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Vennin C, Cattaneo CM, Bosch L, Vegna S, Ma X, Damstra HGJ, Martinovic M, Tsouri E, Ilic M, Azarang L, van Weering JRT, Pulver E, Zeeman AL, Schelfhorst T, Lohuis JO, Rios AC, Dekkers JF, Akkari L, Menezes R, Medema R, Baglio SR, Akhmanova A, Linn SC, Lemeer S, Pegtel DM, Voest EE, van Rheenen J. Taxanes trigger cancer cell killing in vivo by inducing non-canonical T cell cytotoxicity. Cancer Cell 2023; 41:1170-1185.e12. [PMID: 37311414 DOI: 10.1016/j.ccell.2023.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 02/28/2023] [Accepted: 05/11/2023] [Indexed: 06/15/2023]
Abstract
Although treatment with taxanes does not always lead to clinical benefit, all patients are at risk of their detrimental side effects such as peripheral neuropathy. Understanding the in vivo mode of action of taxanes can help design improved treatment regimens. Here, we demonstrate that in vivo, taxanes directly trigger T cells to selectively kill cancer cells in a non-canonical, T cell receptor-independent manner. Mechanistically, taxanes induce T cells to release cytotoxic extracellular vesicles, which lead to apoptosis specifically in tumor cells while leaving healthy epithelial cells intact. We exploit these findings to develop an effective therapeutic approach, based on transfer of T cells pre-treated with taxanes ex vivo, thereby avoiding toxicity of systemic treatment. Our study reveals a different in vivo mode of action of one of the most commonly used chemotherapies, and opens avenues to harness T cell-dependent anti-tumor effects of taxanes while avoiding systemic toxicity.
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Affiliation(s)
- Claire Vennin
- Division of Molecular Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Chiara M Cattaneo
- Oncode Institute, Amsterdam, the Netherlands; Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Leontien Bosch
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081HV Amsterdam, the Netherlands
| | - Serena Vegna
- Oncode Institute, Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Xuhui Ma
- Oncode Institute, Amsterdam, the Netherlands; Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Hugo G J Damstra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584CT Utrecht, the Netherlands
| | - Moreno Martinovic
- Division of Gene Regulation, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Efi Tsouri
- Oncode Institute, Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Mila Ilic
- Oncode Institute, Amsterdam, the Netherlands; Division of Cell Biology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Leyla Azarang
- Biostatistics Centre & Department of Psychosocial Research and Epidemiology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Jan R T van Weering
- Department of Human Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam UMC, 1105AZ Amsterdam, the Netherlands
| | - Emilia Pulver
- Division of Molecular Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Amber L Zeeman
- Oncode Institute, Amsterdam, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC), 3584CT Utrecht, the Netherlands; Princess Maxima Center for Pediatric Oncology, 3584CT Utrecht, the Netherlands
| | - Tim Schelfhorst
- Division of Molecular Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Jeroen O Lohuis
- Division of Molecular Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Anne C Rios
- Oncode Institute, Amsterdam, the Netherlands; Princess Maxima Center for Pediatric Oncology, 3584CT Utrecht, the Netherlands
| | - Johanna F Dekkers
- Oncode Institute, Amsterdam, the Netherlands; Princess Maxima Center for Pediatric Oncology, 3584CT Utrecht, the Netherlands
| | - Leila Akkari
- Oncode Institute, Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Renee Menezes
- Biostatistics Centre & Department of Psychosocial Research and Epidemiology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Rene Medema
- Oncode Institute, Amsterdam, the Netherlands; Division of Cell Biology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Serena R Baglio
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584CT Utrecht, the Netherlands
| | - Sabine C Linn
- Divisions of Molecular Pathology and of Medical Oncology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Department of Pathology, University Medical Center, 1081HV Utrecht, the Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584CT Utrecht, the Netherlands; Netherlands Proteomics Center, 3584CT Utrecht, the Netherlands
| | - Dirk M Pegtel
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081HV Amsterdam, the Netherlands
| | - Emile E Voest
- Oncode Institute, Amsterdam, the Netherlands; Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands
| | - Jacco van Rheenen
- Division of Molecular Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands.
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2
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Prust N, van Breugel PC, Lemeer S. Widespread Arginine Phosphorylation in Staphylococcus aureus. Mol Cell Proteomics 2022; 21:100232. [PMID: 35421590 PMCID: PMC9112008 DOI: 10.1016/j.mcpro.2022.100232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/15/2021] [Accepted: 04/07/2022] [Indexed: 11/25/2022] Open
Abstract
Arginine phosphorylation was only recently discovered to play a significant and relevant role in the Gram-positive bacterium Bacillus subtilis. In addition, arginine phosphorylation was also detected in Staphylococcus aureus, suggesting a widespread role in bacteria. However, the large-scale analysis of protein phosphorylation, and especially those that involve a phosphoramidate bond, comes along with several challenges. The substoichiometric nature of protein phosphorylation requires proper enrichment strategies prior to LC-MS/MS analysis, and the acid instability of phosphoramidates was long thought to impede those enrichments. Furthermore, good spectral quality is required, which can be impeded by the presence of neutral losses of phosphoric acid upon higher energy collision–induced dissociation. Here we show that pArg is stable enough for commonly used Fe3+-IMAC enrichment followed by LC-MS/MS and that HCD is still the gold standard for the analysis of phosphopeptides. By profiling a serine/threonine kinase (Stk1) and phosphatase (Stp1) mutant from a methicillin-resistant S. aureus mutant library, we identified 1062 pArg sites and thus the most comprehensive arginine phosphoproteome to date. Using synthetic arginine phosphorylated peptides, we validated the presence and localization of arginine phosphorylation in S. aureus. Finally, we could show that the knockdown of Stp1 significantly increases the overall amount of arginine phosphorylation in S. aureus. However, our analysis also shows that Stp1 is not a direct protein-arginine phosphatase but only indirectly influences the arginine phosphoproteome. Extensive protein arginine phosphorylation in Staphylococcus aureus. pArg phosphorylation is stable under common phosphor enrichment conditions. Arginine phosphorylation is as widespread as threonine phosphorylation. Phosphatase Stp1 indirectly influences the pArg phosphoproteome in S. aureus.
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Affiliation(s)
- Nadine Prust
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Pieter C van Breugel
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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3
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Sanz-Moreno A, Palomeras S, Pedersen K, Morancho B, Pascual T, Galván P, Benítez S, Gomez-Miragaya J, Ciscar M, Jimenez M, Pernas S, Petit A, Soler-Monsó MT, Viñas G, Alsaleem M, Rakha EA, Green AR, Santamaria PG, Mulder C, Lemeer S, Arribas J, Prat A, Puig T, Gonzalez-Suarez E. RANK signaling increases after anti-HER2 therapy contributing to the emergence of resistance in HER2-positive breast cancer. Breast Cancer Res 2021; 23:42. [PMID: 33785053 PMCID: PMC8008631 DOI: 10.1186/s13058-021-01390-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 01/11/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Around 15-20% of primary breast cancers are characterized by HER2 protein overexpression and/or HER2 gene amplification. Despite the successful development of anti-HER2 drugs, intrinsic and acquired resistance represents a major hurdle. This study was performed to analyze the RANK pathway contribution in HER2-positive breast cancer and anti-HER2 therapy resistance. METHODS RANK and RANKL protein expression was assessed in samples from HER2-positive breast cancer patients resistant to anti-HER2 therapy and treatment-naive patients. RANK and RANKL gene expression was analyzed in paired samples from patients treated with neoadjuvant dual HER2-blockade (lapatinib and trastuzumab) from the SOLTI-1114 PAMELA trial. Additionally, HER2-positive breast cancer cell lines were used to modulate RANK expression and analyze in vitro the contribution of RANK signaling to anti-HER2 resistance and downstream signaling. RESULTS RANK and RANKL proteins are more frequently detected in HER2-positive tumors that have acquired resistance to anti-HER2 therapies than in treatment-naive ones. RANK (but not RANKL) gene expression increased after dual anti-HER2 neoadjuvant therapy in the cohort from the SOLTI-1114 PAMELA trial. Results in HER2-positive breast cancer cell lines recapitulate the clinical observations, with increased RANK expression observed after short-term treatment with the HER2 inhibitor lapatinib or dual anti-HER2 therapy and in lapatinib-resistant cells. After RANKL stimulation, lapatinib-resistant cells show increased NF-κB activation compared to their sensitive counterparts, confirming the enhanced functionality of the RANK pathway in anti-HER2-resistant breast cancer. Overactivation of the RANK signaling pathway enhances ERK and NF-κB signaling and increases lapatinib resistance in different HER2-positive breast cancer cell lines, whereas RANK loss sensitizes lapatinib-resistant cells to the drug. Our results indicate that ErbB signaling is required for RANK/RANKL-driven activation of ERK in several HER2-positive cell lines. In contrast, lapatinib is not able to counteract the NF-κB activation elicited after RANKL treatment in RANK-overexpressing cells. Finally, we show that RANK binds to HER2 in breast cancer cells and that enhanced RANK pathway activation alters HER2 phosphorylation status. CONCLUSIONS Our data support a physical and functional link between RANK and HER2 signaling in breast cancer and demonstrate that increased RANK signaling may contribute to the development of lapatinib resistance through NF-κB activation. Whether HER2-positive breast cancer patients with tumoral RANK expression might benefit from dual HER2 and RANK inhibition therapy remains to be elucidated.
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Affiliation(s)
- Adrián Sanz-Moreno
- Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Present Address: German Mouse Clinic, Institute of Experimental Genetics, HMGU, Neuherberg, 85764, Germany
| | - Sonia Palomeras
- New Therapeutics Targets Lab (TargetsLab), Department of Medical Sciences, University of Girona, Girona, Spain
| | - Kim Pedersen
- Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Beatriz Morancho
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Tomas Pascual
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,SOLTI Breast Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
| | - Patricia Galván
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Sandra Benítez
- Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jorge Gomez-Miragaya
- Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Present Address: Department of Biomedicine, Department of Surgery, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Marina Ciscar
- Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Molecular Oncology, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Maria Jimenez
- Molecular Oncology, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sonia Pernas
- SOLTI Breast Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Breast Unit, Catalan Institute of Oncology (ICO), University Hospital of Bellvitge IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Anna Petit
- Department of Medical Oncology, Breast Unit, Catalan Institute of Oncology (ICO), University Hospital of Bellvitge IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,Pathology Department, University Hospital of Bellvitge, IDIBELL, Barcelona, Spain
| | - María Teresa Soler-Monsó
- Department of Medical Oncology, Breast Unit, Catalan Institute of Oncology (ICO), University Hospital of Bellvitge IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,Pathology Department, University Hospital of Bellvitge, IDIBELL, Barcelona, Spain
| | - Gemma Viñas
- New Therapeutics Targets Lab (TargetsLab), Department of Medical Sciences, University of Girona, Girona, Spain.,Medical Oncology Department, Catalan Institute of Oncology (ICO), Girona, Spain
| | - Mansour Alsaleem
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Emad A Rakha
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Andrew R Green
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, NG7 2RD, UK
| | - Patricia G Santamaria
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Molecular Oncology, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Celine Mulder
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center, Utrecht University, Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center, Utrecht University, Utrecht, The Netherlands
| | - Joaquin Arribas
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Aleix Prat
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,SOLTI Breast Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic, Barcelona, Spain.,Medicine Department, University of Barcelona, Barcelona, Spain
| | - Teresa Puig
- New Therapeutics Targets Lab (TargetsLab), Department of Medical Sciences, University of Girona, Girona, Spain.
| | - Eva Gonzalez-Suarez
- Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. .,Molecular Oncology, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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4
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Leijten NM, Bakker P, Spaink HP, den Hertog J, Lemeer S. Thermal Proteome Profiling in Zebrafish Reveals Effects of Napabucasin on Retinoic Acid Metabolism. Mol Cell Proteomics 2021; 20:100033. [PMID: 33594990 PMCID: PMC7950114 DOI: 10.1074/mcp.ra120.002273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022] Open
Abstract
Thermal proteome profiling (TPP) allows for the unbiased detection of drug-target protein engagements in vivo. Traditionally, 1 cell type is used for TPP studies, with the risk of missing important differentially expressed target proteins. The use of whole organisms would circumvent this problem. Zebrafish embryos are amenable to such an approach. Here, we used TPP on whole zebrafish embryo lysate to identify protein targets of napabucasin, a compound that may affect signal transducer and activator of transcription 3 (Stat3) signaling through an ill-understood mechanism. In zebrafish embryos, napabucasin induced developmental defects consistent with inhibition of Stat3 signaling. TPP profiling showed no distinct shift in Stat3 upon napabucasin treatment, but effects were detected on the oxidoreductase, Pora, which might explain effects on Stat3 signaling. Interestingly, thermal stability of several aldehyde dehydrogenases was affected. Moreover, napabucasin activated aldehyde dehydrogenase enzymatic activity in vitro. Aldehyde dehydrogenases have crucial roles in retinoic acid metabolism, and functionally, we validated napabucasin-mediated activation of the retinoic acid pathway in zebrafish in vivo. We conclude that TPP profiling in whole zebrafish embryo lysate is feasible and facilitates direct correlation of in vivo effects of small molecule drugs with their protein targets.
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Affiliation(s)
- Niels M Leijten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Petra Bakker
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Utrecht, the Netherlands; Institute Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Herman P Spaink
- Institute Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Jeroen den Hertog
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Utrecht, the Netherlands; Institute Biology Leiden, Leiden University, Leiden, the Netherlands.
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands.
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5
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Heider M, Eichner R, Stroh J, Morath V, Kuisl A, Zecha J, Lawatscheck J, Baek K, Garz AK, Rudelius M, Deuschle FC, Keller U, Lemeer S, Verbeek M, Götze KS, Skerra A, Weber WA, Buchner J, Schulman BA, Kuster B, Fernández-Sáiz V, Bassermann F. The IMiD target CRBN determines HSP90 activity toward transmembrane proteins essential in multiple myeloma. Mol Cell 2021; 81:1170-1186.e10. [PMID: 33571422 PMCID: PMC7980223 DOI: 10.1016/j.molcel.2020.12.046] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 11/28/2020] [Accepted: 12/30/2020] [Indexed: 12/23/2022]
Abstract
The complex architecture of transmembrane proteins requires quality control (QC) of folding, membrane positioning, and trafficking as prerequisites for cellular homeostasis and intercellular communication. However, it has remained unclear whether transmembrane protein-specific QC hubs exist. Here we identify cereblon (CRBN), the target of immunomodulatory drugs (IMiDs), as a co-chaperone that specifically determines chaperone activity of HSP90 toward transmembrane proteins by means of counteracting AHA1. This function is abrogated by IMiDs, which disrupt the interaction of CRBN with HSP90. Among the multiple transmembrane protein clients of CRBN-AHA1-HSP90 revealed by cell surface proteomics, we identify the amino acid transporter LAT1/CD98hc as a determinant of IMiD activity in multiple myeloma (MM) and present an Anticalin-based CD98hc radiopharmaceutical for MM radio-theranostics. These data establish the CRBN-AHA1-HSP90 axis in the biogenesis of transmembrane proteins, link IMiD activity to tumor metabolism, and nominate CD98hc and LAT1 as attractive diagnostic and therapeutic targets in MM. CRBN functions as a transmembrane protein-specific co-chaperone of HSP90 Disruption of CRBN-HSP90 interaction determines the anti-tumor activity of IMiDs The CD98hc/LAT1 complex is a central target of IMiDs in multiple myeloma CD98hc-Anticalin is a theranostic tool in multiple myeloma
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Affiliation(s)
- Michael Heider
- Department of Medicine III, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, 81675 Munich, Germany
| | - Ruth Eichner
- Department of Medicine III, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, 81675 Munich, Germany
| | - Jacob Stroh
- Department of Medicine III, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, 81675 Munich, Germany
| | - Volker Morath
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Anna Kuisl
- Department of Medicine III, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, 81675 Munich, Germany
| | - Jana Zecha
- Department of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jannis Lawatscheck
- Center for Integrated Protein Science at the Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Anne-Kathrin Garz
- Department of Medicine III, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Martina Rudelius
- Institute of Pathology, Ludwig-Maximilians University, 80337 Munich, Germany
| | | | - Ulrich Keller
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Hematology, Oncology and Tumor Immunology (Campus Benjamin Franklin), Charité - Universitätsmedizin Berlin, 12200 Berlin, Germany
| | - Simone Lemeer
- Department of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Mareike Verbeek
- Department of Medicine III, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Katharina S Götze
- Department of Medicine III, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technical University of Munich, 85354 Freising, Germany
| | - Wolfgang A Weber
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science at the Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Bernhard Kuster
- Department of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Vanesa Fernández-Sáiz
- Department of Medicine III, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, 81675 Munich, Germany.
| | - Florian Bassermann
- Department of Medicine III, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, 81675 Munich, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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6
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Prust N, van der Laarse S, van den Toorn HWP, van Sorge NM, Lemeer S. In-Depth Characterization of the Staphylococcus aureus Phosphoproteome Reveals New Targets of Stk1. Mol Cell Proteomics 2021; 20:100034. [PMID: 33444734 PMCID: PMC7950182 DOI: 10.1074/mcp.ra120.002232] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/02/2020] [Accepted: 12/10/2020] [Indexed: 11/26/2022] Open
Abstract
Staphylococcus aureus is a major cause of infections worldwide, and infection results in a variety of diseases. As of no surprise, protein phosphorylation is an important game player in signaling cascades and has been shown to be involved in S. aureus virulence. Albeit long neglected, eukaryotic-type serine/threonine kinases in S. aureus have been implicated in this complex signaling cascades. Due to the substoichiometric nature of protein phosphorylation and a lack of suitable analysis tools, the knowledge of these cascades is, however, to date, still limited. Here, were apply an optimized protocol for efficient phosphopeptide enrichment via Fe3+-IMAC followed by LC-MS/MS to get a better understanding of the impact of protein phosphorylation on the complex signaling networks involved in pathogenicity. By profiling a serine/threonine kinase and phosphatase mutant from a methicillin-resistant S. aureus mutant library, we generated the most comprehensive phosphoproteome data set of S. aureus to date, aiding a better understanding of signaling in bacteria. With the identification of 3800 class I p-sites, we were able to increase the number of identifications by more than 21 times compared with recent literature. In addition, we were able to identify 74 downstream targets of the only reported eukaryotic-type Ser/Thr kinase of the S. aureus strain USA300, Stk1. This work allowed an extensive analysis of the bacterial phosphoproteome and indicates that Ser/Thr kinase signaling is far more abundant than previously anticipated in S. aureus.
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Affiliation(s)
- Nadine Prust
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands
| | - Saar van der Laarse
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands
| | - Henk W P van den Toorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands
| | - Nina M van Sorge
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Department of Medical Microbiology and Infection Prevention and Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands.
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7
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Kreutmair S, Erlacher M, Andrieux G, Istvanffy R, Mueller-Rudorf A, Zwick M, Rückert T, Pantic M, Poggio T, Shoumariyeh K, Mueller TA, Kawaguchi H, Follo M, Klingeberg C, Wlodarski M, Baumann I, Pfeifer D, Kulinski M, Rudelius M, Lemeer S, Kuster B, Dierks C, Peschel C, Cabezas-Wallscheid N, Duque-Afonso J, Zeiser R, Cleary ML, Schindler D, Schmitt-Graeff A, Boerries M, Niemeyer CM, Oostendorp RA, Duyster J, Illert AL. Loss of the Fanconi anemia-associated protein NIPA causes bone marrow failure. J Clin Invest 2020; 130:2827-2844. [PMID: 32338640 PMCID: PMC7260023 DOI: 10.1172/jci126215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/26/2018] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFSs) are a heterogeneous group of disorders characterized by defective hematopoiesis, impaired stem cell function, and cancer susceptibility. Diagnosis of IBMFS presents a major challenge due to the large variety of associated phenotypes, and novel, clinically relevant biomarkers are urgently needed. Our study identified nuclear interaction partner of ALK (NIPA) as an IBMFS gene, as it is significantly downregulated in a distinct subset of myelodysplastic syndrome-type (MDS-type) refractory cytopenia in children. Mechanistically, we showed that NIPA is major player in the Fanconi anemia (FA) pathway, which binds FANCD2 and regulates its nuclear abundance, making it essential for a functional DNA repair/FA/BRCA pathway. In a knockout mouse model, Nipa deficiency led to major cell-intrinsic defects, including a premature aging phenotype, with accumulation of DNA damage in hematopoietic stem cells (HSCs). Induction of replication stress triggered a reduction in and functional decline of murine HSCs, resulting in complete bone marrow failure and death of the knockout mice with 100% penetrance. Taken together, the results of our study add NIPA to the short list of FA-associated proteins, thereby highlighting its potential as a diagnostic marker and/or possible target in diseases characterized by hematopoietic failure.
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Affiliation(s)
- Stefanie Kreutmair
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Miriam Erlacher
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, and
| | - Geoffroy Andrieux
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, University Medical Center — University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Rouzanna Istvanffy
- Department of Internal Medicine III, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Alina Mueller-Rudorf
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melissa Zwick
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tamina Rückert
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Milena Pantic
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Teresa Poggio
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Khalid Shoumariyeh
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tony A. Mueller
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hiroyuki Kawaguchi
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Marie Follo
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Cathrin Klingeberg
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcin Wlodarski
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, and
| | - Irith Baumann
- Institute of Pathology, Health Center Böblingen, Böblingen, Germany
| | - Dietmar Pfeifer
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michal Kulinski
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Martina Rudelius
- Institute of Pathology, Ludwig Maximilian University Munich, Munich, Germany
| | - Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Christine Dierks
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christian Peschel
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Internal Medicine III, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | - Jesus Duque-Afonso
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Robert Zeiser
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael L. Cleary
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Detlev Schindler
- Department of Human Genetics, Institute of Human Genetics, Biozentrum, University of Würzburg, Würzburg, Germany
| | | | - Melanie Boerries
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, University Medical Center — University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Charlotte M. Niemeyer
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, and
| | - Robert A.J. Oostendorp
- Department of Internal Medicine III, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Justus Duyster
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Lena Illert
- Department of Internal Medicine I, Medical Center — University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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8
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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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9
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Abstract
![]()
Recent technological
advances have made it possible to investigate
the hitherto rather elusive protein histidine phosphorylation. However,
confident site-specific localization of protein histidine phosphorylation
remains challenging. Here, we address this problem, presenting a mass-spectrometry-based
approach that outperforms classical HCD fragmentation without compromising
sensitivity. We use the phosphohistidine immonium ion as a diagnostic
tool as well as ETD-based fragmentation techniques to achieve unambiguous
identification and localization of histidine-phosphorylation sites.
The work presented here will allow more confident investigation of
the phosphohistidine proteome to reveal the roles of histidine phosphorylation
in cellular signaling events.
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Affiliation(s)
- Clement M Potel
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Center , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Miao-Hsia Lin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Center , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Nadine Prust
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Center , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Henk W P van den Toorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Center , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Center , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Center , Padualaan 8 , 3584 CH Utrecht , The Netherlands
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10
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Affiliation(s)
- Clement M Potel
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
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11
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Lin MH, Potel CM, Tehrani KHME, Heck AJR, Martin NI, Lemeer S. A New Tool to Reveal Bacterial Signaling Mechanisms in Antibiotic Treatment and Resistance. Mol Cell Proteomics 2018; 17:2496-2507. [PMID: 30232125 DOI: 10.1074/mcp.ra118.000880] [Citation(s) in RCA: 16] [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: 05/29/2018] [Revised: 09/12/2018] [Indexed: 11/06/2022] Open
Abstract
The rapid emergence of antimicrobial resistance is a major threat to human health. Antibiotics modulate a wide range of biological processes in bacteria and as such, the study of bacterial cellular signaling could aid the development of urgently needed new antibiotic agents. Due to the advances in bacterial phosphoproteomics, such a systemwide analysis of bacterial signaling in response to antibiotics has recently become feasible. Here we present a dynamic view of differential protein phosphorylation upon antibiotic treatment and antibiotic resistance. Most strikingly, differential phosphorylation was observed on highly conserved residues of resistance regulating transcription factors, implying a previously unanticipated role of phosphorylation mediated regulation. Using the comprehensive phosphoproteomics data presented here as a resource, future research can now focus on deciphering the precise signaling mechanisms contributing to resistance, eventually leading to alternative strategies to combat antimicrobial resistance.
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Affiliation(s)
- Miao-Hsia Lin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, University of Utrecht, Utrecht, The Netherlands
| | - Clement M Potel
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, University of Utrecht, Utrecht, The Netherlands
| | - Kamaleddin H M E Tehrani
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, University of Utrecht, Utrecht, The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, University of Utrecht, Utrecht, The Netherlands.
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12
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Mulder C, Prust N, van Doorn S, Reinecke M, Kuster B, van Bergen en Henegouwen P, Lemeer S. Adaptive Resistance to EGFR-Targeted Therapy by Calcium Signaling in NSCLC Cells. Mol Cancer Res 2018; 16:1773-1784. [DOI: 10.1158/1541-7786.mcr-18-0212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/26/2018] [Accepted: 06/12/2018] [Indexed: 11/16/2022]
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13
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Wu W, Zaal EA, Berkers CR, Lemeer S, Heck AJR. CTGF/VEGFA-activated Fibroblasts Promote Tumor Migration Through Micro-environmental Modulation. Mol Cell Proteomics 2018; 17:1502-1514. [PMID: 29669735 DOI: 10.1074/mcp.ra118.000708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 02/26/2018] [Revised: 04/18/2018] [Indexed: 02/04/2023] Open
Abstract
Fibroblast activation is associated with tumor progression and implicated in metastasis, but the initial triggering signals required to kick-start this process remain largely unknown. Because small cancerous lesions share limited physical contact with neighboring fibroblasts, we reasoned the first tumor-derived signal for fibroblast activation should be secreted and diffusible. By pulsed metabolic labeling and click-chemistry based affinity enrichment, we sieved through the ductal carcinoma secretome for potential fibroblast activators. Using immuno-depletion/supplementation assays on various secreted factors, we pinpointed that tumor-secreted CTGF/VEGFA alone is sufficient to activate paired mammary fibroblasts from the same patient via ROCK1 and JunB signaling. Fibroblasts activated in this manner are distinct in morphology, growth, and adopt a highly tumor-like secretion profile, which in turn promotes tumor migration by counteracting oxidative and lactate stress. These findings reveal a profound division-of-labor between normal and cancer cells under the directive of the latter, and allude to potential metastatic prevention through inhibiting local fibroblast activation.
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Affiliation(s)
- Wei Wu
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.,§Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Esther A Zaal
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Celia R Berkers
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Simone Lemeer
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.,§Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; .,§Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
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14
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Potel CM, Lin MH, Heck AJR, Lemeer S. Defeating Major Contaminants in Fe 3+- Immobilized Metal Ion Affinity Chromatography (IMAC) Phosphopeptide Enrichment. Mol Cell Proteomics 2018; 17:1028-1034. [PMID: 29449344 DOI: 10.1074/mcp.tir117.000518] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/15/2018] [Indexed: 11/06/2022] Open
Abstract
Here we demonstrate that biomolecular contaminants, such as nucleic acid molecules, can seriously interfere with immobilized metal ion affinity chromatography (IMAC)-based phosphopeptide enrichments. We address and largely solve this issue, developing a robust protocol implementing methanol/chloroform protein precipitation and enzymatic digestion using benzonase, which degrades all forms of DNA and RNA, before IMAC-column loading. This simple procedure resulted in a drastic increase of enrichment sensitivity, enabling the identification of around 17,000 unique phosphopeptides and 12,500 unambiguously localized phosphosites in human cell-lines from a single LC-MS/MS run, constituting a 50% increase when compared with the standard protocol. The improved protocol was also applied to bacterial samples, increasing the number of identified bacterial phosphopeptides even more strikingly, by a factor 10, when compared with the standard protocol. For E. coli we detected around 1300 unambiguously localized phosphosites per LC-MS/MS run. The preparation of these ultra-pure phosphopeptide samples only requires marginal extra costs and sample preparation time and should thus be adoptable by every laboratory active in the field of phosphoproteomics.
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Affiliation(s)
- Clement M Potel
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Miao-Hsia Lin
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Simone Lemeer
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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15
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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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16
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Ruprecht B, Zaal EA, Zecha J, Wu W, Berkers CR, Kuster B, Lemeer S. Lapatinib Resistance in Breast Cancer Cells Is Accompanied by Phosphorylation-Mediated Reprogramming of Glycolysis. Cancer Res 2017; 77:1842-1853. [DOI: 10.1158/0008-5472.can-16-2976] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/19/2017] [Accepted: 01/24/2017] [Indexed: 11/16/2022]
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17
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Abstract
Phosphorylation is among the most important post-translational modifications of proteins and has numerous regulatory functions across all domains of life. However, phosphorylation is often substoichiometric, requiring selective and sensitive methods to enrich phosphorylated peptides from complex cellular digests. Various methods have been devised for this purpose and we have recently described a Fe-IMAC HPLC column chromatography setup which is capable of comprehensive, reproducible, and selective enrichment of phosphopeptides out of complex peptide mixtures. In contrast to other formats such as StageTips or batch incubations using TiO2 or Ti-IMAC beads, Fe-IMAC HPLC columns do not suffer from issues regarding incomplete phosphopeptide binding or elution and enrichment efficiency scales linearly with the amount of starting material. Here, we provide a step-by-step protocol for the entire phosphopeptide enrichment procedure including sample preparation (lysis, digestion, desalting), Fe-IMAC column chromatography (column setup, operation, charging), measurement by LC-MS/MS (nHPLC gradient, MS parameters) and data analysis (MaxQuant). To increase throughput, we have optimized several key steps such as the gradient time of the Fe-IMAC separation (15 min per enrichment), the number of consecutive enrichments possible between two chargings (>20) and the column recharging itself (<1 h). We show that the application of this protocol enables the selective (>90 %) identification of more than 10,000 unique phosphopeptides from 1 mg of HeLa digest within 2 h of measurement time (Q Exactive Plus).
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Affiliation(s)
- Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany
| | - Heiner Koch
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Petra Domasinska
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Faculty of Chemical Technology, Department of Biological and Biochemical Sciences, University of Pardubice, Pardubice, Czech Republic
| | - Martin Frejno
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany
- Department of Oncology, University of Oxford, Oxford, UK
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354, 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.
| | - Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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18
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Lebesgue N, Megyeri M, Cristobal A, Scholten A, Chuartzman SG, Voichek Y, Scheltema RA, Mohammed S, Futerman AH, Schuldiner M, Heck AJR, Lemeer S. Combining Deep Sequencing, Proteomics, Phosphoproteomics, and Functional Screens To Discover Novel Regulators of Sphingolipid Homeostasis. J Proteome Res 2016; 16:571-582. [PMID: 28152593 DOI: 10.1021/acs.jproteome.6b00691] [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] [Indexed: 02/03/2023]
Abstract
Sphingolipids (SLs) are essential components of cell membranes and are broad-range bioactive signaling molecules. SL levels must be tightly regulated as imbalances affect cellular function and contribute to pathologies ranging from neurodegenerative and metabolic disorders to cancer and aging. Deciphering how SL homeostasis is maintained and uncovering new regulators is required for understanding lipid biology and for identifying new targets for therapeutic interventions. Here we combine omics technologies to identify the changes of the transcriptome, proteome, and phosphoproteome in the yeast Saccharomyces cerevisiae upon SL depletion induced by myriocin. Surprisingly, while SL depletion triggers important changes in the expression of regulatory proteins involved in SL homeostasis, the most dramatic regulation occurs at the level of the phosphoproteome, suggesting that maintaining SL homeostasis demands rapid responses. To discover which of the phosphoproteomic changes are required for the cell's first-line response to SL depletion, we overlaid our omics results with systematic growth screens for genes required during growth in myriocin. By following the rate of SL biosynthesis in those candidates that are both affecting growth and are phosphorylated in response to the drug, we uncovered Atg9, Stp4, and Gvp36 as putative new regulators of SL homeostasis.
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Affiliation(s)
- Nicolas Lebesgue
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Márton Megyeri
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel.,Department of Chemical Biology, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Alba Cristobal
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Arjen Scholten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Silvia G Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Yoav Voichek
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Anthony H Futerman
- Department of Chemical Biology, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
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19
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Kaplan M, Narasimhan S, de Heus C, Mance D, van Doorn S, Houben K, Popov-Čeleketić D, Damman R, Katrukha EA, Jain P, Geerts WJC, Heck AJR, Folkers GE, Kapitein LC, Lemeer S, van Bergen En Henegouwen PMP, Baldus M. EGFR Dynamics Change during Activation in Native Membranes as Revealed by NMR. Cell 2016; 167:1241-1251.e11. [PMID: 27839865 DOI: 10.1016/j.cell.2016.10.038] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [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: 05/04/2016] [Revised: 08/08/2016] [Accepted: 10/20/2016] [Indexed: 10/20/2022]
Abstract
The epidermal growth factor receptor (EGFR) represents one of the most common target proteins in anti-cancer therapy. To directly examine the structural and dynamical properties of EGFR activation by the epidermal growth factor (EGF) in native membranes, we have developed a solid-state nuclear magnetic resonance (ssNMR)-based approach supported by dynamic nuclear polarization (DNP). In contrast to previous crystallographic results, our experiments show that the ligand-free state of the extracellular domain (ECD) is highly dynamic, while the intracellular kinase domain (KD) is rigid. Ligand binding restricts the overall and local motion of EGFR domains, including the ECD and the C-terminal region. We propose that the reduction in conformational entropy of the ECD by ligand binding favors the cooperative binding required for receptor dimerization, causing allosteric activation of the intracellular tyrosine kinase.
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Affiliation(s)
- Mohammed Kaplan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Cecilia de Heus
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Deni Mance
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Sander van Doorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Klaartje Houben
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Dušan Popov-Čeleketić
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Reinier Damman
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Eugene A Katrukha
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Purvi Jain
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Willie J C Geerts
- Biomolecular Imaging, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Lukas C Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | | | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
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20
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Schmidlin T, Garrigues L, Lane CS, Mulder TC, van Doorn S, Post H, de Graaf EL, Lemeer S, Heck AJR, Altelaar AFM. Assessment of SRM, MRM3, and DIA for the targeted analysis of phosphorylation dynamics in non-small cell lung cancer. Proteomics 2016; 16:2193-205. [DOI: 10.1002/pmic.201500453] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/12/2016] [Accepted: 05/20/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Thierry Schmidlin
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Luc Garrigues
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | | | - T. Celine Mulder
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Sander van Doorn
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Erik L. de Graaf
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
- Current address: Erik L. de Graaf, Fondazione Pisana per la Scienza ONLUS; Via Panfilo Castaldi 2; 56121 Pisa Italy
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
| | - A. F. Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University and Netherlands Proteomics Centre; Utrecht The Netherlands
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21
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Ruprecht B, Roesli C, Lemeer S, Kuster B. MALDI-TOF and nESI Orbitrap MS/MS identify orthogonal parts of the phosphoproteome. Proteomics 2016; 16:1447-56. [PMID: 26990019 DOI: 10.1002/pmic.201500523] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/02/2016] [Accepted: 03/11/2016] [Indexed: 01/01/2023]
Abstract
Phosphorylation is a reversible posttranslational protein modification which plays a pivotal role in intracellular signaling. Despite extensive efforts, phosphorylation site mapping of proteomes is still incomplete motivating the exploration of alternative methods that complement existing workflows. In this study, we compared tandem mass spectrometry (MS/MS) on matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) and nano-electrospray ionization (nESI) Orbitrap instruments with respect to their ability to identify phosphopeptides from complex proteome digests. Phosphopeptides were enriched from tryptic digests of cell lines using Fe-IMAC column chromatography and subjected to LC-MS/MS analysis. We found that the two analytical workflows exhibited considerable orthogonality. For instance, MALDI-TOF MS/MS favored the identification of phosphopeptides encompassing clear motif signatures for acidic residue directed kinases. The extent of orthogonality of the two LC-MS/MS systems was comparable to that of using alternative proteases such as Asp-N, Arg-C, chymotrypsin, Glu-C and Lys-C on just one LC-MS/MS instrument. Notably, MALDI-TOF MS/MS identified an unexpectedly high number and percentage of phosphotyrosine sites (∼20% of all sites), possibly as a direct consequence of more efficient ionization. The data clearly show that LC-MALDI MS/MS can be a useful complement to LC-nESI MS/MS for phosphoproteome mapping and particularly so for acidic and phosphotyrosine containing peptides.
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Affiliation(s)
- Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany.,Center for Protein Science Munich (CIPSM), Freising, Germany
| | - Christoph Roesli
- HI-STEM - Heidelberg, Institute for Stem Cell Technology and Experimental Medicine gemeinnützige GmbH, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany.,Center for Protein Science Munich (CIPSM), Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany.,Center for Protein Science Munich (CIPSM), Freising, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Bavarian Biomolecular Mass Spectrometry Center, Technische Universität München, Freising, Germany
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22
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Abstract
Protein kinases are important mediators of intracellular signaling and are reversibly activated by phosphorylation. Immobilized kinase inhibitors can be used to enrich these often low-abundance proteins, to identify targets of kinase inhibitors, or to probe their selectivity. It has been suggested that the binding of kinases to affinity beads reflects a kinase's activation status, a concept that is under considerable debate. To assess the merits of the idea, we performed a series of experiments including quantitative phosphoproteomics and purification of kinases by single or mixed affinity matrices from signaling activated or resting cancer cells. The data show that mixed affinity beads largely bind kinases independent of their activation status, and experiments using individual immobilized kinase inhibitors show mixed results in terms of preference for binding the active or inactive conformation. Taken together, activity- or conformation-dependent binding to such affinity resins depends (i) on the kinase, (ii) on the affinity probe, and (iii) on the activation status of the lysate or cell. As a result, great caution should be exercised when inferring kinase activity from such binding data. The results also suggest that assaying kinase activity using binding data is restricted to a limited number of well-chosen cases.
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Affiliation(s)
- Benjamin Ruprecht
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
- Center for Protein Science Munich (CIPSM), 85354 Freising, Germany
| | - Jana Zecha
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Stephanie Heinzlmeir
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Guillaume Médard
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
| | - Simone Lemeer
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
- Center for Protein Science Munich (CIPSM), 85354 Freising, Germany
| | - Bernhard Kuster
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
- Center for Protein Science Munich (CIPSM), 85354 Freising, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
- Bavarian
Biomolecular Mass Spectrometry Center, Technische Universität München, 85354 Freising, Germany
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23
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Lemeer S, Gholami AM, Wu Z, Kuster B. Quantitative proteome profiling of human myoma and myometrium tissue reveals kinase expression signatures with potential for therapeutic intervention. Proteomics 2014; 15:356-64. [PMID: 25327614 DOI: 10.1002/pmic.201400213] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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: 05/14/2014] [Revised: 08/18/2014] [Accepted: 10/13/2014] [Indexed: 12/18/2022]
Abstract
Uterine leiomyomas are benign tumors affecting a large proportion of the female population. Despite the very high prevalence, the molecular basis for understanding the onset and development of the disease are still poorly understood. In this study, we profiled the proteomes and kinomes of leiomyoma as well as myometrium samples from patients to a depth of >7000 proteins including 200 kinases. Statistical analysis identified a number of molecular signatures distinguishing healthy from diseased tissue. Among these, nine kinases (ADCK4, CDK5, CSNK2B, DDR1, EPHB1, MAP2K2, PRKCB, PRKG1, and RPS6KA5) representing a number of cellular signaling pathways showed particularly strong discrimination potential. Preliminary statistical analysis by receiver operator characteristics plots revealed very good performance for individual kinases (area under the curve, AUC of 0.70-0.94) as well as binary combinations thereof (AUC 0.70-1.00) that might be used to assess the activity of signaling pathways in myomas. Of note, the receptor tyrosine kinase DDR1 holds future potential as a drug target owing to its strong links to collagen signaling and the excessive formation of extracellular matrix typical for leiomyomas in humans.
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Affiliation(s)
- Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, Freising, Germany
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24
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Ruprecht B, Koch H, Medard G, Mundt M, Kuster B, Lemeer S. Comprehensive and reproducible phosphopeptide enrichment using iron immobilized metal ion affinity chromatography (Fe-IMAC) columns. Mol Cell Proteomics 2014; 14:205-15. [PMID: 25394399 DOI: 10.1074/mcp.m114.043109] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Advances in phosphopeptide enrichment methods enable the identification of thousands of phosphopeptides from complex samples. Current offline enrichment approaches using TiO(2), Ti, and Fe immobilized metal ion affinity chromatography (IMAC) material in batch or microtip format are widely used, but they suffer from irreproducibility and compromised selectivity. To address these shortcomings, we revisited the merits of performing phosphopeptide enrichment in an HPLC column format. We found that Fe-IMAC columns enabled the selective, comprehensive, and reproducible enrichment of phosphopeptides out of complex lysates. Column enrichment did not suffer from bead-to-sample ratio issues and scaled linearly from 100 μg to 5 mg of digest. Direct measurements on an Orbitrap Velos mass spectrometer identified >7500 unique phosphopeptides with 90% selectivity and good quantitative reproducibility (median cv of 15%). The number of unique phosphopeptides could be increased to more than 14,000 when the IMAC eluate was subjected to a subsequent hydrophilic strong anion exchange separation. Fe-IMAC columns outperformed Ti-IMAC and TiO(2) in batch or tip mode in terms of phosphopeptide identification and intensity. Permutation enrichments of flow-throughs showed that all materials largely bound the same phosphopeptide species, independent of physicochemical characteristics. However, binding capacity and elution efficiency did profoundly differ among the enrichment materials and formats. As a result, the often quoted orthogonality of the materials has to be called into question. Our results strongly suggest that insufficient capacity, inefficient elution, and the stochastic nature of data-dependent acquisition in mass spectrometry are the causes of the experimentally observed complementarity. The Fe-IMAC enrichment workflow using an HPLC format developed here enables rapid and comprehensive phosphoproteome analysis that can be applied to a wide range of biological systems.
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Affiliation(s)
- Benjamin Ruprecht
- From the * Chair of 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
| | - Heiner Koch
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Guillaume Medard
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Max Mundt
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Bernhard Kuster
- From the * Chair of 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
| | - Simone Lemeer
- From the * Chair of 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
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25
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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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26
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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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Abstract
Constitutive activity of kinases is known to be crucial for a tumor to maintain its malignant phenotype, a phenomenon which is often referred to as oncogene addiction. The in-depth analysis of aberrant signaling pathways by the analysis of protein phosphorylation has become feasible through recent advances in proteomics technology. In this article we will review developments in the field of phosphoproteomics and its application in cancer research. The most widely used technologies for the generic enrichment of phosphopeptides are discussed as well as targeted approaches for the analysis of a specific subset of phosphopeptides. Validation experiments of phosphorylation sites using targeted mass spectrometry are also explained. Finally, we will highlight applications of phosphoproteomic technology in cancer research using cell lines and tissue.
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Affiliation(s)
- Benjamin Ruprecht
- Technische Universität München, Freising, Germany and Center for Integrated Protein Science Munich, Munich, Germany
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28
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Neumann K, Castiñeiras-Vilariño M, Höckendorf U, Hannesschläger N, Lemeer S, Kupka D, Meyermann S, Lech M, Anders HJ, Kuster B, Busch DH, Gewies A, Naumann R, Groß O, Ruland J. Clec12a is an inhibitory receptor for uric acid crystals that regulates inflammation in response to cell death. Immunity 2014; 40:389-99. [PMID: 24631154 DOI: 10.1016/j.immuni.2013.12.015] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [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: 09/27/2013] [Accepted: 12/24/2013] [Indexed: 12/14/2022]
Abstract
Recognition of cell death by the innate immune system triggers inflammatory responses. However, how these reactions are regulated is not well understood. Here, we identify the inhibitory C-type lectin receptor Clec12a as a specific receptor for dead cells. Both human and mouse Clec12a could physically sense uric acid crystals (monosodium urate, MSU), which are key danger signals for cell-death-induced immunity. Clec12a inhibited inflammatory responses to MSU in vitro, and Clec12a-deficient mice exhibited hyperinflammatory responses after being challenged with MSU or necrotic cells and after radiation-induced thymocyte killing in vivo. Thus, we identified a negative regulatory MSU receptor that controls noninfectious inflammation in response to cell death that has implications for autoimmunity and inflammatory disease.
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Affiliation(s)
- Konstantin Neumann
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Mercedes Castiñeiras-Vilariño
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Ulrike Höckendorf
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Nicole Hannesschläger
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Simone Lemeer
- Lehrstuhl für Proteomik und Bioanalytik, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Danny Kupka
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Svenia Meyermann
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Maciej Lech
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München (LMU), 80336 München, Germany
| | - Hans-Joachim Anders
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München (LMU), 80336 München, Germany
| | - Bernhard Kuster
- Lehrstuhl für Proteomik und Bioanalytik, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Dirk H Busch
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, 81675 Munich, Germany
| | - Andreas Gewies
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Ronald Naumann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Olaf Groß
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Jürgen Ruland
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany.
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29
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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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Pachl F, Ruprecht B, Lemeer S, Kuster B. Characterization of a high field Orbitrap mass spectrometer for proteome analysis. Proteomics 2013; 13:2552-62. [PMID: 23836775 DOI: 10.1002/pmic.201300076] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 02/22/2013] [Revised: 05/08/2013] [Accepted: 06/26/2013] [Indexed: 11/06/2022]
Abstract
The field of proteomics continues to be driven by improvements in analytical technology, notably in peptide separation, quantitative MS, and informatics. In this study, we have characterized a hybrid linear ion trap high field Orbitrap mass spectrometer (Orbitrap Elite) for proteomic applications. The very high resolution available on this instrument allows 95% of all peptide masses to be measured with sub-ppm accuracy that in turn improves protein identification by database searching. We further confirm again that mass accuracy in tandem mass spectra is a valuable parameter for improving the success of protein identification. The new CID rapid scan type of the Orbitrap Elite achieves similar performance as higher energy collision induced dissociation fragmentation and both allow the identification of hundreds of proteins from as little as 0.1 ng of protein digest on column. The new instrument outperforms its predecessor the Orbitrap Velos by a considerable margin on each metric assessed that makes it a valuable and versatile tool for MS-based proteomics.
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Affiliation(s)
- Fiona Pachl
- 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
Protein sequence databases are indispensable tools for life science research including mass spectrometry (MS)-based proteomics. In current database construction processes, sequence similarity clustering is used to reduce redundancies in the source data. Albeit powerful, it ignores the peptide-centric nature of proteomic data and the fact that MS is able to distinguish similar sequences. Therefore, we introduce an approach that structures the protein sequence space at the peptide level using theoretical and empirical information from large-scale proteomic data to generate a mass spectrometry-centric protein sequence database (MScDB). The core modules of MScDB are an in-silico proteolytic digest and a peptide-centric clustering algorithm that groups protein sequences that are indistinguishable by mass spectrometry. Analysis of various MScDB uses cases against five complex human proteomes, resulting in 69 peptide identifications not present in UniProtKB as well as 79 putative single amino acid polymorphisms. MScDB retains ~99% of the identifications in comparison to common databases despite a 3-48% increase in the theoretical peptide search space (but comparable protein sequence space). In addition, MScDB enables cross-species applications such as human/mouse graft models, and our results suggest that the uncertainty in protein assignments to one species can be smaller than 20%.
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Affiliation(s)
- Harald Marx
- Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
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32
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Lemeer S, Zörgiebel C, Ruprecht B, Kohl K, Kuster B. Comparing immobilized kinase inhibitors and covalent ATP probes for proteomic profiling of kinase expression and drug selectivity. J Proteome Res 2013; 12:1723-31. [PMID: 23495751 DOI: 10.1021/pr301073j] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Kinases are involved in the regulation of many cellular processes and aberrant kinase signaling has been implicated in human disease. As a consequence, kinases are attractive drug targets. Assessing kinase function and drug selectivity in a more physiological context is challenging and often hampered by the generally low expression level of kinases and the extensive post-translation modification in vivo. Kinase drug selectivity screens by chemical proteomics have gained attention because they allow the profiling of hundreds of kinases against one drug at the same time. Here, we directly compared two such methods, notably, immobilized broad spectrum kinase inhibitors (kinobeads) and active site labeling using desthiobiotin-ATP and -ADP probes. Affinity purification of ∼ 100 kinases by either kinobeads or ATP/ADP probes was readily achieved using 1 mg of cellular protein. Bioinformatic analysis revealed a high degree of complementarity of the two techniques. Kinobeads covered the Tyrosine Kinase family particularly well and ATP probes enriched higher numbers of STE family kinases. A consecutive combination of both enrichment strategies therefore allowed for the coverage of a larger part of the kinome than any one technique alone. While kinobeads are very selective for kinases, the ATP/ADP probes also enriched a large number of other nucleotide binding proteins. Both methods were applied to the selectivity profiling of the small molecular Aurora kinase inhibitor tozasertib in K562 cells. Our data confirmed Aurora A, B, and BCR-ABL as the main targets of tozasertib and identified TNK1, STK2, RPS6KA1, and RPS6KA3 as submicromolar off targets.
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Affiliation(s)
- Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technische Universität München , Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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33
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Fernández-Sáiz V, Targosz BS, Lemeer S, Eichner R, Langer C, Bullinger L, Reiter C, Slotta-Huspenina J, Schroeder S, Knorn AM, Kurutz J, Peschel C, Pagano M, Kuster B, Bassermann F. SCFFbxo9 and CK2 direct the cellular response to growth factor withdrawal via Tel2/Tti1 degradation and promote survival in multiple myeloma. Nat Cell Biol 2013; 15:72-81. [PMID: 23263282 DOI: 10.1038/ncb2651] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 11/09/2012] [Indexed: 12/17/2022]
Abstract
The Tel2 (also known as Telo2) and Tti1 proteins control the cellular abundance of mammalian PIKKs and are integral components of mTORC1 and mTORC2. Here we report that Tel2 and Tti1 are targeted for degradation within mTORC1 by the SCFFbxo9 ubiquitin ligase to adjust mTOR signalling to growth factor availability. This process is primed by CK2, which translocates to the cytoplasm to mediate mTORC1-specific phosphorylation of Tel2/Tti1, subsequent to growth factor deprivation. As a consequence, mTORC1 is inactivated to restrain cell growth and protein translation whereas relief of feedback inhibition activates the PI(3)K/TORC2/Akt pathway to sustain survival. Significantly, primary human multiple myelomas exhibit high levels of Fbxo9. In this setting, PI(3)K/TORC2/Akt signalling and survival of multiple myeloma cells is dependent on Fbxo9 expression. Thus, mTORC1-specific degradation of the Tel2 and Tti1 proteins represents a central mTOR regulatory mechanism with implications in multiple myeloma, both in promoting survival and in providing targets for the specific treatment of multiple myeloma with high levels of Fbxo9 expression.
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Affiliation(s)
- Vanesa Fernández-Sáiz
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München, Ismaninger Strasse 22, 81675 Munich, Germany
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34
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Bantscheff M, Lemeer S, Savitski MM, Kuster B. Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal Bioanal Chem 2012; 404:939-65. [PMID: 22772140 DOI: 10.1007/s00216-012-6203-4] [Citation(s) in RCA: 539] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/06/2012] [Accepted: 06/15/2012] [Indexed: 02/08/2023]
Abstract
Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also developed into an assay platform capable of measuring hundreds to thousands of proteins in any biological system. The field has progressed at an amazing rate over the past five years in terms of technology as well as the breadth and depth of applications in all areas of the life sciences. Some of the technical approaches that were at an experimental stage back then are considered the gold standard today, and the community is learning to come to grips with the volume and complexity of the data generated. The revolution in DNA/RNA sequencing technology extends the reach of proteomic research to practically any species, and the notion that mass spectrometry has the potential to eventually retire the western blot is no longer in the realm of science fiction. In this review, we focus on the major technical and conceptual developments since 2007 and illustrate these by important recent applications.
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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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36
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Lemeer S, Bluwstein A, Wu Z, Leberfinger J, Müller K, Kramer K, Kuster B. Phosphotyrosine mediated protein interactions of the discoidin domain receptor 1. J Proteomics 2011; 75:3465-77. [PMID: 22057045 DOI: 10.1016/j.jprot.2011.10.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 09/30/2011] [Accepted: 10/06/2011] [Indexed: 11/24/2022]
Abstract
The receptor tyrosine kinase DDR1 has been implicated in multiple human cancers and fibrosis and is targeted by the leukemia drug Gleevec. This suggests that DDR1 might be a new therapeutic target. However, further insight into the DDR1 signaling pathway is required in order to support its further development. Here, we investigated DDR1 proximal signaling by the analysis of protein-protein interactions using proteomic approaches. All known interactors of DDR1 were identified and localized to specific phosphotyrosine residues on the receptor. In addition, we identified numerous signaling proteins as new putative phosphotyrosine mediated interactors including RasGAP, SHIP1, SHIP2, STATs, PI3K and the SRC family kinases. Most of the new proteins contain SH2 and PTB domains and for all interactors we could directly point the site of interaction to specific phosphotyrosine residues on the receptor. The identified proteins have roles in the early steps of the signaling cascade, propagating the signal from the DDR1 receptor into the cell. The map of phosphotyrosine mediated interactors of DDR1 created in this study will serve as a starting point for functional investigations which will enhance our knowledge on the role of the DDR1 receptor in health and disease. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.
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Affiliation(s)
- Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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37
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Wu Z, Doondeea JB, Gholami AM, Janning MC, Lemeer S, Kramer K, Eccles SA, Gollin SM, Grenman R, Walch A, Feller SM, Kuster B. Quantitative chemical proteomics reveals new potential drug targets in head and neck cancer. Mol Cell Proteomics 2011; 10:M111.011635. [PMID: 21955398 DOI: 10.1074/mcp.m111.011635] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tumors of the head and neck represent a molecularly diverse set of human cancers, but relatively few proteins have actually been shown to drive the disease at the molecular level. To identify new targets for individualized diagnosis or therapeutic intervention, we performed a kinase centric chemical proteomics screen and quantified 146 kinases across 34 head and neck squamous cell carcinoma (HNSCC) cell lines using intensity-based label-free mass spectrometry. Statistical analysis of the profiles revealed significant intercell line differences for 42 kinases (p < 0.05), and loss of function experiments using siRNA in high and low expressing cell lines identified kinases including EGFR, NEK9, LYN, JAK1, WEE1, and EPHA2 involved in cell survival and proliferation. EGFR inhibition by the small molecule inhibitors lapatinib, gefitinib, and erlotinib as well as siRNA led to strong reduction of viability in high but not low expressing lines, confirming EGFR as a drug target in 10-20% of HNSCC cell lines. Similarly, high, but not low EPHA2-expressing cells showed strongly reduced viability concomitant with down-regulation of AKT and ERK signaling following EPHA2 siRNA treatment or EPHA1-Fc ligand exposure, suggesting that EPHA2 is a novel drug target in HNSCC. This notion is underscored by immunohistochemical analyses showing that high EPHA2 expression is detected in a subset of HNSCC tissues and is associated with poor prognosis. Given that the approved pan-SRC family kinase inhibitor dasatinib is also a very potent inhibitor of EPHA2, our findings may lead to new therapeutic options for HNSCC patients. Importantly, the strategy employed in this study is generic and therefore also of more general utility for the identification of novel drug targets and molecular pathway markers in tumors. This may ultimately lead to a more rational approach to individualized cancer diagnosis and therapy.
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Affiliation(s)
- Zhixiang Wu
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
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38
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Ding VMY, Boersema PJ, Foong LY, Preisinger C, Koh G, Natarajan S, Lee DY, Boekhorst J, Snel B, Lemeer S, Heck AJR, Choo A. Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells. PLoS One 2011; 6:e17538. [PMID: 21437283 PMCID: PMC3060089 DOI: 10.1371/journal.pone.0017538] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 02/08/2011] [Indexed: 01/05/2023] Open
Abstract
The role of fibroblast growth factor-2 (FGF-2) in maintaining undifferentiated human embryonic stem cells (hESC) was investigated using a targeted phosphoproteomics approach to specifically profile tyrosine phosphorylation events following FGF-2 stimulation. A cumulative total number of 735 unique tyrosine phosphorylation sites on 430 proteins were identified, by far the largest inventory to date for hESC. Early signaling events in FGF-2 stimulated hESC were quantitatively monitored using stable isotope dimethyl labeling, resulting in temporal tyrosine phosphorylation profiles of 316 unique phosphotyrosine peptides originating from 188 proteins. Apart from the rapid activation of all four FGF receptors, trans-activation of several other receptor tyrosine kinases (RTKs) was observed as well as induced tyrosine phosphorylation of downstream proteins such as PI3-K, MAPK and several Src family members. Both PI3-K and MAPK have been linked to hESC maintenance through FGF-2 mediated signaling. The observed activation of the Src kinase family members by FGF-2 and loss of pluripotent marker expression post Src kinase inhibition may point to the regulation of cytoskeletal and actin depending processes to maintain undifferentiated hESC.
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Affiliation(s)
- Vanessa M. Y. Ding
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Centre for Life Sciences (CeLS), NUS Graduate School for Integrative Sciences and Engineering (NGS), Singapore, Singapore
| | - Paul J. Boersema
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Leong Yan Foong
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Christian Preisinger
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Geoffrey Koh
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Subaashini Natarajan
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dong-Yup Lee
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Centre for Life Sciences (CeLS), NUS Graduate School for Integrative Sciences and Engineering (NGS), Singapore, Singapore
| | - Jos Boekhorst
- Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Berend Snel
- Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
- Centre for Biomedical Genetics, Utrecht, The Netherlands
- * E-mail: (AC); (AJRH)
| | - Andre Choo
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Division of Bioengineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore
- * E-mail: (AC); (AJRH)
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Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T, Bantscheff M, Kuster B. Confident phosphorylation site localization using the Mascot Delta Score. Mol Cell Proteomics 2010; 10:M110.003830. [PMID: 21057138 DOI: 10.1074/mcp.m110.003830] [Citation(s) in RCA: 222] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Large scale phosphorylation analysis is more and more getting into focus of proteomic research. Although it is now possible to identify thousands of phosphorylated peptides in a biological system, confident site localization remains challenging. Here we validate the Mascot Delta Score (MD-score) as a simple method that achieves similar sensitivity and specificity for phosphosite localization as the published Ascore, which is mainly used in conjunction with Sequest. The MD-score was evaluated using liquid chromatography-tandem MS data of 180 individually synthesized phosphopeptides with precisely known phosphorylation sites. We tested the MD-score for a wide range of commonly available fragmentation methods and found it to be applicable throughout with high statistical significance. However, the different fragmentation techniques differ strongly in their ability to localize phosphorylation sites. At 1% false localization rate, the highest number of correctly assigned phosphopeptides was achieved by higher energy collision induced dissociation in combination with an Orbitrap mass analyzer followed very closely by low resolution ion trap spectra obtained after electron transfer dissociation. Both these methods are significantly better than low resolution spectra acquired after collision induced dissociation and multi stage activation. Score thresholds determined from simple calibration functions for each fragmentation method were stable over replicate analyses of the phosphopeptide set. The MD-score outperforms the Ascore for tyrosine phosphorylated peptides and we further show that the ability to call sites correctly increases with increasing distance of two candidate sites within a peptide sequence. The MD-score does not require complex computational steps which makes it attractive in terms of practical utility. We provide all mass spectra and the synthetic peptides to the community so that the development of present and future localization software can be benchmarked and any laboratory can determine MD-scores and localization probabilities for their individual analytical set up.
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40
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Boersema PJ, Foong LY, Ding VMY, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo ABH, Heck AJR. In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. Mol Cell Proteomics 2009; 9:84-99. [PMID: 19770167 DOI: 10.1074/mcp.m900291-mcp200] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [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] Open
Abstract
Several mass spectrometry-based assays have emerged for the quantitative profiling of cellular tyrosine phosphorylation. Ideally, these methods should reveal the exact sites of tyrosine phosphorylation, be quantitative, and not be cost-prohibitive. The latter is often an issue as typically several milligrams of (stable isotope-labeled) starting protein material are required to enable the detection of low abundance phosphotyrosine peptides. Here, we adopted and refined a peptidecentric immunoaffinity purification approach for the quantitative analysis of tyrosine phosphorylation by combining it with a cost-effective stable isotope dimethyl labeling method. We were able to identify by mass spectrometry, using just two LC-MS/MS runs, more than 1100 unique non-redundant phosphopeptides in HeLa cells from about 4 mg of starting material without requiring any further affinity enrichment as close to 80% of the identified peptides were tyrosine phosphorylated peptides. Stable isotope dimethyl labeling could be incorporated prior to the immunoaffinity purification, even for the large quantities (mg) of peptide material used, enabling the quantification of differences in tyrosine phosphorylation upon pervanadate treatment or epidermal growth factor stimulation. Analysis of the epidermal growth factor-stimulated HeLa cells, a frequently used model system for tyrosine phosphorylation, resulted in the quantification of 73 regulated unique phosphotyrosine peptides. The quantitative data were found to be exceptionally consistent with the literature, evidencing that such a targeted quantitative phosphoproteomics approach can provide reproducible results. In general, the combination of immunoaffinity purification of tyrosine phosphorylated peptides with large scale stable isotope dimethyl labeling provides a cost-effective approach that can alleviate variation in sample preparation and analysis as samples can be combined early on. Using this approach, a rather complete qualitative and quantitative picture of tyrosine phosphorylation signaling events can be generated.
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Affiliation(s)
- Paul J Boersema
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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Lemeer S, Jopling C, Gouw J, Mohammed S, Heck AJR, Slijper M, den Hertog J. Comparative phosphoproteomics of zebrafish Fyn/Yes morpholino knockdown embryos. Mol Cell Proteomics 2008; 7:2176-87. [PMID: 18550893 DOI: 10.1074/mcp.m800081-mcp200] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [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
The coordinated movement of cells is indispensable for normal vertebrate gastrulation. Several important players and signaling pathways have been identified in convergence and extension (CE) cell movements during gastrulation, including non-canonical Wnt signaling. Fyn and Yes, members of the Src family of kinases, are key regulators of CE movements as well. Here we investigated signaling pathways in early development by comparison of the phosphoproteome of wild type zebrafish embryos with Fyn/Yes knockdown embryos that display specific CE cell movement defects. For quantitation we used differential stable isotope labeling by reductive amination of peptides. Equal amounts of labeled peptides from wild type and Fyn/Yes knockdown embryos were mixed and analyzed by on-line reversed phase TiO(2)-reversed phase LC-MS/MS. Phosphorylated and non-phosphorylated peptides were quantified, and significant changes in protein expression and/or phosphorylation were detected. We identified 348 phosphoproteins of which 69 showed a decrease in phosphorylation in Fyn/Yes knockdown embryos and 72 showed an increase in phosphorylation. Among these phosphoproteins were known regulators of cell movements, including Adducin and PDLIM5. Our results indicate that quantitative phosphoproteomics combined with morpholino-mediated knockdowns can be used to identify novel signaling pathways that act in zebrafish development in vivo.
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Affiliation(s)
- Simone Lemeer
- Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
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Lemeer S, Pinkse MWH, Mohammed S, van Breukelen B, den Hertog J, Slijper M, Heck AJR. Online Automated in Vivo Zebrafish Phosphoproteomics: From Large-Scale Analysis Down to a Single Embryo. J Proteome Res 2008; 7:1555-64. [DOI: 10.1021/pr700667w] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Martijn W. H. Pinkse
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bas van Breukelen
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jeroen den Hertog
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Monique Slijper
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Mohammed S, Kraiczek K, Pinkse MWH, Lemeer S, Benschop JJ, Heck AJR. Chip-Based Enrichment and NanoLC−MS/MS Analysis of Phosphopeptides from Whole Lysates. J Proteome Res 2008; 7:1565-71. [DOI: 10.1021/pr700635a] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Karsten Kraiczek
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Martijn W. H. Pinkse
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Joris J. Benschop
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
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Lemeer S, Ruijtenbeek R, Pinkse MWH, Jopling C, Heck AJR, den Hertog J, Slijper M. Endogenous phosphotyrosine signaling in zebrafish embryos. Mol Cell Proteomics 2007; 6:2088-99. [PMID: 17698882 DOI: 10.1074/mcp.m600482-mcp200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the developing embryo, cell growth, differentiation, and migration are strictly regulated by complex signaling pathways. One of the most important cell signaling mechanisms is protein phosphorylation on tyrosine residues, which is tightly controlled by protein-tyrosine kinases and protein-tyrosine phosphatases. Here we investigated endogenous phosphotyrosine signaling in developing zebrafish embryos. Tyrosine phosphorylated proteins were immunoaffinity-purified from zebrafish embryos at 3 and 5 days postfertilization and identified by multidimensional LC-MS. Among the identified proteins were tyrosine kinases, including Src family kinases, Eph receptor kinases, and focal adhesion kinases, as well as the adaptor proteins paxillin, p130Cas, and Crk. We identified several known and some unknown in vivo tyrosine phosphorylation sites in these proteins. Whereas most immunoaffinity-purified proteins were detected at both developmental stages, significant differences in abundance and/or phosphorylation state were also observed. In addition, multiplex in vitro kinase assays were performed by incubating a microarray of peptide substrates with the lysates of the two developmental stages. Many of the in vivo observations were confirmed by this on-chip in vitro kinase assay. Our experiments are the first to show that global tyrosine phosphorylation-mediated signaling can be studied at endogenous levels in complex multicellular organisms.
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Affiliation(s)
- Simone Lemeer
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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Lemeer S, Jopling C, Naji F, Ruijtenbeek R, Slijper M, Heck AJ, den Hertog J. Protein-tyrosine kinase activity profiling in knock down zebrafish embryos. PLoS One 2007; 2:e581. [PMID: 17611617 PMCID: PMC1895888 DOI: 10.1371/journal.pone.0000581] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Accepted: 05/30/2007] [Indexed: 11/29/2022] Open
Abstract
Background Protein-tyrosine kinases (PTKs) regulate virtually all biological processes. PTKs phosphorylate substrates in a sequence-specific manner and relatively short peptide sequences determine selectivity. Here, we developed new technology to determine PTK activity profiles using peptide arrays. The zebrafish is an excellent model system to investigate signaling in the whole organism, given its wealth of genetic tools, including morpholino-mediated knock down technology. We used zebrafish embryo lysates to determine PTK activity profiles, thus providing the unique opportunity to directly compare the effect of protein knock downs on PTK activity profiles on the one hand and phenotypic changes on the other. Methodology We used multiplex arrays of 144 distinct peptides, spotted on a porous substrate, allowing the sample to be pumped up and down, optimizing reaction kinetics. Kinase reactions were performed using complex zebrafish embryo lysates or purified kinases. Peptide phosphorylation was detected by fluorescent anti-phosphotyrosine antibody binding and the porous chips allowed semi-continuous recording of the signal. We used morpholinos to knock down protein expression in the zebrafish embryos and subsequently, we determined the effects on the PTK activity profiles. Results and Conclusion Reproducible PTK activity profiles were derived from one-day-old zebrafiish embryos. Morpholino-mediated knock downs of the Src family kinases, Fyn and Yes, induced characteristic phenotypes and distinct changes in the PTK activity profiles. Interestingly, the peptide substrates that were less phosphorylated upon Fyn and Yes knock down were preferential substrates of purified Fyn and Yes. Previously, we demonstrated that Wnt11 knock down phenocopied Fyn/Yes knock down. Interestingly, Wnt11 knock down induced similar changes in the PTK activity profile as Fyn/Yes knock down. The control Nacre/Mitfa knock down did not affect the PTK activity profile significantly. Our results indicate that the novel peptide chip technology can be used to unravel kinase signaling pathways in vivo.
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Affiliation(s)
- Simone Lemeer
- Hubrecht Institute, Utrecht, The Netherlands
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | | | - Faris Naji
- Pamgene International B.V., Hertogenbosch, The Netherlands
| | | | - Monique Slijper
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Albert J.R. Heck
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jeroen den Hertog
- Hubrecht Institute, Utrecht, The Netherlands
- * To whom correspondence should be addressed. E-mail:
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Yang J, Groen A, Lemeer S, Jans A, Slijper M, Roe SM, den Hertog J, Barford D. Reversible oxidation of the membrane distal domain of receptor PTPalpha is mediated by a cyclic sulfenamide. Biochemistry 2007; 46:709-19. [PMID: 17223692 DOI: 10.1021/bi061546m] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein tyrosine phosphatases (PTPs) are fundamental to the regulation of cellular signalling cascades triggered by protein tyrosine kinases. Most receptor-like PTPs (RPTPs) comprise two tandem PTP domains, with only the membrane proximal domains (D1) having significant phosphatase activity; the membrane distal domains (D2) display little to no catalytic activity. Intriguingly, however, many RPTP D2s share the catalytically essential Cys and Arg residues of D1s. D2 of RPTPalpha may function as a redox sensor that mediates regulation of D1 via reactive oxygen species. Oxidation of Cys723 of RPTPalpha D2 (equivalent to PTP catalytic Cys residues) stabilizes RPTPalpha dimers, induces rotational coupling, and is required for inactivation of D1 phosphatase activity. Here, we investigated the structural consequences of RPTPalpha D2 oxidation. Exposure of RPTPalpha D2 to oxidants promotes formation of a cyclic sulfenamide species, a reversibly oxidized state of Cys723, accompanied by conformational changes of the D2 catalytic site. The cyclic sulfenamide is highly resistant to terminal oxidation to sulfinic and sulfonic acids. Conformational changes associated with RPTPalpha D2 oxidation have implications for RPTPalpha quaternary structure and allosteric regulation of D1 phosphatase activity.
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MESH Headings
- Amides/chemistry
- Amino Acid Sequence
- Animals
- Chromatography, Gel
- Crystallography, X-Ray
- Cysteine/chemistry
- Dimerization
- Hydrogen Peroxide/chemistry
- Mice
- Models, Molecular
- Oxidation-Reduction
- Protein Conformation/drug effects
- Protein Structure, Quaternary
- Protein Structure, Tertiary
- Protein Tyrosine Phosphatases/chemistry
- Protein Tyrosine Phosphatases/immunology
- Reactive Oxygen Species/chemistry
- Receptor-Like Protein Tyrosine Phosphatases, Class 4
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/immunology
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Sulfenic Acids/chemistry
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Affiliation(s)
- Jing Yang
- Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, United Kingdom
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Groen A, Lemeer S, van der Wijk T, Overvoorde J, Heck AJR, Ostman A, Barford D, Slijper M, den Hertog J. Differential Oxidation of Protein-tyrosine Phosphatases. J Biol Chem 2005; 280:10298-304. [PMID: 15623519 DOI: 10.1074/jbc.m412424200] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxidation is emerging as an important regulatory mechanism of protein-tyrosine phosphatases (PTPs). Here we report that PTPs are differentially oxidized, and we provide evidence for the underlying mechanism. The membrane-proximal RPTPalpha-D1 was catalytically active but not readily oxidized as assessed by immunoprobing with an antibody that recognized oxidized catalytic site cysteines in PTPs (oxPTPs). In contrast, the membrane-distal RPTPalpha-D2, a poor PTP, was readily oxidized. Oxidized catalytic site cysteines in PTP immunoprobing and mass spectrometry demonstrated that mutation of two residues in the Tyr(P) loop and the WPD loop that reverse catalytic activity of RPTPalpha-D1 and RPTPalpha-D2 also reversed oxidizability, suggesting that oxidizability and catalytic activity are coupled. However, catalytically active PTP1B and LAR-D1 were readily oxidized. Oxidizability was strongly dependent on pH, indicating that the microenvironment of the catalytic cysteine has an important role. Crystal structures of PTP domains demonstrated that the orientation of the absolutely conserved PTP loop arginine correlates with oxidizability of PTPs, and consistently, RPTPmu-D1, with a similar conformation as RPTPalpha-D1, was not readily oxidized. In conclusion, PTPs are differentially oxidized at physiological pH and H(2)O(2) concentrations, and the PTP loop arginine is an important determinant for susceptibility to oxidation.
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Affiliation(s)
- Arnoud Groen
- Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Rappoport JZ, Taha BW, Lemeer S, Benmerah A, Simon SM. The AP-2 complex is excluded from the dynamic population of plasma membrane-associated clathrin. J Biol Chem 2003; 278:47357-60. [PMID: 14530274 DOI: 10.1074/jbc.c300390200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Numerous biologically relevant substrates are selectively internalized via clathrin-mediated endocytosis. At the plasma membrane the AP-2 complex plays a major role in clathrin coat formation, interacting with both cargo and clathrin. Utilizing simultaneous dual-channel total internal reflection fluorescence microscopy we have analyzed components of the AP-2 complex (alpha- and beta 2-adaptin) during clathrin-mediated endocytosis. Although in static images enhanced green fluorescent protein-tagged AP-2 markers significantly co-localized with clathrin and other components of clathrin-coated pits, AP-2 did not seem to be present in clathrin spots that appeared to undergo internalization or motility parallel to the plane of the plasma membrane. Two populations of clathrin at the plasma membrane seem to exist, the dynamic and the static, and AP-2 appears to be only found within the latter. These results suggest that colocalized clathrin/AP-2 puncta may represent loci for coated pit production and that previous models that assumed AP-2 was retained within clathrin coats during endocytosis may need to be re-evaluated.
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Affiliation(s)
- Joshua Z Rappoport
- The Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York 10021, USA
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Klapisz E, Sorokina I, Lemeer S, Pijnenburg M, Verkleij AJ, van Bergen en Henegouwen PMP. A ubiquitin-interacting motif (UIM) is essential for Eps15 and Eps15R ubiquitination. J Biol Chem 2002; 277:30746-53. [PMID: 12072436 DOI: 10.1074/jbc.m203004200] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An important negative control mechanism in the signaling of epidermal growth factor (EGF) is the endocytosis and subsequent degradation of activated EGF receptors. Eps15 and its related partner Eps15R play a key role in clathrin-mediated endocytosis of transmembrane receptors. Upon EGF stimulation of the cell, Eps15 becomes both phosphorylated on tyrosine residues and monoubiquitinated. Although tyrosine phosphorylation of Eps15 has been implicated in EGF receptor internalization, the function of Eps15 ubiquitination is not known. Using a mutational approach, we have found that the second ubiquitin-interacting motif (UIM) of Eps15 and Eps15R is essential for their ubiquitination. This UIM partially overlaps with the recently characterized nuclear export signal in Eps15. We show that these two overlapping motifs have different structural requirements with respect to nuclear export signal versus ubiquitination signal activity. Our data demonstrate that the UIM does not contain the ubiquitin acceptor site but functions as a recruitment site for the ubiquitination machinery leading to the monoubiquitination of both Eps15 and Eps15R.
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Affiliation(s)
- Elsa Klapisz
- Molecular Cell Biology, Institute of Biomembranes, Universiteit Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
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