin, Berlin, Germany.
| | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg; Department of Life Sciences and Medicine, University of Luxembourg, L-4367 Belvaux, Luxembourg.
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Berlin Institute of Health (BIH), Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin; Deutsches Zentrum für Herz-Kreislauf-Forschung e. V. (DZHK), Berlin, Germany.
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30
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Ramberger E, Sapozhnikova V, Kowenz-Leutz E, Zimmermann K, Nicot N, Nazarov PV, Perez-Hernandez D, Reimer U, Mertins P, Dittmar G, Leutz A. PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα. iScience 2021; 24:102686. [PMID: 34189442 PMCID: PMC8220391 DOI: 10.1016/j.isci.2021.102686] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/17/2021] [Accepted: 05/30/2021] [Indexed: 01/27/2023] Open
Abstract
C/EBPα represents a paradigm intrinsically disordered transcription factor containing short linear motifs and post-translational modifications (PTM). Unraveling C/EBPα protein interaction networks is a prerequisite for understanding the multi-modal functions of C/EBPα in hematopoiesis and leukemia. Here, we combined arrayed peptide matrix screening (PRISMA) with BioID to generate an in vivo validated and isoform specific interaction map of C/EBPα. The myeloid C/EBPα interactome comprises promiscuous and PTM-regulated interactions with protein machineries involved in gene expression, epigenetics, genome organization, DNA replication, RNA processing, and nuclear transport. C/EBPα interaction hotspots coincide with homologous conserved regions of the C/EBP family that also score as molecular recognition features. PTMs alter the interaction spectrum of C/EBP-motifs to configure a multi-valent transcription factor hub that interacts with multiple co-regulatory components, including BAF/SWI-SNF or Mediator complexes. Combining PRISMA and BioID is a powerful strategy to systematically explore the PTM-regulated interactomes of intrinsically disordered transcription factors. Combining peptide arrays and BioID refines the C/EBPα interactome Hotspots of protein interactions in C/EBPα mostly occur in conserved regions The interaction with the BAF/SWI-SNF complex is modulated by C/EBPα methylation Experimental design suits interactome studies of intrinsically disordered proteins
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Affiliation(s)
- Evelyn Ramberger
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Valeria Sapozhnikova
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Elisabeth Kowenz-Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Karin Zimmermann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Nathalie Nicot
- Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Daniel Perez-Hernandez
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Gunnar Dittmar
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany
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Alfaro JA, Bohländer P, Dai M, Filius M, Howard CJ, van Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Cao C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsay S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M, Yin P, Meller A, Joo C. The emerging landscape of single-molecule protein sequencing technologies. Nat Methods 2021; 18:604-617. [PMID: 34099939 PMCID: PMC8223677 DOI: 10.1038/s41592-021-01143-1] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [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: 06/04/2020] [Accepted: 04/02/2021] [Indexed: 02/04/2023]
Abstract
Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.
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Affiliation(s)
- Javier Antonio Alfaro
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland.
| | - Peggy Bohländer
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - Mingjie Dai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Mike Filius
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Cecil J Howard
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | - Xander F van Kooten
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shilo Ohayon
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Adam Pomorski
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Sonja Schmid
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | - Georges Bedran
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Chan Cao
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Rome, Italy
| | - Etienne Coyaud
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Cees Dekker
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Gunnar Dittmar
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Rienk Eelkema
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - David Goodlett
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
- Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | | | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Rockville, MD, USA
- Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Sung Hyun Kim
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - David Rodriguez-Larrea
- Department of Biochemistry and Molecular Biology, Biofisika Institute (CSIC, UPV/EHU), Leioa, Spain
| | - Stuart Lindsay
- Biodesign Institute, School of Molecular Sciences, Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Rockville, MD, USA
| | | | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Kumar Sarthak
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lusia Sepiashvili
- University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Derek Stein
- Department of Physics, Brown University, Providence, RI, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Amit Meller
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
- Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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Abstract
The analysis of protein-protein interactions (PPIs) is essential for the understanding of cellular signaling. Besides probing PPIs with immunoprecipitation-based techniques, peptide pull-downs are an alternative tool specifically useful to study interactome changes induced by post-translational modifications. Peptides for pull-downs can be chemically synthesized and thus offer the possibility to include amino acid exchanges and post-translational modifications (PTMs) in the pull-down reaction. The combination of peptide pull-down and analysis of the binding partners with mass spectrometry offers the direct measurement of interactome changes induced by PTMs or by amino acid exchanges in the interaction site. The possibility of large-scale peptide synthesis on a membrane surface opened the possibility to systematically analyze interactome changes for mutations of many proteins at the same time. Short linear motifs (SLiMs) are amino acid patterns that can mediate protein binding. A significant number of SLiMs are located in regions of proteins, which are lacking a secondary structure, making the interaction motifs readily available for binding reactions. Peptides are particularly well suited to study protein interactions, which are based on SLiM-mediated binding. New technologies using arrayed peptides for interaction studies are able to identify SLIM-based interaction and identify the interaction motifs.
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Affiliation(s)
- Daniel Perez Hernandez
- Proteomics of Cellular Signalling, Department of Infection and Immunity, Luxembourg Institute of Health, 1 A Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Gunnar Dittmar
- Proteomics of Cellular Signalling, Department of Infection and Immunity, Luxembourg Institute of Health, 1 A Rue Thomas Edison, 1445, Strassen, Luxembourg. .,Department of Life Sciences and Medicine, University of Luxembourg, 4367, Belvaux, Luxembourg.
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Abstract
INTRODUCTION The continuous technical improvement in sensitivity and specificity placed mass spectrometry as an alternative method for analyzing clinical samples. In parallel to the rapid development of discovery proteomics, targeted acquisition has been implemented as a complementary option for measuring a small set of proteins with high sensitivity and robustness in a large sample cohort. The combination of trapped ion mobility with a rapid time-of-flight (TOF) mass spectrometer improves the sensitivity even further and triggers the development of prm-PASEF. AREAS COVERED This article discusses the development of prm-PASEF and its advantages over the existing targeted and discovery methods for analyzing clinical samples. We are also highlighting the different requirements for the use of prm-PASEF on clinical samples. EXPERT OPINION prm-PASEF takes advantage of a dual ion-mobility trap enabling highly multiplexed targeted acquisition. It allows the implementation of a short chromatographic separation setup without sacrificing the number of targeted peptides. Analyzing clinical samples by prm-PASEF holds the promise to significantly improve throughput while maintaining sensitivity to detect the selected target proteins.
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Affiliation(s)
- Antoine Lesur
- Head of the Proteomics Platform, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Gunnar Dittmar
- Co-Head of the Quantitative Biology Unit, Proteomics of Cellular Signaling Research Group Luxembourg Institute of Health, Strassen, Luxembourg
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Mendes ML, Dittmar G. Analysis of the Dynamic Proteasome Structure by Cross-Linking Mass Spectrometry. Biomolecules 2021; 11:biom11040505. [PMID: 33801594 PMCID: PMC8067131 DOI: 10.3390/biom11040505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
The 26S proteasome is a macromolecular complex that degrades proteins maintaining cell homeostasis; thus, determining its structure is a priority to understand its function. Although the 20S proteasome's structure has been known for some years, the highly dynamic nature of the 19S regulatory particle has presented a challenge to structural biologists. Advances in cryo-electron microscopy (cryo-EM) made it possible to determine the structure of the 19S regulatory particle and showed at least seven different conformational states of the proteasome. However, there are still many questions to be answered. Cross-linking mass spectrometry (CLMS) is now routinely used in integrative structural biology studies, and it promises to take integrative structural biology to the next level, answering some of these questions.
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Cano-Galiano A, Oudin A, Fack F, Allega MF, Sumpton D, Martinez-Garcia E, Dittmar G, Hau AC, Herold-Mende C, Bjerkvig R, Meiser J, Tardito S, Niclou SP. FSMP-07. CYSTATHIONINE-Γ-LYASE DRIVES ANTIOXIDANT DEFENSE IN CYSTEINE-RESTRICTED IDH1 MUTANT ASTROCYTOMAS. Neurooncol Adv 2021. [PMCID: PMC7992224 DOI: 10.1093/noajnl/vdab024.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mutations in isocitrate dehydrogenase 1 or 2 (IDH1/2) define glioma subtypes and are considered primary events in gliomagenesis, impacting tumor epigenetics and metabolism. IDH enzymes are crucial for the generation of reducing potential, yet the impact of the mutation on the cellular antioxidant system is not understood. Here, we investigate how glutathione (GSH) levels are maintained in IDH1 mutant gliomas, despite an altered NADPH/NADP balance. We find that IDH1 mutant astrocytomas specifically upregulate cystathionine γ-lyase (CSE), the enzyme responsible for cysteine production upstream of GSH biosynthesis. Genetic and chemical interference with CSE in patient-derived glioma cells carrying the endogenous IDH1 mutation, sensitized tumor cells to cysteine depletion, an effect not observed in IDH1 wild-type gliomas. This correlated with reduced GSH synthesis as shown by in vitro and in vivo serine tracing and led to delayed tumor growth in mice. Thus we show that IDH1 mutant astrocytic gliomas critically rely on NADPH-independent de novo GSH synthesis to maintain the antioxidant defense, which uncovers a novel metabolic vulnerability in this dismal disease.
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Affiliation(s)
| | - Anais Oudin
- Luxembourg Institute of Health, Luxembourg, Luxembourg, Luxembourg
| | - Fred Fack
- Luxembourg Institute of Health, Luxembourg, Luxembourg, Luxembourg
| | | | - David Sumpton
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | | | - Gunnar Dittmar
- Luxembourg Institute of Health, Luxembourg, Luxembourg, Luxembourg
| | - Ann-Christin Hau
- Luxembourg Institute of Health, Luxembourg, Luxembourg, Luxembourg
| | | | - Rolf Bjerkvig
- University of Bergen, Bergen, Norway
- Luxembourg Institute of Health, Luxembourg, Luxembourg, Luxembourg
| | - Johannes Meiser
- Luxembourg Institute of Health, Luxembourg, Luxembourg, Luxembourg
| | - Saverio Tardito
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Simone P Niclou
- Luxembourg Institute of Health, Luxembourg, Luxembourg, Luxembourg
- University of Bergen, Bergen, Norway
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36
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Martin E, Girardello R, Dittmar G, Ludwig A. New insights into the organization and regulation of the apical polarity network in mammalian epithelial cells. FEBS J 2021; 288:7073-7095. [DOI: 10.1111/febs.15710] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 12/11/2022]
Affiliation(s)
- Eleanor Martin
- School of Biological Sciences Nanyang Technological University Singapore City Singapore
- Proteomics of Cellular Signaling Luxembourg Institute of Health Strassen Luxembourg
| | - Rossana Girardello
- School of Biological Sciences Nanyang Technological University Singapore City Singapore
- Proteomics of Cellular Signaling Luxembourg Institute of Health Strassen Luxembourg
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling Luxembourg Institute of Health Strassen Luxembourg
- Department of Life Sciences and Medicine University of Luxembourg Luxembourg
| | - Alexander Ludwig
- School of Biological Sciences Nanyang Technological University Singapore City Singapore
- NTU Institute of Structural Biology (NISB) Experimental Medicine Building Nanyang Technological University Singapore City Singapore
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37
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Imbastari F, Dahlmann M, Sporbert A, Mattioli CC, Mari T, Scholz F, Timm L, Twamley S, Migotti R, Walther W, Dittmar G, Rehm A, Stein U. MACC1 regulates clathrin-mediated endocytosis and receptor recycling of transferrin receptor and EGFR in colorectal cancer. Cell Mol Life Sci 2021; 78:3525-3542. [PMID: 33469705 PMCID: PMC8038998 DOI: 10.1007/s00018-020-03734-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 11/16/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022]
Abstract
Metastasis Associated in Colon Cancer 1 (MACC1) is a novel prognostic, predictive and causal biomarker for tumor progression and metastasis in many cancer types, including colorectal cancer. Besides its clinical value, little is known about its molecular function. Its similarity to SH3BP4, involved in regulating uptake and recycling of transmembrane receptors, suggests a role of MACC1 in endocytosis. By exploring the MACC1 interactome, we identified the clathrin-mediated endocytosis (CME)-associated proteins CLTC, DNM2 and AP-2 as MACC1 binding partners. We unveiled a MACC1-dependent routing of internalized transferrin receptor towards recycling. Elevated MACC1 expression caused also the activation and internalization of EGFR, a higher rate of receptor recycling, as well as earlier and stronger receptor activation and downstream signaling. These effects are limited by deletion of CME-related protein interaction sites in MACC1. Thus, MACC1 regulates CME and receptor recycling, causing increased growth factor-mediated downstream signaling and cell proliferation. This novel mechanism unveils potential therapeutic intervention points restricting MACC1-driven metastasis.
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Affiliation(s)
- Francesca Imbastari
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Mathias Dahlmann
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Anje Sporbert
- Advanced Light Microscopy, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Camilla Ciolli Mattioli
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Tommaso Mari
- Proteome Dynamics, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Florian Scholz
- Tumor Immunology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Lena Timm
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Shailey Twamley
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | | | - Wolfgang Walther
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Armin Rehm
- Tumor Immunology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Ulrike Stein
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.
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Cano-Galiano A, Oudin A, Fack F, Allega MF, Sumpton D, Martinez-Garcia E, Dittmar G, Hau AC, De Falco A, Herold-Mende C, Bjerkvig R, Meiser J, Tardito S, Niclou SP. Cystathionine-γ-lyase drives antioxidant defense in cysteine-restricted IDH1-mutant astrocytomas. Neurooncol Adv 2021; 3:vdab057. [PMID: 34250481 PMCID: PMC8262642 DOI: 10.1093/noajnl/vdab057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Mutations in isocitrate dehydrogenase 1 or 2 (IDH1/2) define glioma subtypes and are considered primary events in gliomagenesis, impacting tumor epigenetics and metabolism. IDH enzyme activity is crucial for the generation of reducing potential in normal cells, yet the impact of the mutation on the cellular antioxidant system in glioma is not understood. The aim of this study was to determine how glutathione (GSH), the main antioxidant in the brain, is maintained in IDH1-mutant gliomas, despite an altered NADPH/NADP balance. METHODS Proteomics, metabolomics, metabolic tracer studies, genetic silencing, and drug targeting approaches in vitro and in vivo were applied. Analyses were done in clinical specimen of different glioma subtypes, in glioma patient-derived cell lines carrying the endogenous IDH1 mutation and corresponding orthotopic xenografts in mice. RESULTS We find that cystathionine-γ-lyase (CSE), the enzyme responsible for cysteine production upstream of GSH biosynthesis, is specifically upregulated in IDH1-mutant astrocytomas. CSE inhibition sensitized these cells to cysteine depletion, an effect not observed in IDH1 wild-type gliomas. This correlated with an increase in reactive oxygen species and reduced GSH synthesis. Propargylglycine (PAG), a brain-penetrant drug specifically targeting CSE, led to delayed tumor growth in mice. CONCLUSIONS We show that IDH1-mutant astrocytic gliomas critically rely on NADPH-independent de novo GSH synthesis via CSE to maintain the antioxidant defense, which highlights a novel metabolic vulnerability that may be therapeutically exploited.
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Affiliation(s)
- Andrés Cano-Galiano
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anais Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Fred Fack
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Maria-Francesca Allega
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Ann-Christin Hau
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Alfonso De Falco
- National Center of Genetics, Laboratoire national de santé, Dudelange, Luxembourg
| | | | - Rolf Bjerkvig
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Johannes Meiser
- Cancer Metabolism Group, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Saverio Tardito
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Department of Biomedicine, University of Bergen, Bergen, Norway
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Wilhelmi I, Grunwald S, Gimber N, Popp O, Dittmar G, Arumughan A, Wanker EE, Laeger T, Schmoranzer J, Daumke O, Schürmann A. The ARFRP1-dependent Golgi scaffolding protein GOPC is required for insulin secretion from pancreatic β-cells. Mol Metab 2020; 45:101151. [PMID: 33359402 PMCID: PMC7811047 DOI: 10.1016/j.molmet.2020.101151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022] Open
Abstract
Objective Hormone secretion from metabolically active tissues, such as pancreatic islets, is governed by specific and highly regulated signaling pathways. Defects in insulin secretion are among the major causes of diabetes. The molecular mechanisms underlying regulated insulin secretion are, however, not yet completely understood. In this work, we studied the role of the GTPase ARFRP1 on insulin secretion from pancreatic β-cells. Methods A β-cell-specific Arfrp1 knockout mouse was phenotypically characterized. Pulldown experiments and mass spectrometry analysis were employed to screen for new ARFRP1-interacting proteins. Co-immunoprecipitation assays as well as super-resolution microscopy were applied for validation. Results The GTPase ARFRP1 interacts with the Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC). Both proteins are co-localized at the trans-Golgi network and regulate the first and second phase of insulin secretion by controlling the plasma membrane localization of the SNARE protein SNAP25. Downregulation of both GOPC and ARFRP1 in Min6 cells interferes with the plasma membrane localization of SNAP25 and enhances its degradation, thereby impairing glucose-stimulated insulin release from β-cells. In turn, overexpression of SNAP25 as well as GOPC restores insulin secretion in islets from β-cell-specific Arfrp1 knockout mice. Conclusion Our results identify a hitherto unrecognized pathway required for insulin secretion at the level of trans-Golgi sorting. β-cell specific deletion of the trans-Golgi residing small GTPase ARFRP1 leads to elevated blood glucose levels in mice. GOPC is a newly identified ARFRP1 dependent scaffolding protein. ARFRP1 and GOPC are required for glucose-stimulated insulin secretion from pancreatic β-cells.
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Affiliation(s)
- Ilka Wilhelmi
- German Institute of Human Nutrition (DIfE) Potsdam-Rehbruecke, Germany; German Center for Diabetes Research (DZD) Munich Neuherberg, Germany
| | - Stephan Grunwald
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Germany
| | - Niclas Gimber
- Advanced Medical Bioimaging Core Facility - AMBIO, Charité-Universitätsmedizin Berlin, Germany
| | - Oliver Popp
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin, Germany
| | - Gunnar Dittmar
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin, Germany
| | - Anup Arumughan
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
| | - Thomas Laeger
- German Institute of Human Nutrition (DIfE) Potsdam-Rehbruecke, Germany; German Center for Diabetes Research (DZD) Munich Neuherberg, Germany
| | - Jan Schmoranzer
- Advanced Medical Bioimaging Core Facility - AMBIO, Charité-Universitätsmedizin Berlin, Germany
| | - Oliver Daumke
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Germany
| | - Annette Schürmann
- German Institute of Human Nutrition (DIfE) Potsdam-Rehbruecke, Germany; German Center for Diabetes Research (DZD) Munich Neuherberg, Germany; University of Potsdam, Institute of Nutritional Sciences, Nuthetal, Germany; Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Germany.
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40
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Stanchev LD, Marek M, Xian F, Klöhn M, Silvestro D, Dittmar G, López-Marqués RL, Günther Pomorski T. Functional Significance of Conserved Cysteines in the Extracellular Loops of the ATP Binding Cassette Transporter Pdr11p. J Fungi (Basel) 2020; 7:jof7010002. [PMID: 33375075 PMCID: PMC7822014 DOI: 10.3390/jof7010002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
The pleiotropic drug resistance (PDR) transporter Pdr11p is expressed under anaerobic growth conditions at the plasma membrane of the yeast Saccharomyces cerevisiae, where it facilitates the uptake of exogenous sterols. Members of the fungal PDR family contain six conserved cysteines in their extracellular loops (ECL). For the functional analysis of these cysteine residues in Pdr11p, we generated a series of single cysteine-to-serine mutants. All mutant proteins expressed well and displayed robust ATPase activity upon purification. Mass-spectrometry analysis identified two cysteine residues (C582 and C603) in ECL3 forming a disulfide bond. Further characterization by cell-based assays showed that all mutants are compromised in facilitating sterol uptake, protein stability, and trafficking to the plasma membrane. Our data highlight the fundamental importance of all six extracellular cysteine residues for the functional integrity of Pdr11p and provide new structural insights into the PDR family of transporters.
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Affiliation(s)
- Lyubomir Dimitrov Stanchev
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (L.D.S.); (M.K.)
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Magdalena Marek
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Feng Xian
- Proteomics of Cellular Signaling, Luxembourg Institute of Health, Rue Thomas Edison 1A-B, L-1445 Strassen, Luxembourg; (F.X.); (G.D.)
| | - Mara Klöhn
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (L.D.S.); (M.K.)
| | - Daniele Silvestro
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Luxembourg Institute of Health, Rue Thomas Edison 1A-B, L-1445 Strassen, Luxembourg; (F.X.); (G.D.)
| | - Rosa Laura López-Marqués
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (L.D.S.); (M.K.)
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
- Correspondence: ; Tel.: +49-234-322-4430
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41
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Lesur A, Schmit PO, Bernardin F, Letellier E, Brehmer S, Decker J, Dittmar G. Highly Multiplexed Targeted Proteomics Acquisition on a TIMS-QTOF. Anal Chem 2020; 93:1383-1392. [DOI: 10.1021/acs.analchem.0c03180] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Antoine Lesur
- Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, L-1445 Strassen, Luxembourg
| | | | - François Bernardin
- Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - Elisabeth Letellier
- Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, Campus Belval, L-4367 Belvaux, Luxembourg
| | - Sven Brehmer
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Jens Decker
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, L-1445 Strassen, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, Campus Belval, L-4367 Belvaux, Luxembourg
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42
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Schuster A, Klein E, Neirinckx V, Knudsen AM, Fabian C, Hau AC, Dieterle M, Oudin A, Nazarov PV, Golebiewska A, Muller A, Perez-Hernandez D, Rodius S, Dittmar G, Bjerkvig R, Herold-Mende C, Klink B, Kristensen BW, Niclou SP. AN1-type zinc finger protein 3 (ZFAND3) is a transcriptional regulator that drives Glioblastoma invasion. Nat Commun 2020; 11:6366. [PMID: 33311477 PMCID: PMC7732990 DOI: 10.1038/s41467-020-20029-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 11/04/2020] [Indexed: 01/12/2023] Open
Abstract
The infiltrative nature of Glioblastoma (GBM), the most aggressive primary brain tumor, critically prevents complete surgical resection and masks tumor cells behind the blood brain barrier reducing the efficacy of systemic treatment. Here, we use a genome-wide interference screen to determine invasion-essential genes and identify the AN1/A20 zinc finger domain containing protein 3 (ZFAND3) as a crucial driver of GBM invasion. Using patient-derived cellular models, we show that loss of ZFAND3 hampers the invasive capacity of GBM, whereas ZFAND3 overexpression increases motility in cells that were initially not invasive. At the mechanistic level, we find that ZFAND3 activity requires nuclear localization and integral zinc-finger domains. Our findings indicate that ZFAND3 acts within a nuclear protein complex to activate gene transcription and regulates the promoter of invasion-related genes such as COL6A2, FN1, and NRCAM. Further investigation in ZFAND3 function in GBM and other invasive cancers is warranted. Glioblastomas (GBMs) are highly invasive brain tumours, but the underlying mechanisms of GBM invasion are unclear. Here, the authors perform an RNA interference screen and identify AN1-Type Zinc Finger protein 3 (ZFAND3) as a regulator of GBM invasion, and find that it acts through the transcriptional regulation of invasion-related genes.
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Affiliation(s)
- Anne Schuster
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Eliane Klein
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Virginie Neirinckx
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Arnon Møldrup Knudsen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Carina Fabian
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ann-Christin Hau
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Monika Dieterle
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anais Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Arnaud Muller
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | | | - Sophie Rodius
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Rolf Bjerkvig
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Christel Herold-Mende
- Division of Neurosurgical Research, Department of Neurosurgery, University of Heidelberg, Heidelberg, Germany
| | - Barbara Klink
- National Center of Genetics, Laboratoire National de Santé, Dudelange, Luxembourg.,Functional Tumor Genetics, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Bjarne Winther Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg. .,Department of Biomedicine, University of Bergen, Bergen, Norway.
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43
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Aladdin A, Yao Y, Yang C, Kahlert G, Ghani M, Király N, Boratkó A, Uray K, Dittmar G, Tar K. The Proteasome Activators Blm10/PA200 Enhance the Proteasomal Degradation of N-Terminal Huntingtin. Biomolecules 2020; 10:biom10111581. [PMID: 33233776 PMCID: PMC7699873 DOI: 10.3390/biom10111581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/22/2022] Open
Abstract
The Blm10/PA200 family of proteasome activators modulates the peptidase activity of the core particle (20S CP). They participate in opening the 20S CP gate, thus facilitating the degradation of unstructured proteins such as tau and Dnm1 in a ubiquitin- and ATP-independent manner. Furthermore, PA200 also participates in the degradation of acetylated histones. In our study, we use a combination of yeast and human cell systems to investigate the role of Blm10/PA200 in the degradation of N-terminal Huntingtin fragments (N-Htt). We demonstrate that the human PA200 binds to N-Htt. The loss of Blm10 in yeast or PA200 in human cells results in increased mutant N-Htt aggregate formation and elevated cellular toxicity. Furthermore, Blm10 in vitro accelerates the proteasomal degradation of soluble N-Htt. Collectively, our data suggest N-Htt as a new substrate for Blm10/PA200-proteasomes and point to new approaches in Huntington's disease (HD) research.
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Affiliation(s)
- Azzam Aladdin
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
- Doctoral School of Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Yanhua Yao
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10460, USA;
- Correspondence: (Y.Y.); (G.D.); (K.T.); Tel.: +86-21-6384-6590 (Y.Y.); +352-26970-944 (G.D.); +36-52-412-345 (K.T.)
| | - Ciyu Yang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10460, USA;
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Marvi Ghani
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
- Doctoral School of Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Nikolett Király
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
- Doctoral School of Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Anita Boratkó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
| | - Karen Uray
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
| | - Gunnar Dittmar
- Proteomics of Cellular Signalling, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Department of Life Science and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
- Correspondence: (Y.Y.); (G.D.); (K.T.); Tel.: +86-21-6384-6590 (Y.Y.); +352-26970-944 (G.D.); +36-52-412-345 (K.T.)
| | - Krisztina Tar
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10460, USA;
- Correspondence: (Y.Y.); (G.D.); (K.T.); Tel.: +86-21-6384-6590 (Y.Y.); +352-26970-944 (G.D.); +36-52-412-345 (K.T.)
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44
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Coll-de la Rubia E, Martinez-Garcia E, Dittmar G, Gil-Moreno A, Cabrera S, Colas E. Prognostic Biomarkers in Endometrial Cancer: A Systematic Review and Meta-Analysis. J Clin Med 2020; 9:E1900. [PMID: 32560580 PMCID: PMC7356541 DOI: 10.3390/jcm9061900] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 12/23/2022] Open
Abstract
Endometrial cancer (EC) is the sixth most common cancer in women worldwide and its mortality is directly associated with the presence of poor prognostic factors driving tumor recurrence. Stratification systems are based on few molecular, and mostly clinical and pathological parameters, but these systems remain inaccurate. Therefore, identifying prognostic EC biomarkers is crucial for improving risk assessment pre- and postoperatively and to guide treatment decisions. This systematic review gathers all protein biomarkers associated with clinical prognostic factors of EC, recurrence and survival. Relevant studies were identified by searching the PubMed database from 1991 to February 2020. A total number of 398 studies matched our criteria, which compiled 255 proteins associated with the prognosis of EC. MUC16, ESR1, PGR, TP53, WFDC2, MKI67, ERBB2, L1CAM, CDH1, PTEN and MMR proteins are the most validated biomarkers. On the basis of our meta-analysis ESR1, TP53 and WFDC2 showed potential usefulness for predicting overall survival in EC. Limitations of the published studies in terms of appropriate study design, lack of high-throughput measurements, and statistical deficiencies are highlighted, and new approaches and perspectives for the identification and validation of clinically valuable EC prognostic biomarkers are discussed.
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Affiliation(s)
- Eva Coll-de la Rubia
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain;
| | - Elena Martinez-Garcia
- Quantitative Biology Unit, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (E.M.-G.); (G.D.)
| | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (E.M.-G.); (G.D.)
| | - Antonio Gil-Moreno
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain;
- Gynecological Department, Vall Hebron University Hospital, CIBERONC, 08035 Barcelona, Spain
| | - Silvia Cabrera
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain;
- Gynecological Department, Vall Hebron University Hospital, CIBERONC, 08035 Barcelona, Spain
| | - Eva Colas
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain;
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45
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Longworth J, Mendes ML, Dittmar G. Ubiquitin Chain Analysis by Parallel Reaction Monitoring. J Vis Exp 2020. [PMID: 32628175 DOI: 10.3791/60702] [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: 10/31/2022] Open
Abstract
Assessment of the global profile of ubiquitin chain topologies within a proteome is of interest to answer a wide range of biological questions. The protocol outlined here takes advantage of the di-glycine (-GG) modification left after the tryptic digestion of ubiquitin incorporated in a chain. By quantifying these topology-characteristic peptides the relative abundance of each ubiquitin chain topology can be determined. The steps required to quantify these peptides by a parallel reaction monitoring experiment are reported taking into consideration the stabilization of ubiquitin chains. Preparation of heavy controls, cell lysis, and digestion are described along with the appropriate mass spectrometer setup and data analysis workflow. An example data set with perturbations in ubiquitin topology is presented, accompanied by examples of how optimization of the protocol can affect results. By following the steps outlined, a user will be able to perform a global assessment of the ubiquitin topology landscape within their biological context.
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Affiliation(s)
| | - Marta L Mendes
- Quantitative Biology Unit, Luxembourg Institute of Health
| | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health;
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46
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Ihantola T, Di Bucchianico S, Happo M, Ihalainen M, Uski O, Bauer S, Kuuspalo K, Sippula O, Tissari J, Oeder S, Hartikainen A, Rönkkö TJ, Martikainen MV, Huttunen K, Vartiainen P, Suhonen H, Kortelainen M, Lamberg H, Leskinen A, Sklorz M, Michalke B, Dilger M, Weiss C, Dittmar G, Beckers J, Irmler M, Buters J, Candeias J, Czech H, Yli-Pirilä P, Abbaszade G, Jakobi G, Orasche J, Schnelle-Kreis J, Kanashova T, Karg E, Streibel T, Passig J, Hakkarainen H, Jokiniemi J, Zimmermann R, Hirvonen MR, Jalava PI. Influence of wood species on toxicity of log-wood stove combustion aerosols: a parallel animal and air-liquid interface cell exposure study on spruce and pine smoke. Part Fibre Toxicol 2020; 17:27. [PMID: 32539833 PMCID: PMC7296712 DOI: 10.1186/s12989-020-00355-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/26/2020] [Indexed: 12/11/2022] Open
Abstract
Background Wood combustion emissions have been studied previously either by in vitro or in vivo models using collected particles, yet most studies have neglected gaseous compounds. Furthermore, a more accurate and holistic view of the toxicity of aerosols can be gained with parallel in vitro and in vivo studies using direct exposure methods. Moreover, modern exposure techniques such as air-liquid interface (ALI) exposures enable better assessment of the toxicity of the applied aerosols than, for example, the previous state-of-the-art submerged cell exposure techniques. Methods We used three different ALI exposure systems in parallel to study the toxicological effects of spruce and pine combustion emissions in human alveolar epithelial (A549) and murine macrophage (RAW264.7) cell lines. A whole-body mouse inhalation system was also used to expose C57BL/6 J mice to aerosol emissions. Moreover, gaseous and particulate fractions were studied separately in one of the cell exposure systems. After exposure, the cells and animals were measured for various parameters of cytotoxicity, inflammation, genotoxicity, transcriptome and proteome. Results We found that diluted (1:15) exposure pine combustion emissions (PM1 mass 7.7 ± 6.5 mg m− 3, 41 mg MJ− 1) contained, on average, more PM and polycyclic aromatic hydrocarbons (PAHs) than spruce (PM1 mass 4.3 ± 5.1 mg m− 3, 26 mg MJ− 1) emissions, which instead showed a higher concentration of inorganic metals in the emission aerosol. Both A549 cells and mice exposed to these emissions showed low levels of inflammation but significantly increased genotoxicity. Gaseous emission compounds produced similar genotoxicity and a higher inflammatory response than the corresponding complete combustion emission in A549 cells. Systems biology approaches supported the findings, but we detected differing responses between in vivo and in vitro experiments. Conclusions Comprehensive in vitro and in vivo exposure studies with emission characterization and systems biology approaches revealed further information on the effects of combustion aerosol toxicity than could be achieved with either method alone. Interestingly, in vitro and in vivo exposures showed the opposite order of the highest DNA damage. In vitro measurements also indicated that the gaseous fraction of emission aerosols may be more important in causing adverse toxicological effects. Combustion aerosols of different wood species result in mild but aerosol specific in vitro and in vivo effects.
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Affiliation(s)
- Tuukka Ihantola
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland.
| | - Sebastiano Di Bucchianico
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Mikko Happo
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland.,Ramboll Finland, P.O.Box 25 Itsehallintokuja 3, FI-02601, Espoo, Finland
| | - Mika Ihalainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Oskari Uski
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Stefanie Bauer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Kari Kuuspalo
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland.,Present address: Savonia University of applied sciences, Microkatu 1, FI-70210, Kuopio, Finland
| | - Olli Sippula
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Jarkko Tissari
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Sebastian Oeder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Anni Hartikainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Teemu J Rönkkö
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Maria-Viola Martikainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Kati Huttunen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Petra Vartiainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Heikki Suhonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Miika Kortelainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Heikki Lamberg
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Ari Leskinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland.,Finnish Meteorological Institute, Yliopistonranta 1 F, FI-70210, Kuopio, Finland
| | - Martin Sklorz
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany.,Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr. Lorenzweg 2, D-18051, Rostock, Germany
| | - Bernhard Michalke
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Marco Dilger
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Campus North, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Carsten Weiss
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Campus North, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Gunnar Dittmar
- Luxembourg institute of health, 1A-B rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Johannes Beckers
- Institute of Experimental Genetics (IEG), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany.,Technical University of Munich, Chair of Experimental Genetics, D-85350, Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), D-85764, Neuherberg, Germany
| | - Martin Irmler
- Institute of Experimental Genetics (IEG), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Jeroen Buters
- ZAUM - Center of Allergy & Environment, Technical University Munich/Helmholtz Center Munich, Biedersteiner Str. 29, D-80802, Munich, Germany
| | - Joana Candeias
- ZAUM - Center of Allergy & Environment, Technical University Munich/Helmholtz Center Munich, Biedersteiner Str. 29, D-80802, Munich, Germany
| | - Hendryk Czech
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland.,Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Pasi Yli-Pirilä
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Gülcin Abbaszade
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Gert Jakobi
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Jürgen Orasche
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Jürgen Schnelle-Kreis
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Tamara Kanashova
- Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr. Lorenzweg 2, D-18051, Rostock, Germany.,Max-Delbrück-Centrum für Molekulare Medizin (MDC), Robert-Rössle-Str. 10, D-13125, Berlin, Germany
| | - Erwin Karg
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Thorsten Streibel
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany.,Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr. Lorenzweg 2, D-18051, Rostock, Germany
| | - Johannes Passig
- Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr. Lorenzweg 2, D-18051, Rostock, Germany
| | - Henri Hakkarainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Jorma Jokiniemi
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Ralf Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany.,Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr. Lorenzweg 2, D-18051, Rostock, Germany
| | - Maija-Riitta Hirvonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
| | - Pasi I Jalava
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O.Box 1627, FI-70210, Kuopio, Finland
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47
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Malik AR, Szydlowska K, Nizinska K, Asaro A, van Vliet EA, Popp O, Dittmar G, Fritsche-Guenther R, Kirwan JA, Nykjaer A, Lukasiuk K, Aronica E, Willnow TE. SorCS2 Controls Functional Expression of Amino Acid Transporter EAAT3 and Protects Neurons from Oxidative Stress and Epilepsy-Induced Pathology. Cell Rep 2020; 26:2792-2804.e6. [PMID: 30840898 PMCID: PMC6410498 DOI: 10.1016/j.celrep.2019.02.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 01/20/2019] [Accepted: 02/07/2019] [Indexed: 01/05/2023] Open
Abstract
VPS10P domain receptors emerge as central regulators of intracellular protein sorting in neurons with relevance for various brain pathologies. Here, we identified a role for the family member SorCS2 in protection of neurons from oxidative stress and epilepsy-induced cell death. We show that SorCS2 acts as sorting receptor that sustains cell surface expression of the neuronal amino acid transporter EAAT3 to facilitate import of cysteine, required for synthesis of the reactive oxygen species scavenger glutathione. Lack of SorCS2 causes depletion of EAAT3 from the plasma membrane and impairs neuronal cysteine uptake. As a consequence, SorCS2-deficient mice exhibit oxidative brain damage that coincides with enhanced neuronal cell death and increased mortality during epilepsy. Our findings highlight a protective role for SorCS2 in neuronal stress response and provide a possible explanation for upregulation of this receptor seen in surviving neurons of the human epileptic brain.
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Affiliation(s)
- Anna R Malik
- Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany.
| | - Kinga Szydlowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Karolina Nizinska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Antonino Asaro
- Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Erwin A van Vliet
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, the Netherlands; Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Oliver Popp
- Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Gunnar Dittmar
- Department of Oncology, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - Raphaela Fritsche-Guenther
- Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany; Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany
| | - Jennifer A Kirwan
- Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany; Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany
| | - Anders Nykjaer
- MIND Center, Danish Research Institute of Translational Neuroscience - DANDRITE, The Danish Research Foundation Center PROMEMO, Departments of Biomedicine, Aarhus University, and Neurosurgery, Aarhus University Hospital, 8000C Aarhus, Denmark
| | - Katarzyna Lukasiuk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, the Netherlands; Stichting Epilepsie Instellingen Nederland (SEIN), 2103 SW Heemstede, the Netherlands
| | - Thomas E Willnow
- Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany.
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48
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Zhao X, Nedvetsky P, Stanchi F, Vion AC, Popp O, Zühlke K, Dittmar G, Klussmann E, Gerhardt H. Correction: Endothelial PKA activity regulates angiogenesis by limiting autophagy through phosphorylation of ATG16L1. eLife 2020; 9:58195. [PMID: 32338607 PMCID: PMC7185991 DOI: 10.7554/elife.58195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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49
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Walbrecq G, Lecha O, Gaigneaux A, Fougeras MR, Philippidou D, Margue C, Tetsi Nomigni M, Bernardin F, Dittmar G, Behrmann I, Kreis S. Hypoxia-Induced Adaptations of miRNomes and Proteomes in Melanoma Cells and Their Secreted Extracellular Vesicles. Cancers (Basel) 2020; 12:cancers12030692. [PMID: 32183388 PMCID: PMC7140034 DOI: 10.3390/cancers12030692] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/12/2020] [Indexed: 12/13/2022] Open
Abstract
Reduced levels of intratumoural oxygen are associated with hypoxia-induced pro-oncogenic events such as invasion, metabolic reprogramming, epithelial–mesenchymal transition, metastasis and resistance to therapy, all favouring cancer progression. Small extracellular vesicles (EV) shuttle various cargos (proteins, miRNAs, DNA and others). Tumour-derived EVs can be taken up by neighbouring or distant cells in the tumour microenvironment, thus facilitating intercellular communication. The quantity of extracellular vesicle secretion and their composition can vary with changing microenvironmental conditions and disease states. Here, we investigated in melanoma cells the influence of hypoxia on the content and number of secreted EVs. Whole miRNome and proteome profiling revealed distinct expression patterns in normoxic or hypoxic growth conditions. Apart from the well-known miR-210, we identified miR-1290 as a novel hypoxia-associated microRNA, which was highly abundant in hypoxic EVs. On the other hand, miR-23a-5p and -23b-5p were consistently downregulated in hypoxic conditions, while the protein levels of the miR-23a/b-5p-predicted target IPO11 were concomitantly upregulated. Furthermore, hypoxic melanoma EVs exhibit a signature consisting of six proteins (AKR7A2, DDX39B, EIF3C, FARSA, PRMT5, VARS), which were significantly associated with a poor prognosis for melanoma patients, indicating that proteins and/or miRNAs secreted by cancer cells may be exploited as biomarkers.
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Affiliation(s)
- Geoffroy Walbrecq
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Odile Lecha
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Anthoula Gaigneaux
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Miriam R. Fougeras
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg; (M.R.F.)
- Doctoral School in Science and Engineering (DSSE), Faculty of Science, Technology and Medicine, University of Luxembourg, 2 avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg
| | - Demetra Philippidou
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Christiane Margue
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Milène Tetsi Nomigni
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - François Bernardin
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg; (M.R.F.)
| | - Gunnar Dittmar
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg; (M.R.F.)
| | - Iris Behrmann
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Stephanie Kreis
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
- Correspondence:
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50
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Rodius S, de Klein N, Jeanty C, Sánchez-Iranzo H, Crespo I, Ibberson M, Xenarios I, Dittmar G, Mercader N, Niclou SP, Azuaje F. Fisetin protects against cardiac cell death through reduction of ROS production and caspases activity. Sci Rep 2020; 10:2896. [PMID: 32076073 PMCID: PMC7031222 DOI: 10.1038/s41598-020-59894-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 01/28/2020] [Indexed: 12/16/2022] Open
Abstract
Myocardial infarction (MI) is a leading cause of death worldwide. Reperfusion is considered as an optimal therapy following cardiac ischemia. However, the promotion of a rapid elevation of O2 levels in ischemic cells produces high amounts of reactive oxygen species (ROS) leading to myocardial tissue injury. This phenomenon is called ischemia reperfusion injury (IRI). We aimed at identifying new and effective compounds to treat MI and minimize IRI. We previously studied heart regeneration following myocardial injury in zebrafish and described each step of the regeneration process, from the day of injury until complete recovery, in terms of transcriptional responses. Here, we mined the data and performed a deep in silico analysis to identify drugs highly likely to induce cardiac regeneration. Fisetin was identified as the top candidate. We validated its effects in an in vitro model of MI/IRI in mammalian cardiac cells. Fisetin enhances viability of rat cardiomyocytes following hypoxia/starvation – reoxygenation. It inhibits apoptosis, decreases ROS generation and caspase activation and protects from DNA damage. Interestingly, fisetin also activates genes involved in cell proliferation. Fisetin is thus a highly promising candidate drug with clinical potential to protect from ischemic damage following MI and to overcome IRI.
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Affiliation(s)
- Sophie Rodius
- Quantitative Biology Unit, Luxembourg Institute of Health (LIH), Luxembourg, 1445, Strassen, Luxembourg.
| | - Niek de Klein
- Department of Genetics, University of Groningen, Groningen, 9700 RB, The Netherlands.,The author completed this work at the Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, 1445, Strassen, Luxembourg
| | - Céline Jeanty
- Quantitative Biology Unit, Luxembourg Institute of Health (LIH), Luxembourg, 1445, Strassen, Luxembourg
| | - Héctor Sánchez-Iranzo
- Development of the Epicardium and Its Role During Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029, Madrid, Spain
| | - Isaac Crespo
- Vital-IT Systems Biology Division, SIB Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland
| | - Mark Ibberson
- Vital-IT Systems Biology Division, SIB Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland
| | - Ioannis Xenarios
- Vital-IT Systems Biology Division, SIB Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, CH-1015, Switzerland.,Department of Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health (LIH), Luxembourg, 1445, Strassen, Luxembourg
| | - Nadia Mercader
- Development of the Epicardium and Its Role During Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029, Madrid, Spain.,Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Simone P Niclou
- Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, 1445, Strassen, Luxembourg
| | - Francisco Azuaje
- Quantitative Biology Unit, Luxembourg Institute of Health (LIH), Luxembourg, 1445, Strassen, Luxembourg. .,Current affiliation: Data and Translational Sciences, UCB Celltech, 208 Bath Road, Slough, SL1 3WE, United Kingdom.
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