1
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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.
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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.
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2
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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.
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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
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3
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Ruprecht B, Wei L, Zheng L, Bodea S, Mo X, Maschberger M, Stoehr G, Hahne H, Cornella-Taracido I, Chi A. Chemoproteomic profiling to identify activity changes and functional inhibitors of DNA-binding proteins. Cell Chem Biol 2022; 29:1639-1648.e4. [PMID: 36356585 DOI: 10.1016/j.chembiol.2022.10.008] [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: 09/25/2021] [Revised: 07/04/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022]
Abstract
DNA-binding proteins are promising therapeutic targets but are notoriously difficult to drug. Here, we evaluate a chemoproteomic DNA interaction platform as a complementary strategy for parallelized compound profiling. To enable this approach, we determined the proteomic binding landscape of 92 immobilized DNA sequences. Perturbation-induced activity changes of captured transcription factors in disease-relevant settings demonstrated functional relevance of the enriched subproteome. Chemoproteomic profiling of >300 cysteine-directed compounds against a coverage optimized bead mixture, which specifically captures >150 DNA binders, revealed competition of several DNA-binding proteins, including the transcription factors ELF1 and ELF2. We also discovered the first compound that displaces the DNA-repair complex MSH2-MSH3 from DNA. Compound binding to cysteine 252 on MSH3 was confirmed using chemoproteomic reactive cysteine profiling. Overall, these results suggested that chemoproteomic DNA bead pull-downs enable the specific readout of transcription factor activity and can identify functional "hotspots" on DNA binders toward expanding the druggable proteome.
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Affiliation(s)
| | - Lan Wei
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | - Li Zheng
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | - Smaranda Bodea
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | - Xuan Mo
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | | | | | - Hannes Hahne
- OmicScouts GmbH, 85354 Freising, Bavaria, Germany
| | | | - An Chi
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA.
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4
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Dieter SM, Siegl C, Codó PL, Huerta M, Ostermann-Parucha AL, Schulz E, Zowada MK, Martin S, Laaber K, Nowrouzi A, Blatter M, Kreth S, Westermann F, Benner A, Uhrig U, Putzker K, Lewis J, Haegebarth A, Mumberg D, Holton SJ, Weiske J, Toepper LM, Scheib U, Siemeister G, Ball CR, Kuster B, Stoehr G, Hahne H, Johannes S, Lange M, Herbst F, Glimm H. Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer. Cell Rep 2021; 36:109394. [PMID: 34289372 DOI: 10.1016/j.celrep.2021.109394] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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: 09/23/2020] [Revised: 04/08/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Novel treatment options for metastatic colorectal cancer (CRC) are urgently needed to improve patient outcome. Here, we screen a library of non-characterized small molecules against a heterogeneous collection of patient-derived CRC spheroids. By prioritizing compounds with inhibitory activity in a subset of-but not all-spheroid cultures, NCT02 is identified as a candidate with minimal risk of non-specific toxicity. Mechanistically, we show that NCT02 acts as molecular glue that induces ubiquitination of cyclin K (CCNK) and proteasomal degradation of CCNK and its complex partner CDK12. Knockout of CCNK or CDK12 decreases proliferation of CRC cells in vitro and tumor growth in vivo. Interestingly, sensitivity to pharmacological CCNK/CDK12 degradation is associated with TP53 deficiency and consensus molecular subtype 4 in vitro and in patient-derived xenografts. We thus demonstrate the efficacy of targeted CCNK/CDK12 degradation for a CRC subset, highlighting the potential of drug-induced proteolysis for difficult-to-treat types of cancer.
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Affiliation(s)
- Sebastian M Dieter
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany.
| | | | - Paula L Codó
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; CureVac AG, 60325 Frankfurt am Main, Germany
| | - Mario Huerta
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Anna L Ostermann-Parucha
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Erik Schulz
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Martina K Zowada
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Sylvia Martin
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Karin Laaber
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Ali Nowrouzi
- Division of Molecular and Translational Radiation Oncology, Heidelberg Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Mona Blatter
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Sina Kreth
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Ulrike Uhrig
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Kerstin Putzker
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Joe Lewis
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Andrea Haegebarth
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Dominik Mumberg
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Simon J Holton
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Joerg Weiske
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Lena-Marit Toepper
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Ulrike Scheib
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Gerhard Siemeister
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Claudia R Ball
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 01307 Dresden, Germany; Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden at TU Dresden, 01307 Dresden, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | | | | | - Sarah Johannes
- Bayer AG, Research & Development, Pharmaceuticals, 42117 Wuppertal, Germany
| | - Martin Lange
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Friederike Herbst
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 01307 Dresden, Germany; Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden at TU Dresden, 01307 Dresden, Germany.
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5
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Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Angelov A, Werner T, Bantscheff M, Wilhelm M, Klingenspor M, Lemeer S, Liebl W, Hahne H, Savitski MM, Kuster B. Meltome atlas-thermal proteome stability across the tree of life. Nat Methods 2020; 17:495-503. [PMID: 32284610 DOI: 10.1038/s41592-020-0801-4] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans and covering melting temperatures of 30-90 °C. Protein sequence, composition and size affect thermal stability in prokaryotes and eukaryotic proteins show a nonlinear relationship between the degree of disordered protein structure and thermal stability. The data indicate that evolutionary conservation of protein complexes is reflected by similar thermal stability of their proteins, and we show examples in which genomic alterations can affect thermal stability. Proteins of the respiratory chain were found to be very stable in many organisms, and human mitochondria showed close to normal respiration at 46 °C. We also noted cell-type-specific effects that can affect protein stability or the efficacy of drugs. This meltome atlas broadly defines the proteome amenable to thermal profiling in biology and drug discovery and can be explored online at http://meltomeatlas.proteomics.wzw.tum.de:5003/ and http://www.proteomicsdb.org.
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Affiliation(s)
- Anna Jarzab
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Nils Kurzawa
- Genome Biology Unit, EMBL, Heidelberg, Germany.,Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | | | - Matthias Moerch
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Niels Leijten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Yangyang Bian
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Eva Musiol
- Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
| | | | | | | | - Charlotte Daly
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Mergner
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Britta Spanier
- Chair of Nutritional Physiology, Technical University of Munich, Freising, Germany
| | - Angel Angelov
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | | | | | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Wolfgang Liebl
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | | | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
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6
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Wang D, Eraslan B, Wieland T, Hallström B, Hopf T, Zolg DP, Zecha J, Asplund A, Li LH, Meng C, Frejno M, Schmidt T, Schnatbaum K, Wilhelm M, Ponten F, Uhlen M, Gagneur J, Hahne H, Kuster B. A deep proteome and transcriptome abundance atlas of 29 healthy human tissues. Mol Syst Biol 2019; 15:e8503. [PMID: 30777892 PMCID: PMC6379049 DOI: 10.15252/msb.20188503] [Citation(s) in RCA: 394] [Impact Index Per Article: 78.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 01/01/2019] [Accepted: 01/08/2019] [Indexed: 11/28/2022] Open
Abstract
Genome-, transcriptome- and proteome-wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we generated a quantitative proteome and transcriptome abundance atlas of 29 paired healthy human tissues from the Human Protein Atlas project representing human genes by 18,072 transcripts and 13,640 proteins including 37 without prior protein-level evidence. The analysis revealed that hundreds of proteins, particularly in testis, could not be detected even for highly expressed mRNAs, that few proteins show tissue-specific expression, that strong differences between mRNA and protein quantities within and across tissues exist and that protein expression is often more stable across tissues than that of transcripts. Only 238 of 9,848 amino acid variants found by exome sequencing could be confidently detected at the protein level showing that proteogenomics remains challenging, needs better computational methods and requires rigorous validation. Many uses of this resource can be envisaged including the study of gene/protein expression regulation and biomarker specificity evaluation.
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Affiliation(s)
- Dongxue Wang
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Basak Eraslan
- Computational Biology, Department of Informatics, Technical University of Munich, Garching bei München, Germany
- Department of Biochemistry, Quantitative Biosciences Munich, Gene Center, Ludwig Maximilian Universität, München, Germany
| | | | - Björn Hallström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | | | - Daniel Paul Zolg
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Anna Asplund
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Li-Hua Li
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Chen Meng
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Martin Frejno
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | | | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Frederik Ponten
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Julien Gagneur
- Computational Biology, Department of Informatics, Technical University of Munich, Garching bei München, Germany
| | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
- Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
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7
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Eraslan B, Wang D, Gusic M, Prokisch H, Hallström BM, Uhlén M, Asplund A, Pontén F, Wieland T, Hopf T, Hahne H, Kuster B, Gagneur J. Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues. Mol Syst Biol 2019; 15:e8513. [PMID: 30777893 PMCID: PMC6379048 DOI: 10.15252/msb.20188513] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Despite their importance in determining protein abundance, a comprehensive catalogue of sequence features controlling protein-to-mRNA (PTR) ratios and a quantification of their effects are still lacking. Here, we quantified PTR ratios for 11,575 proteins across 29 human tissues using matched transcriptomes and proteomes. We estimated by regression the contribution of known sequence determinants of protein synthesis and degradation in addition to 45 mRNA and 3 protein sequence motifs that we found by association testing. While PTR ratios span more than 2 orders of magnitude, our integrative model predicts PTR ratios at a median precision of 3.2-fold. A reporter assay provided functional support for two novel UTR motifs, and an immobilized mRNA affinity competition-binding assay identified motif-specific bound proteins for one motif. Moreover, our integrative model led to a new metric of codon optimality that captures the effects of codon frequency on protein synthesis and degradation. Altogether, this study shows that a large fraction of PTR ratio variation in human tissues can be predicted from sequence, and it identifies many new candidate post-transcriptional regulatory elements.
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Affiliation(s)
- Basak Eraslan
- Computational Biology, Department of Informatics, Technical University of Munich, Garching Munich, Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dongxue Wang
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Mirjana Gusic
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Björn M Hallström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Frederik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thomas Wieland
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Thomas Hopf
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- Center For Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Julien Gagneur
- Computational Biology, Department of Informatics, Technical University of Munich, Garching Munich, Germany
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8
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Yoon H, Schaubeck M, Lagkouvardos I, Blesl A, Heinzlmeir S, Hahne H, Clavel T, Panda S, Ludwig C, Kuster B, Manichanh C, Kump P, Haller D, Hörmannsperger G. Increased Pancreatic Protease Activity in Response to Antibiotics Impairs Gut Barrier and Triggers Colitis. Cell Mol Gastroenterol Hepatol 2018; 6:370-388.e3. [PMID: 30182050 PMCID: PMC6121113 DOI: 10.1016/j.jcmgh.2018.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/15/2018] [Indexed: 12/19/2022]
Abstract
Background & Aims Antibiotic (ABx) therapy is associated with increased risk for Crohn's disease but underlying mechanisms are unknown. We observed high fecal serine protease activity (PA) to be a frequent side effect of ABx therapy. The aim of the present study was to unravel whether this rise in large intestinal PA may promote colitis development via detrimental effects on the large intestinal barrier. Methods Transwell experiments were used to assess the impact of high PA in ABx-treated patients or vancomycin/metronidazole-treated mice on the epithelial barrier. Serine protease profiling was performed using liquid chromatography-mass spectrometry/mass spectrometry analysis. The impact of high large intestinal PA on the intestinal barrier in wild-type and interleukin (IL)10-/- mice and on colitis development in IL10-/- mice was investigated using vancomycin/metronidazole with or without oral serine protease inhibitor (AEBSF) treatment. Results The ABx-induced, high large intestinal PA was caused by significantly increased levels of pancreatic proteases and impaired epithelial barrier integrity. In wild-type mice, the rise in PA caused a transient increase in intestinal permeability but did not affect susceptibility to chemically induced acute colitis. In IL10-/- mice, increased PA caused a consistent impairment of the intestinal barrier associated with inflammatory activation in the large intestinal tissue. In the long term, the vancomycin/metronidazole-induced lasting increase in PA aggravated colitis development in IL10-/- mice. Conclusions High large intestinal PA is a frequent adverse effect of ABx therapy, which is detrimental to the large intestinal barrier and may contribute to the development of chronic intestinal inflammation in susceptible individuals.
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Key Words
- ABx, antibiotics
- AEBSF, 4-(2-aminoethyl) benzenesulfonyl fluoride hydrochloride
- DSS, dextran sulfate sodium
- Epithelial Barrier
- GF, germ-free
- Gut Microbiota
- IBD, inflammatory bowel diseases
- IL, interleukin
- Inflammatory Bowel Diseases
- LC-MS/MS, liquid chromatography–mass spectrometry/mass spectrometry
- PA, protease activity
- PBS, phosphate-buffered saline
- PMSF, phenylmethane-sulfonylfluoride
- SPF, specific pathogen-free
- Serine Proteases
- TEER, transepithelial electrical resistance
- V/M, vancomycin/metronidazole
- WT, wild-type
- cecal-sup, cecal-supernatants
- ctr, control
- stool-sup, stool-supernatants
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Affiliation(s)
- Hongsup Yoon
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
| | - Monika Schaubeck
- Max Planck Institute of Neurobiology, Department of Neuroimmunology, Martinsried, Germany
| | - Ilias Lagkouvardos
- Technische Universität München, Junior Research Group Microbial Bioinformatics, ZIEL – Institute for Food and Health, Freising-Weihenstephan, Germany
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
| | - Andreas Blesl
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Stephanie Heinzlmeir
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | - Hannes Hahne
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- OmicScouts GmbH, Freising, Germany
| | - Thomas Clavel
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
- RWTH University Hospital, Institute of Medical Microbiology, Functional Microbiome Research Group, Aachen, Germany
| | - Suchita Panda
- Vall d'Hebron Research Institute, Digestive Research Unit, Barcelona, Spain
| | - Christina Ludwig
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | - Bernhard Kuster
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | | | - Patrizia Kump
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Dirk Haller
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
| | - Gabriele Hörmannsperger
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
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9
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Lee CY, Wang D, Wilhelm M, Zolg DP, Schmidt T, Schnatbaum K, Reimer U, Pontén F, Uhlén M, Hahne H, Kuster B. Mining the Human Tissue Proteome for Protein Citrullination. Mol Cell Proteomics 2018; 17:1378-1391. [PMID: 29610271 DOI: 10.1074/mcp.ra118.000696] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/28/2018] [Indexed: 11/06/2022] Open
Abstract
Citrullination is a posttranslational modification of arginine catalyzed by five peptidylarginine deiminases (PADs) in humans. The loss of a positive charge may cause structural or functional alterations, and while the modification has been linked to several diseases, including rheumatoid arthritis (RA) and cancer, its physiological or pathophysiological roles remain largely unclear. In part, this is owing to limitations in available methodology to robustly enrich, detect, and localize the modification. As a result, only a few citrullination sites have been identified on human proteins with high confidence. In this study, we mined data from mass-spectrometry-based deep proteomic profiling of 30 human tissues to identify citrullination sites on endogenous proteins. Database searching of ∼70 million tandem mass spectra yielded ∼13,000 candidate spectra, which were further triaged by spectrum quality metrics and the detection of the specific neutral loss of isocyanic acid from citrullinated peptides to reduce false positives. Because citrullination is easily confused with deamidation, we synthetized ∼2,200 citrullinated and 1,300 deamidated peptides to build a library of reference spectra. This led to the validation of 375 citrullination sites on 209 human proteins. Further analysis showed that >80% of the identified modifications sites were new, and for 56% of the proteins, citrullination was detected for the first time. Sequence motif analysis revealed a strong preference for Asp and Gly, residues around the citrullination site. Interestingly, while the modification was detected in 26 human tissues with the highest levels found in the brain and lung, citrullination levels did not correlate well with protein expression of the PAD enzymes. Even though the current work represents the largest survey of protein citrullination to date, the modification was mostly detected on high abundant proteins, arguing that the development of specific enrichment methods would be required in order to study the full extent of cellular protein citrullination.
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Affiliation(s)
- Chien-Yun Lee
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,§Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan.,¶Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
| | - Dongxue Wang
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Daniel P Zolg
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tobias Schmidt
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | - Ulf Reimer
- ‖JPT Peptide Technologies GmbH, Berlin, Germany
| | - Fredrik Pontén
- **Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- ‡‡Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | - Bernhard Kuster
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; .,¶¶Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
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10
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Buhner S, Hahne H, Hartwig K, Li Q, Vignali S, Ostertag D, Meng C, Hörmannsperger G, Braak B, Pehl C, Frieling T, Barbara G, De Giorgio R, Demir IE, Ceyhan GO, Zeller F, Boeckxstaens G, Haller D, Kuster B, Schemann M. Protease signaling through protease activated receptor 1 mediate nerve activation by mucosal supernatants from irritable bowel syndrome but not from ulcerative colitis patients. PLoS One 2018. [PMID: 29529042 PMCID: PMC5846775 DOI: 10.1371/journal.pone.0193943] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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] [Indexed: 12/12/2022] Open
Abstract
Background & aims The causes of gastrointestinal complaints in irritable bowel syndrome (IBS) remain poorly understood. Altered nerve function has emerged as an important pathogenic factor as IBS mucosal biopsy supernatants consistently activate enteric and sensory neurons. We investigated the neurally active molecular components of such supernatants from patients with IBS and quiescent ulcerative colitis (UC). Method Effects of supernatants from 7 healthy controls (HC), 20 IBS and 12 UC patients on human and guinea pig submucous neurons were studied with neuroimaging techniques. We identify differentially expressed proteins with proteome analysis. Results Nerve activation by IBS supernatants was prevented by the protease activated receptor 1 (PAR1) antagonist SCHE79797. UC supernatants also activated enteric neurons through protease dependent mechanisms but without PAR1 involvement. Proteome analysis of the supernatants identified 204 proteins, among them 17 proteases as differentially expressed between IBS, UC and HC. Of those the four proteases elastase 3a, chymotrypsin C, proteasome subunit type beta-2 and an unspecified isoform of complement C3 were significantly more abundant in IBS compared to HC and UC supernatants. Of eight proteases, which were upregulated in IBS, the combination of elastase 3a, cathepsin L and proteasome alpha subunit-4 showed the highest prediction accuracy of 98% to discriminate between IBS and HC groups. Elastase synergistically potentiated the effects of histamine and serotonin–the two other main neuroactive substances in the IBS supernatants. A serine protease inhibitor isolated from the probiotic Bifidobacterium longum NCC2705 (SERPINBL), known to inhibit elastase-like proteases, prevented nerve activation by IBS supernatants. Conclusion Proteases in IBS and UC supernatants were responsible for nerve activation. Our data demonstrate that proteases, particularly those signalling through neuronal PAR1, are biomarker candidates for IBS, and protease profiling may be used to characterise IBS.
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Affiliation(s)
- Sabine Buhner
- Human Biology, Technische Universität München, Freising, Germany
| | - Hannes Hahne
- Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Kerstin Hartwig
- Human Biology, Technische Universität München, Freising, Germany
| | - Qin Li
- Human Biology, Technische Universität München, Freising, Germany
- Department of Physiology, Shangdong University, Shangdong, China
| | - Sheila Vignali
- Human Biology, Technische Universität München, Freising, Germany
| | - Daniela Ostertag
- Human Biology, Technische Universität München, Freising, Germany
| | - Chen Meng
- Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | | | - Breg Braak
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | | | | | - Giovanni Barbara
- Department of Medical and Surgical Sciences, St. Orsola Hospital, Bologna, Italy
| | - Roberto De Giorgio
- Department of Clinical Sciences, Nuovo Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Ihsan Ekin Demir
- Department of General Surgery, University Hospital Rechts der Isar, Technische Universität München, Germany
| | - Güralp Onur Ceyhan
- Department of General Surgery, University Hospital Rechts der Isar, Technische Universität München, Germany
| | | | - Guy Boeckxstaens
- Translational Research Centre for Gastrointestinal Disorders, University Hospital Gasthuisberg, Catholic University of Leuven, Leuven, Belgium
| | - Dirk Haller
- Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Michael Schemann
- Human Biology, Technische Universität München, Freising, Germany
- * E-mail:
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11
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Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B. The target landscape of clinical kinase drugs. Science 2018; 358:358/6367/eaan4368. [PMID: 29191878 DOI: 10.1126/science.aan4368] [Citation(s) in RCA: 490] [Impact Index Per Article: 81.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/20/2017] [Indexed: 02/06/2023]
Abstract
Kinase inhibitors are important cancer therapeutics. Polypharmacology is commonly observed, requiring thorough target deconvolution to understand drug mechanism of action. Using chemical proteomics, we analyzed the target spectrum of 243 clinically evaluated kinase drugs. The data revealed previously unknown targets for established drugs, offered a perspective on the "druggable" kinome, highlighted (non)kinase off-targets, and suggested potential therapeutic applications. Integration of phosphoproteomic data refined drug-affected pathways, identified response markers, and strengthened rationale for combination treatments. We exemplify translational value by discovering SIK2 (salt-inducible kinase 2) inhibitors that modulate cytokine production in primary cells, by identifying drugs against the lung cancer survival marker MELK (maternal embryonic leucine zipper kinase), and by repurposing cabozantinib to treat FLT3-ITD-positive acute myeloid leukemia. This resource, available via the ProteomicsDB database, should facilitate basic, clinical, and drug discovery research and aid clinical decision-making.
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Affiliation(s)
- Susan Klaeger
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephanie Heinzlmeir
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Harald Polzer
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Binje Vick
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, German Center for Environmental Health (HMGU), Munich, Germany
| | | | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Svenja Petzoldt
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chen Meng
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katrin Reiter
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Huichao Qiao
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Dominic Helm
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Heiner Koch
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Schoof
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | | | - Elena Casale
- Oncology, Nerviano Medical Sciences Srl, Milan, Italy
| | | | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Zhixiang Wu
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | | | | | | | - Anne-Kathrin Garz
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany
| | - Bjoern-Oliver Gohlke
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Structural Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
| | - Daniel Paul Zolg
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Gian Kayser
- Institute of Surgical Pathology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tonu Vooder
- Center of Thoracic Surgery, Krefeld, Germany.,Estonian Genome Center, University of Tartu, Tartu, Estonia.,Tartu University Hospital, Tartu, Estonia
| | - Robert Preissner
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Structural Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
| | - Hannes Hahne
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Neeme Tõnisson
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Tartu University Hospital, Tartu, Estonia
| | - Karl Kramer
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Katharina Götze
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany
| | - Florian Bassermann
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany
| | | | | | | | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Philipp A Greif
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Sabine Schneider
- Department of Chemistry, TUM, Garching, Germany.,Center For Integrated Protein Science Munich (CIPSM), Munich, Germany
| | | | - Juergen Ruland
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institut für Klinische Chemie und Pathobiochemie, TUM, Munich, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Irmela Jeremias
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, German Center for Environmental Health (HMGU), Munich, Germany.,Department of Pediatrics, Dr von Hauner Children's Hospital, LMU, Munich, Germany
| | - Karsten Spiekermann
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Center For Integrated Protein Science Munich (CIPSM), Munich, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, Freising, Germany
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12
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Schott AS, Behr J, Geißler AJ, Kuster B, Hahne H, Vogel RF. Quantitative Proteomics for the Comprehensive Analysis of Stress Responses of Lactobacillus paracasei subsp. paracasei F19. J Proteome Res 2017; 16:3816-3829. [PMID: 28862000 DOI: 10.1021/acs.jproteome.7b00474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lactic acid bacteria are broadly employed as starter cultures in the manufacture of foods. Upon technological preparation, they are confronted with drying stress that amalgamates numerous stress conditions resulting in losses of fitness and survival. To better understand and differentiate physiological stress responses, discover general and specific markers for the investigated stress conditions, and predict optimal preconditioning for starter cultures, we performed a comprehensive genomic and quantitative proteomic analysis of a commonly used model system, Lactobacillus paracasei subsp. paracasei TMW 1.1434 (isogenic with F19) under 11 typical stress conditions, including among others oxidative, osmotic, pH, and pressure stress. We identified and quantified >1900 proteins in triplicate analyses, representing 65% of all genes encoded in the genome. The identified genes were thoroughly annotated in terms of subcellular localization prediction and biological functions, suggesting unbiased and comprehensive proteome coverage. In total, 427 proteins were significantly differentially expressed in at least one condition. Most notably, our analysis suggests that optimal preconditioning toward drying was predicted to be alkaline and high-pressure stress preconditioning. Taken together, we believe the presented strategy may serve as a prototypic example for the analysis and utility of employing quantitative-mass-spectrometry-based proteomics to study bacterial physiology.
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Affiliation(s)
- Ann-Sophie Schott
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
| | - Jürgen Behr
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising 85354, Germany
| | - Andreas J Geißler
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
| | - Bernhard Kuster
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising 85354, Germany.,Chair of Proteomics and Bioanalytics, Technische Universität München , Freising 85354, Germany.,Center for Integrated Protein Science Munich, Freising 85354, Germany
| | | | - Rudi F Vogel
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
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13
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Affiliation(s)
- Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Hannes Hahne
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Mikhail Savitski
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Harald Marx
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
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14
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Abstract
The pig is one of the earliest domesticated animals in the history of human civilization and represents one of the most important livestock animals. The recent sequencing of the Sus scrofa genome was a major step toward the comprehensive understanding of porcine biology, evolution, and its utility as a promising large animal model for biomedical and xenotransplantation research. However, the functional and structural annotation of the Sus scrofa genome is far from complete. Here, we present mass spectrometry-based quantitative proteomics data of nine juvenile organs and six embryonic stages between 18 and 39 days after gestation. We found that the data provide evidence for and improve the annotation of 8176 protein-coding genes including 588 novel and 321 refined gene models. The analysis of tissue-specific proteins and the temporal expression profiles of embryonic proteins provides an initial functional characterization of expressed protein interaction networks and modules including as yet uncharacterized proteins. Comparative transcript and protein expression analysis to human organs reveal a moderate conservation of protein translation across species. We anticipate that this resource will facilitate basic and applied research on Sus scrofa as well as its porcine relatives.
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Affiliation(s)
| | | | | | | | | | - Dmitrij Frishman
- Institute of Bioinformatics and Systems Biology , German Research Center for Environmental Health, Neuherberg, Germany.,St Petersburg State Polytechnical University , St Petersburg, Russia
| | - Bernhard Kuster
- Center for Integrated Protein Science Munich , Munich, Germany
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15
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Feil G, Horres R, Schulte J, Mack AF, Petzoldt S, Arnold C, Meng C, Jost L, Boxleitner J, Kiessling-Wolf N, Serbest E, Helm D, Kuster B, Hartmann I, Korff T, Hahne H. Bacterial Cellulose Shifts Transcriptome and Proteome of Cultured Endothelial Cells Towards Native Differentiation. Mol Cell Proteomics 2017. [PMID: 28637836 DOI: 10.1074/mcp.ra117.000001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Preserving the native phenotype of primary cells in vitro is a complex challenge. Recently, hydrogel-based cellular matrices have evolved as alternatives to conventional cell culture techniques. We developed a bacterial cellulose-based aqueous gel-like biomaterial, dubbed Xellulin, which mimics a cellular microenvironment and seems to maintain the native phenotype of cultured and primary cells. When applied to human umbilical vein endothelial cells (HUVEC), it allowed the continuous cultivation of cell monolayers for more than one year without degradation or dedifferentiation. To investigate the impact of Xellulin on the endothelial cell phenotype in detail, we applied quantitative transcriptomics and proteomics and compared the molecular makeup of native HUVEC, HUVEC on collagen-coated Xellulin and collagen-coated cell culture plastic (polystyrene).Statistical analysis of 12,475 transcripts and 7831 proteins unveiled massive quantitative differences of the compared transcriptomes and proteomes. K-means clustering followed by network analysis showed that HUVEC on plastic upregulate transcripts and proteins controlling proliferation, cell cycle and protein biosynthesis. In contrast, HUVEC on Xellulin maintained, by and large, the expression levels of genes supporting their native biological functions and signaling networks such as integrin, receptor tyrosine kinase MAP/ERK and PI3K signaling pathways, while decreasing the expression of proliferation associated proteins. Moreover, CD34-an endothelial cell differentiation marker usually lost early during cell culture - was re-expressed within 2 weeks on Xellulin but not on plastic. And HUVEC on Xellulin showed a significantly stronger functional responsiveness to a prototypic pro-inflammatory stimulus than HUVEC on plastic.Taken together, this is one of the most comprehensive transcriptomic and proteomic studies of native and propagated HUVEC, which underscores the importance of the morphology of the cellular microenvironment to regulate cellular differentiation, and demonstrates, for the first time, the potential of Xellulin as versatile tool promoting an in vivo-like phenotype in primary and propagated cell culture.
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Affiliation(s)
- Gerhard Feil
- From the ‡Xellutec GmbH, Eichenstraβe 15, 82061 Neuried, Germany
| | - Ralf Horres
- §GenXPro GmbH, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Julia Schulte
- From the ‡Xellutec GmbH, Eichenstraβe 15, 82061 Neuried, Germany
| | - Andreas F Mack
- ¶Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Österbergstraβe 3, 72074 Tübingen, Germany
| | - Svenja Petzoldt
- ‖OmicScouts GmbH, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Caroline Arnold
- **Institute of Physiology and Pathophysiology, Division of Cardiovascular Physiology, University of Heidelberg, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany
| | - Chen Meng
- ‡‡Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Lukas Jost
- §GenXPro GmbH, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | | | | | - Ender Serbest
- From the ‡Xellutec GmbH, Eichenstraβe 15, 82061 Neuried, Germany
| | - Dominic Helm
- ‖OmicScouts GmbH, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Bernhard Kuster
- ‡‡Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany.,§§Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische Universität München, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Isabel Hartmann
- From the ‡Xellutec GmbH, Eichenstraβe 15, 82061 Neuried, Germany
| | - Thomas Korff
- §§Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische Universität München, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Hannes Hahne
- ‖OmicScouts GmbH, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany;
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16
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Ruprecht B, Wang D, Chiozzi RZ, Li LH, Hahne H, Kuster B. Hydrophilic Strong Anion Exchange (hSAX) Chromatography Enables Deep Fractionation of Tissue Proteomes. Methods Mol Biol 2017; 1550:69-82. [PMID: 28188524 DOI: 10.1007/978-1-4939-6747-6_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The bottom-up proteomic analysis of cell line and tissue samples to a depth > 10,000 proteins still represents a considerable challenge because of the sheer number of peptides generated by proteolytic digestions and the high dynamic range of protein expression. As a result, comprehensive protein coverage requires multidimensional peptide separation. Recently, off-line hydrophilic strong cation exchange (hSAX) chromatography has proven its merits for high resolution separation of peptides due to its high degree of orthogonality to reversed-phase liquid chromatography. Here we describe the use of hSAX for the deep analysis of tissue proteomes. The protocol includes optimized sample preparation steps (lysis with the aid of mechanical disruption, one-step disulfide bridge reduction and alkylation), setup and operation of hSAX columns and gradients, desalting of hSAX fractions prior to LC-MS/MS analysis, and suggestions for the choice of data acquisition parameters and data analysis using MaxQuant. Application of the protocol to the fractionation of 300 μg human brain tissue digest led to the identification of more than 100,000 unique peptide sequences representing over 10,195 proteins and 9,500 genes in 3 days of measurement time on a Q Exactive Plus mass spectrometer.
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Affiliation(s)
- Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany
| | - Dongxue Wang
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | | | - Li-Hua Li
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany.
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Biomolecular Mass Spectrometry Center, Technische Universität München, Freising, Germany.
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17
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Yu P, Hahne H, Wilhelm M, Kuster B. Ethylene glycol improves electrospray ionization efficiency in bottom-up proteomics. Anal Bioanal Chem 2016; 409:1049-1057. [PMID: 27766361 DOI: 10.1007/s00216-016-0023-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/09/2016] [Accepted: 10/07/2016] [Indexed: 10/20/2022]
Abstract
Liquid chromatography coupled online to nano-electrospray ionization (nESI) tandem mass spectrometry is the analytical workhorse in the field of proteome research. Dimethyl sulfoxide (DMSO) was recently shown to improve nESI efficiency by a factor of three to ten thus improving the sensitivity and coverage of proteomic experiments. However, relatively few investigations into which solvent additives promote nESI response have been performed at a proteomic scale. Here, we systematically evaluated the concept by screening about 30 compounds with various physico-chemical properties. Detailed further analysis showed that ethylene glycol performed similarly to DMSO and the results indicate that enhancing the nESI response of peptides by simple solvent additives is a valid and promising approach. Ethylene glycol may serve as a viable alternative to DMSO in applications where DMSO has disadvantages. In keeping with nESI theory, the key properties of an effective solvent additive for proteomic applications are a boiling point higher than water, low surface tension, and preferably high polarity for reversed phase LC-MS/MS applications. Graphical Abstract Ethylene glycol substantially improves peptide ionization.
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Affiliation(s)
- Peng Yu
- Technical University of Munich, Emil-Erlenmeyer-Forum-5, 85354, Freising, Germany
| | - Hannes Hahne
- Technical University of Munich, Emil-Erlenmeyer-Forum-5, 85354, Freising, Germany.,OmicScouts GmbH, St.-Valentin-Straße 5, 85356, Freising, Germany
| | - Mathias Wilhelm
- Technical University of Munich, Emil-Erlenmeyer-Forum-5, 85354, Freising, Germany
| | - Bernhard Kuster
- Technical University of Munich, Emil-Erlenmeyer-Forum-5, 85354, Freising, Germany. .,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Gregor-Mendel-Straße 4, 85354, Freising, Germany.
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18
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Hao Y, Colak R, Teyra J, Corbi-Verge C, Ignatchenko A, Hahne H, Wilhelm M, Kuster B, Braun P, Kaida D, Kislinger T, Kim PM. Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins. Cell Rep 2015. [PMID: 26146086 DOI: 10.1016/j.celrep.2015.06.031:183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Alternative splicing acts on transcripts from almost all human multi-exon genes. Notwithstanding its ubiquity, fundamental ramifications of splicing on protein expression remain unresolved. The number and identity of spliced transcripts that form stably folded proteins remain the sources of considerable debate, due largely to low coverage of experimental methods and the resulting absence of negative data. We circumvent this issue by developing a semi-supervised learning algorithm, positive unlabeled learning for splicing elucidation (PULSE; http://www.kimlab.org/software/pulse), which uses 48 features spanning various categories. We validated its accuracy on sets of bona fide protein isoforms and directly on mass spectrometry (MS) spectra for an overall AU-ROC of 0.85. We predict that around 32% of "exon skipping" alternative splicing events produce stable proteins, suggesting that the process engenders a significant number of previously uncharacterized proteins. We also provide insights into the distribution of positive isoforms in various functional classes and into the structural effects of alternative splicing.
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Affiliation(s)
- Yanqi Hao
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1AS, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Recep Colak
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1AS, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Joan Teyra
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1AS, Canada
| | - Carles Corbi-Verge
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1AS, Canada
| | - Alexander Ignatchenko
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Hannes Hahne
- Chair for Proteomics and Bioanalytics, TU Muenchen, Freising 85354, Germany
| | - Mathias Wilhelm
- Chair for Proteomics and Bioanalytics, TU Muenchen, Freising 85354, Germany
| | - Bernhard Kuster
- Chair for Proteomics and Bioanalytics, TU Muenchen, Freising 85354, Germany; German Cancer Consortium (DKTK), Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Center for Integrated Protein Science Munich, Munich, Germany; Bavarian Biomolecular Mass Spectrometry Center, Technische Universität München, Freising, Germany
| | - Pascal Braun
- Lehrstuhl fuer Systembiologie der Pflanzen, TU Muenchen, Munich, Germany
| | - Daisuke Kaida
- Frontier Research Core for Life Sciences, University of Toyama, Toyama 930-8555, Japan
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5T 2M9, Canada
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1AS, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1AS, Canada.
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19
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Hao Y, Colak R, Teyra J, Corbi-Verge C, Ignatchenko A, Hahne H, Wilhelm M, Kuster B, Braun P, Kaida D, Kislinger T, Kim PM. Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins. Cell Rep 2015; 12:183-9. [PMID: 26146086 DOI: 10.1016/j.celrep.2015.06.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 02/18/2015] [Accepted: 06/09/2015] [Indexed: 12/30/2022] Open
Abstract
Alternative splicing acts on transcripts from almost all human multi-exon genes. Notwithstanding its ubiquity, fundamental ramifications of splicing on protein expression remain unresolved. The number and identity of spliced transcripts that form stably folded proteins remain the sources of considerable debate, due largely to low coverage of experimental methods and the resulting absence of negative data. We circumvent this issue by developing a semi-supervised learning algorithm, positive unlabeled learning for splicing elucidation (PULSE; http://www.kimlab.org/software/pulse), which uses 48 features spanning various categories. We validated its accuracy on sets of bona fide protein isoforms and directly on mass spectrometry (MS) spectra for an overall AU-ROC of 0.85. We predict that around 32% of "exon skipping" alternative splicing events produce stable proteins, suggesting that the process engenders a significant number of previously uncharacterized proteins. We also provide insights into the distribution of positive isoforms in various functional classes and into the structural effects of alternative splicing.
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Affiliation(s)
- Yanqi Hao
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1AS, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Recep Colak
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1AS, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Joan Teyra
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1AS, Canada
| | - Carles Corbi-Verge
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1AS, Canada
| | - Alexander Ignatchenko
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Hannes Hahne
- Chair for Proteomics and Bioanalytics, TU Muenchen, Freising 85354, Germany
| | - Mathias Wilhelm
- Chair for Proteomics and Bioanalytics, TU Muenchen, Freising 85354, Germany
| | - Bernhard Kuster
- Chair for Proteomics and Bioanalytics, TU Muenchen, Freising 85354, Germany; German Cancer Consortium (DKTK), Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Center for Integrated Protein Science Munich, Munich, Germany; Bavarian Biomolecular Mass Spectrometry Center, Technische Universität München, Freising, Germany
| | - Pascal Braun
- Lehrstuhl fuer Systembiologie der Pflanzen, TU Muenchen, Munich, Germany
| | - Daisuke Kaida
- Frontier Research Core for Life Sciences, University of Toyama, Toyama 930-8555, Japan
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5T 2M9, Canada
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1AS, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1AS, Canada.
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20
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Savitski MM, Wilhelm M, Hahne H, Kuster B, Bantscheff M. A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets. Mol Cell Proteomics 2015; 14:2394-404. [PMID: 25987413 DOI: 10.1074/mcp.m114.046995] [Citation(s) in RCA: 280] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Indexed: 02/06/2023] Open
Abstract
Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological and technical heterogeneity in proteomic experiments further add to the challenge and there are strong differences in opinion regarding the conceptual validity of a protein FDR and no consensus regarding the methodology for protein FDR determination. There are also limitations inherent to the widely used classic target-decoy strategy that particularly show when analyzing very large data sets and that lead to a strong over-representation of decoy identifications. In this study, we investigated the merits of the classic, as well as a novel target-decoy-based protein FDR estimation approach, taking advantage of a heterogeneous data collection comprised of ∼19,000 LC-MS/MS runs deposited in ProteomicsDB (https://www.proteomicsdb.org). The "picked" protein FDR approach treats target and decoy sequences of the same protein as a pair rather than as individual entities and chooses either the target or the decoy sequence depending on which receives the highest score. We investigated the performance of this approach in combination with q-value based peptide scoring to normalize sample-, instrument-, and search engine-specific differences. The "picked" target-decoy strategy performed best when protein scoring was based on the best peptide q-value for each protein yielding a stable number of true positive protein identifications over a wide range of q-value thresholds. We show that this simple and unbiased strategy eliminates a conceptual issue in the commonly used "classic" protein FDR approach that causes overprediction of false-positive protein identification in large data sets. The approach scales from small to very large data sets without losing performance, consistently increases the number of true-positive protein identifications and is readily implemented in proteomics analysis software.
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Affiliation(s)
| | - Mathias Wilhelm
- §Chair for Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany; ¶SAP SE, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany
| | - Hannes Hahne
- §Chair for Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Bernhard Kuster
- §Chair for Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany; ‖Center for Integrated Protein Science Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Marcus Bantscheff
- From the ‡Cellzome GmbH, Meyerhofstrasse 1, 69117 Heidelberg, Germany;
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21
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Schurr BC, Hahne H, Kuster B, Behr J, Vogel RF. Molecular mechanisms behind the antimicrobial activity of hop iso-α-acids in Lactobacillus brevis. Food Microbiol 2014; 46:553-563. [PMID: 25475328 DOI: 10.1016/j.fm.2014.09.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [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: 06/10/2014] [Revised: 09/24/2014] [Accepted: 09/28/2014] [Indexed: 11/30/2022]
Abstract
The main bittering component in beer, hop iso-α-acids, have been characterised as weak acids, which act as ionophores impairing microbial cells' function under acidic conditions as present in beer. Besides medium pH, divalent cations play a central role regarding the efficacy of the antimicrobial effect. The iso-α-acids' non-bitter derivatives humulinic acids can be found in isomerised hop extracts and can be generated during hop storage. Therefore, they have been under investigation concerning their influence on beer sensory properties. This study sketches the molecular mechanism behind iso-α-acids' antimicrobial activity in Lactobacillus (L.) brevis regarding their ionophore activity versus the dependence of the inhibitory potential on manganese binding, and suggests humulinic acids as novel tasteless food preservatives. We designed and synthesised chemically modified iso-α-acids to enhance the basic understanding of the molecular mechanism of antimicrobial iso-α-acids. It could be observed that a manganese-binding dependent transmembrane redox reaction (oxidative stress) plays a crucial role in inhibition. Privation of an acidic hydroxyl group neither erased ionophore activity, nor did it entirely abolish antimicrobial activity. Humulinic acids proved to be highly inhibitory, even outperforming iso-α-acids.
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Affiliation(s)
- Benjamin C Schurr
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, 85354 Freising, Germany
| | - Hannes Hahne
- Chair for Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Bernhard Kuster
- Chair for Proteomics and Bioanalytics, Technische Universität München, Freising, Germany; Center for Integrated Protein Science Munich, Germany
| | - Jürgen Behr
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, 85354 Freising, Germany.
| | - Rudi F Vogel
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, 85354 Freising, Germany
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22
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Helm D, Vissers JPC, Hughes CJ, Hahne H, Ruprecht B, Pachl F, Grzyb A, Richardson K, Wildgoose J, Maier SK, Marx H, Wilhelm M, Becher I, Lemeer S, Bantscheff M, Langridge JI, Kuster B. Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics. Mol Cell Proteomics 2014; 13:3709-15. [PMID: 25106551 DOI: 10.1074/mcp.m114.041038] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
One of the limiting factors in determining the sensitivity of tandem mass spectrometry using hybrid quadrupole orthogonal acceleration time-of-flight instruments is the duty cycle of the orthogonal ion injection system. As a consequence, only a fraction of the generated fragment ion beam is collected by the time-of-flight analyzer. Here we describe a method utilizing postfragmentation ion mobility spectrometry of peptide fragment ions in conjunction with mobility time synchronized orthogonal ion injection leading to a substantially improved duty cycle and a concomitant improvement in sensitivity of up to 10-fold for bottom-up proteomic experiments. This enabled the identification of 7500 human proteins within 1 day and 8600 phosphorylation sites within 5 h of LC-MS/MS time. The method also proved powerful for multiplexed quantification experiments using tandem mass tags exemplified by the chemoproteomic interaction analysis of histone deacetylases with Trichostatin A.
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Affiliation(s)
- Dominic Helm
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | | | - Hannes Hahne
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Benjamin Ruprecht
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Fiona Pachl
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | | | | | - Stefan K Maier
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Harald Marx
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Mathias Wilhelm
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | - Simone Lemeer
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | | | - Bernhard Kuster
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany; ‖Center for Integrated Protein Science Munich, Germany
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23
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Wilhelm M, Schlegl J, Hahne H, Gholami AM, Lieberenz M, Savitski MM, Ziegler E, Butzmann L, Gessulat S, Marx H, Mathieson T, Lemeer S, Schnatbaum K, Reimer U, Wenschuh H, Mollenhauer M, Slotta-Huspenina J, Boese JH, Bantscheff M, Gerstmair A, Faerber F, Kuster B. Mass-spectrometry-based draft of the human proteome. Nature 2014; 509:582-7. [PMID: 24870543 DOI: 10.1038/nature13319] [Citation(s) in RCA: 1321] [Impact Index Per Article: 132.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 04/11/2014] [Indexed: 12/15/2022]
Abstract
Proteomes are characterized by large protein-abundance differences, cell-type- and time-dependent expression patterns and post-translational modifications, all of which carry biological information that is not accessible by genomics or transcriptomics. Here we present a mass-spectrometry-based draft of the human proteome and a public, high-performance, in-memory database for real-time analysis of terabytes of big data, called ProteomicsDB. The information assembled from human tissues, cell lines and body fluids enabled estimation of the size of the protein-coding genome, and identified organ-specific proteins and a large number of translated lincRNAs (long intergenic non-coding RNAs). Analysis of messenger RNA and protein-expression profiles of human tissues revealed conserved control of protein abundance, and integration of drug-sensitivity data enabled the identification of proteins predicting resistance or sensitivity. The proteome profiles also hold considerable promise for analysing the composition and stoichiometry of protein complexes. ProteomicsDB thus enables navigation of proteomes, provides biological insight and fosters the development of proteomic technology.
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Affiliation(s)
- Mathias Wilhelm
- 1] Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany [2] SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany [3]
| | - Judith Schlegl
- 1] SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany [2]
| | - Hannes Hahne
- 1] Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany [2]
| | - Amin Moghaddas Gholami
- 1] Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany [2]
| | | | | | | | - Lars Butzmann
- SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany
| | | | - Harald Marx
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Toby Mathieson
- Cellzome GmbH, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | | | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstraße 5, 12489 Berlin, Germany
| | - Holger Wenschuh
- JPT Peptide Technologies GmbH, Volmerstraße 5, 12489 Berlin, Germany
| | - Martin Mollenhauer
- Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675 München, Germany
| | - Julia Slotta-Huspenina
- Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675 München, Germany
| | | | | | | | - Franz Faerber
- SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany
| | - Bernhard Kuster
- 1] Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany [2] Center for Integrated Protein Science Munich, Germany
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Haedke UR, Frommel SC, Hansen F, Hahne H, Kuster B, Bogyo M, Verhelst SHL. Phosphoramidates as Novel Activity-Based Probes for Serine Proteases. Chembiochem 2014; 15:1106-10. [DOI: 10.1002/cbic.201400013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Indexed: 01/06/2023]
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25
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Pauly M, Sroka M, Reiss J, Rinke G, Albarghash A, Vogelgesang R, Hahne H, Kuster B, Sesterhenn J, Kern K, Rauschenbach S. A hydrodynamically optimized nano-electrospray ionization source and vacuum interface. Analyst 2014; 139:1856-67. [DOI: 10.1039/c3an01836a] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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26
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Weis C, Pfeilmeier S, Glawischnig E, Isono E, Pachl F, Hahne H, Kuster B, Eichmann R, Hückelhoven R. Co-immunoprecipitation-based identification of putative BAX INHIBITOR-1-interacting proteins involved in cell death regulation and plant-powdery mildew interactions. Mol Plant Pathol 2013; 14:791-802. [PMID: 23782494 PMCID: PMC6638788 DOI: 10.1111/mpp.12050] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The endoplasmic reticulum (ER)-resident BAX INHIBITOR-1 (BI-1) protein is one of a few cell death suppressors known to be conserved in animals and plants. The function of BI-1 proteins in response to various biotic and abiotic stress factors is well established. However, little is known about the underlying mechanisms. We conducted co-immunoprecipitation (co-IP) experiments to identify Arabidopsis thaliana BI-1-interacting proteins to obtain a potentially better understanding of how BI-1 functions during plant-pathogen interactions and as a suppressor of cell death. Liquid chromatography and tandem mass spectrometry (LC-MS/MS) identified 95 proteins co-immunoprecipitated with green fluorescing protein (GFP)-tagged BI-1. Five selected candidate proteins, a RIBOPHORIN II (RPN2) family protein, VACUOLAR ATP SYNTHASE SUBUNIT A (VHA-A), cytochrome P450 83A1 (CYP83A1), H(+) -ATPASE 1 (AHA1) and PROHIBITIN 2 (PHB2), were further investigated with regard to their role in BI-1-associated processes. To this end, we analysed a set of Arabidopsis mutants in the interaction with the adapted powdery mildew fungus Erysiphe cruciferarum and on cell death-inducing treatments. Two independent rpn2 knock-down mutants tended to better support powdery mildew, and a phb2 mutant showed altered responses to cell death-inducing Alternaria alternata f.sp. lycopersici (AAL) toxin treatment. Two independent cyp83a1 mutants showed a strong powdery mildew resistance phenotype and enhanced sensitivity to AAL toxin. Moreover, co-localization studies and fluorescence resonance energy transfer (FRET) experiments suggested a direct interaction of BI-1 with CYP83A1 at the ER.
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Affiliation(s)
- Corina Weis
- Lehrstuhl für Phytopathologie, Technische Universität München, 85354 Freising, Germany
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27
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Hahne H, Pachl F, Ruprecht B, Maier SK, Klaeger S, Helm D, Médard G, Wilm M, Lemeer S, Kuster B. DMSO enhances electrospray response, boosting sensitivity of proteomic experiments. Nat Methods 2013; 10:989-91. [DOI: 10.1038/nmeth.2610] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 07/15/2013] [Indexed: 11/09/2022]
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28
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Gholami A, Hahne H, Wu Z, Auer F, Meng C, Wilhelm M, Kuster B. Global Proteome Analysis of the NCI-60 Cell Line Panel. Cell Rep 2013; 4:609-20. [DOI: 10.1016/j.celrep.2013.07.018] [Citation(s) in RCA: 244] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 05/23/2013] [Accepted: 07/18/2013] [Indexed: 12/12/2022] Open
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29
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Maier SK, Hahne H, Gholami AM, Balluff B, Meding S, Schoene C, Walch AK, Kuster B. Comprehensive identification of proteins from MALDI imaging. Mol Cell Proteomics 2013; 12:2901-10. [PMID: 23782541 DOI: 10.1074/mcp.m113.027599] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful tool for the visualization of proteins in tissues and has demonstrated considerable diagnostic and prognostic value. One main challenge is that the molecular identity of such potential biomarkers mostly remains unknown. We introduce a generic method that removes this issue by systematically identifying the proteins embedded in the MALDI matrix using a combination of bottom-up and top-down proteomics. The analyses of ten human tissues lead to the identification of 1400 abundant and soluble proteins constituting the set of proteins detectable by MALDI IMS including >90% of all IMS biomarkers reported in the literature. Top-down analysis of the matrix proteome identified 124 mostly N- and C-terminally fragmented proteins indicating considerable protein processing activity in tissues. All protein identification data from this study as well as the IMS literature has been deposited into MaTisse, a new publically available database, which we anticipate will become a valuable resource for the IMS community.
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Affiliation(s)
- Stefan K Maier
- Chair for Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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30
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Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DMF, Agnew B, Kuster B. Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry. J Proteome Res 2013; 12:927-36. [PMID: 23301498 DOI: 10.1021/pr300967y] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The post-translational modification of proteins with N-acetylglucosamine (O-GlcNAc) is involved in the regulation of a wide variety of cellular processes and associated with a number of chronic diseases. Despite its emerging biological significance, the systematic identification of O-GlcNAc proteins is still challenging. In the present study, we demonstrate a significantly improved O-GlcNAc protein enrichment procedure, which exploits metabolic labeling of cells by azide-modified GlcNAc and copper-mediated Click chemistry for purification of modified proteins on an alkyne-resin. On-resin proteolysis using trypsin followed by LC-MS/MS afforded the identification of around 1500 O-GlcNAc proteins from a single cell line. Subsequent elution of covalently resin bound O-GlcNAc peptides using selective β-elimination enabled the identification of 185 O-GlcNAc modification sites on 80 proteins. To demonstrate the practical utility of the developed approach, we studied the global effects of the O-GlcNAcase inhibitor GlcNAcstatin G on the level of O-GlcNAc modification of cellular proteins. About 200 proteins including several key players involved in the hexosamine signaling pathway showed significantly increased O-GlcNAcylation levels in response to the drug, which further strengthens the link of O-GlcNAc protein modification to cellular nutrient sensing and response.
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Affiliation(s)
- Hannes Hahne
- Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences, Weihenstephan, Technische Universität München, Freising, Germany
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31
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Abstract
The study of metabolically labeled or probe-modified proteins is an important area in chemical proteomics. Isolation and purification of the protein targets is a necessary step before MS identification. The biotin-streptavidin system is widely used in this process, but the harsh denaturing conditions also release natively biotinylated proteins and non-selectively bound proteins. A cleavable linker strategy is a promising approach for solving this problem. Though several cleavable linkers have been developed and tested, an efficient, easily synthesized, and inexpensive cleavable linker is a desirable addition to the proteomics toolbox. Here, we describe the chemical proteomics application of a vicinal diol cleavable linker. Through easy-to-handle chemistry we incorporate this linker into an activity-based probe and a biotin alkyne tag amenable for bioorthogonal ligation. With these reagents, background protein identifications are significantly reduced relative to standard on-bead digestion.
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Affiliation(s)
- Yinliang Yang
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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32
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Abstract
Phosphorylated O-GlcNAc is a novel post-translational modification that has so far only been found on the neuronal protein AP180 from the rat (Graham et al., J. Proteome Res. 2011, 10, 2725-2733). Upon collision induced dissociation, the modification generates a highly mass deficient fragment ion (m/z 284.0530) that can be used as a reporter for the identification of phosphorylated O-GlcNAc. Using a publically available mouse brain phosphoproteome data set, we employed our recently developed Oscore software to re-evaluate high resolution/high accuracy tandem mass spectra and discovered the modification on 23 peptides corresponding to 11 mouse proteins. The systematic analysis of 220 candidate phosphoGlcNAc tandem mass spectra as well as a synthetic standard enabled the dissection of the major phosphoGlcNAc fragmentation pathways, suggesting that the modification is O-GlcNAc-6-phosphate. We find that the classical O-GlcNAc modification often exists on the same peptides indicating that O-GlcNAc-6-phosphate may biosynthetically arise in two steps involving the O-GlcNAc transferase and a currently unknown kinase. Many of the identified proteins are involved in synaptic transmission and for Ca(2+)/calmodulin kinase IV, the O-GlcNAc-6-phosphate modification was found in the vicinity of two autophosphorylation sites required for full activation of the kinase suggesting a potential regulatory role for O-GlcNAc-6-phosphate. By re-analyzing mass spectrometric data from human embryonic and induced pluripotent stem cells, our study also identified Zinc finger protein 462 (ZNF462) as the first human O-GlcNAc-6-phosphate modified protein. Collectively, the data suggests that O-GlcNAc-6-phosphate is a general post-translation modification of mammalian proteins with a variety of possible cellular functions.
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Affiliation(s)
- Hannes Hahne
- Center of Life and Food Sciences Weihenstephan, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
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Grüner BM, Hahne H, Mazur PK, Trajkovic-Arsic M, Maier S, Esposito I, Kalideris E, Michalski CW, Kleeff J, Rauser S, Schmid RM, Küster B, Walch A, Siveke JT. MALDI imaging mass spectrometry for in situ proteomic analysis of preneoplastic lesions in pancreatic cancer. PLoS One 2012; 7:e39424. [PMID: 22761793 PMCID: PMC3383687 DOI: 10.1371/journal.pone.0039424] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [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: 01/15/2012] [Accepted: 05/20/2012] [Indexed: 01/07/2023] Open
Abstract
The identification of new biomarkers for preneoplastic pancreatic lesions (PanINs, IPMNs) and early pancreatic ductal adenocarcinoma (PDAC) is crucial due to the diseases high mortality rate upon late detection. To address this task we used the novel technique of matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) on genetically engineered mouse models (GEM) of pancreatic cancer. Various GEM were analyzed with MALDI IMS to investigate the peptide/protein-expression pattern of precursor lesions in comparison to normal pancreas and PDAC with cellular resolution. Statistical analysis revealed several discriminative m/z-species between normal and diseased tissue. Intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasm (IPMN) could be distinguished from normal pancreatic tissue and PDAC by 26 significant m/z-species. Among these m/z-species, we identified Albumin and Thymosin-beta 4 by liquid chromatography and tandem mass spectrometry (LC-MS/MS), which were further validated by immunohistochemistry, western blot, quantitative RT-PCR and ELISA in both murine and human tissue. Thymosin-beta 4 was found significantly increased in sera of mice with PanIN lesions. Upregulated PanIN expression of Albumin was accompanied by increased expression of liver-restricted genes suggesting a hepatic transdifferentiation program of preneoplastic cells. In conclusion we show that GEM of endogenous PDAC are a suitable model system for MALDI-IMS and subsequent LC-MS/MS analysis, allowing in situ analysis of small precursor lesions and identification of differentially expressed peptides and proteins.
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Affiliation(s)
- Barbara M. Grüner
- II. Medizinische Klinik, Technische Universität München, Munich, Germany
| | - Hannes Hahne
- Chair of Proteomics and Bioanalytics, Center of Life and Food Sciences, Technische Universität München, Munich, Germany
| | - Pawel K. Mazur
- II. Medizinische Klinik, Technische Universität München, Munich, Germany
| | | | - Stefan Maier
- Chair of Proteomics and Bioanalytics, Center of Life and Food Sciences, Technische Universität München, Munich, Germany
- Institute of Pathology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Irene Esposito
- Institute of Pathology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Evdokia Kalideris
- II. Medizinische Klinik, Technische Universität München, Munich, Germany
| | | | - Jörg Kleeff
- Department of Surgery, Technische Universität München, Munich, Germany
| | - Sandra Rauser
- Institute of Pathology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Roland M. Schmid
- II. Medizinische Klinik, Technische Universität München, Munich, Germany
| | - Bernhard Küster
- Chair of Proteomics and Bioanalytics, Center of Life and Food Sciences, Technische Universität München, Munich, Germany
- Center for Integrated Protein Science Munich, Munich, Germany
| | - Axel Walch
- Institute of Pathology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Jens T. Siveke
- II. Medizinische Klinik, Technische Universität München, Munich, Germany
- * E-mail:
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Abstract
The attachment of N-acetylglucosamine to serine or threonine residues (O-GlcNAc) is a post-translational modification on nuclear and cytoplasmic proteins with emerging roles in numerous cellular processes, such as signal transduction, transcription, and translation. It is further presumed that O-GlcNAc can exhibit a site-specific, dynamic and possibly functional interplay with phosphorylation. O-GlcNAc proteins are commonly identified by tandem mass spectrometry following some form of biochemical enrichment. In the present study, we assessed if, and to which extent, O-GlcNAc-modified proteins can be discovered from existing large-scale proteome data sets. To this end, we conceived a straightforward O-GlcNAc identification strategy based on our recently developed Oscore software that automatically analyzes tandem mass spectra for the presence and intensity of O-GlcNAc diagnostic fragment ions. Using the Oscore, we discovered hundreds of O-GlcNAc peptides not initially identified in these studies, and most of which have not been described before. Merely re-searching this data extended the number of known O-GlcNAc proteins by almost 100 suggesting that this modification exists even more widely than previously anticipated and the modification is often sufficiently abundant to be detected without enrichment. However, a comparison of O-GlcNAc and phospho-identifications from the very same data indicates that the O-GlcNAc modification is considerably less abundant than phosphorylation. The discovery of numerous doubly modified peptides (i.e. peptides with one or multiple O-GlcNAc or phosphate moieties), suggests that O-GlcNAc and phosphorylation are not necessarily mutually exclusive, but can occur simultaneously at adjacent sites.
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Affiliation(s)
- Hannes Hahne
- Center of Life and Food Sciences Weihenstephan, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
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35
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Hahne H, Neubert P, Kuhn K, Etienne C, Bomgarden R, Rogers JC, Kuster B. Carbonyl-Reactive Tandem Mass Tags for the Proteome-Wide Quantification of N-Linked Glycans. Anal Chem 2012; 84:3716-24. [DOI: 10.1021/ac300197c] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hannes Hahne
- Chair for Proteomics
and Bioanalytics,
Center of Life and Food Sciences Weihenstephan, Technische Universität München, Emil-Erlenmeyer-Forum
5, 85354 Freising, Germany
| | - Patrick Neubert
- Chair for Proteomics
and Bioanalytics,
Center of Life and Food Sciences Weihenstephan, Technische Universität München, Emil-Erlenmeyer-Forum
5, 85354 Freising, Germany
| | - Karsten Kuhn
- Proteome Sciences R&D GmbH & Co. KG, Frankfurt am Main, Germany
| | - Chris Etienne
- Thermo Scientific Pierce Protein
Research, Thermo Fisher Scientific, Rockford,
Illinois 61105, United States
| | - Ryan Bomgarden
- Thermo Scientific Pierce Protein
Research, Thermo Fisher Scientific, Rockford,
Illinois 61105, United States
| | - John C. Rogers
- Thermo Scientific Pierce Protein
Research, Thermo Fisher Scientific, Rockford,
Illinois 61105, United States
| | - Bernhard Kuster
- Chair for Proteomics
and Bioanalytics,
Center of Life and Food Sciences Weihenstephan, Technische Universität München, Emil-Erlenmeyer-Forum
5, 85354 Freising, Germany
- Center for Integrated Protein Science Munich, Emil-Erlenmeyer-Forum 5, 85354
Freising, Germany
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Abstract
Proteomics is turning more and more towards quantitative measurements of biological systems. This in turn has spurred the development of numerous experimental methods that enable such measurements. Vast quantities of mostly mass spectrometric data are often generated as a result which requires the use of software tools that turns raw data into useful quantitative information from which knowledge about the biological system can eventually be derived. This chapter gives a brief overview of available software tools for mass spectrometry based quantitative proteomics.
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Affiliation(s)
- Simone Lemeer
- Chair of Proteomcis and Bioanalytics, Technische Universität München, Freising, Germany
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37
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Steck N, Hoffmann M, Sava IG, Kim SC, Hahne H, Tonkonogy SL, Mair K, Krueger D, Pruteanu M, Shanahan F, Vogelmann R, Schemann M, Kuster B, Sartor RB, Haller D. Enterococcus faecalis metalloprotease compromises epithelial barrier and contributes to intestinal inflammation. Gastroenterology 2011; 141:959-71. [PMID: 21699778 DOI: 10.1053/j.gastro.2011.05.035] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 05/01/2011] [Accepted: 05/12/2011] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS Matrix metalloproteases (MMPs) mediate pathogenesis of chronic intestinal inflammation. We characterized the role of the gelatinase (GelE), a metalloprotease from Enterococcus faecalis, in the development of colitis in mice. METHODS Germ-free, interleukin-10-deficient (IL-10(-/-)) mice were monoassociated with the colitogenic E faecalis strain OG1RF and isogenic, GelE-mutant strains. Barrier function was determined by measuring E-cadherin expression, transepithelial electrical resistance (TER), and translocation of permeability markers in colonic epithelial cells and colon segments from IL-10(-/-) and TNF(ΔARE/Wt) mice. GelE specificity was shown with the MMP inhibitor marimastat. RESULTS Histologic analysis (score 0-4) of E faecalis monoassociated IL-10(-/-) mice revealed a significant reduction in colonic tissue inflammation in the absence of bacteria-derived GelE. We identified cleavage sites for GelE in the sequence of recombinant mouse E-cadherin, indicating that it might be degraded by GelE. Experiments with Ussing chambers and purified GelE revealed the loss of barrier function and extracellular E-cadherin in mice susceptible to intestinal inflammation (IL-10(-/-) and TNF(ΔARE/Wt) mice) before inflammation developed. Colonic epithelial cells had reduced TER and increased translocation of permeability markers after stimulation with GelE from OG1RF or strains of E faecalis isolated from patients with Crohn's disease and ulcerative colitis. CONCLUSIONS The metalloprotease GelE, produced by commensal strains of E faecalis, contributes to development of chronic intestinal inflammation in mice that are susceptible to intestinal inflammation (IL-10(-/-) and TNF(ΔARE/Wt) mice) by impairing epithelial barrier integrity.
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Affiliation(s)
- Natalie Steck
- Chair for Biofunctionality, ZIEL-Research Center for Nutrition and Food Science, CDD Center for Diet and Disease, Technische Universität München, Freising-Weihenstephan, Germany
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38
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Pohl S, Tu WY, Aldridge PD, Gillespie C, Hahne H, Mäder U, Read TD, Harwood CR. Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis
to oxidative stress. Proteomics 2011; 11:3036-55. [DOI: 10.1002/pmic.201100085] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/28/2011] [Accepted: 04/05/2011] [Indexed: 11/12/2022]
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Albaum SP, Hahne H, Otto A, Haußmann U, Becher D, Poetsch A, Goesmann A, Nattkemper TW. A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study. Proteome Sci 2011; 9:30. [PMID: 21663690 PMCID: PMC3142201 DOI: 10.1186/1477-5956-9-30] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 06/11/2011] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Mass spectrometry-based proteomics has reached a stage where it is possible to comprehensively analyze the whole proteome of a cell in one experiment. Here, the employment of stable isotopes has become a standard technique to yield relative abundance values of proteins. In recent times, more and more experiments are conducted that depict not only a static image of the up- or down-regulated proteins at a distinct time point but instead compare developmental stages of an organism or varying experimental conditions. RESULTS Although the scientific questions behind these experiments are of course manifold, there are, nevertheless, two questions that commonly arise: 1) which proteins are differentially regulated regarding the selected experimental conditions, and 2) are there groups of proteins that show similar abundance ratios, indicating that they have a similar turnover? We give advice on how these two questions can be answered and comprehensively compare a variety of commonly applied computational methods and their outcomes. CONCLUSIONS This work provides guidance through the jungle of computational methods to analyze mass spectrometry-based isotope-labeled datasets and recommends an effective and easy-to-use evaluation strategy. We demonstrate our approach with three recently published datasets on Bacillus subtilis 12 and Corynebacterium glutamicum 3. Special focus is placed on the application and validation of cluster analysis methods. All applied methods were implemented within the rich internet application QuPE 4. Results can be found at http://qupe.cebitec.uni-bielefeld.de.
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Affiliation(s)
- Stefan P Albaum
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University,
Germany
- Biodata Mining Group, Faculty of Technology, Bielefeld University, Germany
| | - Hannes Hahne
- Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences
Weihenstephan, Technische Universität München, Germany
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, Germany
- Current Address: Chair for Proteomics and Bioanalytics, Center of Life and Food
Sciences Weihenstephan, Technische Universität München, Germany
| | - Andreas Otto
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, Germany
| | - Ute Haußmann
- Plant Biochemistry, Ruhr University Bochum, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, Germany
| | | | - Alexander Goesmann
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University,
Germany
- Bioinformatics Resource Facility, CeBiTec, Bielefeld University, Germany
| | - Tim W Nattkemper
- Biodata Mining Group, Faculty of Technology, Bielefeld University, Germany
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40
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Hahne H, Kuster B. A novel two-stage tandem mass spectrometry approach and scoring scheme for the identification of O-GlcNAc modified peptides. J Am Soc Mass Spectrom 2011; 22:931-942. [PMID: 21472528 DOI: 10.1007/s13361-011-0107-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 02/16/2011] [Accepted: 02/21/2011] [Indexed: 05/30/2023]
Abstract
The modification of serine and threonine residues in proteins by a single N-acetylglucosamine (O-GlcNAc) residue is an emerging post-translational modification (PTM) with broad biological implications. However, the systematic or large-scale analysis of this PTM is hampered by several factors, including low stoichiometry and the lability of the O-glycosidic bond during tandem mass spectrometry. Using a library of 72 synthetic glycopeptides, we developed a two-stage tandem MS approach consisting of pulsed Q dissociation (PQD) for O-GlcNAc peptide detection and electron transfer dissociation (ETD) for identification and site localization. Based on a set of O-GlcNAc specific fragment ions, we further developed a score (OScore) that discriminates O-GlcNAc peptide spectra from spectra of unmodified peptides with 95% sensitivity and >99% specificity. Integrating the OScore into the two-stage LC-MS/MS approach detected O-GlcNAc peptides in the low fmol range and at 10-fold better sensitivity than a single data-dependent ETD tandem MS experiment.
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Affiliation(s)
- Hannes Hahne
- Department of Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
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Friedrich L, Stangl S, Hahne H, Küster B, Köhler P, Multhoff G, Skerra A. Bacterial production and functional characterization of the Fab fragment of the murine IgG1/lambda monoclonal antibody cmHsp70.1, a reagent for tumour diagnostics. Protein Eng Des Sel 2010; 23:161-8. [PMID: 20123884 DOI: 10.1093/protein/gzp095] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hsp70, the major stress-inducible member of the 70 kDa heat shock protein family, is frequently exposed on the plasma membrane of human tumours and, even more pronounced, on metastases but not detectable on normal tissues. The mouse monoclonal antibody cmHsp70.1, which recognizes a peptide epitope in the C-terminal substrate binding domain of both human and murine Hsp70, provides a promising reagent for the monitoring of Hsp70-positive tumours during cancer therapy. Here, we describe the variable domain sequences of the antibody produced by the hybridoma cell line and attempts to secrete the corresponding recombinant Fab fragment in Escherichia coli. Initially, the yield of soluble functional Fab fragment that could be purified from the periplasmic cell extract was extremely low, even when preparing different chimeric versions with constant domains of human or murine origin or with the light chain constant domain belonging to the kappa or lambda class. Surprisingly, this yield could be raised dramatically by more than a factor 100 in the presence of the folding helper plasmid pTUM4, which overexpresses two periplasmic disulphide oxido-reductases as well as two chaperones with proline-cis/trans-isomerase activity. Thus, more than 15 mg functional recombinant Fab fragment could be purified per litre E.coli culture from a bench top fermenter. This Fab fragment showed high and specific Hsp70 binding activity in ELISA and SPR measurements, revealing a dissociation constant of 35 nM. Notably, the Fab fragment sensitively recognizes the membrane-associated Hsp70 on tumour cell lines both in immunofluorescence microscopy and flow cytometry, thus showing potential for tumour detection in vitro and in vivo.
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Affiliation(s)
- Lars Friedrich
- Munich Center for Integrated Protein Science and Lehrstuhl für Biologische Chemie, Technische Universität München, München, Germany
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Hahne H, Wolff S, Hecker M, Becher D. From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 2009; 8:4123-36. [PMID: 18763711 DOI: 10.1002/pmic.200800258] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The analysis of integral membrane proteins (IMPs) with mass spectrometry-centered technologies has undergone great progress during the past few years, allowing for the analysis of several hundreds of IMPs. In this study, we investigated three promising shotgun approaches for the identification of IMPs of the model organism Bacillus subtilis. One comprises a classical membrane preparation procedure with carbonate and high-ionic-strength buffers, followed by SDS-PAGE and LC-MS/MS analysis. The two others are based on enzymatic trimming of the crude membrane fraction either with trypsin or proteinase K and subsequent gel-free analysis. As a result, we observed the highest degree of complementarity between the gel-based and the proteinase K approach, since the first exclusively addresses soluble loops and domains of IMPs and gave rise to 8709 unique peptides, whereas the latter contributed 1180 unique peptide identifications from otherwise inaccessible transmembrane helices (TMHs). All three methods contribute significant numbers (381, 284, and 276, respectively) to the total of 527 IMP identifications from the membrane fraction of exponentially growing B. subtilis cells, thus representing approximately 69% of all transcribed IMPs.
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Affiliation(s)
- Hannes Hahne
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
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Wolff S, Hahne H, Hecker M, Becher D. Complementary analysis of the vegetative membrane proteome of the human pathogen Staphylococcus aureus. Mol Cell Proteomics 2008; 7:1460-8. [PMID: 18460691 DOI: 10.1074/mcp.m700554-mcp200] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The Gram-positive bacterium Staphylococcus aureus is a serious human pathogen causing a wide variety of diseases, and its increasing resistance toward all available antibiotics makes its further investigation absolutely essential. We examined the membrane proteome of exponentially growing cells of S. aureus COL because this subproteome plays a major role in the virulence of the bacterium in its host. In general, an analysis of membrane proteins is impeded by their hydrophobic nature as well as by a high abundance of many cytosolic proteins. The implementation of three different technologies, one-dimensional gel-LC, two-dimensional LC, and a membrane shaving approach combined with MS/MS analyses, enabled an identification of 271 integral and 86 peripheral membrane proteins from exponentially growing cells. In particular, the latter approach that combined membrane shaving with a subsequent chymotrypsin digest of integral membrane domains of proteins greatly facilitated the detection of hydrophobic peptides derived from membrane-spanning segments (713 peptides, 60% of all peptides) and therefore yielded almost exclusively highly hydrophobic integral membrane proteins (96.7%). A comparison of the various methods disclosed the one-dimensional gel-LC and the shaving approach to be highly complementary techniques. A combination of them will reveal a most comprehensive view on membrane proteomes.
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Affiliation(s)
- Susanne Wolff
- Institute for Microbiology, Ernst Moritz Arndt University, D-17489 Greifswald, Germany
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Giannadakis K, Gehling H, Sitter H, Achenbach S, Hahne H, Gotzen L. [Is a general pharmacologic thromboembolism prophylaxis necessary in ambulatory treatment by plaster cast immobilization in lower limb injuries?]. Unfallchirurg 2000; 103:475-8. [PMID: 10925650 DOI: 10.1007/s001130050568] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Selected patients with minor lower limb injuries and low risk for deep vein thrombosis (DVT), who required cast immobilizing and did not receive medical thrombosis prophylaxis, were included in a prospective study. The decision to give not medical thrombosis prophylaxis depended on an concept of individualised prophylaxis for patients at risk for thromboembolism. From March 1994 to March 1996 in 178 outpatients (118 men, 60 women, mean age 25.8 [16-39] years) a clinical examination and a colour-coded duplex sonography were performed after removal of the cast for detection of DVT of the lower limb. A phlebography was performed when thrombosis was suspected. Two patients developed a one bundle thrombosis of the calf. Clinical appearance of lung embolism was not observed. These results suggest, that low risk patients with minor injuries of the lower limb and plaster cast immobilisation do not need a medical thrombosis prophylaxis.
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Affiliation(s)
- K Giannadakis
- Klinik für Unfallchirurgie, Philipps-Universität Marburg
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Liappis N, Kochbeck E, Eckhardt G, Hahne H, Kesseler K, Bantzer P. [Amino acid losses in human sweat. Influence of oral contraceptives, physical exercise and sex on the excretion of amino acids in sweat (author's transl)]. Arch Dermatol Res 1980; 269:311-23. [PMID: 7235735 DOI: 10.1007/bf00406425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
UNLABELLED With the aid of ion exchange column chromatography we determined quantitatively the free amino acids in thermal sweat of the total human body surface. Sweat of 60 healthy men and 63 healthy women (aged 18-31 years) collected during 12 min of sauna bathing was investigated. Thirty men and 31 women were well trained, 33 women were taking oral, hormonal contraceptives. Sweat was deproteinised by adding an equal volume of 5% sulphosalicylic acid. RESULTS 1. The comparison of the women taking oral contraceptives with the women not taking oral contraceptives showed no qualitative or significant quantitative differences in the excretion of amino acids in thermal sweat collected from the total body surface. 2. The comparison of the trained women with the untrained women neither revealed qualitative or significant quantitative differences in the excretion of amino acids in thermal sweat collected from the total body surface. 3. As compared to the trained men, untrained men excreted in thermal sweat collected from the total body surface significantly more alanine, arginine, citrulline, cystine, glycine, histidine, isoleucine, leucine, lysine, phenylalanine, serine, threonine, tyrosine, and valine. 4. The sex-specific comparison of the amino acid excretion in sweat showed that men had a significantly increased excretion of cystine, histidine, leucine, and taurine. Proline was detected only in the sweat of women. 5. The quantitative results obtained for the amino acid excretions during 12 min of sauna bathing suggest that persons exposed to hard, physical activity and/or high environmental temperatures have quite equal amino acid losses in sweat and in 24 h urine.
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