1
|
Reinecke M, Brear P, Vornholz L, Berger BT, Seefried F, Wilhelm S, Samaras P, Gyenis L, Litchfield DW, Médard G, Müller S, Ruland J, Hyvönen M, Wilhelm M, Kuster B. Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors. Nat Chem Biol 2024; 20:577-585. [PMID: 37904048 PMCID: PMC11062922 DOI: 10.1038/s41589-023-01459-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/22/2023] [Indexed: 11/01/2023]
Abstract
Medicinal chemistry has discovered thousands of potent protein and lipid kinase inhibitors. These may be developed into therapeutic drugs or chemical probes to study kinase biology. Because of polypharmacology, a large part of the human kinome currently lacks selective chemical probes. To discover such probes, we profiled 1,183 compounds from drug discovery projects in lysates of cancer cell lines using Kinobeads. The resulting 500,000 compound-target interactions are available in ProteomicsDB and we exemplify how this molecular resource may be used. For instance, the data revealed several hundred reasonably selective compounds for 72 kinases. Cellular assays validated GSK986310C as a candidate SYK (spleen tyrosine kinase) probe and X-ray crystallography uncovered the structural basis for the observed selectivity of the CK2 inhibitor GW869516X. Compounds targeting PKN3 were discovered and phosphoproteomics identified substrates that indicate target engagement in cells. We anticipate that this molecular resource will aid research in drug discovery and chemical biology.
Collapse
Affiliation(s)
- Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Larsen Vornholz
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Benedict-Tilmann Berger
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Florian Seefried
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - David William Litchfield
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Jürgen Ruland
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany.
| |
Collapse
|
2
|
Lier S, Sellmer A, Orben F, Heinzlmeir S, Krauß L, Schneeweis C, Hassan Z, Schneider C, Schäfer A, Pongratz H, Engleitner T, Öllinger R, Kuisl A, Bassermann F, Schlag C, Kong B, Dove S, Kuster B, Rad R, Reichert M, Wirth M, Saur D, Mahboobi S, Schneider G. Corrigendum to "A novel Cereblon E3 ligase modulator with antitumor activity in gastrointestinal cancer" [Bioorgan. Chem. 119 (2022) 105505]. Bioorg Chem 2024; 146:107248. [PMID: 38458892 DOI: 10.1016/j.bioorg.2024.107248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Affiliation(s)
- Svenja Lier
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Andreas Sellmer
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany
| | - Felix Orben
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | | | - Lukas Krauß
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Christian Schneeweis
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Zonera Hassan
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Carolin Schneider
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Arlette Schäfer
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Herwig Pongratz
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, MRI, TU Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, MRI, TU Munich, Germany
| | - Anna Kuisl
- Medical Clinic and Policlinic III, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Florian Bassermann
- Medical Clinic and Policlinic III, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Christoph Schlag
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Bo Kong
- Department of Surgery, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany; Department of General Surgery, University of Ulm, 89081 Ulm, Germany
| | - Stefan Dove
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TU Munich, 85354 Freising, Germany; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TU Munich, 85354 Freising, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, MRI, TU Munich, Germany; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Maximilian Reichert
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Center for Protein Assemblies (CPA), Technische Universität München, 85747 Garching, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charit́e - Universitätsmedizin Berlin, 12203 Berlin, Germany
| | - Dieter Saur
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Institute for Translational Cancer Research and Experimental Cancer Therapy, Klinikum Rechts der Isar, TU Munich, Germany
| | - Siavosh Mahboobi
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany.
| | - Günter Schneider
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany; University Medical Center Göttingen, Department of General, Visceral and Pediatric Surgery, 37075 Göttingen, Germany.
| |
Collapse
|
3
|
Stepan J, Heinz DE, Dethloff F, Wiechmann S, Martinelli S, Hafner K, Ebert T, Junglas E, Häusl AS, Pöhlmann ML, Jakovcevski M, Pape JC, Zannas AS, Bajaj T, Hermann A, Ma X, Pavenstädt H, Schmidt MV, Philipsen A, Turck CW, Deussing JM, Rammes G, Robinson AC, Payton A, Wehr MC, Stein V, Murgatroyd C, Kremerskothen J, Kuster B, Wotjak CT, Gassen NC. Inhibiting Hippo pathway kinases releases WWC1 to promote AMPAR-dependent synaptic plasticity and long-term memory in mice. Sci Signal 2024; 17:eadj6603. [PMID: 38687825 DOI: 10.1126/scisignal.adj6603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 04/11/2024] [Indexed: 05/02/2024]
Abstract
The localization, number, and function of postsynaptic AMPA-type glutamate receptors (AMPARs) are crucial for synaptic plasticity, a cellular correlate for learning and memory. The Hippo pathway member WWC1 is an important component of AMPAR-containing protein complexes. However, the availability of WWC1 is constrained by its interaction with the Hippo pathway kinases LATS1 and LATS2 (LATS1/2). Here, we explored the biochemical regulation of this interaction and found that it is pharmacologically targetable in vivo. In primary hippocampal neurons, phosphorylation of LATS1/2 by the upstream kinases MST1 and MST2 (MST1/2) enhanced the interaction between WWC1 and LATS1/2, which sequestered WWC1. Pharmacologically inhibiting MST1/2 in male mice and in human brain-derived organoids promoted the dissociation of WWC1 from LATS1/2, leading to an increase in WWC1 in AMPAR-containing complexes. MST1/2 inhibition enhanced synaptic transmission in mouse hippocampal brain slices and improved cognition in healthy male mice and in male mouse models of Alzheimer's disease and aging. Thus, compounds that disrupt the interaction between WWC1 and LATS1/2 might be explored for development as cognitive enhancers.
Collapse
Affiliation(s)
- Jens Stepan
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany
- Department of Obstetrics and Gynecology, Paracelsus Medical University, 5020 Salzburg, Austria
- Department of Gynecology and Obstetrics, Technical University of Munich, 81675 Munich, Germany
| | - Daniel E Heinz
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany
- Research Group Neuronal Plasticity, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Max Planck School of Cognition, 04103 Leipzig, Germany
| | - Frederik Dethloff
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Metabolomics Core Facility, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Svenja Wiechmann
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
- German Cancer Consortium (DKTK), 80336 Munich, Germany
- German Cancer Center (DKFZ), 69120 Heidelberg, Germany
| | - Silvia Martinelli
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Kathrin Hafner
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Tim Ebert
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany
- Research Group Neuronal Plasticity, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Ellen Junglas
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany
| | - Alexander S Häusl
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Max L Pöhlmann
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Mira Jakovcevski
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Julius C Pape
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Anthony S Zannas
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Thomas Bajaj
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany
| | - Anke Hermann
- Department of Medicine D, Division of General Internal Medicine, Nephrology, and Rheumatology, University Hospital Münster, 48149 Münster, Germany
| | - Xiao Ma
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Hermann Pavenstädt
- Department of Medicine D, Division of General Internal Medicine, Nephrology, and Rheumatology, University Hospital Münster, 48149 Münster, Germany
| | - Mathias V Schmidt
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Alexandra Philipsen
- Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany
| | - Christoph W Turck
- Proteomics and Biomarkers, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
| | - Jan M Deussing
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Research Group Molecular Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Gerhard Rammes
- Department of Anaesthesiology and Intensive Care Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Andrew C Robinson
- Division of Neuroscience, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Salford Royal Hospital, Salford M6 8HD, UK
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre (MAHSC), Salford M6 8HD, UK
| | - Antony Payton
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester M13 9NT, UK
| | - Michael C Wehr
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Valentin Stein
- Institute of Physiology II, Medical Faculty University of Bonn, 53115 Bonn, Germany
| | | | - Joachim Kremerskothen
- Department of Medicine D, Division of General Internal Medicine, Nephrology, and Rheumatology, University Hospital Münster, 48149 Münster, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
- German Cancer Consortium (DKTK), 80336 Munich, Germany
- German Cancer Center (DKFZ), 69120 Heidelberg, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | - Carsten T Wotjak
- Research Group Neuronal Plasticity, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Central Nervous System Diseases Research, Boehringer Ingelheim Pharmaceuticals GmbH & Co. KG, 88397 Biberach an der Riß, Germany
| | - Nils C Gassen
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany
| |
Collapse
|
4
|
Yoshida T, Mergner J, Yang Z, Liu J, Kuster B, Fernie AR, Grill E. Integrating multi-omics data reveals energy and stress signaling activated by abscisic acid in Arabidopsis. Plant J 2024. [PMID: 38613775 DOI: 10.1111/tpj.16765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 03/24/2024] [Accepted: 03/31/2024] [Indexed: 04/15/2024]
Abstract
Phytohormones are essential signaling molecules regulating various processes in growth, development, and stress responses. Genetic and molecular studies, especially using Arabidopsis thaliana (Arabidopsis), have discovered many important players involved in hormone perception, signal transduction, transport, and metabolism. Phytohormone signaling pathways are extensively interconnected with other endogenous and environmental stimuli. However, our knowledge of the huge and complex molecular network governed by a hormone remains limited. Here we report a global overview of downstream events of an abscisic acid (ABA) receptor, REGULATORY COMPONENTS OF ABA RECEPTOR (RCAR) 6 (also known as PYRABACTIN RESISTANCE 1 [PYR1]-LIKE [PYL] 12), by integrating phosphoproteomic, proteomic and metabolite profiles. Our data suggest that the RCAR6 overexpression constitutively decreases the protein levels of its coreceptors, namely clade A protein phosphatases of type 2C, and activates sucrose non-fermenting-1 (SNF1)-related protein kinase 1 (SnRK1) and SnRK2, the central regulators of energy and ABA signaling pathways. Furthermore, several enzymes in sugar metabolism were differentially phosphorylated and expressed in the RCAR6 line, and the metabolite profile revealed altered accumulations of several organic acids and amino acids. These results indicate that energy- and water-saving mechanisms mediated by the SnRK1 and SnRK2 kinases, respectively, are under the control of the ABA receptor-coreceptor complexes.
Collapse
Affiliation(s)
- Takuya Yoshida
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany
| | - Julia Mergner
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Zhenyu Yang
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Jinghui Liu
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany
| | - Erwin Grill
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
| |
Collapse
|
5
|
Picciani M, Gabriel W, Giurcoiu VG, Shouman O, Hamood F, Lautenbacher L, Jensen CB, Müller J, Kalhor M, Soleymaniniya A, Kuster B, The M, Wilhelm M. Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit. Proteomics 2024; 24:e2300112. [PMID: 37672792 DOI: 10.1002/pmic.202300112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
Machine learning (ML) and deep learning (DL) models for peptide property prediction such as Prosit have enabled the creation of high quality in silico reference libraries. These libraries are used in various applications, ranging from data-independent acquisition (DIA) data analysis to data-driven rescoring of search engine results. Here, we present Oktoberfest, an open source Python package of our spectral library generation and rescoring pipeline originally only available online via ProteomicsDB. Oktoberfest is largely search engine agnostic and provides access to online peptide property predictions, promoting the adoption of state-of-the-art ML/DL models in proteomics analysis pipelines. We demonstrate its ability to reproduce and even improve our results from previously published rescoring analyses on two distinct use cases. Oktoberfest is freely available on GitHub (https://github.com/wilhelm-lab/oktoberfest) and can easily be installed locally through the cross-platform PyPI Python package.
Collapse
Affiliation(s)
- Mario Picciani
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wassim Gabriel
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Victor-George Giurcoiu
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Omar Shouman
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Firas Hamood
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Ludwig Lautenbacher
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Cecilia Bang Jensen
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Julian Müller
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mostafa Kalhor
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Armin Soleymaniniya
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| |
Collapse
|
6
|
Tretter C, de Andrade Krätzig N, Pecoraro M, Lange S, Seifert P, von Frankenberg C, Untch J, Zuleger G, Wilhelm M, Zolg DP, Dreyer FS, Bräunlein E, Engleitner T, Uhrig S, Boxberg M, Steiger K, Slotta-Huspenina J, Ochsenreither S, von Bubnoff N, Bauer S, Boerries M, Jost PJ, Schenck K, Dresing I, Bassermann F, Friess H, Reim D, Grützmann K, Pfütze K, Klink B, Schröck E, Haller B, Kuster B, Mann M, Weichert W, Fröhling S, Rad R, Hiltensperger M, Krackhardt AM. Author Correction: Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nat Commun 2024; 15:2364. [PMID: 38491045 PMCID: PMC10943035 DOI: 10.1038/s41467-024-46724-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024] Open
Affiliation(s)
- Celina Tretter
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Niklas de Andrade Krätzig
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Matteo Pecoraro
- Department of Proteomics and Signal Transduction, Max Plank Institute of Biochemistry, Munich, Germany
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Sebastian Lange
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Philipp Seifert
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Clara von Frankenberg
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Johannes Untch
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Gabriela Zuleger
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Mathias Wilhelm
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
- Technical University of Munich, TUM School of Life Sciences, Computational Mass Spectrometry, Freising, Germany
| | - Daniel P Zolg
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
| | - Florian S Dreyer
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Eva Bräunlein
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Thomas Engleitner
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Sebastian Uhrig
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Precision Oncology Program, NCT Heidelberg, Heidelberg, Germany
| | - Melanie Boxberg
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Julia Slotta-Huspenina
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Sebastian Ochsenreither
- German Cancer Consortium (DKTK), partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nikolas von Bubnoff
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Hematology and Oncology, Medical Center, University of Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Sebastian Bauer
- German Cancer Consortium (DKTK), partner site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp J Jost
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
- Clinical Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- University Comprehensive Cancer Center Graz, Medical University of Graz, Graz, Austria
| | - Kristina Schenck
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Iska Dresing
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Florian Bassermann
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Helmut Friess
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany
| | - Daniel Reim
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany
| | - Konrad Grützmann
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Core Unit Molecular Tumor Diagnostics (CMTD), NCT Dresden, Dresden, Germany
- Institute for Medical Informatics and Biometry, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Katrin Pfütze
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Klink
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Evelin Schröck
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC), Dresden, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Bernhard Haller
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of AI and Informatics in Medicine, Munich, Germany
| | - Bernhard Kuster
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
- Technical University of Munich, TUM School of Life Sciences, Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Freising, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Plank Institute of Biochemistry, Munich, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Michael Hiltensperger
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Angela M Krackhardt
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany.
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany.
- Malteser Krankenhaus St. Franziskus-Hospital, Flensburg, Germany.
| |
Collapse
|
7
|
Kuster B, Tüshaus J, Bayer FP. A new mass analyzer shakes up the proteomics field. Nat Biotechnol 2024:10.1038/s41587-024-02129-y. [PMID: 38302752 DOI: 10.1038/s41587-024-02129-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Affiliation(s)
- Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany.
- Partner Site Munich, German Cancer Consortium (DKTK), Munich, Germany.
- Clinspect-M, Munich, Germany.
| | - Johanna Tüshaus
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
- Clinspect-M, Munich, Germany
| | - Florian P Bayer
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
| |
Collapse
|
8
|
Graf A, Bassukas AEL, Xiao Y, Barbosa ICR, Mergner J, Grill P, Michalke B, Kuster B, Schwechheimer C. D6PK plasma membrane polarity requires a repeated CXX(X)P motif and PDK1-dependent phosphorylation. Nat Plants 2024; 10:300-314. [PMID: 38278951 PMCID: PMC10881395 DOI: 10.1038/s41477-023-01615-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/15/2023] [Indexed: 01/28/2024]
Abstract
D6 PROTEIN KINASE (D6PK) is a polarly localized plasma-membrane-associated kinase from Arabidopsis thaliana that activates polarly distributed PIN-FORMED auxin transporters. D6PK moves rapidly to and from the plasma membrane, independent of its PIN-FORMED targets. The middle D6PK domain, an insertion between kinase subdomains VII and VIII, is required and sufficient for association and polarity of the D6PK plasma membrane. How D6PK polarity is established and maintained remains to be shown. Here we show that cysteines from repeated middle domain CXX(X)P motifs are S-acylated and required for D6PK membrane association. While D6PK S-acylation is not detectably regulated during intracellular transport, phosphorylation of adjacent serine residues, in part in dependence on the upstream 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE, promotes D6PK transport, controls D6PK residence time at the plasma membrane and prevents its lateral diffusion. We thus identify new mechanisms for the regulation of D6PK plasma membrane interaction and polarity.
Collapse
Affiliation(s)
- Alina Graf
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | | | - Yao Xiao
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Inês C R Barbosa
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Julia Mergner
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar, Center for Translational Cancer Research, Munich, Germany
| | - Peter Grill
- Helmholtz Zentrum München, German Research Center for Environmental Health, Analytical BioGeoChemistry, Neuherberg, Germany
| | - Bernhard Michalke
- Helmholtz Zentrum München, German Research Center for Environmental Health, Analytical BioGeoChemistry, Neuherberg, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Claus Schwechheimer
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| |
Collapse
|
9
|
Kardell O, von Toerne C, Merl-Pham J, König AC, Blindert M, Barth TK, Mergner J, Ludwig C, Tüshaus J, Eckert S, Müller SA, Breimann S, Giesbertz P, Bernhardt AM, Schweizer L, Albrecht V, Teupser D, Imhof A, Kuster B, Lichtenthaler SF, Mann M, Cox J, Hauck SM. Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens. J Proteome Res 2024; 23:117-129. [PMID: 38015820 PMCID: PMC10775142 DOI: 10.1021/acs.jproteome.3c00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/02/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023]
Abstract
The foundation for integrating mass spectrometry (MS)-based proteomics into systems medicine is the development of standardized start-to-finish and fit-for-purpose workflows for clinical specimens. An essential step in this pursuit is to highlight the common ground in a diverse landscape of different sample preparation techniques and liquid chromatography-mass spectrometry (LC-MS) setups. With the aim to benchmark and improve the current best practices among the proteomics MS laboratories of the CLINSPECT-M consortium, we performed two consecutive round-robin studies with full freedom to operate in terms of sample preparation and MS measurements. The six study partners were provided with two clinically relevant sample matrices: plasma and cerebrospinal fluid (CSF). In the first round, each laboratory applied their current best practice protocol for the respective matrix. Based on the achieved results and following a transparent exchange of all lab-specific protocols within the consortium, each laboratory could advance their methods before measuring the same samples in the second acquisition round. Both time points are compared with respect to identifications (IDs), data completeness, and precision, as well as reproducibility. As a result, the individual performances of participating study centers were improved in the second measurement, emphasizing the effect and importance of the expert-driven exchange of best practices for direct practical improvements.
Collapse
Affiliation(s)
- Oliver Kardell
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
| | - Christine von Toerne
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
| | - Juliane Merl-Pham
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
| | - Ann-Christine König
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
| | - Marcel Blindert
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
| | - Teresa K. Barth
- Clinical
Protein Analysis Unit (ClinZfP), Biomedical Center (BMC), Faculty
of Medicine, Ludwig-Maximilians-University
(LMU) Munich, Großhaderner Straße 9, Martinsried 82152, Germany
| | - Julia Mergner
- Bavarian
Center for Biomolecular Mass Spectrometry at Klinikum Rechts der Isar
(BayBioMS@MRI), Technical University of
Munich, Munich 80333, Germany
| | - Christina Ludwig
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of
Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Johanna Tüshaus
- Chair
of Proteomics and Bioanalytics, Technical
University of Munich, Freising 85354, Germany
| | - Stephan Eckert
- Chair
of Proteomics and Bioanalytics, Technical
University of Munich, Freising 85354, Germany
| | - Stephan A. Müller
- German
Center
for Neurodegenerative Diseases (DZNE) Munich, DZNE, Munich 81377, Germany
- Neuroproteomics,
School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich 81675, Germany
| | - Stephan Breimann
- German
Center
for Neurodegenerative Diseases (DZNE) Munich, DZNE, Munich 81377, Germany
- Neuroproteomics,
School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich 81675, Germany
| | - Pieter Giesbertz
- German
Center
for Neurodegenerative Diseases (DZNE) Munich, DZNE, Munich 81377, Germany
- Neuroproteomics,
School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich 81675, Germany
| | - Alexander M. Bernhardt
- German
Center
for Neurodegenerative Diseases (DZNE) Munich, DZNE, Munich 81377, Germany
- Department
of Neurology, Ludwig-Maximilians-Universität
München, Munich 80539, Germany
| | - Lisa Schweizer
- Department
of Proteomics and Signal Transduction, Max-Planck
Institute of Biochemistry, Martinsried 82152, Germany
| | - Vincent Albrecht
- Department
of Proteomics and Signal Transduction, Max-Planck
Institute of Biochemistry, Martinsried 82152, Germany
| | - Daniel Teupser
- Institute
of Laboratory Medicine, University Hospital,
LMU Munich, Munich 81377, Germany
| | - Axel Imhof
- Clinical
Protein Analysis Unit (ClinZfP), Biomedical Center (BMC), Faculty
of Medicine, Ludwig-Maximilians-University
(LMU) Munich, Großhaderner Straße 9, Martinsried 82152, Germany
| | - Bernhard Kuster
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of
Life Sciences, Technical University of Munich, Freising 85354, Germany
- Chair
of Proteomics and Bioanalytics, Technical
University of Munich, Freising 85354, Germany
| | - Stefan F. Lichtenthaler
- German
Center
for Neurodegenerative Diseases (DZNE) Munich, DZNE, Munich 81377, Germany
- Neuroproteomics,
School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich 81675, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich 81377, Germany
| | - Matthias Mann
- Department
of Proteomics and Signal Transduction, Max-Planck
Institute of Biochemistry, Martinsried 82152, Germany
| | - Jürgen Cox
- Computational Systems
Biochemistry Research Group, Max-Planck
Institute of Biochemistry, Martinsried 82152, Germany
| | - Stefanie M. Hauck
- Metabolomics
and Proteomics Core (MPC), Helmholtz Zentrum
München,German Research Center for Environmental Health (GmbH), Munich 80939, Germany
| |
Collapse
|
10
|
Lee CY, The M, Meng C, Bayer FP, Putzker K, Müller J, Streubel J, Woortman J, Sakhteman A, Resch M, Schneider A, Wilhelm S, Kuster B. Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics. Mol Syst Biol 2024; 20:28-55. [PMID: 38177929 PMCID: PMC10883282 DOI: 10.1038/s44320-023-00004-7] [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: 12/23/2022] [Revised: 11/06/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Kinase inhibitors (KIs) are important cancer drugs but often feature polypharmacology that is molecularly not understood. This disconnect is particularly apparent in cancer entities such as sarcomas for which the oncogenic drivers are often not clear. To investigate more systematically how the cellular proteotypes of sarcoma cells shape their response to molecularly targeted drugs, we profiled the proteomes and phosphoproteomes of 17 sarcoma cell lines and screened the same against 150 cancer drugs. The resulting 2550 phenotypic profiles revealed distinct drug responses and the cellular activity landscapes derived from deep (phospho)proteomes (9-10,000 proteins and 10-27,000 phosphorylation sites per cell line) enabled several lines of analysis. For instance, connecting the (phospho)proteomic data with drug responses revealed known and novel mechanisms of action (MoAs) of KIs and identified markers of drug sensitivity or resistance. All data is publicly accessible via an interactive web application that enables exploration of this rich molecular resource for a better understanding of active signalling pathways in sarcoma cells, identifying treatment response predictors and revealing novel MoA of clinical KIs.
Collapse
Affiliation(s)
- Chien-Yun Lee
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Kerstin Putzker
- Chemical Biology Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Julian Müller
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Johanna Streubel
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Woortman
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Moritz Resch
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Annika Schneider
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany.
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
11
|
Tüshaus J, Sakhteman A, Lechner S, The M, Mucha E, Krisp C, Schlegel J, Delbridge C, Kuster B. A region-resolved proteomic map of the human brain enabled by high-throughput proteomics. EMBO J 2023; 42:e114665. [PMID: 37916885 PMCID: PMC10690467 DOI: 10.15252/embj.2023114665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
Substantial efforts are underway to deepen our understanding of human brain morphology, structure, and function using high-resolution imaging as well as high-content molecular profiling technologies. The current work adds to these approaches by providing a comprehensive and quantitative protein expression map of 13 anatomically distinct brain regions covering more than 11,000 proteins. This was enabled by the optimization, characterization, and implementation of a high-sensitivity and high-throughput microflow liquid chromatography timsTOF tandem mass spectrometry system (LC-MS/MS) capable of analyzing more than 2,000 consecutive samples prepared from formalin-fixed paraffin embedded (FFPE) material. Analysis of this proteomic resource highlighted brain region-enriched protein expression patterns and functional protein classes, protein localization differences between brain regions and individual markers for specific areas. To facilitate access to and ease further mining of the data by the scientific community, all data can be explored online in a purpose-built R Shiny app (https://brain-region-atlas.proteomics.ls.tum.de).
Collapse
Affiliation(s)
- Johanna Tüshaus
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Amirhossein Sakhteman
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Severin Lechner
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Matthew The
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Eike Mucha
- Bruker Daltonics GmbH & Co. KGBremenGermany
| | | | - Jürgen Schlegel
- Department of Neuropathology, Klinikum Rechts der ISAR, School of MedicineTechnical University MunichMunichGermany
| | - Claire Delbridge
- Department of Neuropathology, Klinikum Rechts der ISAR, School of MedicineTechnical University MunichMunichGermany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
- German Cancer Consortium (DKTK), Munich SiteHeidelbergGermany
| |
Collapse
|
12
|
Bayer FP, Gander M, Kuster B, The M. CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose-response curves. Nat Commun 2023; 14:7902. [PMID: 38036588 PMCID: PMC10689459 DOI: 10.1038/s41467-023-43696-z] [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: 08/25/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
Dose-response curves are key metrics in pharmacology and biology to assess phenotypic or molecular actions of bioactive compounds in a quantitative fashion. Yet, it is often unclear whether or not a measured response significantly differs from a curve without regulation, particularly in high-throughput applications or unstable assays. Treating potency and effect size estimates from random and true curves with the same level of confidence can lead to incorrect hypotheses and issues in training machine learning models. Here, we present CurveCurator, an open-source software that provides reliable dose-response characteristics by computing p-values and false discovery rates based on a recalibrated F-statistic and a target-decoy procedure that considers dataset-specific effect size distributions. The application of CurveCurator to three large-scale datasets enables a systematic drug mode of action analysis and demonstrates its scalable utility across several application areas, facilitated by a performant, interactive dashboard for fast data exploration.
Collapse
Affiliation(s)
- Florian P Bayer
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Manuel Gander
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, 80336, Munich, Germany
| | - Matthew The
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
| |
Collapse
|
13
|
Ecker V, Brandmeier L, Stumpf M, Giansanti P, Moreira AV, Pfeuffer L, Fens MHAM, Lu J, Kuster B, Engleitner T, Heidegger S, Rad R, Ringshausen I, Zenz T, Wendtner CM, Müschen M, Jellusova J, Ruland J, Buchner M. Negative feedback regulation of MAPK signaling is an important driver of chronic lymphocytic leukemia progression. Cell Rep 2023; 42:113017. [PMID: 37792532 DOI: 10.1016/j.celrep.2023.113017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/08/2023] [Accepted: 08/06/2023] [Indexed: 10/06/2023] Open
Abstract
Despite available targeted treatments for the disease, drug-resistant chronic lymphocytic leukemia (CLL) poses a clinical challenge. The objective of this study is to examine whether the dual-specific phosphatases DUSP1 and DUSP6 are required to negatively regulate mitogen-activated protein kinases (MAPKs) and thus counterbalance excessive MAPK activity. We show that high expression of DUSP6 in CLL correlates with poor clinical prognosis. Importantly, genetic deletion of the inhibitory phosphatase DUSP1 or DUSP6 and blocking DUSP1/6 function using a small-molecule inhibitor reduces CLL cell survival in vitro and in vivo. Using global phospho-proteome approaches, we observe acute activation of MAPK signaling by DUSP1/6 inhibition. This promotes accumulation of mitochondrial reactive oxygen species and, thereby, DNA damage and apoptotic cell death in CLL cells. Finally, we observe that DUSP1/6 inhibition is particularly effective against treatment-resistant CLL and therefore suggest transient DUSP1/6 inhibition as a promising treatment concept to eliminate drug-resistant CLL cells.
Collapse
Affiliation(s)
- Veronika Ecker
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Lisa Brandmeier
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Martina Stumpf
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Piero Giansanti
- TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany; Bavarian Center for Biomolecular Mass Spectrometry at the University hospital rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany
| | - Aida Varela Moreira
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lisa Pfeuffer
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Marcel H A M Fens
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Junyan Lu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany; Bavarian Center for Biomolecular Mass Spectrometry at the University hospital rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Munich Partner Site, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Engleitner
- TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany; Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Simon Heidegger
- TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany; Department of Medicine III, School of Medicine, Technical University of Munich, Munich, Germany
| | - Roland Rad
- TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany; German Cancer Consortium (DKTK), Munich Partner Site, Munich, Germany; Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Ingo Ringshausen
- Wellcome Trust/MRC Cambridge Stem Cell Institute and Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AH, UK
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, 8091 Zurich, Switzerland
| | - Clemens-Martin Wendtner
- Munich Clinic Schwabing, Academic Teaching Hospital, Ludwig-Maximilian University (LMU), Munich, Germany
| | - Markus Müschen
- Center of Molecular and Cellular Oncology, Yale School of Medicine, 300 George Street, New Haven, CT 06520, USA
| | - Julia Jellusova
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Jürgen Ruland
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany; German Cancer Consortium (DKTK), Munich Partner Site, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Maike Buchner
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; TranslaTUM - Central Institute for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany.
| |
Collapse
|
14
|
Kücükdisli M, Bel-Abed H, Cirillo D, Lo WT, Efrém NL, Horatscheck A, Perepelittchenko L, Prokofeva P, Ehret TAL, Radetzki S, Neuenschwander M, Specker E, Médard G, Müller S, Wilhelm S, Kuster B, von Kries JP, Haucke V, Nazaré M. Structural Basis for Highly Selective Class II Alpha Phosphoinositide-3-Kinase Inhibition. J Med Chem 2023; 66:14278-14302. [PMID: 37819647 DOI: 10.1021/acs.jmedchem.3c01319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Class II phosphoinositide-3-kinases (PI3Ks) play central roles in cell signaling, division, migration, and survival. Despite evidence that all PI3K class II isoforms serve unique cellular functions, the lack of isoform-selective inhibitors severely hampers the systematic investigation of their potential relevance as pharmacological targets. Here, we report the structural evaluation and molecular determinants for selective PI3K-C2α inhibition by a structure-activity relationship study based on a pteridinone scaffold, leading to the discovery of selective PI3K-C2α inhibitors called PITCOINs. Cocrystal structures and docking experiments supported the rationalization of the structural determinants essential for inhibitor activity and high selectivity. Profiling of PITCOINs in a panel of more than 118 diverse kinases showed no off-target kinase inhibition. Notably, by addressing a selectivity pocket, PITCOIN4 showed nanomolar inhibition of PI3K-C2α and >100-fold selectivity in a general kinase panel. Our study paves the way for the development of novel therapies for diseases related to PI3K-C2α function.
Collapse
Affiliation(s)
- Murat Kücükdisli
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - Hassen Bel-Abed
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - Davide Cirillo
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - Wen-Ting Lo
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - Nina-Louisa Efrém
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - André Horatscheck
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - Liudmila Perepelittchenko
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - Polina Prokofeva
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Theresa A L Ehret
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Silke Radetzki
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - Edgar Specker
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, 13125 Berlin, Germany
| |
Collapse
|
15
|
Adamowicz K, Arend L, Maier A, Schmidt JR, Kuster B, Tsoy O, Zolotareva O, Baumbach J, Laske T. Proteomic meta-study harmonization, mechanotyping and drug repurposing candidate prediction with ProHarMeD. NPJ Syst Biol Appl 2023; 9:49. [PMID: 37816770 PMCID: PMC10564802 DOI: 10.1038/s41540-023-00311-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Proteomics technologies, which include a diverse range of approaches such as mass spectrometry-based, array-based, and others, are key technologies for the identification of biomarkers and disease mechanisms, referred to as mechanotyping. Despite over 15,000 published studies in 2022 alone, leveraging publicly available proteomics data for biomarker identification, mechanotyping and drug target identification is not readily possible. Proteomic data addressing similar biological/biomedical questions are made available by multiple research groups in different locations using different model organisms. Furthermore, not only various organisms are employed but different assay systems, such as in vitro and in vivo systems, are used. Finally, even though proteomics data are deposited in public databases, such as ProteomeXchange, they are provided at different levels of detail. Thus, data integration is hampered by non-harmonized usage of identifiers when reviewing the literature or performing meta-analyses to consolidate existing publications into a joint picture. To address this problem, we present ProHarMeD, a tool for harmonizing and comparing proteomics data gathered in multiple studies and for the extraction of disease mechanisms and putative drug repurposing candidates. It is available as a website, Python library and R package. ProHarMeD facilitates ID and name conversions between protein and gene levels, or organisms via ortholog mapping, and provides detailed logs on the loss and gain of IDs after each step. The web tool further determines IDs shared by different studies, proposes potential disease mechanisms as well as drug repurposing candidates automatically, and visualizes these results interactively. We apply ProHarMeD to a set of four studies on bone regeneration. First, we demonstrate the benefit of ID harmonization which increases the number of shared genes between studies by 50%. Second, we identify a potential disease mechanism, with five corresponding drug targets, and the top 20 putative drug repurposing candidates, of which Fondaparinux, the candidate with the highest score, and multiple others are known to have an impact on bone regeneration. Hence, ProHarMeD allows users to harmonize multi-centric proteomics research data in meta-analyses, evaluates the success of the ID conversions and remappings, and finally, it closes the gaps between proteomics, disease mechanism mining and drug repurposing. It is publicly available at https://apps.cosy.bio/proharmed/ .
Collapse
Affiliation(s)
- Klaudia Adamowicz
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, 22607, Germany
| | - Lis Arend
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, 22607, Germany
| | - Andreas Maier
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, 22607, Germany
| | - Johannes R Schmidt
- Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Olga Tsoy
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, 22607, Germany
| | - Olga Zolotareva
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, 22607, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, 22607, Germany
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, 5230, Denmark
| | - Tanja Laske
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, 22607, Germany.
| |
Collapse
|
16
|
Krumm J, Petrova E, Lechner S, Mergner J, Boehm HH, Prestipino A, Steinbrunn D, Deline ML, Koetzner L, Schindler C, Helming L, Fromme T, Klingenspor M, Hahne H, Pieck JC, Kuster B. High-Throughput Screening and Proteomic Characterization of Compounds Targeting Myeloid-Derived Suppressor Cells. Mol Cell Proteomics 2023; 22:100632. [PMID: 37586548 PMCID: PMC10518717 DOI: 10.1016/j.mcpro.2023.100632] [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: 12/27/2022] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023] Open
Abstract
Myeloid-derived suppressor cells (MDSC) are a heterogeneous cell population of incompletely differentiated immune cells. They are known to suppress T cell activity and are implicated in multiple chronic diseases, which make them an attractive cell population for drug discovery. Here, we characterized the baseline proteomes and phospho-proteomes of mouse MDSC differentiated from a progenitor cell line to a depth of 7000 proteins and phosphorylation sites. We also validated the cellular system for drug discovery by recapitulating and identifying known and novel molecular responses to the well-studied MDSC drugs entinostat and mocetinostat. We established a high-throughput drug screening platform using a MDSC/T cell coculture system and assessed the effects of ∼21,000 small molecule compounds on T cell proliferation and IFN-γ secretion to identify novel MDSC modulator. The most promising candidates were validated in a human MDSC system, and subsequent proteomic experiments showed significant upregulation of several proteins associated with the reduction of reactive oxygen species (ROS). Proteome-wide solvent-induced protein stability assays identified Acyp1 and Cd74 as potential targets, and the ROS-reducing drug phenotype was validated by measuring ROS levels in cells in response to compound, suggesting a potential mode of action. We anticipate that the data and chemical tools developed in this study will be valuable for further research on MDSC and related drug discovery.
Collapse
Affiliation(s)
- Johannes Krumm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Elissaveta Petrova
- Global Research & Development, Discovery and Development Technologies, Discovery Pharmacology, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Severin Lechner
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Mergner
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany
| | - Hans-Henning Boehm
- Global Research & Development, TIP-Oncology & Immunooncology, Myeloid Cell Research, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Alessandro Prestipino
- Global Research & Development, Discovery and Development Technologies, Discovery Pharmacology, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | | | - Marshall L Deline
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Lisa Koetzner
- Global Research & Development, Discovery and Development Technologies, Global Medicinal Chemistry, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Christina Schindler
- Global Research & Development, Discovery Technologies, Computational Chemistry & Biologics, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Laura Helming
- Global Research & Development, TIP-Oncology & Immunooncology, Myeloid Cell Research, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Tobias Fromme
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | | | - Jan-Carsten Pieck
- Global Research & Development, Discovery and Development Technologies, Discovery Pharmacology, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany.
| |
Collapse
|
17
|
Knecht S, Eberl HC, Kreisz N, Ugwu UJ, Starikova T, Kuster B, Wilhelm S. An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry-Based Secretomics. Mol Cell Proteomics 2023; 22:100636. [PMID: 37597723 PMCID: PMC10518356 DOI: 10.1016/j.mcpro.2023.100636] [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: 02/27/2023] [Revised: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
The active release of proteins into the extracellular space and the proteolytic cleavage of cell surface proteins are key processes that coordinate and fine-tune a multitude of physiological functions. The entirety of proteins that fulfill these extracellular tasks are referred to as the secretome and are of special interest for the investigation of biomarkers of disease states and physiological processes related to cell-cell communication. LC-MS-based proteomics approaches are a valuable tool for the comprehensive and unbiased characterization of this important subproteome. This review discusses procedures, opportunities, and limitations of mass spectrometry-based secretomics to better understand and navigate the complex analytical landscape for studying protein secretion in biomedical science.
Collapse
Affiliation(s)
- Sascha Knecht
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - H Christian Eberl
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany
| | - Norbert Kreisz
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Ukamaka Juliet Ugwu
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tatiana Starikova
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
| |
Collapse
|
18
|
Tretter C, de Andrade Krätzig N, Pecoraro M, Lange S, Seifert P, von Frankenberg C, Untch J, Zuleger G, Wilhelm M, Zolg DP, Dreyer FS, Bräunlein E, Engleitner T, Uhrig S, Boxberg M, Steiger K, Slotta-Huspenina J, Ochsenreither S, von Bubnoff N, Bauer S, Boerries M, Jost PJ, Schenck K, Dresing I, Bassermann F, Friess H, Reim D, Grützmann K, Pfütze K, Klink B, Schröck E, Haller B, Kuster B, Mann M, Weichert W, Fröhling S, Rad R, Hiltensperger M, Krackhardt AM. Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nat Commun 2023; 14:4632. [PMID: 37532709 PMCID: PMC10397250 DOI: 10.1038/s41467-023-39570-7] [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: 09/27/2022] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 patients across 25 tumor types for proteogenomic-based discovery of neoantigens. By using an optimized computational approach, we discover a large number of tumor-specific and tumor-associated antigens. To create a pipeline for the identification of neoantigens in our cohort, we combine DNA and RNA sequencing with MS-based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity and an in-depth validation process. We detect a broad variety of non-canonical HLA-binding peptides in the majority of patients demonstrating partially immunogenicity. Our validation process allows for the selection of 32 potential neoantigen candidates. The majority of neoantigen candidates originates from variants identified in the RNA data set, illustrating the relevance of RNA as a still understudied source of cancer antigens. This study underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates.
Collapse
Affiliation(s)
- Celina Tretter
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Niklas de Andrade Krätzig
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Matteo Pecoraro
- Department of Proteomics and Signal Transduction, Max Plank Institute of Biochemistry, Munich, Germany
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Sebastian Lange
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Philipp Seifert
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Clara von Frankenberg
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Johannes Untch
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Gabriela Zuleger
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Mathias Wilhelm
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
- Technical University of Munich, TUM School of Life Sciences, Computational Mass Spectrometry, Freising, Germany
| | - Daniel P Zolg
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
| | - Florian S Dreyer
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Eva Bräunlein
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Thomas Engleitner
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Sebastian Uhrig
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Precision Oncology Program, NCT Heidelberg, Heidelberg, Germany
| | - Melanie Boxberg
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Julia Slotta-Huspenina
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Sebastian Ochsenreither
- German Cancer Consortium (DKTK), partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nikolas von Bubnoff
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Hematology and Oncology, Medical Center, University of Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Sebastian Bauer
- German Cancer Consortium (DKTK), partner site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp J Jost
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
- Clinical Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- University Comprehensive Cancer Center Graz, Medical University of Graz, Graz, Austria
| | - Kristina Schenck
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Iska Dresing
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Florian Bassermann
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Helmut Friess
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany
| | - Daniel Reim
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany
| | - Konrad Grützmann
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Core Unit Molecular Tumor Diagnostics (CMTD), NCT Dresden, Dresden, Germany
- Institute for Medical Informatics and Biometry, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Katrin Pfütze
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Klink
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Evelin Schröck
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC), Dresden, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Bernhard Haller
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of AI and Informatics in Medicine, Munich, Germany
| | - Bernhard Kuster
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
- Technical University of Munich, TUM School of Life Sciences, Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Freising, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Plank Institute of Biochemistry, Munich, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Michael Hiltensperger
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Angela M Krackhardt
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany.
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany.
- Malteser Krankenhaus St. Franziskus-Hospital, Flensburg, Germany.
| |
Collapse
|
19
|
Abele M, Doll E, Bayer FP, Meng C, Lomp N, Neuhaus K, Scherer S, Kuster B, Ludwig C. Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes. Mol Cell Proteomics 2023; 22:100612. [PMID: 37391045 PMCID: PMC10407251 DOI: 10.1016/j.mcpro.2023.100612] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/18/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023] Open
Abstract
Bacteria are the most abundant and diverse organisms among the kingdoms of life. Due to this excessive variance, finding a unified, comprehensive, and safe workflow for quantitative bacterial proteomics is challenging. In this study, we have systematically evaluated and optimized sample preparation, mass spectrometric data acquisition, and data analysis strategies in bacterial proteomics. We investigated workflow performances on six representative species with highly different physiologic properties to mimic bacterial diversity. The best sample preparation strategy was a cell lysis protocol in 100% trifluoroacetic acid followed by an in-solution digest. Peptides were separated on a 30-min linear microflow liquid chromatography gradient and analyzed in data-independent acquisition mode. Data analysis was performed with DIA-NN using a predicted spectral library. Performance was evaluated according to the number of identified proteins, quantitative precision, throughput, costs, and biological safety. With this rapid workflow, over 40% of all encoded genes were detected per bacterial species. We demonstrated the general applicability of our workflow on a set of 23 taxonomically and physiologically diverse bacterial species. We could confidently identify over 45,000 proteins in the combined dataset, of which 30,000 have not been experimentally validated before. Our work thereby provides a valuable resource for the microbial scientific community. Finally, we grew Escherichia coli and Bacillus cereus in replicates under 12 different cultivation conditions to demonstrate the high-throughput suitability of the workflow. The proteomic workflow we present in this manuscript does not require any specialized equipment or commercial software and can be easily applied by other laboratories to support and accelerate the proteomic exploration of the bacterial kingdom.
Collapse
Affiliation(s)
- Miriam Abele
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Division of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Etienne Doll
- Division of Microbial Ecology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Florian P Bayer
- Division of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Nina Lomp
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Klaus Neuhaus
- Division of Microbial Ecology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Core Facility Microbiome, ZIEL - Institute for Food & Health, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Siegfried Scherer
- Division of Microbial Ecology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Division of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
| |
Collapse
|
20
|
Lechner S, Steimbach RR, Wang L, Deline ML, Chang YC, Fromme T, Klingenspor M, Matthias P, Miller AK, Médard G, Kuster B. Chemoproteomic target deconvolution reveals Histone Deacetylases as targets of (R)-lipoic acid. Nat Commun 2023; 14:3548. [PMID: 37322067 PMCID: PMC10272112 DOI: 10.1038/s41467-023-39151-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
Lipoic acid is an essential enzyme cofactor in central metabolic pathways. Due to its claimed antioxidant properties, racemic (R/S)-lipoic acid is used as a food supplement but is also investigated as a pharmaceutical in over 180 clinical trials covering a broad range of diseases. Moreover, (R/S)-lipoic acid is an approved drug for the treatment of diabetic neuropathy. However, its mechanism of action remains elusive. Here, we performed chemoproteomics-aided target deconvolution of lipoic acid and its active close analog lipoamide. We find that histone deacetylases HDAC1, HDAC2, HDAC3, HDAC6, HDAC8, and HDAC10 are molecular targets of the reduced form of lipoic acid and lipoamide. Importantly, only the naturally occurring (R)-enantiomer inhibits HDACs at physiologically relevant concentrations and leads to hyperacetylation of HDAC substrates. The inhibition of HDACs by (R)-lipoic acid and lipoamide explain why both compounds prevent stress granule formation in cells and may also provide a molecular rationale for many other phenotypic effects elicited by lipoic acid.
Collapse
Affiliation(s)
- Severin Lechner
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Raphael R Steimbach
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Biosciences Faculty, Heidelberg University, Heidelberg, Germany
| | - Longlong Wang
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland
- Faculty of Sciences, University of Basel, 4031, Basel, Switzerland
| | - Marshall L Deline
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Yun-Chien Chang
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Tobias Fromme
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland
- Faculty of Sciences, University of Basel, 4031, Basel, Switzerland
| | - Aubry K Miller
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany.
| |
Collapse
|
21
|
Tröster A, DiPrima M, Jores N, Kudlinzki D, Sreeramulu S, Gande SL, Linhard V, Ludig D, Schug A, Saxena K, Reinecke M, Heinzlmeir S, Leisegang MS, Wollenhaupt J, Lennartz F, Weiss MS, Kuster B, Tosato G, Schwalbe H. Optimization of the Lead Compound NVP-BHG712 as a Colorectal Cancer Inhibitor. Chemistry 2023; 29:e202203967. [PMID: 36799129 PMCID: PMC10133194 DOI: 10.1002/chem.202203967] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
The ephrin type-A receptor 2 (EPHA2) kinase belongs to the largest family of receptor tyrosine kinases. There are several indications of an involvement of EPHA2 in the development of infectious diseases and cancer. Despite pharmacological potential, EPHA2 is an under-examined target protein. In this study, we synthesized a series of derivatives of the inhibitor NVP-BHG712 and triazine-based compounds. These compounds were evaluated to determine their potential as kinase inhibitors of EPHA2, including elucidation of their binding mode (X-ray crystallography), affinity (microscale thermophoresis), and selectivity (Kinobeads assay). Eight inhibitors showed affinities in the low-nanomolar regime (KD <10 nM). Testing in up to seven colon cancer cell lines that express EPHA2 reveals that several derivatives feature promising effects for the control of human colon carcinoma. Thus, we have developed a set of powerful tool compounds for fundamental new research on the interplay of EPH receptors in a cellular context.
Collapse
Affiliation(s)
- Alix Tröster
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Michael DiPrima
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), 37 Convent Drive, NIH Bethesda Campus, Building 37, Room 4124, Bethesda, MD 20892, USA
| | - Nathalie Jores
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Denis Kudlinzki
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Santosh L. Gande
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
| | - Verena Linhard
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Damian Ludig
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Alexander Schug
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Krishna Saxena
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
- German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
| | - Stephanie Heinzlmeir
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
| | - Matthias S. Leisegang
- Institute for Cardiovascular Physiology, Johann Wolfgang Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main (Germany)
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, 12489 Berlin (Germany)
| | - Frank Lennartz
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, 12489 Berlin (Germany)
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, 12489 Berlin (Germany)
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
- German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
| | - Giovanna Tosato
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), 37 Convent Drive, NIH Bethesda Campus, Building 37, Room 4124, Bethesda, MD 20892, USA
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
| |
Collapse
|
22
|
Zecha J, Bayer FP, Wiechmann S, Woortman J, Berner N, Müller J, Schneider A, Kramer K, Abril-Gil M, Hopf T, Reichart L, Chen L, Hansen FM, Lechner S, Samaras P, Eckert S, Lautenbacher L, Reinecke M, Hamood F, Prokofeva P, Vornholz L, Falcomatà C, Dorsch M, Schröder A, Venhuizen A, Wilhelm S, Médard G, Stoehr G, Ruland J, Grüner BM, Saur D, Buchner M, Ruprecht B, Hahne H, The M, Wilhelm M, Kuster B. Decrypting drug actions and protein modifications by dose- and time-resolved proteomics. Science 2023; 380:93-101. [PMID: 36926954 PMCID: PMC7615311 DOI: 10.1126/science.ade3925] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [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: 08/12/2022] [Accepted: 02/21/2023] [Indexed: 03/18/2023]
Abstract
Although most cancer drugs modulate the activities of cellular pathways by changing posttranslational modifications (PTMs), little is known regarding the extent and the time- and dose-response characteristics of drug-regulated PTMs. In this work, we introduce a proteomic assay called decryptM that quantifies drug-PTM modulation for thousands of PTMs in cells to shed light on target engagement and drug mechanism of action. Examples range from detecting DNA damage by chemotherapeutics, to identifying drug-specific PTM signatures of kinase inhibitors, to demonstrating that rituximab kills CD20-positive B cells by overactivating B cell receptor signaling. DecryptM profiling of 31 cancer drugs in 13 cell lines demonstrates the broad applicability of the approach. The resulting 1.8 million dose-response curves are provided as an interactive molecular resource in ProteomicsDB.
Collapse
Affiliation(s)
- Jana Zecha
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Florian P. Bayer
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Svenja Wiechmann
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Julia Woortman
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Nicola Berner
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Julian Müller
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Annika Schneider
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Karl Kramer
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Mar Abril-Gil
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Thomas Hopf
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Leonie Reichart
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Lin Chen
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Fynn M. Hansen
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Severin Lechner
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Patroklos Samaras
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Stephan Eckert
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Ludwig Lautenbacher
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Maria Reinecke
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Firas Hamood
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Polina Prokofeva
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Larsen Vornholz
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Chiara Falcomatà
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
- Technical University of Munich, School of Medicine, Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, 80336 Munich, Germany
| | - Madeleine Dorsch
- West German Cancer Center, University Hospital Essen, Department of Medical Oncology, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Ayla Schröder
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Anton Venhuizen
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Stephanie Wilhelm
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Guillaume Médard
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Gabriele Stoehr
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Jürgen Ruland
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), 81675 Munich, Germany
| | - Barbara M. Grüner
- West German Cancer Center, University Hospital Essen, Department of Medical Oncology, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Dieter Saur
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
- Technical University of Munich, School of Medicine, Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, 80336 Munich, Germany
| | - Maike Buchner
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Benjamin Ruprecht
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Hannes Hahne
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Matthew The
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Mathias Wilhelm
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Bernhard Kuster
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| |
Collapse
|
23
|
Tröster A, DiPrima M, Jores N, Kudlinzki D, Sreeramulu S, Gande SL, Linhard V, Ludig D, Schug A, Saxena K, Reinecke M, Heinzlmeir S, Leisegang MS, Wollenhaupt J, Lennartz F, Weiss MS, Kuster B, Tosato G, Schwalbe H. Optimization of the Lead Compound NVP−BHG712 as a Colorectal Cancer Inhibitor. Chemistry 2023. [DOI: 10.1002/chem.202300918] [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: 03/30/2023]
|
24
|
Němec V, Khirsariya P, Janovská P, Moyano PM, Maier L, Procházková P, Kebková P, Gybel' T, Berger BT, Chaikuad A, Reinecke M, Kuster B, Knapp S, Bryja V, Paruch K. Discovery of Potent and Exquisitely Selective Inhibitors of Kinase CK1 with Tunable Isoform Selectivity. Angew Chem Int Ed Engl 2023; 62:e202217532. [PMID: 36625768 DOI: 10.1002/anie.202217532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
Casein kinases 1 (CK1) are key signaling molecules that have emerged recently as attractive therapeutic targets in particular for the treatment of hematological malignancies. Herein, we report the identification of a new class of potent and highly selective inhibitors of CK1α, δ and ϵ. Based on their optimal in vitro and in vivo profiles and their exclusive selectivity, MU1250, MU1500 and MU1742 were selected as quality chemical probes for those CK1 isoforms. At proper concentrations, MU1250 and MU1500 allow for specific targeting of CK1δ or dual inhibition of CK1δ/ϵ in cells. The compound MU1742 also efficiently inhibits CK1α and, to our knowledge, represents the first potent and highly selective inhibitor of this enzyme. In addition, we demonstrate that the central 1H-pyrrolo[2,3-b]pyridine-imidazole pharmacophore can be used as the basis of highly selective inhibitors of other therapeutically relevant protein kinases, e.g. p38α, as exemplified by the compound MU1299.
Collapse
Affiliation(s)
- Václav Němec
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| | - Prashant Khirsariya
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| | - Pavlína Janovská
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Paula Martín Moyano
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Lukáš Maier
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| | - Petra Procházková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Pavlína Kebková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Tomáš Gybel'
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354, Freising, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kamil Paruch
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| |
Collapse
|
25
|
Bernhardt AM, Tiedt S, Teupser D, Dichgans M, Meyer B, Gempt J, Kuhn PH, Simons M, Palleis C, Weidinger E, Nübling G, Holdt L, Hönikl L, Gasperi C, Giesbertz P, Müller SA, Breimann S, Lichtenthaler SF, Kuster B, Mann M, Imhof A, Barth T, Hauck SM, Zetterberg H, Otto M, Weichert W, Hemmer B, Levin J. A unified classification approach rating clinical utility of protein biomarkers across neurologic diseases. EBioMedicine 2023; 89:104456. [PMID: 36745974 PMCID: PMC9931915 DOI: 10.1016/j.ebiom.2023.104456] [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: 08/29/2022] [Revised: 12/22/2022] [Accepted: 01/17/2023] [Indexed: 02/07/2023] Open
Abstract
A major evolution from purely clinical diagnoses to biomarker supported clinical diagnosing has been occurring over the past years in neurology. High-throughput methods, such as next-generation sequencing and mass spectrometry-based proteomics along with improved neuroimaging methods, are accelerating this development. This calls for a consensus framework that is broadly applicable and provides a spot-on overview of the clinical validity of novel biomarkers. We propose a harmonized terminology and a uniform concept that stratifies biomarkers according to clinical context of use and evidence levels, adapted from existing frameworks in oncology with a strong focus on (epi)genetic markers and treatment context. We demonstrate that this framework allows for a consistent assessment of clinical validity across disease entities and that sufficient evidence for many clinical applications of protein biomarkers is lacking. Our framework may help to identify promising biomarker candidates and classify their applications by clinical context, aiming for routine clinical use of (protein) biomarkers in neurology.
Collapse
Affiliation(s)
- Alexander M Bernhardt
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Neurodegenerative Diseases, Site Munich, Germany
| | - Steffen Tiedt
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Martin Dichgans
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, Germany
| | - Bernhard Meyer
- Department of Neurosurgery, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Jens Gempt
- Department of Neurosurgery, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Peer-Hendrik Kuhn
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Mikael Simons
- German Center for Neurodegenerative Diseases, Site Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, Germany; Institute of Neuronal Cell Biology, Technical University Munich, 80802, Munich, Germany
| | - Carla Palleis
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Neurodegenerative Diseases, Site Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Endy Weidinger
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Neurodegenerative Diseases, Site Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Georg Nübling
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Neurodegenerative Diseases, Site Munich, Germany
| | - Lesca Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Lisa Hönikl
- Department of Neurosurgery, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christiane Gasperi
- Department of Neurology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Pieter Giesbertz
- German Center for Neurodegenerative Diseases, Site Munich, Germany; Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases, Site Munich, Germany; Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Stephan Breimann
- German Center for Neurodegenerative Diseases, Site Munich, Germany; Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technical University of Munich, Freising, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases, Site Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; German Cancer Consortium (DKTK), Munich Partner Site, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Axel Imhof
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Großhaderner Straße 9, 82152, Martinsried, Germany
| | - Teresa Barth
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Großhaderner Straße 9, 82152, Martinsried, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Centre Munich, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK; UK Dementia Research Institute at UCL, London, UK; Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
| | - Markus Otto
- Department of Neurology, Halle University Hospital, Martin Luther University Halle/Wittenberg, Saale, Germany
| | - Wilko Weichert
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Bernhard Hemmer
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Department of Neurology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.
| | - Johannes Levin
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Neurodegenerative Diseases, Site Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| |
Collapse
|
26
|
Arfelli VC, Chang YC, Bagnoli JW, Kerbs P, Ciamponi FE, Paz LMDS, Pankivskyi S, de Matha Salone J, Maucuer A, Massirer KB, Enard W, Kuster B, Greif PA, Archangelo LF. UHMK1 is a novel splicing regulatory kinase. J Biol Chem 2023; 299:103041. [PMID: 36803961 PMCID: PMC10033318 DOI: 10.1016/j.jbc.2023.103041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/18/2023] [Accepted: 02/04/2023] [Indexed: 02/19/2023] Open
Abstract
The U2AF Homology Motif Kinase 1 (UHMK1) is the only kinase that contains the U2AF homology motif, a common protein interaction domain among splicing factors. Through this motif, UHMK1 interacts with the splicing factors SF1 and SF3B1, known to participate in the 3' splice site recognition during the early steps of spliceosome assembly. Although UHMK1 phosphorylates these splicing factors in vitro, the involvement of UHMK1 in RNA processing has not previously been demonstrated. Here, we identify novel putative substrates of this kinase and evaluate UHMK1 contribution to overall gene expression and splicing, by integrating global phosphoproteomics, RNA-seq, and bioinformatics approaches. Upon UHMK1 modulation, 163 unique phosphosites were differentially phosphorylated in 117 proteins, of which 106 are novel potential substrates of this kinase. Gene Ontology analysis showed enrichment of terms previously associated with UHMK1 function, such as mRNA splicing, cell cycle, cell division, and microtubule organization. The majority of the annotated RNA-related proteins are components of the spliceosome but are also involved in several steps of gene expression. Comprehensive analysis of splicing showed that UHMK1 affected over 270 alternative splicing events. Moreover, splicing reporter assay further supported UHMK1 function on splicing. Overall, RNA-seq data demonstrated that UHMK1 knockdown had a minor impact on transcript expression and pointed to UHMK1 function in epithelial-mesenchymal transition. Functional assays demonstrated that UHMK1 modulation affects proliferation, colony formation, and migration. Taken together, our data implicate UHMK1 as a splicing regulatory kinase, connecting protein regulation through phosphorylation and gene expression in key cellular processes.
Collapse
Affiliation(s)
- Vanessa C Arfelli
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil
| | - Yun-Chien Chang
- Proteomics and Bioanalytics, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Johannes W Bagnoli
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University (LMU), Martinsried, Germany
| | - Paul Kerbs
- Laboratory for Experimental Leukemia and Lymphoma Research, Munich University Hospital, Ludwig-Maximilians University (LMU), Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felipe E Ciamponi
- Center for Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Laissa M da S Paz
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil
| | - Serhii Pankivskyi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | | | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Katlin B Massirer
- Center for Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University (LMU), Martinsried, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Philipp A Greif
- Laboratory for Experimental Leukemia and Lymphoma Research, Munich University Hospital, Ludwig-Maximilians University (LMU), Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Leticia Fröhlich Archangelo
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil.
| |
Collapse
|
27
|
Brajkovic S, Rugen N, Agius C, Berner N, Eckert S, Sakhteman A, Schwechheimer C, Kuster B. Getting Ready for Large-Scale Proteomics in Crop Plants. Nutrients 2023; 15:nu15030783. [PMID: 36771489 PMCID: PMC9921824 DOI: 10.3390/nu15030783] [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: 01/04/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Plants are an indispensable cornerstone of sustainable global food supply. While immense progress has been made in decoding the genomes of crops in recent decades, the composition of their proteomes, the entirety of all expressed proteins of a species, is virtually unknown. In contrast to the model plant Arabidopsis thaliana, proteomic analyses of crop plants have often been hindered by the presence of extreme concentrations of secondary metabolites such as pigments, phenolic compounds, lipids, carbohydrates or terpenes. As a consequence, crop proteomic experiments have, thus far, required individually optimized protein extraction protocols to obtain samples of acceptable quality for downstream analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). In this article, we present a universal protein extraction protocol originally developed for gel-based experiments and combined it with an automated single-pot solid-phase-enhanced sample preparation (SP3) protocol on a liquid handling robot to prepare high-quality samples for proteomic analysis of crop plants. We also report an automated offline peptide separation protocol and optimized micro-LC-MS/MS conditions that enables the identification and quantification of ~10,000 proteins from plant tissue within 6 h of instrument time. We illustrate the utility of the workflow by analyzing the proteomes of mature tomato fruits to an unprecedented depth. The data demonstrate the robustness of the approach which we propose for use in upcoming large-scale projects that aim to map crop tissue proteomes.
Collapse
Affiliation(s)
- Sarah Brajkovic
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Nils Rugen
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- Institute of Plant Genetics, Leibniz University Hannover, 30167 Hannover, Germany
| | - Carlos Agius
- Chair of Plant Systems Biology, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Nicola Berner
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Stephan Eckert
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Claus Schwechheimer
- Chair of Plant Systems Biology, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- Correspondence:
| |
Collapse
|
28
|
Lo WT, Belabed H, Kücükdisli M, Metag J, Roske Y, Prokofeva P, Ohashi Y, Horatscheck A, Cirillo D, Krauss M, Schmied C, Neuenschwander M, von Kries JP, Médard G, Kuster B, Perisic O, Williams RL, Daumke O, Payrastre B, Severin S, Nazaré M, Haucke V. Development of selective inhibitors of phosphatidylinositol 3-kinase C2α. Nat Chem Biol 2023; 19:18-27. [PMID: 36109648 PMCID: PMC7613998 DOI: 10.1038/s41589-022-01118-z] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/20/2022] [Indexed: 01/01/2023]
Abstract
Phosphatidylinositol 3-kinase type 2α (PI3KC2α) and related class II PI3K isoforms are of increasing biomedical interest because of their crucial roles in endocytic membrane dynamics, cell division and signaling, angiogenesis, and platelet morphology and function. Herein we report the development and characterization of PhosphatidylInositol Three-kinase Class twO INhibitors (PITCOINs), potent and highly selective small-molecule inhibitors of PI3KC2α catalytic activity. PITCOIN compounds exhibit strong selectivity toward PI3KC2α due to their unique mode of interaction with the ATP-binding site of the enzyme. We demonstrate that acute inhibition of PI3KC2α-mediated synthesis of phosphatidylinositol 3-phosphates by PITCOINs impairs endocytic membrane dynamics and membrane remodeling during platelet-dependent thrombus formation. PITCOINs are potent and selective cell-permeable inhibitors of PI3KC2α function with potential biomedical applications ranging from thrombosis to diabetes and cancer.
Collapse
Affiliation(s)
- Wen-Ting Lo
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Hassane Belabed
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Murat Kücükdisli
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Juliane Metag
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Yvette Roske
- grid.419491.00000 0001 1014 0849Max-Delbrück-Centrum für Molekulare Medizin, Kristallographie, Berlin, Germany
| | - Polina Prokofeva
- grid.6936.a0000000123222966Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Yohei Ohashi
- grid.42475.300000 0004 0605 769XMRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - André Horatscheck
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Davide Cirillo
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Michael Krauss
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Christopher Schmied
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Martin Neuenschwander
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Jens Peter von Kries
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Guillaume Médard
- grid.6936.a0000000123222966Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- grid.6936.a0000000123222966Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Olga Perisic
- grid.42475.300000 0004 0605 769XMRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Roger L. Williams
- grid.42475.300000 0004 0605 769XMRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Oliver Daumke
- grid.419491.00000 0001 1014 0849Max-Delbrück-Centrum für Molekulare Medizin, Kristallographie, Berlin, Germany
| | - Bernard Payrastre
- Inserm, U1297-Université, Toulouse III, Institut des Maladies Métaboliques et Cardiovasculaires, Toulouse, France ,grid.411175.70000 0001 1457 2980Centre Hospitalier Universitaire de Toulouse, Laboratoire d’Hématologie, Toulouse, France
| | - Sonia Severin
- Inserm, U1297-Université, Toulouse III, Institut des Maladies Métaboliques et Cardiovasculaires, Toulouse, France
| | - Marc Nazaré
- Departments of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany. .,Departments of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
| |
Collapse
|
29
|
Stepan J, Heinz DE, Dethloff F, Bajaj T, Zellner A, Hafner K, Wiechmann S, Mackert S, Mecdad Y, Rabenstein M, Ebert T, Martinelli S, Häusl AS, Pöhlmann ML, Hermann A, Ma X, Pavenstädt H, Schmidt MV, Philipsen A, Turck CW, Deussing JM, Kuster B, Wehr MC, Stein V, Kremerskothen J, Wotjak CT, Gassen NC. Hippo-released WWC1 facilitates AMPA receptor regulatory complexes for hippocampal learning. Cell Rep 2022; 41:111766. [PMID: 36476872 DOI: 10.1016/j.celrep.2022.111766] [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: 04/08/2022] [Revised: 08/23/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022] Open
Abstract
Learning and memory rely on changes in postsynaptic glutamergic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type receptor (AMPAR) number, spatial organization, and function. The Hippo pathway component WW and C2 domain-containing protein 1 (WWC1) regulates AMPAR surface expression and impacts on memory performance. However, synaptic binding partners of WWC1 and its hierarchical position in AMPAR complexes are largely unclear. Using cell-surface proteomics in hippocampal tissue of Wwc1-deficient mice and by generating a hippocampus-specific interactome, we show that WWC1 is a major regulatory platform in AMPAR signaling networks. Under basal conditions, the Hippo pathway members WWC1 and large tumor-suppressor kinase (LATS) are associated, which might prevent WWC1 effects on synaptic proteins. Reduction of WWC1/LATS binding through a point mutation at WWC1 elevates the abundance of WWC1 in AMPAR complexes and improves hippocampal-dependent learning and memory. Thus, uncoupling of WWC1 from the Hippo pathway to AMPAR-regulatory complexes provides an innovative strategy to enhance synaptic transmission.
Collapse
Affiliation(s)
- Jens Stepan
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany; Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany; Department of Obstetrics and Gynecology, Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Daniel E Heinz
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany; Research Group Neuronal Plasticity, Max Planck Institute of Psychiatry, 80804 Munich, Germany; Max Planck School of Cognition, 04103 Leipzig, Germany
| | - Frederik Dethloff
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany; Metabolomics Core Facility, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Thomas Bajaj
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany
| | - Andreas Zellner
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany; Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Kathrin Hafner
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Svenja Wiechmann
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; German Cancer Consortium (DKTK), 80336 Munich, Germany; German Cancer Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah Mackert
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany
| | - Yara Mecdad
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany
| | - Michael Rabenstein
- Institute of Physiology II, University Hospital Bonn, 53115 Bonn, Germany
| | - Tim Ebert
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany; Research Group Neuronal Plasticity, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Silvia Martinelli
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Alexander S Häusl
- Department Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Maximilian L Pöhlmann
- Department Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Anke Hermann
- Department of Medicine D, Division of General Internal Medicine, Nephrology, and Rheumatology, University Hospital Münster, 48149 Münster, Germany
| | - Xiao Ma
- Research Group Signal Transduction, Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Hermann Pavenstädt
- Department of Medicine D, Division of General Internal Medicine, Nephrology, and Rheumatology, University Hospital Münster, 48149 Münster, Germany
| | - Mathias V Schmidt
- Department Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Alexandra Philipsen
- Clinic for Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany
| | - Chris W Turck
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Jan M Deussing
- Research Group Molecular Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; German Cancer Consortium (DKTK), 80336 Munich, Germany; German Cancer Center (DKFZ), 69120 Heidelberg, Germany; Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | - Michael C Wehr
- Research Group Signal Transduction, Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Valentin Stein
- Institute of Physiology II, University Hospital Bonn, 53115 Bonn, Germany
| | - Joachim Kremerskothen
- Department of Medicine D, Division of General Internal Medicine, Nephrology, and Rheumatology, University Hospital Münster, 48149 Münster, Germany
| | - Carsten T Wotjak
- Research Group Neuronal Plasticity, Max Planck Institute of Psychiatry, 80804 Munich, Germany; Central Nervous System Diseases Research, Boehringer-Ingelheim Pharma GmbH & Co KG, 88400 Biberach, Germany.
| | - Nils C Gassen
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany; Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University Hospital Bonn, 53127 Bonn, Germany.
| |
Collapse
|
30
|
Prokofeva P, Höfer S, Hornisch M, Abele M, Kuster B, Médard G. Merits of Diazirine Photo-Immobilization for Target Profiling of Natural Products and Cofactors. ACS Chem Biol 2022; 17:3100-3109. [PMID: 36302507 PMCID: PMC9680877 DOI: 10.1021/acschembio.2c00500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/05/2022] [Indexed: 01/20/2023]
Abstract
Finding the targets of natural products is of key importance in both chemical biology and drug discovery, and deconvolution of cofactor interactomes contributes to the functional annotation of the proteome. Identifying the proteins that underlie natural compound activity in phenotypic screens helps to validate the respective targets and, potentially, expand the druggable proteome. Here, we present a generally applicable protocol for the photoactivated immobilization of unmodified and microgram quantities of natural products on diazirine-decorated beads and their use for systematic affinity-based proteome profiling. We show that among 31 molecules of very diverse reported activity and biosynthetic origin, 25 could indeed be immobilized. Dose-response competition binding experiments using lysates of human or bacterial cells followed by quantitative mass spectrometry recapitulated targets of 9 molecules with <100 μM affinity. Among them, immobilization of coenzyme A produced a tool to interrogate proteins containing a HotDog domain. Surprisingly, immobilization of the cofactor flavin adenine dinucleotide (FAD) led to the identification of nanomolar interactions with dozens of RNA-binding proteins.
Collapse
Affiliation(s)
- Polina Prokofeva
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Höfer
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Maximilian Hornisch
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Miriam Abele
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354 Freising, Germany
| | - Bernhard Kuster
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354 Freising, Germany
| | - Guillaume Médard
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| |
Collapse
|
31
|
Lageveen‐Kammeijer GSM, Kuster B, Reusch D, Wuhrer M. High sensitivity glycomics in biomedicine. Mass Spectrom Rev 2022; 41:1014-1039. [PMID: 34494287 PMCID: PMC9788051 DOI: 10.1002/mas.21730] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 05/15/2023]
Abstract
Many analytical challenges in biomedicine arise from the generally high heterogeneity and complexity of glycan- and glycoconjugate-containing samples, which are often only available in minute amounts. Therefore, highly sensitive workflows and detection methods are required. In this review mass spectrometric workflows and detection methods are evaluated for glycans and glycoproteins. Furthermore, glycomic methodologies and innovations that are tailored for enzymatic treatments, chemical derivatization, purification, separation, and detection at high sensitivity are highlighted. The discussion is focused on the analysis of mammalian N-linked and GalNAc-type O-linked glycans.
Collapse
Affiliation(s)
| | - Bernhard Kuster
- Chair for Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
| | - Dietmar Reusch
- Pharma Technical Development EuropeRoche Diagnostics GmbHPenzbergGermany
| | - Manfred Wuhrer
- Leiden University Medical CenterCenter for Proteomics and MetabolomicsLeidenThe Netherlands
| |
Collapse
|
32
|
Steimbach RR, Herbst-Gervasoni CJ, Lechner S, Murray Stewart T, Klinke G, Ridinger J, Géraldy MNE, Tihanyi G, Foley JR, Uhrig U, Kuster B, Poschet G, Casero RA, Médard G, Oehme I, Christianson DW, Gunkel N, Miller AK. Aza-SAHA Derivatives Are Selective Histone Deacetylase 10 Chemical Probes That Inhibit Polyamine Deacetylation and Phenocopy HDAC10 Knockout. J Am Chem Soc 2022; 144:18861-18875. [PMID: 36200994 PMCID: PMC9588710 DOI: 10.1021/jacs.2c05030] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the first well-characterized selective chemical probe for histone deacetylase 10 (HDAC10) with unprecedented selectivity over other HDAC isozymes. HDAC10 deacetylates polyamines and has a distinct substrate specificity, making it unique among the 11 zinc-dependent HDAC hydrolases. Taking inspiration from HDAC10 polyamine substrates, we systematically inserted an amino group ("aza-scan") into the hexyl linker moiety of the approved drug Vorinostat (SAHA). This one-atom replacement (C→N) transformed SAHA from an unselective pan-HDAC inhibitor into a specific HDAC10 inhibitor. Optimization of the aza-SAHA structure yielded the HDAC10 chemical probe DKFZ-748, with potency and selectivity demonstrated by cellular and biochemical target engagement, as well as thermal shift assays. Cocrystal structures of our aza-SAHA derivatives with HDAC10 provide a structural rationale for potency, and chemoproteomic profiling confirmed exquisite cellular HDAC10-selectivity of DKFZ-748 across the target landscape of HDAC drugs. Treatment of cells with DKFZ-748, followed by quantification of selected polyamines, validated for the first time the suspected cellular function of HDAC10 as a polyamine deacetylase. Finally, in a polyamine-limiting in vitro tumor model, DKFZ-748 showed dose-dependent growth inhibition of HeLa cells. We expect DKFZ-748 and related probes to enable further studies on the enigmatic biology of HDAC10 and acetylated polyamines in both physiological and pathological settings.
Collapse
Affiliation(s)
- Raphael R. Steimbach
- Cancer Drug Development, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Biosciences Faculty, Heidelberg University, 69120, Heidelberg, Germany
| | - Corey J. Herbst-Gervasoni
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6323, USA
| | - Severin Lechner
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354, Freising, Germany
| | - Tracy Murray Stewart
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21231, USA
| | - Glynis Klinke
- Center for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Johannes Ridinger
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany
| | - Magalie N. E. Géraldy
- Cancer Drug Development, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Gergely Tihanyi
- Cancer Drug Development, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Jackson R. Foley
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21231, USA
| | - Ulrike Uhrig
- Chemical Biology Core Facility, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354, Freising, Germany
| | - Gernot Poschet
- Center for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Robert A. Casero
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21231, USA
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354, Freising, Germany
| | - Ina Oehme
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6323, USA
| | - Nikolas Gunkel
- Cancer Drug Development, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Aubry K. Miller
- Cancer Drug Development, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| |
Collapse
|
33
|
Hanke T, Mathea S, Woortman J, Salah E, Berger BT, Tumber A, Kashima R, Hata A, Kuster B, Müller S, Knapp S. Development and Characterization of Type I, Type II, and Type III LIM-Kinase Chemical Probes. J Med Chem 2022; 65:13264-13287. [PMID: 36136092 DOI: 10.1021/acs.jmedchem.2c01106] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
LIMKs are important regulators of actin and microtubule dynamics, and they play essential roles in many cellular processes. Deregulation of LIMKs has been linked to the development of diverse diseases, including cancers and cognitive disabilities, but well-characterized inhibitors known as chemical probes are still lacking. Here, we report the characterization of three highly selective LIMK1/2 inhibitors covering all canonical binding modes (type I/II/III) and the structure-based design of the type II/III inhibitors. Characterization of these chemical probes revealed a low nanomolar affinity for LIMK1/2, and all inhibitors 1 (LIMKi3; type I), 48 (TH470; type II), and 15 (TH257; type III) showed excellent selectivity in a comprehensive scanMAX kinase selectivity panel. Phosphoproteomics revealed remarkable differences between type I and type II inhibitors compared with the allosteric inhibitor 15. In phenotypic assays such as neurite outgrowth models of fragile X-chromosome, 15 showed promising activity, suggesting the potential application of allosteric LIMK inhibitors treating this orphan disease.
Collapse
Affiliation(s)
- Thomas Hanke
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Julia Woortman
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Eidarus Salah
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Risa Kashima
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, United States
| | - Akiko Hata
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, United States
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany.,German Translational Cancer Network (DKTK), Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany.,German Translational Cancer Network (DKTK), Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| |
Collapse
|
34
|
Paulmann C, Spallek R, Karpiuk O, Heider M, Schäffer I, Zecha J, Klaeger S, Walzik M, Öllinger R, Engleitner T, Wirth M, Keller U, Krönke J, Rudelius M, Kossatz S, Rad R, Kuster B, Bassermann F. The OTUD6B-LIN28B-MYC axis determines the proliferative state in multiple myeloma. EMBO J 2022; 41:e110871. [PMID: 36059274 PMCID: PMC9574752 DOI: 10.15252/embj.2022110871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Deubiquitylases (DUBs) are therapeutically amenable components of the ubiquitin machinery that stabilize substrate proteins. Their inhibition can destabilize oncoproteins that may otherwise be undruggable. Here, we screened for DUB vulnerabilities in multiple myeloma, an incurable malignancy with dependency on the ubiquitin proteasome system and identified OTUD6B as an oncogene that drives the G1/S‐transition. LIN28B, a suppressor of microRNA biogenesis, is specified as a bona fide cell cycle‐specific substrate of OTUD6B. Stabilization of LIN28B drives MYC expression at G1/S, which in turn allows for rapid S‐phase entry. Silencing OTUD6B or LIN28B inhibits multiple myeloma outgrowth in vivo and high OTUD6B expression evolves in patients that progress to symptomatic multiple myeloma and results in an adverse outcome of the disease. Thus, we link proteolytic ubiquitylation with post‐transcriptional regulation and nominate OTUD6B as a potential mediator of the MGUS‐multiple myeloma transition, a central regulator of MYC, and an actionable vulnerability in multiple myeloma and other tumors with an activated OTUD6B‐LIN28B axis.
Collapse
Affiliation(s)
- Carmen Paulmann
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Ria Spallek
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Oleksandra Karpiuk
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Michael Heider
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Isabell Schäffer
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Susan Klaeger
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Michaela Walzik
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Rupert Öllinger
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.,Department of Medicine II, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, Technical University of Munich, Munich, Germany
| | - Thomas Engleitner
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.,Department of Medicine II, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, Technical University of Munich, Munich, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany.,Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Jan Krönke
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany
| | - Martina Rudelius
- Institute of Pathology, Ludwigs Maximilians University, Munich, Germany
| | - Susanne Kossatz
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.,Department of Nuclear Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Roland Rad
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.,Department of Medicine II, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, Technical University of Munich, Munich, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany
| | - Florian Bassermann
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany
| |
Collapse
|
35
|
Lechner S, Malgapo MIP, Grätz C, Steimbach RR, Baron A, Rüther P, Nadal S, Stumpf C, Loos C, Ku X, Prokofeva P, Lautenbacher L, Heimburg T, Würf V, Meng C, Wilhelm M, Sippl W, Kleigrewe K, Pauling JK, Kramer K, Miller AK, Pfaffl MW, Linder ME, Kuster B, Médard G. Author Correction: Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target. Nat Chem Biol 2022; 18:913. [PMID: 35840679 DOI: 10.1038/s41589-022-01112-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Severin Lechner
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Martin Ian P Malgapo
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Christian Grätz
- Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Raphael R Steimbach
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Agnes Baron
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Patrick Rüther
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Simon Nadal
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Carmen Stumpf
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christina Loos
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Xin Ku
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Polina Prokofeva
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Ludwig Lautenbacher
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Tino Heimburg
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Vivian Würf
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Josch K Pauling
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karl Kramer
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Aubry K Miller
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael W Pfaffl
- Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Maurine E Linder
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
| |
Collapse
|
36
|
Giansanti P, Samaras P, Bian Y, Meng C, Coluccio A, Frejno M, Jakubowsky H, Dobiasch S, Hazarika RR, Rechenberger J, Calzada-Wack J, Krumm J, Mueller S, Lee CY, Wimberger N, Lautenbacher L, Hassan Z, Chang YC, Falcomatà C, Bayer FP, Bärthel S, Schmidt T, Rad R, Combs SE, The M, Johannes F, Saur D, de Angelis MH, Wilhelm M, Schneider G, Kuster B. Mass spectrometry-based draft of the mouse proteome. Nat Methods 2022; 19:803-811. [PMID: 35710609 DOI: 10.1038/s41592-022-01526-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/17/2022] [Indexed: 01/06/2023]
Abstract
The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and several lines of analyses exemplify which insights can be gleaned from the data. For instance, tissue- and cell-type resolved profiles provide protein evidence for the expression of 17,000 genes, thousands of isoforms and 50,000 phosphorylation sites in vivo. Proteogenomic comparison of mouse, human and Arabidopsis reveal common and distinct mechanisms of gene expression regulation and, despite many similarities, numerous differentially abundant orthologs that likely serve species-specific functions. We leverage the mouse proteome by integrating phenotypic drug (n > 400) and radiation response data with the proteomes of 66 pancreatic ductal adenocarcinoma (PDAC) cell lines to reveal molecular markers for sensitivity and resistance. This unique atlas complements other molecular resources for the mouse and can be explored online via ProteomicsDB and PACiFIC.
Collapse
Affiliation(s)
- Piero Giansanti
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Yangyang Bian
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,College of Life Science, Northwest University, Xi'an, China
| | - Chen Meng
- Bavarian Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany
| | - Andrea Coluccio
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Martin Frejno
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Hannah Jakubowsky
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Sophie Dobiasch
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Radiation Medicine, Department of Radiation Sciences, Helmholtz Zentrum München, Neuherberg, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rashmi R Hazarika
- Population epigenetics and epigenomics, Technical University of Munich, Freising, Germany.,Institute of Advanced Study (IAS), Technical University of Munich, Freising, Germany
| | - Julia Rechenberger
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Calzada-Wack
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Krumm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Sebastian Mueller
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Chien-Yun Lee
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Nicole Wimberger
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Ludwig Lautenbacher
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Zonera Hassan
- Medical Clinic and Policlinic II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Yun-Chien Chang
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Chiara Falcomatà
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Roland Rad
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Stephanie E Combs
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Radiation Medicine, Department of Radiation Sciences, Helmholtz Zentrum München, Neuherberg, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Frank Johannes
- Population epigenetics and epigenomics, Technical University of Munich, Freising, Germany.,Institute of Advanced Study (IAS), Technical University of Munich, Freising, Germany
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Experimental Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Günter Schneider
- Medical Clinic and Policlinic II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,University Medical Center Göttingen, Department of General, Visceral and Pediatric Surgery, Göttingen, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany. .,Bavarian Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany. .,German Cancer Consortium (DKTK), Munich, Germany. .,German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Institute of Advanced Study (IAS), Technical University of Munich, Freising, Germany.
| |
Collapse
|
37
|
Orben F, Lankes K, Schneeweis C, Hassan Z, Jakubowsky H, Krauß L, Boniolo F, Schneider C, Schäfer A, Murr J, Schlag C, Kong B, Öllinger R, Wang C, Beyer G, Mahajan UM, Xue Y, Mayerle J, Schmid RM, Kuster B, Rad R, Braun CJ, Wirth M, Reichert M, Saur D, Schneider G. Epigenetic drug screening defines a PRMT5 inhibitor-sensitive pancreatic cancer subtype. JCI Insight 2022; 7:e151353. [PMID: 35439169 PMCID: PMC9220834 DOI: 10.1172/jci.insight.151353] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 04/12/2022] [Indexed: 11/17/2022] Open
Abstract
Systemic therapies for pancreatic ductal adenocarcinoma (PDAC) remain unsatisfactory. Clinical prognosis is particularly poor for tumor subtypes with activating aberrations in the MYC pathway, creating an urgent need for novel therapeutic targets. To unbiasedly find MYC-associated epigenetic dependencies, we conducted a drug screen in pancreatic cancer cell lines. Here, we found that protein arginine N-methyltransferase 5 (PRMT5) inhibitors triggered an MYC-associated dependency. In human and murine PDACs, a robust connection of MYC and PRMT5 was detected. By the use of gain- and loss-of-function models, we confirmed the increased efficacy of PRMT5 inhibitors in MYC-deregulated PDACs. Although inhibition of PRMT5 was inducing DNA damage and arresting PDAC cells in the G2/M phase of the cell cycle, apoptotic cell death was executed predominantly in cells with high MYC expression. Experiments in primary patient-derived PDAC models demonstrated the existence of a highly PRMT5 inhibitor-sensitive subtype. Our work suggests developing PRMT5 inhibitor-based therapies for PDAC.
Collapse
Affiliation(s)
- Felix Orben
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
| | | | - Christian Schneeweis
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich (TUM), Munich, Germany
| | - Zonera Hassan
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
| | - Hannah Jakubowsky
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich (TUM), Munich, Germany
| | - Lukas Krauß
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- University Medical Center Göttingen, Department of General, Visceral and Pediatric Surgery, Göttingen, Germany
| | - Fabio Boniolo
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich (TUM), Munich, Germany
| | - Carolin Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- University Medical Center Göttingen, Department of General, Visceral and Pediatric Surgery, Göttingen, Germany
| | - Arlett Schäfer
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
| | - Janine Murr
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
| | | | - Bo Kong
- Department of Surgery, Klinikum rechts der Isar, TUM, Munich, Germany
- Department of General Surgery, University of Ulm, Ulm, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine and
| | - Chengdong Wang
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, TUM, Freising, Germany
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Department of Surgery, Children’s Hospital of Soochow University, Suzhou, China
| | - Georg Beyer
- Department of Medicine II, LMU University Hospital, Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Ujjwal M. Mahajan
- Department of Medicine II, LMU University Hospital, Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Yonggan Xue
- Department of Medicine II, LMU University Hospital, Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Julia Mayerle
- Department of Medicine II, LMU University Hospital, Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Roland M. Schmid
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, TUM, Freising, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM, Freising, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine and
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christian J. Braun
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Maximilian Reichert
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Center for Protein Assemblies (CPA), TUM, Garching, Germany
- Translational Pancreatic Research Cancer Center, Medical Clinic and Polyclinic II, Klinikum rechts der Isar, TUM, Munich, Germany
| | - Dieter Saur
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich (TUM), Munich, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Günter Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- University Medical Center Göttingen, Department of General, Visceral and Pediatric Surgery, Göttingen, Germany
| |
Collapse
|
38
|
Abstract
Proteins are intimately involved in executing and controlling virtually all cellular processes. To understand the molecular mechanisms that underlie plant phenotypes, it is essential to investigate protein expression, interactions, and modifications, to name a few. The proteome is highly dynamic in time and space, and a plethora of protein modifications, protein interactions, and network constellations are at play under specific conditions and developmental stages. Analysis of proteomes aims to characterize the entire protein complement of a particular cell type, tissue, or organism-a challenging task, given the dynamic nature of the proteome. Modern mass spectrometry-based proteomics technology can be used to address this complexity at a system-wide scale by the global identification and quantification of thousands of proteins. In this review, we present current methods and technologies employed in mass spectrometry-based proteomics and provide examples of dynamic changes in the plant proteome elucidated by proteomic approaches.
Collapse
Affiliation(s)
- Julia Mergner
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany;
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| |
Collapse
|
39
|
Gabriel W, The M, Zolg DP, Bayer FP, Shouman O, Lautenbacher L, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Huhmer A, Wenschuh H, Reimer U, Médard G, Kuster B, Wilhelm M. Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides. Anal Chem 2022; 94:7181-7190. [PMID: 35549156 DOI: 10.1021/acs.analchem.1c05435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The prediction of fragment ion intensities and retention time of peptides has gained significant attention over the past few years. However, the progress shown in the accurate prediction of such properties focused primarily on unlabeled peptides. Tandem mass tags (TMT) are chemical peptide labels that are coupled to free amine groups usually after protein digestion to enable the multiplexed analysis of multiple samples in bottom-up mass spectrometry. It is a standard workflow in proteomics ranging from single-cell to high-throughput proteomics. Particularly for TMT, increasing the number of confidently identified spectra is highly desirable as it provides identification and quantification information with every spectrum. Here, we report on the generation of an extensive resource of synthetic TMT-labeled peptides as part of the ProteomeTools project and present the extension of the deep learning model Prosit to accurately predict the retention time and fragment ion intensities of TMT-labeled peptides with high accuracy. Prosit-TMT supports CID and HCD fragmentation and ion trap and Orbitrap mass analyzers in a single model. Reanalysis of published TMT data sets show that this single model extracts substantial additional information. Applying Prosit-TMT, we discovered that the expression of many proteins in human breast milk follows a distinct daily cycle which may prime the newborn for nutritional or environmental cues.
Collapse
Affiliation(s)
- Wassim Gabriel
- Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Daniel P Zolg
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Omar Shouman
- Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | - Ludwig Lautenbacher
- Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | | | | | - Tobias Knaute
- JPT Peptide Technologies GmbH, 12489 Berlin, Germany
| | | | - Andreas Huhmer
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Ulf Reimer
- JPT Peptide Technologies GmbH, 12489 Berlin, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry, 85354 Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| |
Collapse
|
40
|
Lechner S, Malgapo MIP, Grätz C, Steimbach RR, Baron A, Rüther P, Nadal S, Stumpf C, Loos C, Ku X, Prokofeva P, Lautenbacher L, Heimburg T, Würf V, Meng C, Wilhelm M, Sippl W, Kleigrewe K, Pauling JK, Kramer K, Miller AK, Pfaffl MW, Linder ME, Kuster B, Médard G. Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target. Nat Chem Biol 2022; 18:812-820. [PMID: 35484434 PMCID: PMC9339481 DOI: 10.1038/s41589-022-01015-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 03/15/2022] [Indexed: 01/22/2023]
Abstract
Histone deacetylase (HDAC) targeting drugs have entered the pharmacopoeia in the 2000s. However, some enigmatic phenotypes suggest off-target engagement. Here, we developed a quantitative chemical proteomics assay using immobilized HDAC inhibitors and mass spectrometry that we deployed to establish the target landscape of 53 drugs. The assay covers 9 of the 11 human zinc-dependent HDACs, questions the reported selectivity of some widely-used molecules, notably for HDAC6, and delineates how the composition of HDAC complexes influences drug potency. Unexpectedly, metallo-beta-lactamase domain-containing protein 2 (MBLAC2) featured as a frequent off-target of hydroxamate drugs. This poorly characterized palmitoyl-CoA hydrolase is inhibited by 24 HDAC inhibitors at low nM potency. MBLAC2 enzymatic inhibition and knock down led to the accumulation of extracellular vesicles. Given the importance of extracellular vesicle biology in neurological diseases and cancer, this HDAC-independent drug effect may qualify MBLAC2 as a target for drug discovery.
Collapse
Affiliation(s)
- Severin Lechner
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Martin Ian P Malgapo
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Christian Grätz
- Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Raphael R Steimbach
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Agnes Baron
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Patrick Rüther
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Simon Nadal
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Carmen Stumpf
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christina Loos
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Xin Ku
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Polina Prokofeva
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Ludwig Lautenbacher
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Tino Heimburg
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Vivian Würf
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Josch K Pauling
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karl Kramer
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Aubry K Miller
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael W Pfaffl
- Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Maurine E Linder
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
| |
Collapse
|
41
|
Hamood F, Bayer FP, Wilhelm M, Kuster B, The M. SIMSI-Transfer: Software-assisted reduction of missing values in phosphoproteomic and proteomic isobaric labeling data using tandem mass spectrum clustering. Mol Cell Proteomics 2022; 21:100238. [PMID: 35462064 PMCID: PMC9389303 DOI: 10.1016/j.mcpro.2022.100238] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/18/2022] [Accepted: 03/27/2022] [Indexed: 12/11/2022] Open
Abstract
Isobaric stable isotope labeling techniques such as tandem mass tags (TMTs) have become popular in proteomics because they enable the relative quantification of proteins with high precision from up to 18 samples in a single experiment. While missing values in peptide quantification are rare in a single TMT experiment, they rapidly increase when combining multiple TMT experiments. As the field moves toward analyzing ever higher numbers of samples, tools that reduce missing values also become more important for analyzing TMT datasets. To this end, we developed SIMSI-Transfer (Similarity-based Isobaric Mass Spectra 2 [MS2] Identification Transfer), a software tool that extends our previously developed software MaRaCluster (© Matthew The) by clustering similar tandem MS2 from multiple TMT experiments. SIMSI-Transfer is based on the assumption that similarity-clustered MS2 spectra represent the same peptide. Therefore, peptide identifications made by database searching in one TMT batch can be transferred to another TMT batch in which the same peptide was fragmented but not identified. To assess the validity of this approach, we tested SIMSI-Transfer on masked search engine identification results and recovered >80% of the masked identifications while controlling errors in the transfer procedure to below 1% false discovery rate. Applying SIMSI-Transfer to six published full proteome and phosphoproteome datasets from the Clinical Proteomic Tumor Analysis Consortium led to an increase of 26 to 45% of identified MS2 spectra with TMT quantifications. This significantly decreased the number of missing values across batches and, in turn, increased the number of peptides and proteins identified in all TMT batches by 43 to 56% and 13 to 16%, respectively. Spectrum clustering enables peptide identification transfer between LC–MS/MS runs. The SIMSI pipeline supports processing full proteome and phosphoproteome data. SIMSI increases the number of quantifiable PSMs by 26 to 45%. SIMSI reduces missing values in multibatch TMT labeling experiments by up to 21%.
Collapse
Affiliation(s)
- Firas Hamood
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
| |
Collapse
|
42
|
Oeckl J, Janovska P, Adamcova K, Bardova K, Brunner S, Dieckmann S, Ecker J, Fromme T, Funda J, Gantert T, Giansanti P, Hidrobo MS, Kuda O, Kuster B, Li Y, Pohl R, Schmitt S, Schweizer S, Zischka H, Zouhar P, Kopecky J, Klingenspor M. Loss of UCP1 function augments recruitment of futile lipid cycling for thermogenesis in murine brown fat. Mol Metab 2022; 61:101499. [PMID: 35470094 PMCID: PMC9097615 DOI: 10.1016/j.molmet.2022.101499] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Josef Oeckl
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Petra Janovska
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Katerina Adamcova
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Kristina Bardova
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Sarah Brunner
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Sebastian Dieckmann
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Josef Ecker
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Tobias Fromme
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Jiri Funda
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Thomas Gantert
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Piero Giansanti
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Maria Soledad Hidrobo
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Ondrej Kuda
- Laboratory of Metabolism of Bioactive Lipids, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Yongguo Li
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Radek Pohl
- NMR spectroscopy, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Czech Republic
| | - Sabine Schmitt
- Institute of Toxicology and Environmental Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sabine Schweizer
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Hans Zischka
- Institute of Toxicology and Environmental Hygiene, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, Munich, Germany
| | - Petr Zouhar
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Jan Kopecky
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic.
| | - Martin Klingenspor
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany.
| |
Collapse
|
43
|
Krumm J, Sekine K, Samaras P, Brazovskaja A, Breunig M, Yasui R, Kleger A, Taniguchi H, Wilhelm M, Treutlein B, Camp JG, Kuster B. High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development. Cell Rep 2022; 38:110604. [PMID: 35354033 DOI: 10.1016/j.celrep.2022.110604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/29/2021] [Accepted: 03/09/2022] [Indexed: 11/29/2022] Open
Abstract
Primary human hepatocytes are widely used to evaluate liver toxicity of drugs, but they are scarce and demanding to culture. Stem cell-derived hepatocytes are increasingly discussed as alternatives. To obtain a better appreciation of the molecular processes during the differentiation of induced pluripotent stem cells into hepatocytes, we employ a quantitative proteomic approach to follow the expression of 9,000 proteins, 12,000 phosphorylation sites, and 800 acetylation sites over time. The analysis reveals stage-specific markers, a major molecular switch between hepatic endoderm versus immature hepatocyte-like cells impacting, e.g., metabolism, the cell cycle, kinase activity, and the expression of drug transporters. Comparing the proteomes of two- (2D) and three-dimensional (3D)-derived hepatocytes with fetal and adult liver indicates a fetal-like status of the in vitro models and lower expression of important ADME/Tox proteins. The collective data enable constructing a molecular roadmap of hepatocyte development that serves as a valuable resource for future research.
Collapse
Affiliation(s)
- Johannes Krumm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Keisuke Sekine
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Agnieska Brazovskaja
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Markus Breunig
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany
| | - Ryota Yasui
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan
| | - Alexander Kleger
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany
| | - Hideki Taniguchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan; Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, 4056 Basel, Switzerland
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, 85354 Freising, Germany.
| |
Collapse
|
44
|
Weiß L, Gaelings L, Reiner T, Mergner J, Kuster B, Fehér A, Hensel G, Gahrtz M, Kumlehn J, Engelhardt S, Hückelhoven R. Posttranslational modification of the RHO of plants protein RACB by phosphorylation and cross-kingdom conserved ubiquitination. PLoS One 2022; 17:e0258924. [PMID: 35333858 PMCID: PMC8956194 DOI: 10.1371/journal.pone.0258924] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/10/2021] [Indexed: 11/19/2022] Open
Abstract
Small RHO-type G-proteins act as signaling hubs and master regulators of polarity in eukaryotic cells. Their activity is tightly controlled, as defective RHO signaling leads to aberrant growth and developmental defects. Two major processes regulate G-protein activity: canonical shuttling between different nucleotide bound states and posttranslational modification (PTM), of which the latter can support or suppress RHO signaling, depending on the individual PTM. In plants, regulation of Rho of plants (ROPs) signaling activity has been shown to act through nucleotide exchange and GTP hydrolysis, as well as through lipid modification, but there is little data available on phosphorylation or ubiquitination of ROPs. Hence, we applied proteomic analyses to identify PTMs of the barley ROP RACB. We observed in vitro phosphorylation by barley ROP binding kinase 1 and in vivo ubiquitination of RACB. Comparative analyses of the newly identified RACB phosphosites and human RHO protein phosphosites revealed conservation of modified amino acid residues, but no overlap of actual phosphorylation patterns. However, the identified RACB ubiquitination site is conserved in all ROPs from Hordeum vulgare, Arabidopsis thaliana and Oryza sativa and in mammalian Rac1 and Rac3. Point mutation of this ubiquitination site leads to stabilization of RACB. Hence, this highly conserved lysine residue may regulate protein stability across different kingdoms.
Collapse
Affiliation(s)
- Lukas Weiß
- Chair of Phytopathology, Technical University of Munich (TUM), Freising, Germany
| | - Lana Gaelings
- Chair of Phytopathology, Technical University of Munich (TUM), Freising, Germany
| | - Tina Reiner
- Chair of Phytopathology, Technical University of Munich (TUM), Freising, Germany
| | - Julia Mergner
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, Freising, Germany
| | - Attila Fehér
- Chair of Plant Biology, University of Szeged, and Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Götz Hensel
- Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Manfred Gahrtz
- Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jochen Kumlehn
- Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Stefan Engelhardt
- Chair of Phytopathology, Technical University of Munich (TUM), Freising, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, Technical University of Munich (TUM), Freising, Germany
- * E-mail:
| |
Collapse
|
45
|
Abstract
INTRODUCTION Due to its excellent sensitivity, nano-flow liquid chromatography tandem mass spectrometry (LC-MS/MS) is the mainstay in proteome research; however, this comes at the expense of limited throughput and robustness. In contrast, micro-flow LC-MS/MS enables high-throughput, robustness, quantitative reproducibility, and precision while retaining a moderate degree of sensitivity. Such features make it an attractive technology for a wide range of proteomic applications. In particular, large-scale projects involving the analysis of hundreds to thousands of samples. AREAS COVERED This review summarizes the history of chromatographic separation in discovery proteomics with a focus on micro-flow LC-MS/MS, discusses the current state-of-the-art, highlights advances in column development and instrumentation, and provides guidance on which LC flow best supports different types of proteomic applications. EXPERT OPINION Micro-flow LC-MS/MS will replace nano-flow LC-MS/MS in many proteomic applications, particularly when sample quantities are not limited and sample cohorts are large. Examples include clinical analyses of body fluids, tissues, drug discovery and chemical biology investigations, plus systems biology projects across all kingdoms of life. When combined with rapid and sensitive MS, intelligent data acquisition, and informatics approaches, it will soon become possible to analyze large cohorts of more than 10,000 samples in a comprehensive and fully quantitative fashion.
Collapse
Affiliation(s)
- Yangyang Bian
- The College of Life Science, Northwest University, Xi'an, P.R. China
| | - Chunli Gao
- The College of Life Science, Northwest University, Xi'an, P.R. China
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| |
Collapse
|
46
|
Lier S, Sellmer A, Orben F, Heinzlmeir S, Krauß L, Schneeweis C, Hassan Z, Schneider C, Patricia Gloria Schäfer A, Pongratz H, Engleitner T, Öllinger R, Kuisl A, Bassermann F, Schlag C, Kong B, Dove S, Kuster B, Rad R, Reichert M, Wirth M, Saur D, Mahboobi S, Schneider G. A novel Cereblon E3 ligase modulator with antitumor activity in gastrointestinal cancer. Bioorg Chem 2022; 119:105505. [PMID: 34838332 DOI: 10.1016/j.bioorg.2021.105505] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/06/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022]
Abstract
Targeted protein degradation offers new opportunities to inactivate cancer drivers and has successfully entered the clinic. Ways to induce selective protein degradation include proteolysis targeting chimera (PROTAC) technology and immunomodulatory (IMiDs) / next-generation Cereblon (CRBN) E3 ligase modulating drugs (CELMoDs). Here, we aimed to develop a MYC PROTAC based on the MYC-MAX dimerization inhibitor 10058-F4 derivative 28RH and Thalidomide, called MDEG-541. We show that a subgroup of gastrointestinal cancer cell lines and primary patient-derived organoids are MDEG-541 sensitive. Although MYC expression was regulated in a CRBN-, proteasome- and ubiquitin-dependent manner, we provide evidence that MDEG-541 induced the degradation of CRBN neosubstrates, including G1 to S phase transition 1/2 (GSPT1/2) and the Polo-like kinase 1 (PLK1). In sum, we have established a CRBN-dependent degrader of relevant cancer targets with activity in gastrointestinal cancers.
Collapse
Affiliation(s)
- Svenja Lier
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Andreas Sellmer
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany
| | - Felix Orben
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | | | - Lukas Krauß
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Christian Schneeweis
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Zonera Hassan
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Carolin Schneider
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | | | - Herwig Pongratz
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, MRI, TU Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, MRI, TU Munich, Germany
| | - Anna Kuisl
- Medical Clinic and Policlinic III, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Florian Bassermann
- Medical Clinic and Policlinic III, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Christoph Schlag
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany
| | - Bo Kong
- Department of Surgery, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany; Department of General Surgery, University of Ulm, 89081 Ulm, Germany
| | - Stefan Dove
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TU Munich, 85354 Freising, Germany; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TU Munich, 85354 Freising, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, MRI, TU Munich, Germany; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Maximilian Reichert
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Center for Protein Assemblies (CPA), Technische Universität München, 85747 Garching, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, 12203 Berlin, Germany
| | - Dieter Saur
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Institute for Translational Cancer Research and Experimental Cancer Therapy, Klinikum Rechts der Isar, TU Munich, Germany
| | - Siavosh Mahboobi
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany.
| | - Günter Schneider
- Medical Clinic and Policlinic II, Klinikum Rechts der Isar, TU Munich, 81675 Munich, Germany; University Medical Center Göttingen, Department of General, Visceral and Pediatric Surgery, 37075 Göttingen, Germany.
| |
Collapse
|
47
|
Zellner A, Müller SA, Lindner B, Beaufort N, Rozemuller AJM, Arzberger T, Gassen NC, Lichtenthaler SF, Kuster B, Haffner C, Dichgans M. Proteomic profiling in cerebral amyloid angiopathy reveals an overlap with CADASIL highlighting accumulation of HTRA1 and its substrates. Acta Neuropathol Commun 2022; 10:6. [PMID: 35074002 PMCID: PMC8785498 DOI: 10.1186/s40478-021-01303-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022] Open
Abstract
Cerebral amyloid angiopathy (CAA) is an age-related condition and a major cause of intracerebral hemorrhage and cognitive decline that shows close links with Alzheimer's disease (AD). CAA is characterized by the aggregation of amyloid-β (Aβ) peptides and formation of Aβ deposits in the brain vasculature resulting in a disruption of the angioarchitecture. Capillaries are a critical site of Aβ pathology in CAA type 1 and become dysfunctional during disease progression. Here, applying an advanced protocol for the isolation of parenchymal microvessels from post-mortem brain tissue combined with liquid chromatography tandem mass spectrometry (LC-MS/MS), we determined the proteomes of CAA type 1 cases (n = 12) including a patient with hereditary cerebral hemorrhage with amyloidosis-Dutch type (HCHWA-D), and of AD cases without microvascular amyloid pathology (n = 13) in comparison to neurologically healthy controls (n = 12). ELISA measurements revealed microvascular Aβ1-40 levels to be exclusively enriched in CAA samples (mean: > 3000-fold compared to controls). The proteomic profile of CAA type 1 was characterized by massive enrichment of multiple predominantly secreted proteins and showed significant overlap with the recently reported brain microvascular proteome of patients with cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), a hereditary cerebral small vessel disease (SVD) characterized by the aggregation of the Notch3 extracellular domain. We found this overlap to be largely attributable to the accumulation of high-temperature requirement protein A1 (HTRA1), a serine protease with an established role in the brain vasculature, and several of its substrates. Notably, this signature was not present in AD cases. We further show that HTRA1 co-localizes with Aβ deposits in brain capillaries from CAA type 1 patients indicating a pathologic recruitment process. Together, these findings suggest a central role of HTRA1-dependent protein homeostasis in the CAA microvasculature and a molecular connection between multiple types of brain microvascular disease.
Collapse
Affiliation(s)
- Andreas Zellner
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Barbara Lindner
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Nathalie Beaufort
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Annemieke J M Rozemuller
- Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
| | - Thomas Arzberger
- Department of Psychiatry and Psychotherapy, Klinikum der Universität München, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nils C Gassen
- Research Group Neurohomeostasis, Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Christof Haffner
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 17, 81377, Munich, Germany.
- Department of Psychiatry and Psychotherapy, School of Medicine, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675, Munich, Germany.
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 17, 81377, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| |
Collapse
|
48
|
Lautenbacher L, Samaras P, Muller J, Grafberger A, Shraideh M, Rank J, Fuchs ST, Schmidt TK, The M, Dallago C, Wittges H, Rost B, Krcmar H, Kuster B, Wilhelm M. ProteomicsDB: toward a FAIR open-source resource for life-science research. Nucleic Acids Res 2022; 50:D1541-D1552. [PMID: 34791421 PMCID: PMC8728203 DOI: 10.1093/nar/gkab1026] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022] Open
Abstract
ProteomicsDB (https://www.ProteomicsDB.org) is a multi-omics and multi-organism resource for life science research. In this update, we present our efforts to continuously develop and expand ProteomicsDB. The major focus over the last two years was improving the findability, accessibility, interoperability and reusability (FAIR) of the data as well as its implementation. For this purpose, we release a new application programming interface (API) that provides systematic access to essentially all data in ProteomicsDB. Second, we release a new open-source user interface (UI) and show the advantages the scientific community gains from such software. With the new interface, two new visualizations of protein primary, secondary and tertiary structure as well an updated spectrum viewer were added. Furthermore, we integrated ProteomicsDB with our deep-neural-network Prosit that can predict the fragmentation characteristics and retention time of peptides. The result is an automatic processing pipeline that can be used to reevaluate database search engine results stored in ProteomicsDB. In addition, we extended the data content with experiments investigating different human biology as well as a newly supported organism.
Collapse
Affiliation(s)
- Ludwig Lautenbacher
- Technical University of Munich, Computational Mass Spectrometry, 85354 Freising, Bavaria, Germany
| | - Patroklos Samaras
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
| | - Julian Muller
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
| | - Andreas Grafberger
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
| | - Marwin Shraideh
- Technical University of Munich, Chair for Information Systems, 85748 Garching, Bavaria, Germany
- Technical University of Munich, SAP University Competence Center, 85748 Garching, Bavaria, Germany
| | - Johannes Rank
- Technical University of Munich, Chair for Information Systems, 85748 Garching, Bavaria, Germany
- Technical University of Munich, SAP University Competence Center, 85748 Garching, Bavaria, Germany
| | - Simon T Fuchs
- Technical University of Munich, Chair for Information Systems, 85748 Garching, Bavaria, Germany
- Technical University of Munich, SAP University Competence Center, 85748 Garching, Bavaria, Germany
| | - Tobias K Schmidt
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
| | - Matthew The
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
| | - Christian Dallago
- Technical University of Munich, Department for Bioinformatics and Computational Biology, 85748 Garching, Bavaria, Germany
- Technical University of Munich, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), 85748 Garching, Bavaria, Germany
| | - Holger Wittges
- Technical University of Munich, Chair for Information Systems, 85748 Garching, Bavaria, Germany
- Technical University of Munich, SAP University Competence Center, 85748 Garching, Bavaria, Germany
| | - Burkhard Rost
- Technical University of Munich, Department for Bioinformatics and Computational Biology, 85748 Garching, Bavaria, Germany
- Technical University of Munich, Institute for Advanced Study (TUM-IAS), 85748 Freising, Bavaria, Germany
| | - Helmut Krcmar
- Technical University of Munich, Chair for Information Systems, 85748 Garching, Bavaria, Germany
- Technical University of Munich, SAP University Competence Center, 85748 Garching, Bavaria, Germany
| | - Bernhard Kuster
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
- Technical University of Munich, Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), 85354 Freising, Bavaria, Germany
| | - Mathias Wilhelm
- Technical University of Munich, Computational Mass Spectrometry, 85354 Freising, Bavaria, Germany
| |
Collapse
|
49
|
Zhang X, Schuhmachers P, Mourão A, Giansanti P, Murer A, Thumann S, Kuklik‐Roos C, Beer S, Hauck SM, Hammerschmidt W, Küppers R, Kuster B, Raab M, Strebhardt K, Sattler M, Münz C, Kempkes B. PLK1-dependent phosphorylation restrains EBNA2 activity and lymphomagenesis in EBV-infected mice. EMBO Rep 2021; 22:e53007. [PMID: 34605140 PMCID: PMC8647151 DOI: 10.15252/embr.202153007] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/17/2021] [Accepted: 09/10/2021] [Indexed: 01/17/2023] Open
Abstract
While Epstein-Barr virus (EBV) establishes a life-long latent infection in apparently healthy human immunocompetent hosts, immunodeficient individuals are at particular risk to develop lymphoproliferative B-cell malignancies caused by EBV. A key EBV protein is the transcription factor EBV nuclear antigen 2 (EBNA2), which initiates B-cell proliferation. Here, we combine biochemical, cellular, and in vivo experiments demonstrating that the mitotic polo-like kinase 1 (PLK1) binds to EBNA2, phosphorylates its transactivation domain, and thereby inhibits its biological activity. EBNA2 mutants that impair PLK1 binding or prevent EBNA2 phosphorylation are gain-of-function mutants. They exhibit enhanced transactivation capacities, accelerate the proliferation of infected B cells, and promote the development of monoclonal B-cell lymphomas in infected mice. Thus, PLK1 coordinates the activity of EBNA2 to attenuate the risk of tumor incidences in favor of the establishment of latency in the infected but healthy host.
Collapse
Affiliation(s)
- Xiang Zhang
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Patrick Schuhmachers
- Viral ImmunbiologyInstitute of Experimental ImmunologyUniversity of ZürichZürichSwitzerland
| | - André Mourão
- Institute of Structural BiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- Department of ChemistryBavarian NMR CenterTechnical University of MunichGarchingGermany
| | - Piero Giansanti
- Chair of Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
| | - Anita Murer
- Viral ImmunbiologyInstitute of Experimental ImmunologyUniversity of ZürichZürichSwitzerland
| | - Sybille Thumann
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Cornelia Kuklik‐Roos
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Sophie Beer
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core FacilityHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research)University Hospital EssenEssenGermany
| | - Bernhard Kuster
- Chair of Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
- Bavarian Center for Biomolecular Mass SpectrometryTechnical University of MunichFreisingGermany
| | - Monika Raab
- Department of Gynecology and ObstetricsJohann Wolfgang Goethe UniversityFrankfurt am MainGermany
| | - Klaus Strebhardt
- Department of Gynecology and ObstetricsJohann Wolfgang Goethe UniversityFrankfurt am MainGermany
| | - Michael Sattler
- Institute of Structural BiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- Department of ChemistryBavarian NMR CenterTechnical University of MunichGarchingGermany
| | - Christian Münz
- Viral ImmunbiologyInstitute of Experimental ImmunologyUniversity of ZürichZürichSwitzerland
| | - Bettina Kempkes
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| |
Collapse
|
50
|
Eckert S, Chang YC, Bayer FP, The M, Kuhn PH, Weichert W, Kuster B. Evaluation of Disposable Trap Column nanoLC-FAIMS-MS/MS for the Proteomic Analysis of FFPE Tissue. J Proteome Res 2021; 20:5402-5411. [PMID: 34735149 DOI: 10.1021/acs.jproteome.1c00695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteomic biomarker discovery using formalin-fixed paraffin-embedded (FFPE) tissue requires robust workflows to support the analysis of large cohorts of patient samples. It also requires finding a reasonable balance between achieving a high proteomic depth and limiting the overall analysis time. To this end, we evaluated the merits of online coupling of single-use disposable trap column nanoflow liquid chromatography, high-field asymmetric-waveform ion-mobility spectrometry (FAIMS), and tandem mass spectrometry (nLC-FAIMS-MS/MS). The data show that ≤600 ng of peptide digest should be loaded onto the chromatographic part of the system. Careful characterization of the FAIMS settings enabled the choice of optimal combinations of compensation voltages (CVs) as a function of the employed LC gradient time. We found nLC-FAIMS-MS/MS to be on par with StageTip-based off-line basic pH reversed-phase fractionation in terms of proteomic depth and reproducibility of protein quantification (coefficient of variation ≤15% for 90% of all proteins) but requiring 50% less sample and substantially reducing sample handling. Using FFPE materials from the lymph node, lung, and prostate tissue as examples, we show that nLC-FAIMS-MS/MS can identify 5000-6000 proteins from the respective tissue within a total of 3 h of analysis time.
Collapse
Affiliation(s)
- Stephan Eckert
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany.,Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Yun-Chien Chang
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Peer-Hendrik Kuhn
- Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising 85354, Germany
| |
Collapse
|