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Offensperger F, Tin G, Duran-Frigola M, Hahn E, Dobner S, Ende CWA, Strohbach JW, Rukavina A, Brennsteiner V, Ogilvie K, Marella N, Kladnik K, Ciuffa R, Majmudar JD, Field SD, Bensimon A, Ferrari L, Ferrada E, Ng A, Zhang Z, Degliesposti G, Boeszoermenyi A, Martens S, Stanton R, Müller AC, Hannich JT, Hepworth D, Superti-Furga G, Kubicek S, Schenone M, Winter GE. Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells. Science 2024; 384:eadk5864. [PMID: 38662832 DOI: 10.1126/science.adk5864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 03/22/2024] [Indexed: 05/04/2024]
Abstract
Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advanced fragment-based ligand discovery toward cellular systems, but throughput limitations have stymied the scalable identification of fragment-protein interactions. We report proteome-wide maps of protein-binding propensity for 407 structurally diverse small-molecule fragments. We verified that identified interactions can be advanced to active chemical probes of E3 ubiquitin ligases, transporters, and kinases. Integrating machine learning binary classifiers further enabled interpretable predictions of fragment behavior in cells. The resulting resource of fragment-protein interactions and predictive models will help to elucidate principles of molecular recognition and expedite ligand discovery efforts for hitherto undrugged proteins.
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Affiliation(s)
- Fabian Offensperger
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gary Tin
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Miquel Duran-Frigola
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Ersilia Open Source Initiative, Cambridge CB1 3DE, UK
| | - Elisa Hahn
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sarah Dobner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Andrea Rukavina
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vincenth Brennsteiner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Kevin Ogilvie
- Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Nara Marella
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Katharina Kladnik
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Rodolfo Ciuffa
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Ariel Bensimon
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Luca Ferrari
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Evandro Ferrada
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Amanda Ng
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Zhechun Zhang
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - Gianluca Degliesposti
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andras Boeszoermenyi
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Robert Stanton
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - André C Müller
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - J Thomas Hannich
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Giulio Superti-Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Georg E Winter
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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2
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Bernhardt D, Peeken JC, Kehl V, Eitz K, Guckenberger M, Andratschke N, Mayinger MC, Lindel K, Dieckmann K, El Shafie R, Debus J, Riesterer O, Rogers S, Blanck O, Wolff R, Grosu A, Bilger A, Henkenberens C, Schulze K, Gani C, Müller AC, Radlanski K, Janssen S, Ferentinos K, Combs SE. Post-Operative Stereotactic Radiotherapy for Resected Brain Metastases: Results of the Multicenter Analysis (AURORA) of the German Working Group "Stereotactic Radiotherapy". Int J Radiat Oncol Biol Phys 2023; 117:e87-e88. [PMID: 37786203 DOI: 10.1016/j.ijrobp.2023.06.842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) While the results of prospective studies support the use of postoperative stereotactic radiotherapy (RT) to the resection cavity (RC) as the standard of care after surgery, there are several issues that need to be investigated such as factors for improving local control, risk of leptomeningeal disease and radiation necrosis. Further, the optimal dose and fractionation is still under debate. MATERIALS/METHODS The working group "Stereotactic Radiotherapy" of the German Society of Radiation Oncology (DEGRO) analyzed its multi-institutional database with 661 patients who received postoperative stereotactic RT to the RC. Treatment was performed at 13 centers between 2008 and 2021. Patient characteristics, treatment details, and follow-up data including overall survival (OS), local control (LC) were evaluated. Cox Regression and Kaplan-Meier curves with Log-rank Tests were calculated for selected variables. RESULTS In this retrospective study, overall survival was 61.5% at 1 year, 47.6% at 2 years, and 35.5% at 3 years, and local control was 84.6% at 1 year, 74.8% at 2 years, and 72.8% at 3 years. 96% of patients were treated with hypofractionated stereotactic radiotherapy (HSRT), only 26 patients received single fraction radiosurgery (4%). Prognostic factors associated with overall survival were Karnofsky Performance Status, RPA and GPA class, controlled primary tumor and absence of extracranial metastases, whereas prognostic factor associated with local control was planning target volume (23 mL or less). CONCLUSION HSRT is the most common fractionation form in the treatment of RCs in this multicenter analysis. This approach results in excellent OS and LC outcomes. OS in patients with resected brain metastases is mainly influenced by performance status. In regard to local control, RT of large cavities remain a challenge with significantly worse outcome.
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Affiliation(s)
- D Bernhardt
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, Germany, Munich, Germany
| | - J C Peeken
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany; Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Center Munich, Munich, Germany
| | - V Kehl
- Institute for AI and Informatics in Medicine, Munich, NA, Germany
| | - K Eitz
- Department of Radiation Oncology - Klinikum rechts der Isar, Technical University of Munich (TUM), Munich, Germany
| | - M Guckenberger
- Department of Radiation Oncology, University Hospital Zurich (USZ), University of Zurich (UZH), Zurich, Switzerland
| | - N Andratschke
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - M C Mayinger
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - K Lindel
- Municipal Hospital, Department for Radiation Oncology, Karlsruhe, Germany
| | - K Dieckmann
- Department of Radiation Oncology, Vienna, Austria
| | - R El Shafie
- 8Department of Radiation Oncology, University Hospital Göttingen, Göttingen, Germany
| | - J Debus
- CCU Translational Radiation Oncology, German Cancer Consortium (DKTK) Core-Center Heidelberg, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany; Radiation Oncology University Hospital Heidelberg, Heidelberg, Germany
| | - O Riesterer
- Center for Radiation Oncology KSA-KSB, Cantonal Hospital Aarau, Aarau, Switzerland
| | - S Rogers
- Radiation Oncology Center KSA-KSB, Kantonsspital Aarau, Aarau, Switzerland
| | - O Blanck
- Department of Radiation Oncology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - R Wolff
- University Hospital Frankfurt, Department of Neurosurgery, Frankfurt, Germany
| | - A Grosu
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany; Department of Radiation Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - A Bilger
- Department of Radiation Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - C Henkenberens
- Department of Radiotherapy and Special Oncology, Medical School Hannover, Hannover, Germany
| | - K Schulze
- Klinikum Fulda, 36251 Bad Hersfeld, Germany
| | - C Gani
- Department of Radiation Oncology, University Hospital and Medical Faculty Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany
| | - A C Müller
- Department of Radiotherapy, Klinikum Ludwigsburg, Ludwigsburg, Germany
| | - K Radlanski
- Radiation Oncology and Radiotherapy, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - S Janssen
- Department of Radiation Oncology, University of Lübeck, Lübeck, Germany
| | - K Ferentinos
- Radiation Oncology Department, German Oncology Center, Limassol, Cyprus
| | - S E Combs
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany; Institute of Innovative Radiotherapy (iRT), Department of Radiation Sciences (DRS), Helmholtz Zentrum München, Neuherberg, Germany
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3
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Moretton A, Kourtis S, Gañez Zapater A, Calabrò C, Espinar Calvo ML, Fontaine F, Darai E, Abad Cortel E, Block S, Pascual-Reguant L, Pardo-Lorente N, Ghose R, Vander Heiden MG, Janic A, Müller AC, Loizou JI, Sdelci S. A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability. Mol Syst Biol 2023:e11267. [PMID: 37259925 DOI: 10.15252/msb.202211267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Abstract
While cellular metabolism impacts the DNA damage response, a systematic understanding of the metabolic requirements that are crucial for DNA damage repair has yet to be achieved. Here, we investigate the metabolic enzymes and processes that are essential for the resolution of DNA damage. By integrating functional genomics with chromatin proteomics and metabolomics, we provide a detailed description of the interplay between cellular metabolism and the DNA damage response. Further analysis identified that Peroxiredoxin 1, PRDX1, contributes to the DNA damage repair. During the DNA damage response, PRDX1 translocates to the nucleus where it reduces DNA damage-induced nuclear reactive oxygen species. Moreover, PRDX1 loss lowers aspartate availability, which is required for the DNA damage-induced upregulation of de novo nucleotide synthesis. In the absence of PRDX1, cells accumulate replication stress and DNA damage, leading to proliferation defects that are exacerbated in the presence of etoposide, thus revealing a role for PRDX1 as a DNA damage surveillance factor.
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Affiliation(s)
- Amandine Moretton
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Savvas Kourtis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antoni Gañez Zapater
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Chiara Calabrò
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Maria Lorena Espinar Calvo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Frédéric Fontaine
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Evangelia Darai
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Etna Abad Cortel
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Samuel Block
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laura Pascual-Reguant
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Natalia Pardo-Lorente
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ritobrata Ghose
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ana Janic
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Joanna I Loizou
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sara Sdelci
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
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4
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Casteels T, Bajew S, Reiniš J, Enders L, Schuster M, Fontaine F, Müller AC, Wagner BK, Bock C, Kubicek S. SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression. Cell Rep 2022; 40:111288. [PMID: 36044849 DOI: 10.1016/j.celrep.2022.111288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 04/06/2022] [Accepted: 08/09/2022] [Indexed: 11/28/2022] Open
Abstract
Insulin expression is primarily restricted to the pancreatic β cells, which are physically or functionally depleted in diabetes. Identifying targetable pathways repressing insulin in non-β cells, particularly in the developmentally related glucagon-secreting α cells, is an important aim of regenerative medicine. Here, we perform an RNA interference screen in a murine α cell line to identify silencers of insulin expression. We discover that knockdown of the splicing factor Smndc1 triggers a global repression of α cell gene-expression programs in favor of increased β cell markers. Mechanistically, Smndc1 knockdown upregulates the β cell transcription factor Pdx1 by modulating the activities of the BAF and Atrx chromatin remodeling complexes. SMNDC1's repressive role is conserved in human pancreatic islets, its loss triggering enhanced insulin secretion and PDX1 expression. Our study identifies Smndc1 as a key factor connecting splicing and chromatin remodeling to the control of insulin expression in human and mouse islet cells.
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Affiliation(s)
- Tamara Casteels
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Simon Bajew
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Jiří Reiniš
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Lennart Enders
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Frédéric Fontaine
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | | | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria; Medical University of Vienna, Center for Medical Statistics, Informatics, and Intelligent Systems, Institute of Artificial Intelligence, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria.
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5
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Mötz M, Stas MR, Hammer SE, Duckova T, Fontaine F, Kiesler A, Seitz K, Ladinig A, Müller AC, Riedel C, Saalmüller A, Rümenapf T. Identification of MHC-I-Presented Porcine Respiratory and Reproductive Syndrome Virus (PRRSV) Peptides Reveals Immunogenic Epitopes within Several Non-Structural Proteins Recognized by CD8+ T Cells. Viruses 2022; 14:v14091891. [PMID: 36146698 PMCID: PMC9502253 DOI: 10.3390/v14091891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most relevant porcine pathogens worldwide. Active control of the disease relies on modified live virus vaccines (MLVs), as most inactivated vaccines provide very limited protection. Neutralizing antibodies occur late in infection; therefore, CD8+ T cells are considered important correlates of protection and are a frequent focus of investigation. Our aim was to identify viral peptides naturally bound by the class I major histocompatibility complex (MHC-I) and to confirm their ability to stimulate CD8+ T cells. For this purpose, we immunoprecipitated MHC-I/peptide complexes of PRRSV (strain AUT15-33) -infected cells (SLA-I Lr-Hp 35.0/24 mod) to isolate the viral epitopes and analyzed them with liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Furthermore, we employed these identified peptides to stimulate peripheral blood mononuclear cells (PBMCs) of previously PRRSV-infected pigs and measured the PRRSV-specific CD8+ T-cell response with an intracellular cytokine staining (ICS). Our data revealed that PRRSV non-structural proteins (NSPs), encoded in open reading frame 1a and 1b (ORF1), present the major source of MHC-I-presented peptides. Additionally, we show that our identified epitopes are able to trigger IFNγ responses in vitro. These findings are a basis for understanding the proteasomal degradation of PRRSV proteins, the cellular ability to display them via MHC-I, and their potential to restimulate CD8+ T cells.
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Affiliation(s)
- Marlene Mötz
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
- Correspondence: (M.M.); (T.R.)
| | - Melissa R. Stas
- Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Sabine E. Hammer
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Tereza Duckova
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Frederic Fontaine
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Alexandra Kiesler
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Kerstin Seitz
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Andrea Ladinig
- Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - André C. Müller
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Christiane Riedel
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Armin Saalmüller
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Till Rümenapf
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
- Correspondence: (M.M.); (T.R.)
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6
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Tabata K, Prasad V, Paul D, Lee JY, Pham MT, Twu WI, Neufeldt CJ, Cortese M, Cerikan B, Stahl Y, Joecks S, Tran CS, Lüchtenborg C, V'kovski P, Hörmann K, Müller AC, Zitzmann C, Haselmann U, Beneke J, Kaderali L, Erfle H, Thiel V, Lohmann V, Superti-Furga G, Brügger B, Bartenschlager R. Convergent use of phosphatidic acid for hepatitis C virus and SARS-CoV-2 replication organelle formation. Nat Commun 2021; 12:7276. [PMID: 34907161 PMCID: PMC8671429 DOI: 10.1038/s41467-021-27511-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/22/2021] [Indexed: 11/09/2022] Open
Abstract
Double membrane vesicles (DMVs) serve as replication organelles of plus-strand RNA viruses such as hepatitis C virus (HCV) and SARS-CoV-2. Viral DMVs are morphologically analogous to DMVs formed during autophagy, but lipids driving their biogenesis are largely unknown. Here we show that production of the lipid phosphatidic acid (PA) by acylglycerolphosphate acyltransferase (AGPAT) 1 and 2 in the ER is important for DMV biogenesis in viral replication and autophagy. Using DMVs in HCV-replicating cells as model, we found that AGPATs are recruited to and critically contribute to HCV and SARS-CoV-2 replication and proper DMV formation. An intracellular PA sensor accumulated at viral DMV formation sites, consistent with elevated levels of PA in fractions of purified DMVs analyzed by lipidomics. Apart from AGPATs, PA is generated by alternative pathways and their pharmacological inhibition also impaired HCV and SARS-CoV-2 replication as well as formation of autophagosome-like DMVs. These data identify PA as host cell lipid involved in proper replication organelle formation by HCV and SARS-CoV-2, two phylogenetically disparate viruses causing very different diseases, i.e. chronic liver disease and COVID-19, respectively. Host-targeting therapy aiming at PA synthesis pathways might be suitable to attenuate replication of these viruses.
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Affiliation(s)
- Keisuke Tabata
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Vibhu Prasad
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - David Paul
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ji-Young Lee
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Minh-Tu Pham
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Woan-Ing Twu
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Yannick Stahl
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Sebastian Joecks
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- LI-COR Biosciences GmbH, Siemensstrasse 25A, Bad Homburg, Germany
| | - Cong Si Tran
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | | | - Philip V'kovski
- Institute of Virology and Immunology IVI, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Katrin Hörmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Carolin Zitzmann
- Institute of Bioinformatics and Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, NM, USA
| | - Uta Haselmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Jürgen Beneke
- BioQuant, Heidelberg University, Heidelberg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics and Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
| | - Holger Erfle
- BioQuant, Heidelberg University, Heidelberg, Germany
| | - Volker Thiel
- Institute of Virology and Immunology IVI, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Britta Brügger
- Biochemistry Center Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany.
- Division Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany.
- German Center for Infection Research, Heidelberg Partner Site, Heidelberg, Germany.
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Zhu C, Boucheron N, Müller AC, Májek P, Claudel T, Halilbasic E, Baazim H, Lercher A, Viczenczova C, Hainberger D, Preglej T, Sandner L, Alteneder M, Gülich AF, Khan M, Hamminger P, Remetic J, Ohradanova-Repic A, Schatzlmaier P, Donner C, Fuchs CD, Stojakovic T, Scharnagl H, Sakaguchi S, Weichhart T, Bergthaler A, Stockinger H, Ellmeier W, Trauner M. 24-Norursodeoxycholic acid reshapes immunometabolism in CD8 + T cells and alleviates hepatic inflammation. J Hepatol 2021; 75:1164-1176. [PMID: 34242699 PMCID: PMC8522806 DOI: 10.1016/j.jhep.2021.06.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND & AIMS 24-Norursodeoxycholic acid (NorUDCA) is a novel therapeutic bile acid used to treat immune-mediated cholestatic liver diseases, such as primary sclerosing cholangitis (PSC), where dysregulated T cells including CD8+ T cells contribute to hepatobiliary immunopathology. We hypothesized that NorUDCA may directly modulate CD8+ T cell function thus contributing to its therapeutic efficacy. METHODS NorUDCA's immunomodulatory effects were first studied in Mdr2-/- mice, as a cholestatic model of PSC. To differentiate NorUDCA's immunomodulatory effects on CD8+ T cell function from its anticholestatic actions, we also used a non-cholestatic model of hepatic injury induced by an excessive CD8+ T cell immune response upon acute non-cytolytic lymphocytic choriomeningitis virus (LCMV) infection. Studies included molecular and biochemical approaches, flow cytometry and metabolic assays in murine CD8+ T cells in vitro. Mass spectrometry was used to identify potential CD8+ T cell targets modulated by NorUDCA. The signaling effects of NorUDCA observed in murine cells were validated in circulating T cells from patients with PSC. RESULTS NorUDCA demonstrated immunomodulatory effects by reducing hepatic innate and adaptive immune cells, including CD8+ T cells in the Mdr2-/- model. In the non-cholestatic model of CD8+ T cell-driven immunopathology induced by acute LCMV infection, NorUDCA ameliorated hepatic injury and systemic inflammation. Mechanistically, NorUDCA demonstrated strong immunomodulatory efficacy in CD8+ T cells affecting lymphoblastogenesis, expansion, glycolysis and mTORC1 signaling. Mass spectrometry identified that NorUDCA regulates CD8+ T cells by targeting mTORC1. NorUDCA's impact on mTORC1 signaling was further confirmed in circulating PSC CD8+ T cells. CONCLUSIONS NorUDCA has a direct modulatory impact on CD8+ T cells and attenuates excessive CD8+ T cell-driven hepatic immunopathology. These findings are relevant for treatment of immune-mediated liver diseases such as PSC. LAY SUMMARY Elucidating the mechanisms by which 24-norursodeoxycholic acid (NorUDCA) works for the treatment of immune-mediated liver diseases, such as primary sclerosing cholangitis, is of considerable clinical interest. Herein, we uncovered an unrecognized property of NorUDCA in the immunometabolic regulation of CD8+ T cells, which has therapeutic relevance for immune-mediated liver diseases, including PSC.
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Affiliation(s)
- Ci Zhu
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria,Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Nicole Boucheron
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Peter Májek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thierry Claudel
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Emina Halilbasic
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Hatoon Baazim
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexander Lercher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Csilla Viczenczova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniela Hainberger
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Teresa Preglej
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Lisa Sandner
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Marlis Alteneder
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Alexandra F. Gülich
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Matarr Khan
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Patricia Hamminger
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Jelena Remetic
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Anna Ohradanova-Repic
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Philipp Schatzlmaier
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Clemens Donner
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Claudia D. Fuchs
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Tatjana Stojakovic
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, University Hospital Graz, Graz, Austria
| | - Hubert Scharnagl
- Clinical Institute of Medical and Chemical Laboratory of Diagnostics, Medical University of Graz, Graz, Austria
| | - Shinya Sakaguchi
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Thomas Weichhart
- Institute of Medical Genetics, Center of Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hannes Stockinger
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Wilfried Ellmeier
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Michael Trauner
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria.
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8
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Terlecki-Zaniewicz S, Humer T, Eder T, Schmoellerl J, Heyes E, Manhart G, Kuchynka N, Parapatics K, Liberante FG, Müller AC, Tomazou EM, Grebien F. Biomolecular condensation of NUP98 fusion proteins drives leukemogenic gene expression. Nat Struct Mol Biol 2021; 28:190-201. [PMID: 33479542 DOI: 10.1038/s41594-020-00550-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/14/2020] [Indexed: 01/15/2023]
Abstract
NUP98 fusion proteins cause leukemia via unknown molecular mechanisms. All NUP98 fusion proteins share an intrinsically disordered region (IDR) in the NUP98 N terminus, featuring repeats of phenylalanine-glycine (FG), and C-terminal fusion partners often function in gene control. We investigated whether mechanisms of oncogenic transformation by NUP98 fusion proteins are hardwired in their protein interactomes. Affinity purification coupled to mass spectrometry (MS) and confocal imaging of five NUP98 fusion proteins expressed in human leukemia cells revealed that shared interactors were enriched for proteins involved in biomolecular condensation and that they colocalized with NUP98 fusion proteins in nuclear puncta. We developed biotinylated isoxazole-mediated condensome MS (biCon-MS) to show that NUP98 fusion proteins alter the global composition of biomolecular condensates. An artificial FG-repeat-containing fusion protein phenocopied the nuclear localization patterns of NUP98 fusion proteins and their capability to drive oncogenic gene expression programs. Thus, we propose that IDR-containing fusion proteins combine biomolecular condensation with transcriptional control to induce cancer.
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Affiliation(s)
- Stefan Terlecki-Zaniewicz
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria.,Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Theresa Humer
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Eder
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Johannes Schmoellerl
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Elizabeth Heyes
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Gabriele Manhart
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | | | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fabio G Liberante
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Eleni M Tomazou
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria.
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9
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Mayor-Ruiz C, Bauer S, Brand M, Kozicka Z, Siklos M, Imrichova H, Kaltheuner IH, Hahn E, Seiler K, Koren A, Petzold G, Fellner M, Bock C, Müller AC, Zuber J, Geyer M, Thomä NH, Kubicek S, Winter GE. Rational discovery of molecular glue degraders via scalable chemical profiling. Nat Chem Biol 2020; 16:1199-1207. [PMID: 32747809 PMCID: PMC7116640 DOI: 10.1038/s41589-020-0594-x] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/15/2020] [Indexed: 11/09/2022]
Abstract
Targeted protein degradation is a new therapeutic modality based on drugs that destabilize proteins by inducing their proximity to E3 ubiquitin ligases. Of particular interest are molecular glues that can degrade otherwise unligandable proteins by orchestrating direct interactions between target and ligase. However, their discovery has so far been serendipitous, thus hampering broad translational efforts. Here, we describe a scalable strategy toward glue degrader discovery that is based on chemical screening in hyponeddylated cells coupled to a multi-omics target deconvolution campaign. This approach led us to identify compounds that induce ubiquitination and degradation of cyclin K by prompting an interaction of CDK12-cyclin K with a CRL4B ligase complex. Notably, this interaction is independent of a dedicated substrate receptor, thus functionally segregating this mechanism from all described degraders. Collectively, our data outline a versatile and broadly applicable strategy to identify degraders with nonobvious mechanisms and thus empower future drug discovery efforts.
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Affiliation(s)
- Cristina Mayor-Ruiz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sophie Bauer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Brand
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Zuzanna Kozicka
- FMI Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Elisa Hahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kristina Seiler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Georg Petzold
- FMI Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Michaela Fellner
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Nicolas H Thomä
- FMI Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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10
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Heinz LX, Lee J, Kapoor U, Kartnig F, Sedlyarov V, Papakostas K, César-Razquin A, Essletzbichler P, Goldmann U, Stefanovic A, Bigenzahn JW, Scorzoni S, Pizzagalli MD, Bensimon A, Müller AC, King FJ, Li J, Girardi E, Mbow ML, Whitehurst CE, Rebsamen M, Superti-Furga G. TASL is the SLC15A4-associated adaptor for IRF5 activation by TLR7-9. Nature 2020; 581:316-322. [PMID: 32433612 PMCID: PMC7610944 DOI: 10.1038/s41586-020-2282-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/07/2020] [Indexed: 12/20/2022]
Abstract
Toll-like receptors (TLRs) have a crucial role in the recognition of pathogens and initiation of immune responses1–3. Here we show that a previously uncharacterized protein encoded by CXorf21—a gene that is associated with systemic lupus erythematosus4,5—interacts with the endolysosomal transporter SLC15A4, an essential but poorly understood component of the endolysosomal TLR machinery also linked to autoimmune disease4,6–9. Loss of this type-I-interferon-inducible protein, which we refer to as ‘TLR adaptor interacting with SLC15A4 on the lysosome’ (TASL), abrogated responses to endolysosomal TLR agonists in both primary and transformed human immune cells. Deletion of SLC15A4 or TASL specifically impaired the activation of the IRF pathway without affecting NF-κB and MAPK signalling, which indicates that ligand recognition and TLR engagement in the endolysosome occurred normally. Extensive mutagenesis of TASL demonstrated that its localization and function relies on the interaction with SLC15A4. TASL contains a conserved pLxIS motif (in which p denotes a hydrophilic residue and x denotes any residue) that mediates the recruitment and activation of IRF5. This finding shows that TASL is an innate immune adaptor for TLR7, TLR8 and TLR9 signalling, revealing a clear mechanistic analogy with the IRF3 adaptors STING, MAVS and TRIF10,11. The identification of TASL as the component that links endolysosomal TLRs to the IRF5 transcription factor via SLC15A4 provides a mechanistic explanation for the involvement of these proteins in systemic lupus erythematosus12–14.
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Affiliation(s)
- Leonhard X Heinz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - JangEun Lee
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Utkarsh Kapoor
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Felix Kartnig
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Konstantinos Papakostas
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Adrian César-Razquin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Patrick Essletzbichler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ulrich Goldmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Adrijana Stefanovic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefania Scorzoni
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Mattia D Pizzagalli
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ariel Bensimon
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - F James King
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Jun Li
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Enrico Girardi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - M Lamine Mbow
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | | | - Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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11
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Bigenzahn JW, Collu GM, Kartnig F, Pieraks M, Vladimer GI, Heinz LX, Sedlyarov V, Schischlik F, Fauster A, Rebsamen M, Parapatics K, Blomen VA, Müller AC, Winter GE, Kralovics R, Brummelkamp TR, Mlodzik M, Superti-Furga G. Abstract A08: Genetic drug resistance screen identifies LZTR1 as regulator of RAS ubiquitination and signaling. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-a08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Small-molecule tyrosine kinase inhibitor (TKI)-based treatment of chronic myeloid leukemia (CML), directed by the presence of the Philadelphia chromosome (Ph+) encoded BCR-ABL tyrosine kinase, is a paradigm of targeted cancer therapy. However, the development of TKI resistance limits the long-term success of these therapeutics. We used a genetic screening approach in the near-haploid CML cell line KBM-7 to identify six genes whose individual loss of function led to TKI drug resistance. We investigated in detail the role of the leucine zipper-like transcription regulator 1 (LZTR1) gene, as it was mechanistically enigmatic despite its involvement in many human developmental and oncologic diseases including glioblastoma, schwannomatosis and Noonan syndrome. We found that LZTR1 inactivation led to enhanced MAPK pathway activity and reduced TKI sensitivity of CML cells in a RAS-dependent way. LZTR1 missense mutations identified in human diseases failed to revert the loss-of-function phenotype. Knockdown of the LZTR1 orthologue CG3711 in Drosophila led to an increase in ectopic wing vein formation that could be rescued by impairment of RAS gene function, confirming the epistatic relationship and suggesting an evolutionary conserved role for LZTR1 in RAS regulation. Endogenous LZTR1 protein associated with the four main RAS isoforms KRAS4A, KRAS4B, NRAS and HRAS in proximity biotinylation proteomic and immunoprecipitation experiments in a manner that for KRAS required farnesylation and palmitoylation. Ectopic expression of LZTR1 along with all four RAS proteins led to their ubiquitination, compatible with the proposed role of LZTR1 as a cullin (CUL)-3 E3 ligase adaptor. Loss of LZTR1 led to reduced ubiquitination of endogenous KRAS and its increased abundance as well as enhanced localization at the plasma membrane. Together with the work on the role of LZTR1 in diseases driven by the dysregulation of RAS ubiquitination and signaling (Steklov, Pandolfi, Baietti et al., Anna Sablina lab, KU Leuven; see separate abstract), we propose that LZTR1 acts as a conserved regulator of RAS ubiquitination and MAPK pathway activation, providing a mechanistic explanation to its genetic involvement across a variety of human pathologies.
Citation Format: Johannes W. Bigenzahn, Giovanna M. Collu, Felix Kartnig, Melanie Pieraks, Gregory I. Vladimer, Leonhard X. Heinz, Vitaly Sedlyarov, Fiorella Schischlik, Astrid Fauster, Manuele Rebsamen, Katja Parapatics, Vincent A. Blomen, André C. Müller, Georg E. Winter, Robert Kralovics, Thijn R. Brummelkamp, Marek Mlodzik, Giulio Superti-Furga. Genetic drug resistance screen identifies LZTR1 as regulator of RAS ubiquitination and signaling [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A08.
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Affiliation(s)
| | | | - Felix Kartnig
- 1CeMM Center for Molecular Medicine, Vienna, Austria,
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- 2Icahn School of Medicine at Mount Sinai, New York, NY,
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12
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Superti-Furga G, Lackner D, Wiedmer T, Ingles-Prieto A, Barbosa B, Girardi E, Goldmann U, Gürtl B, Klavins K, Klimek C, Lindinger S, Liñeiro-Retes E, Müller AC, Onstein S, Redinger G, Reil D, Sedlyarov V, Wolf G, Crawford M, Everley R, Hepworth D, Liu S, Noell S, Piotrowski M, Stanton R, Zhang H, Corallino S, Faedo A, Insidioso M, Maresca G, Redaelli L, Sassone F, Scarabottolo L, Stucchi M, Tarroni P, Tremolada S, Batoulis H, Becker A, Bender E, Chang YN, Ehrmann A, Müller-Fahrnow A, Pütter V, Zindel D, Hamilton B, Lenter M, Santacruz D, Viollet C, Whitehurst C, Johnsson K, Leippe P, Baumgarten B, Chang L, Ibig Y, Pfeifer M, Reinhardt J, Schönbett J, Selzer P, Seuwen K, Bettembourg C, Biton B, Czech J, de Foucauld H, Didier M, Licher T, Mikol V, Pommereau A, Puech F, Yaligara V, Edwards A, Bongers BJ, Heitman LH, IJzerman AP, Sijben HJ, van Westen GJ, Grixti J, Kell DB, Mughal F, Swainston N, Wright-Muelas M, Bohstedt T, Burgess-Brown N, Carpenter L, Dürr K, Hansen J, Scacioc A, Banci G, Colas C, Digles D, Ecker G, Füzi B, Gamsjäger V, Grandits M, Martini R, Troger F, Altermatt P, Doucerain C, Dürrenberger F, Manolova V, Steck AL, Sundström H, Wilhelm M, Steppan CM. The RESOLUTE consortium: unlocking SLC transporters for drug discovery. Nat Rev Drug Discov 2020; 19:429-430. [DOI: 10.1038/d41573-020-00056-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Schmidt-Hegemann NS, Kroeze SGC, Henkenberens C, Vogel MME, Kirste S, Becker J, Burger IA, Derlin T, Bartenstein P, Eiber M, Mix M, la Fougère C, Müller AC, Grosu AL, Combs SE, Christiansen H, Guckenberger M, Belka C. Influence of localization of PSMA-positive oligo-metastases on efficacy of metastasis-directed external-beam radiotherapy-a multicenter retrospective study. Eur J Nucl Med Mol Imaging 2020; 47:1852-1863. [PMID: 32002591 DOI: 10.1007/s00259-020-04708-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/22/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE Approximately 40-70% of biochemically persistent or recurrent prostate cancer (PCa) patients after radical prostatectomy (RPE) are oligo-metastatic in 68gallium-prostate-specific membrane antigen positron emission tomography (68Ga-PSMA PET). Those lesions are frequently located outside the prostate bed, and therefore not cured by the current standards of care like external-beam radiotherapy (EBRT) of the prostatic fossa. This retrospective study analyzes the influence of oligo-metastases' site on outcome after metastasis-directed radiotherapy (MDR). METHODS Retrospectively, 359 patients with PET-positive PCa recurrences after RPE were analyzed. Biochemical recurrence-free survival (BRFS) (prostate-specific antigen (PSA) < post-radiotherapy nadir + 0.2 ng/mL) was assessed using Kaplan-Meier survival and Cox regression analysis. RESULTS All patients were initially clinically without distant metastases (cM0). Seventy-five patients had local recurrence within the prostatic fossa, 32 patients had pelvic nodal plus local recurrence, 117 patients had pelvic nodal recurrence, 51 patients had paraaortic lymph node metastases with/without locoregional recurrence, and 84 patients had bone or visceral metastases with/without locoregional recurrence. Median PSA before MDR was 1.2 ng/mL (range, 0.04-47.5). Additive androgen deprivation therapy (ADT) was given in 35% (125/359) of patients. Median PSA nadir after MDR was 0.23 ng/mL (range, < 0.03-18.30). After a median follow-up of 16 months (1-57), 239/351 (68%) patients had no biochemical recurrence. Patients with distant lymph node and/or distant metastases, the so-called oligo-body cohort, had an overall in-field control of 90/98 (91%) but at the same time, an ex-field progress of 44/96 (46%). In comparison, an ex-field progress was detected in 28/154 (18%) patients with local and/or pelvic nodal recurrence (oligo-pelvis group). Compared with the oligo-pelvis group, there was a significantly lower BRFS in oligo-body patients at the last follow-up. CONCLUSION Overall, BRFS was dependent on patterns of metastatic disease. Thus, MDR of PSMA PET-positive oligo-metastases can be offered considering that about one-third of the patients progressed within a median follow-up of 16 months.
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Affiliation(s)
- N-S Schmidt-Hegemann
- Department of Radiation Oncology, University Hospital LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.
| | - S G C Kroeze
- Department of Radiation Oncology, University Hospital Zürich, Zurich, Switzerland
| | - C Henkenberens
- Department of Radiotherapy and Special Oncology, Medical School Hannover, Hannover, Germany
| | - M M E Vogel
- Department of Radiation Oncology, Technical University of Munich, Munich, Germany.,Institute of Radiation Medicine (IRM), Department of Radiation Sciences, Helmholtz Zentrum München, Unterschleissheim, Munich, Germany
| | - S Kirste
- Department of Radiation Oncology, University of Freiburg, Freiburg im Breisgau, Germany
| | - J Becker
- Department of Radiation Oncology, University Hospital Tübingen, Tübingen, Germany
| | - I A Burger
- Department of Nuclear Medicine, University Hospital Zürich, Zürich, Switzerland
| | - T Derlin
- Department of Nuclear Medicine, Hannover Medical School, Hannover, Germany
| | - P Bartenstein
- Department of Nuclear Medicine, University Hospital LMU Munich, Munich, Germany
| | - M Eiber
- Department of Nuclear Medicine, Technical University Munich, Munich, Germany
| | - M Mix
- Department of Nuclear Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Ch la Fougère
- Department of Nuclear Medicine, University Hospital Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - A C Müller
- Department of Radiation Oncology, University Hospital Tübingen, Tübingen, Germany
| | - A L Grosu
- Department of Radiation Oncology, University of Freiburg, Freiburg im Breisgau, Germany.,German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany
| | - S E Combs
- Department of Radiation Oncology, Technical University of Munich, Munich, Germany.,Institute of Radiation Medicine (IRM), Department of Radiation Sciences, Helmholtz Zentrum München, Unterschleissheim, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - H Christiansen
- Department of Radiotherapy and Special Oncology, Medical School Hannover, Hannover, Germany
| | - M Guckenberger
- Department of Radiation Oncology, University Hospital Zürich, Zurich, Switzerland
| | - C Belka
- Department of Radiation Oncology, University Hospital LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
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14
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Bigenzahn JW, Collu GM, Kartnig F, Pieraks M, Vladimer GI, Heinz LX, Sedlyarov V, Schischlik F, Fauster A, Rebsamen M, Parapatics K, Blomen VA, Müller AC, Winter GE, Kralovics R, Brummelkamp TR, Mlodzik M, Superti-Furga G. LZTR1 is a regulator of RAS ubiquitination and signaling. Science 2018; 362:1171-1177. [PMID: 30442766 DOI: 10.1126/science.aap8210] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 06/26/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
In genetic screens aimed at understanding drug resistance mechanisms in chronic myeloid leukemia cells, inactivation of the cullin 3 adapter protein-encoding leucine zipper-like transcription regulator 1 (LZTR1) gene led to enhanced mitogen-activated protein kinase (MAPK) pathway activity and reduced sensitivity to tyrosine kinase inhibitors. Knockdown of the Drosophila LZTR1 ortholog CG3711 resulted in a Ras-dependent gain-of-function phenotype. Endogenous human LZTR1 associates with the main RAS isoforms. Inactivation of LZTR1 led to decreased ubiquitination and enhanced plasma membrane localization of endogenous KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog). We propose that LZTR1 acts as a conserved regulator of RAS ubiquitination and MAPK pathway activation. Because LZTR1 disease mutations failed to revert loss-of-function phenotypes, our findings provide a molecular rationale for LZTR1 involvement in a variety of inherited and acquired human disorders.
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Affiliation(s)
- Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Giovanna M Collu
- Department of Cell, Developmental, and Regenerative Biology and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Felix Kartnig
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Melanie Pieraks
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gregory I Vladimer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Leonhard X Heinz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Fiorella Schischlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Astrid Fauster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vincent A Blomen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Thijn R Brummelkamp
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.,Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.,Cancer Genomics Center (CGC.nl), Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Marek Mlodzik
- Department of Cell, Developmental, and Regenerative Biology and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria. .,Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
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15
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Skucha A, Ebner J, Schmöllerl J, Roth M, Eder T, César-Razquin A, Stukalov A, Vittori S, Muhar M, Lu B, Aichinger M, Jude J, Müller AC, Győrffy B, Vakoc CR, Valent P, Bennett KL, Zuber J, Superti-Furga G, Grebien F. MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity. Nat Commun 2018; 9:1983. [PMID: 29777171 PMCID: PMC5959866 DOI: 10.1038/s41467-018-04329-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/23/2018] [Indexed: 12/21/2022] Open
Abstract
MLL-fusions represent a large group of leukemia drivers, whose diversity originates from the vast molecular heterogeneity of C-terminal fusion partners of MLL. While studies of selected MLL-fusions have revealed critical molecular pathways, unifying mechanisms across all MLL-fusions remain poorly understood. We present the first comprehensive survey of protein-protein interactions of seven distantly related MLL-fusion proteins. Functional investigation of 128 conserved MLL-fusion-interactors identifies a specific role for the lysine methyltransferase SETD2 in MLL-leukemia. SETD2 loss causes growth arrest and differentiation of AML cells, and leads to increased DNA damage. In addition to its role in H3K36 tri-methylation, SETD2 is required to maintain high H3K79 di-methylation and MLL-AF9-binding to critical target genes, such as Hoxa9. SETD2 loss synergizes with pharmacologic inhibition of the H3K79 methyltransferase DOT1L to induce DNA damage, growth arrest, differentiation, and apoptosis. These results uncover a dependency for SETD2 during MLL-leukemogenesis, revealing a novel actionable vulnerability in this disease.
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Affiliation(s)
- Anna Skucha
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria
| | - Jessica Ebner
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria
| | | | - Mareike Roth
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Thomas Eder
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria
| | - Adrián César-Razquin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Sarah Vittori
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Matthias Muhar
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Bin Lu
- Cold Spring Harbor Larboratory, Cold Spring Harbor, 11724, NY, USA
| | - Martin Aichinger
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Second Department of Pediatrics, Semmelweis University, Budapest, 1094, Hungary
| | | | - Peter Valent
- Department of Internal Medicine I. Division of Hematology and Hemostaseology, Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, Vienna, 1090, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, 1090, Austria
| | - Florian Grebien
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria.
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, 1210, Austria.
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16
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Lee SE, Song J, Bösl K, Müller AC, Vitko D, Bennett KL, Superti-Furga G, Pandey A, Kandasamy RK, Kim MS. Proteogenomic Analysis to Identify Missing Proteins from Haploid Cell Lines. Proteomics 2018; 18:e1700386. [DOI: 10.1002/pmic.201700386] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/14/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Seung-Eun Lee
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
- Department of Biomedical Science and TechnologyKyung Hee Medical Science Research Institute; Kyung Hee University; Yongin-si Republic of Korea
| | - JongKeon Song
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
| | - Korbinian Bösl
- Centre of Molecular Inflammation Research (SFF-CEMIR), and Department of Clinical and Molecular Medicine (IKOM); Norwegian University of Science and Technology; Trondheim Norway
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Dijana Vitko
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
- Center for Physiology and Pharmacology; Medical University of Vienna; Vienna Austria
| | - Akhilesh Pandey
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore MD USA
| | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (SFF-CEMIR), and Department of Clinical and Molecular Medicine (IKOM); Norwegian University of Science and Technology; Trondheim Norway
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
- Centre for Molecular Medicine Norway (NCMM) Nordic EMBL Partnership; University of Oslo and Oslo University Hospital; Oslo Norway
| | - Min-Sik Kim
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
- Department of Biomedical Science and TechnologyKyung Hee Medical Science Research Institute; Kyung Hee University; Yongin-si Republic of Korea
- Global Center for Pharmaceutical Ingredient Materials; Kyung Hee University; Yongin-si Republic of Korea
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17
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Lee SE, Song J, Bösl K, Müller AC, Vitko D, Bennett KL, Superti-Furga G, Pandey A, Kandasamy RK, Kim MS. Front Cover: Proteogenomic Analysis to Identify Missing Proteins from Haploid Cell Lines. Proteomics 2018. [DOI: 10.1002/pmic.201870061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Ishoey M, Chorn S, Singh N, Jaeger MG, Brand M, Paulk J, Bauer S, Erb MA, Parapatics K, Müller AC, Bennett KL, Ecker GF, Bradner JE, Winter GE. Translation Termination Factor GSPT1 Is a Phenotypically Relevant Off-Target of Heterobifunctional Phthalimide Degraders. ACS Chem Biol 2018; 13:553-560. [PMID: 29356495 DOI: 10.1021/acschembio.7b00969] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein degradation is an emerging therapeutic strategy with a unique molecular pharmacology that enables the disruption of all functions associated with a target. This is particularly relevant for proteins depending on molecular scaffolding, such as transcription factors or receptor tyrosine kinases (RTKs). To address tractability of multiple RTKs for chemical degradation by the E3 ligase CUL4-RBX1-DDB1-CRBN (CRL4CRBN), we synthesized a series of phthalimide degraders based on the promiscuous kinase inhibitors sunitinib and PHA665752. While both series failed to induce degradation of their consensus targets, individual molecules displayed pronounced efficacy in leukemia cell lines. Orthogonal target identification supported by molecular docking led us to identify the translation termination factor G1 to S phase transition 1 (GSPT1) as a converging off-target, resulting from inadvertent E3 ligase modulation. This research highlights the importance of monitoring degradation events that are independent of the respective targeting ligand as a unique feature of small-molecule degraders.
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Affiliation(s)
- Mette Ishoey
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Someth Chorn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Natesh Singh
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - Martin G. Jaeger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Matthias Brand
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Sophie Bauer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Michael A. Erb
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Gerhard F. Ecker
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - James E. Bradner
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Georg E. Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
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19
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Perego M, Maurer M, Wang JX, Shaffer S, Müller AC, Parapatics K, Li L, Hristova D, Shin S, Keeney F, Liu S, Xu X, Raj A, Jensen JK, Bennett KL, Wagner SN, Somasundaram R, Herlyn M. A slow-cycling subpopulation of melanoma cells with highly invasive properties. Oncogene 2018; 37:302-312. [PMID: 28925403 PMCID: PMC5799768 DOI: 10.1038/onc.2017.341] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/02/2017] [Accepted: 08/12/2017] [Indexed: 12/16/2022]
Abstract
Melanoma is a heterogeneous tumor with different subpopulations showing different proliferation rates. Slow-cycling cells were previously identified in melanoma, but not fully biologically characterized. Using the label-retention method, we identified a subpopulation of slow-cycling cells, defined as label-retaining cells (LRC), with strong invasive properties. We demonstrate through live imaging that LRC are leaving the primary tumor mass at a very early stage and disseminate to peripheral organs. Through global proteome analyses, we identified the secreted protein SerpinE2/protease nexin-1 as causative for the highly invasive potential of LRC in melanomas.
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Affiliation(s)
- M Perego
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - M Maurer
- Division of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna, Austria
| | - J X Wang
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - S Shaffer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - A C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - K Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - L Li
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - D Hristova
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - S Shin
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - F Keeney
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - S Liu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - X Xu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - A Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - J K Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - K L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - S N Wagner
- Division of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna, Austria
| | - R Somasundaram
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - M Herlyn
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
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20
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Licciardello MP, Ringler A, Markt P, Klepsch F, Lardeau CH, Sdelci S, Schirghuber E, Müller AC, Caldera M, Wagner A, Herzog R, Penz T, Schuster M, Boidol B, Dürnberger G, Folkvaljon Y, Stattin P, Ivanov V, Colinge J, Bock C, Kratochwill K, Menche J, Bennett KL, Kubicek S. A combinatorial screen of the CLOUD uncovers a synergy targeting the androgen receptor. Nat Chem Biol 2017; 13:771-778. [DOI: 10.1038/nchembio.2382] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/02/2017] [Indexed: 12/24/2022]
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21
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Bigenzahn JW, Fauster A, Rebsamen M, Kandasamy RK, Scorzoni S, Vladimer GI, Müller AC, Gstaiger M, Zuber J, Bennett KL, Superti-Furga G. An Inducible Retroviral Expression System for Tandem Affinity Purification Mass-Spectrometry-Based Proteomics Identifies Mixed Lineage Kinase Domain-like Protein (MLKL) as an Heat Shock Protein 90 (HSP90) Client. Mol Cell Proteomics 2016; 15:1139-50. [PMID: 26933192 PMCID: PMC4813694 DOI: 10.1074/mcp.o115.055350] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tandem affinity purification–mass spectrometry (TAP-MS) is a popular strategy for the identification of protein–protein interactions, characterization of protein complexes, and entire networks. Its employment in cellular settings best fitting the relevant physiology is limited by convenient expression vector systems. We developed an easy-to-handle, inducible, dually selectable retroviral expression vector allowing dose- and time-dependent control of bait proteins bearing the efficient streptavidin-hemagglutinin (SH)-tag at their N- or C termini. Concomitant expression of a reporter fluorophore allows to monitor bait-expressing cells by flow cytometry or microscopy and enables high-throughput phenotypic assays. We used the system to successfully characterize the interactome of the neuroblastoma RAS viral oncogene homolog (NRAS) Gly12Asp (G12D) mutant and exploited the advantage of reporter fluorophore expression by tracking cytokine-independent cell growth using flow cytometry. Moreover, we tested the feasibility of studying cytotoxicity-mediating proteins with the vector system on the cell death-inducing mixed lineage kinase domain-like protein (MLKL) Ser358Asp (S358D) mutant. Interaction proteomics analysis of MLKL Ser358Asp (S358D) identified heat shock protein 90 (HSP90) as a high-confidence interacting protein. Further phenotypic characterization established MLKL as a novel HSP90 client. In summary, this novel inducible expression system enables SH-tag-based interaction studies in the cell line proficient for the respective phenotypic or signaling context and constitutes a valuable tool for experimental approaches requiring inducible or traceable protein expression.
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Affiliation(s)
- Johannes W Bigenzahn
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Astrid Fauster
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Manuele Rebsamen
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Richard K Kandasamy
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefania Scorzoni
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gregory I Vladimer
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André C Müller
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Gstaiger
- §Department of Biology, Institute of Mol. Syst. Biol., ETH Zürich, Zürich, Switzerland
| | - Johannes Zuber
- ¶Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Keiryn L Bennett
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; ‖Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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22
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Sialana FJ, Gulyassy P, Májek P, Sjöstedt E, Kis V, Müller AC, Rudashevskaya EL, Mulder J, Bennett KL, Lubec G. Mass spectrometric analysis of synaptosomal membrane preparations for the determination of brain receptors, transporters and channels. Proteomics 2016; 16:2911-2920. [DOI: 10.1002/pmic.201600234] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 09/26/2016] [Accepted: 10/17/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Fernando J. Sialana
- Department of Pharmaceutical Chemistry; University of Vienna; Vienna Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Peter Gulyassy
- Laboratory of Proteomics; Institute of Biology; Eötvös Loránd University; Budapest Hungary
| | - Peter Májek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Evelina Sjöstedt
- Science for Life Laboratory; School of Biotechnology; KTH-Royal Institute of Technology; Stockholm Sweden
- Science for Life Laboratory; Department of Immunology; Genetics and Pathology; Uppsala University; Uppsala Sweden
| | - Viktor Kis
- Department of Anatomy; Cell and Developmental Biology; Eötvös Loránd University; Budapest Hungary
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | | | - Jan Mulder
- Science for Life Laboratory; Department of Neuroscience; Uppsala University; Uppsala Sweden
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Gert Lubec
- Department of Pharmaceutical Chemistry; University of Vienna; Vienna Austria
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23
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Müller AC, Giambruno R, Weißer J, Májek P, Hofer A, Bigenzahn JW, Superti-Furga G, Jessen HJ, Bennett KL. Identifying Kinase Substrates via a Heavy ATP Kinase Assay and Quantitative Mass Spectrometry. Sci Rep 2016; 6:28107. [PMID: 27346722 PMCID: PMC4921819 DOI: 10.1038/srep28107] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 05/31/2016] [Indexed: 01/17/2023] Open
Abstract
Mass spectrometry-based in vitro kinase screens play an essential role in the discovery of kinase substrates, however, many suffer from biological and technical noise or necessitate genetically-altered enzyme-cofactor systems. We describe a method that combines stable γ-[(18)O2]-ATP with classical in vitro kinase assays within a contemporary quantitative proteomic workflow. Our approach improved detection of known substrates of the non-receptor tyrosine kinase ABL1; and identified potential, new in vitro substrates.
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Affiliation(s)
- André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Roberto Giambruno
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Juliane Weißer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Peter Májek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandre Hofer
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Henning J Jessen
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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24
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Mazouzi A, Stukalov A, Müller AC, Chen D, Wiedner M, Prochazkova J, Chiang SC, Schuster M, Breitwieser FP, Pichlmair A, El-Khamisy SF, Bock C, Kralovics R, Colinge J, Bennett KL, Loizou JI. A Comprehensive Analysis of the Dynamic Response to Aphidicolin-Mediated Replication Stress Uncovers Targets for ATM and ATMIN. Cell Rep 2016; 15:893-908. [PMID: 27149854 DOI: 10.1016/j.celrep.2016.03.077] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 01/21/2016] [Accepted: 03/21/2016] [Indexed: 01/01/2023] Open
Abstract
The cellular response to replication stress requires the DNA-damage-responsive kinase ATM and its cofactor ATMIN; however, the roles of this signaling pathway following replication stress are unclear. To identify the functions of ATM and ATMIN in response to replication stress, we utilized both transcriptomics and quantitative mass-spectrometry-based phosphoproteomics. We found that replication stress induced by aphidicolin triggered widespread changes in both gene expression and protein phosphorylation patterns. These changes gave rise to distinct early and late replication stress responses. Furthermore, our analysis revealed previously unknown targets of ATM and ATMIN downstream of replication stress. We demonstrate ATMIN-dependent phosphorylation of H2AX and of CRMP2, a protein previously implicated in Alzheimer's disease but not in the DNA damage response. Overall, our dataset provides a comprehensive resource for discovering the cellular responses to replication stress and, potentially, associated pathologies.
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Affiliation(s)
- Abdelghani Mazouzi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria; Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Doris Chen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Marc Wiedner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Jana Prochazkova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Shih-Chieh Chiang
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Florian P Breitwieser
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Andreas Pichlmair
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Sherif F El-Khamisy
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria.
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Hörmann K, Stukalov A, Müller AC, Heinz LX, Superti-Furga G, Colinge J, Bennett KL. A Surface Biotinylation Strategy for Reproducible Plasma Membrane Protein Purification and Tracking of Genetic and Drug-Induced Alterations. J Proteome Res 2016; 15:647-58. [PMID: 26699813 DOI: 10.1021/acs.jproteome.5b01066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plasma membrane (PM) proteins contribute to the identity of a cell, mediate contact and communication, and account for more than two-thirds of known drug targets.1-8 In the past years, several protocols for the proteomic profiling of PM proteins have been described. Nevertheless, comparative analyses have mainly focused on different variations of one approach.9-11 We compared sulfo-NHS-SS-biotinylation, aminooxy-biotinylation, and surface coating with silica beads to isolate PM proteins for subsequent analysis by one-dimensional gel-free liquid chromatography mass spectrometry. Absolute and relative numbers of PM proteins and reproducibility parameters on a qualitative and quantitative level were assessed. Sulfo-NHS-SS-biotinylation outperformed aminooxy-biotinylation and surface coating using silica beads for most of the monitored criteria. We further simplified this procedure by a competitive biotin elution strategy achieving an average PM annotated protein fraction of 54% (347 proteins). Computational analysis using additional databases and prediction tools revealed that in total over 90% of the purified proteins were associated with the PM, mostly as interactors. The modified sulfo-NHS-SS-biotinylation protocol was validated by tracking changes in the plasma membrane proteome composition induced by genetic alteration and drug treatment. Glycosylphosphatidylinositol (GPI)-anchored proteins were depleted in PM purifications from cells deficient in the GPI transamidase component PIGS, and treatment of cells with tunicamycin significantly reduced the abundance of N-glycoproteins in surface purifications.
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Affiliation(s)
- Katrin Hörmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
| | - Leonhard X Heinz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria.,Center for Physiology and Pharmacology, Medical University of Vienna , 1090 Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
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Radic-Sarikas B, Rix U, Stukalov A, Gridling M, Müller AC, Colinge J, Superti-Furga G, Bennett KL. Enhancing cognate target elution efficiency in gel-free chemical proteomics. EuPA Open Proteomics 2015. [DOI: 10.1016/j.euprot.2015.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. PLoS One 2015; 10:e0142162. [PMID: 26539827 PMCID: PMC4634858 DOI: 10.1371/journal.pone.0142162] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/19/2015] [Indexed: 11/19/2022] Open
Abstract
We performed a pilot proteogenomic study to compare lung adenocarcinoma to lung squamous cell carcinoma using quantitative proteomics (6-plex TMT) combined with a customized Affymetrix GeneChip. Using MaxQuant software, we identified 51,001 unique peptides that mapped to 7,241 unique proteins and from these identified 6,373 genes with matching protein expression for further analysis. We found a minor correlation between gene expression and protein expression; both datasets were able to independently recapitulate known differences between the adenocarcinoma and squamous cell carcinoma subtypes. We found 565 proteins and 629 genes to be differentially expressed between adenocarcinoma and squamous cell carcinoma, with 113 of these consistently differentially expressed at both the gene and protein levels. We then compared our results to published adenocarcinoma versus squamous cell carcinoma proteomic data that we also processed with MaxQuant. We selected two proteins consistently overexpressed in squamous cell carcinoma in all studies, MCT1 (SLC16A1) and GLUT1 (SLC2A1), for further investigation. We found differential expression of these same proteins at the gene level in our study as well as in other public gene expression datasets. These findings combined with survival analysis of public datasets suggest that MCT1 and GLUT1 may be potential prognostic markers in adenocarcinoma and druggable targets in squamous cell carcinoma. Data are available via ProteomeXchange with identifier PXD002622.
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Affiliation(s)
- Paul A. Stewart
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Eric A. Welsh
- Cancer Informatics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Haoyun Cao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Bin Fang
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - John M. Koomen
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Steven A. Eschrich
- Cancer Informatics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
- * E-mail:
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Huber KVM, Olek KM, Müller AC, Tan CSH, Bennett KL, Colinge J, Superti-Furga G. Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling. Nat Methods 2015; 12:1055-7. [PMID: 26389571 PMCID: PMC4629415 DOI: 10.1038/nmeth.3590] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/30/2015] [Indexed: 01/20/2023]
Abstract
Thermal stabilization of proteins after ligand binding provides an efficient means to assess the binding of small molecules to proteins. We show here that in combination with quantitative mass spectrometry, the approach allows for the systematic survey of protein engagement by cellular metabolites and drugs. We profiled the targets of the drugs methotrexate and (S)-crizotinib and the metabolite 2'3'-cGAMP in intact cells and identified the 2'3'-cGAMP cognate transmembrane receptor STING, involved in immune signaling.
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Affiliation(s)
- Kilian V M Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Karin M Olek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Chris Soon Heng Tan
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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29
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Heinz LX, Baumann CL, Köberlin MS, Snijder B, Gawish R, Shui G, Sharif O, Aspalter IM, Müller AC, Kandasamy RK, Breitwieser FP, Pichlmair A, Bruckner M, Rebsamen M, Blüml S, Karonitsch T, Fauster A, Colinge J, Bennett KL, Knapp S, Wenk MR, Superti-Furga G. The Lipid-Modifying Enzyme SMPDL3B Negatively Regulates Innate Immunity. Cell Rep 2015; 11:1919-28. [PMID: 26095358 PMCID: PMC4508342 DOI: 10.1016/j.celrep.2015.05.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/23/2015] [Accepted: 05/01/2015] [Indexed: 12/26/2022] Open
Abstract
Lipid metabolism and receptor-mediated signaling are highly intertwined processes that cooperate to fulfill cellular functions and safeguard cellular homeostasis. Activation of Toll-like receptors (TLRs) leads to a complex cellular response, orchestrating a diverse range of inflammatory events that need to be tightly controlled. Here, we identified the GPI-anchored Sphingomyelin Phosphodiesterase, Acid-Like 3B (SMPDL3B) in a mass spectrometry screening campaign for membrane proteins co-purifying with TLRs. Deficiency of Smpdl3b in macrophages enhanced responsiveness to TLR stimulation and profoundly changed the cellular lipid composition and membrane fluidity. Increased cellular responses could be reverted by re-introducing affected ceramides, functionally linking membrane lipid composition and innate immune signaling. Finally, Smpdl3b-deficient mice displayed an intensified inflammatory response in TLR-dependent peritonitis models, establishing its negative regulatory role in vivo. Taken together, our results identify the membrane-modulating enzyme SMPDL3B as a negative regulator of TLR signaling that functions at the interface of membrane biology and innate immunity. Identification of SMPDL3B as lipid-modulating phosphodiesterase on macrophages Negative regulatory role for SMPDL3B in Toll-like receptor function Strong influence of SMPDL3B on membrane lipid composition and fluidity Smpdl3b-deficient mice show enhanced responsiveness in TLR-dependent peritonitis
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Affiliation(s)
- Leonhard X Heinz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Christoph L Baumann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Marielle S Köberlin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Berend Snijder
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Riem Gawish
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Department of Medicine I, Laboratory of Infection Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Omar Sharif
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Department of Medicine I, Laboratory of Infection Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Irene M Aspalter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Richard K Kandasamy
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Florian P Breitwieser
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andreas Pichlmair
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Manuela Bruckner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Stephan Blüml
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Division of Rheumatology, Department of Medicine III, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas Karonitsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Astrid Fauster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sylvia Knapp
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Department of Medicine I, Laboratory of Infection Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Markus R Wenk
- Department of Biochemistry and Department of Biological Sciences, National University of Singapore, Singapore 117456, Singapore; Swiss Tropical and Public Health Institute, University of Basel, 4003 Basel, Switzerland
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria.
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Hofer A, Cremosnik GS, Müller AC, Giambruno R, Trefzer C, Superti-Furga G, Bennett KL, Jessen HJ. A Modular Synthesis of Modified Phosphoanhydrides. Chemistry 2015; 21:10116-22. [PMID: 26033174 DOI: 10.1002/chem.201500838] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/11/2022]
Abstract
Phosphoanhydrides (P-anhydrides) are ubiquitously occurring modifications in nature. Nucleotides and their conjugates, for example, are among the most important building blocks and signaling molecules in cell biology. To study and manipulate their biological functions, a diverse range of analogues have been developed. Phosphate-modified analogues have been successfully applied to study proteins that depend on these abundant cellular building blocks, but very often both the preparation and purification of these molecules are challenging. This study discloses a general access to P-anhydrides, including different nucleotide probes, that greatly facilitates their preparation and isolation. The convenient and scalable synthesis of, for example, (18) O labeled nucleoside triphosphates holds promise for future applications in phosphoproteomics.
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Affiliation(s)
- Alexandre Hofer
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland)
| | - Gregor S Cremosnik
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA (UK)
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Roberto Giambruno
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Claudia Trefzer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Henning J Jessen
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland).
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Planyavsky M, Huber ML, Staller NA, Müller AC, Bennett KL. A longitudinal proteomic assessment of peptide degradation and loss under acidic storage conditions. Anal Biochem 2015; 473:11-3. [DOI: 10.1016/j.ab.2014.11.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 10/24/2022]
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Muellner MK, Mair B, Ibrahim Y, Kerzendorfer C, Lechtermann H, Trefzer C, Klepsch F, Müller AC, Leitner E, Macho-Maschler S, Superti-Furga G, Bennett KL, Baselga J, Rix U, Kubicek S, Colinge J, Serra V, Nijman SMB. Targeting a cell state common to triple-negative breast cancers. Mol Syst Biol 2015; 11:789. [PMID: 25699542 PMCID: PMC4358660 DOI: 10.15252/msb.20145664] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Some mutations in cancer cells can be exploited for therapeutic intervention. However, for many cancer subtypes, including triple-negative breast cancer (TNBC), no frequently recurring aberrations could be identified to make such an approach clinically feasible. Characterized by a highly heterogeneous mutational landscape with few common features, many TNBCs cluster together based on their ‘basal-like’ transcriptional profiles. We therefore hypothesized that targeting TNBC cells on a systems level by exploiting the transcriptional cell state might be a viable strategy to find novel therapies for this highly aggressive disease. We performed a large-scale chemical genetic screen and identified a group of compounds related to the drug PKC412 (midostaurin). PKC412 induced apoptosis in a subset of TNBC cells enriched for the basal-like subtype and inhibited tumor growth in vivo. We employed a multi-omics approach and computational modeling to address the mechanism of action and identified spleen tyrosine kinase (SYK) as a novel and unexpected target in TNBC. Quantitative phosphoproteomics revealed that SYK inhibition abrogates signaling to STAT3, explaining the selectivity for basal-like breast cancer cells. This non-oncogene addiction suggests that chemical SYK inhibition may be beneficial for a specific subset of TNBC patients and demonstrates that targeting cell states could be a viable strategy to discover novel treatment strategies.
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Affiliation(s)
- Markus K Muellner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Barbara Mair
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Yasir Ibrahim
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Claudia Kerzendorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hannelore Lechtermann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Claudia Trefzer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Freya Klepsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ernestine Leitner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - José Baselga
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Uwe Rix
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Sebastian M B Nijman
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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33
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Eberle CA, Zayas M, Stukalov A, Pichlmair A, Alvisi G, Müller AC, Bennett KL, Bartenschlager R, Superti-Furga G. The lysine methyltransferase SMYD3 interacts with hepatitis C virus NS5A and is a negative regulator of viral particle production. Virology 2014; 462-463:34-41. [PMID: 25092459 PMCID: PMC4139193 DOI: 10.1016/j.virol.2014.05.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 02/28/2014] [Accepted: 05/14/2014] [Indexed: 01/19/2023]
Abstract
Hepatitis C virus (HCV) is a considerable global health and economic burden. The HCV nonstructural protein (NS) 5A is essential for the viral life cycle. The ability of NS5A to interact with different host and viral proteins allow it to manipulate cellular pathways and regulate viral processes, including RNA replication and virus particle assembly. As part of a proteomic screen, we identified several NS5A-binding proteins, including the lysine methyltransferase SET and MYND domain containing protein 3 (SMYD3). We confirmed the interaction in the context of viral replication by co-immunoprecipitation and co-localization studies. Mutational analyses revealed that the MYND-domain of SMYD3 and domain III of NS5A are required for the interaction. Overexpression of SMYD3 resulted in decreased intracellular and extracellular virus titers, whilst viral RNA replication remained unchanged, suggesting that SMYD3 negatively affects HCV particle production in a NS5A-dependent manner. Identification of SMYD3 as interactor of the HCV protein NS5A using a proteomic approach. Confirmation of SMYD3 as interactor of NS5A in the context of active viral replication. Identification of SMYD3 as negative regulator of HCV infectious particle assembly.
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Affiliation(s)
- Carol-Ann Eberle
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Margarita Zayas
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Andreas Pichlmair
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria; Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Gualtiero Alvisi
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany; Department of Molecular Medicine, Via Gabelli 63, 35121 Padua, Italy
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria.
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Maurer M, Müller AC, Parapatics K, Pickl WF, Wagner C, Rudashevskaya EL, Breitwieser FP, Colinge J, Garg K, Griss J, Bennett KL, Wagner SN. Comprehensive comparative and semiquantitative proteome of a very low number of native and matched epstein-barr-virus-transformed B lymphocytes infiltrating human melanoma. J Proteome Res 2014; 13:2830-45. [PMID: 24803318 DOI: 10.1021/pr401270y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Melanoma, the deadliest form of skin cancer, is highly immunogenic and frequently infiltrated with immune cells including B cells. The role of tumor-infiltrating B cells (TIBCs) in melanoma is as yet unresolved, possibly due to technical challenges in obtaining TIBCs in sufficient quantity for extensive studies and due to the limited life span of B cells in vitro. A comprehensive workflow has thus been developed for successful isolation and proteomic analysis of a low number of TIBCs from fresh, human melanoma tissue. In addition, we generated in vitro-proliferating TIBC cultures using simultaneous stimulation with Epstein-Barr virus (EBV) and the TLR9 ligand CpG-oligodesoxynucleotide (CpG ODN). The FASP method and iTRAQ labeling were utilized to obtain a comparative, semiquantitative proteome to assess EBV-induced changes in TIBCs. By using as few as 100 000 B cells (∼5 μg protein)/sample for our proteomic study, a total number of 6507 proteins were identified. EBV-induced changes in TIBCs are similar to those already reported for peripheral B cells and largely involve changes in cell cycle proliferation, apoptosis, and interferon response, while most of the proteins were not significantly altered. This study provides an essential, further step toward detailed characterization of TIBCs including functional in vitro analysis.
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Affiliation(s)
- Margarita Maurer
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna , Waehringer Guertel 18-20, A-1090 Vienna, Austria
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Huber ML, Sacco R, Parapatics K, Skucha A, Khamina K, Müller AC, Rudashevskaya EL, Bennett KL. abFASP-MS: affinity-based filter-aided sample preparation mass spectrometry for quantitative analysis of chemically labeled protein complexes. J Proteome Res 2014; 13:1147-55. [PMID: 24400740 PMCID: PMC3923452 DOI: 10.1021/pr4009892] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Affinity
purification coupled to 1-D gel-free liquid chromatography
mass spectrometry (LC–MS) is a well-established and widespread
approach for the analyses of noncovalently interacting protein complexes.
In this study, two proteins conjugated to a streptavidin-binding peptide
and hemagglutinin double tag were expressed in the respective Flp-In
HEK293 cell lines: green fluorescent protein (SH-GFP) and TANK binding
kinase 1 (SH-TBK1_MOUSE). Fluorescent anti-HA immunoblots revealed
that the expression level of SH-GFP was ∼50% lower than that
of SH-TBK1_MOUSE. Subsequently, the input material was normalized
to obtain a similar quantity of purified SH-tagged proteins. Optimization
of the release of protein complexes from the anti-HA-agarose with different eluting agents was then assessed. With
respect to the total number of protein groups identified in the purified
complexes, elution with 2% SDS surpassed both 100 mM glycine and 100
mM formic acid. Relative quantitation of the purified protein complexes
using TMT 6-plex reagents confirmed the higher efficiency of the 2%
SDS elution followed by filter-aided sample preparation (FASP). The
data presented in this study provide a new application of FASP to
quantitative MS analysis of affinity-purified protein complexes. We
have termed the approach abFASP-MS, or affinity-based filter-aided
sample preparation mass spectrometry.
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Affiliation(s)
- Marie L Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , Lazarettgasse 14, 1090 Vienna, Austria
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Chamrád I, Rix U, Stukalov A, Gridling M, Parapatics K, Müller AC, Altiok S, Colinge J, Superti-Furga G, Haura EB, Bennett KL. A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies. J Proteome Res 2013; 12:4005-17. [PMID: 23901793 DOI: 10.1021/pr400309p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
While targeted therapy based on the idea of attenuating the activity of a preselected, therapeutically relevant protein has become one of the major trends in modern cancer therapy, no truly specific targeted drug has been developed and most clinical agents have displayed a degree of polypharmacology. Therefore, the specificity of anticancer therapeutics has emerged as a highly important but severely underestimated issue. Chemical proteomics is a powerful technique combining postgenomic drug-affinity chromatography with high-end mass spectrometry analysis and bioinformatic data processing to assemble a target profile of a desired therapeutic molecule. Due to high demands on the starting material, however, chemical proteomic studies have been mostly limited to cancer cell lines. Herein, we report a down-scaling of the technique to enable the analysis of very low abundance samples, as those obtained from needle biopsies. By a systematic investigation of several important parameters in pull-downs with the multikinase inhibitor bosutinib, the standard experimental protocol was optimized to 100 μg protein input. At this level, more than 30 well-known targets were detected per single pull-down replicate with high reproducibility. Moreover, as presented by the comprehensive target profile obtained from miniaturized pull-downs with another clinical drug, dasatinib, the optimized protocol seems to be extendable to other drugs of interest. Sixty distinct human and murine targets were finally identified for bosutinib and dasatinib in chemical proteomic experiments utilizing core needle biopsy samples from xenotransplants derived from patient tumor tissue. Altogether, the developed methodology proves robust and generic and holds many promises for the field of personalized health care.
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Affiliation(s)
- Ivo Chamrád
- Department of Protein Biochemistry and Proteomics, Technological Centre of the Palacký University, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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Dürnberger G, Bürckstümmer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Müller AC, Schönegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J. Experimental characterization of the human non-sequence-specific nucleic acid interactome. Genome Biol 2013; 14:R81. [PMID: 23902751 PMCID: PMC4053969 DOI: 10.1186/gb-2013-14-7-r81] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 07/31/2013] [Indexed: 12/17/2022] Open
Abstract
Background The interactions between proteins and nucleic acids have a fundamental function in many biological processes, including gene transcription, RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins that bind individual mRNAs in mammalian cells has been greatly augmented by recent surveys, no systematic study on the non-sequence-specific engagement of native human proteins with various types of nucleic acids has been reported. Results We designed an experimental approach to achieve broad coverage of the non-sequence-specific RNA and DNA binding space, including methylated cytosine, and tested for interaction potential with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high-confidence direct binders, 139 of which were novel and 237 devoid of previous experimental evidence. We could assign specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and individual domains. The evolutionarily conserved protein YB-1, previously associated with cancer and drug resistance, was shown to bind methylated cytosine preferentially, potentially conferring upon YB-1 an epigenetics-related function. Conclusions The dataset described here represents a rich resource of experimentally determined nucleic acid-binding proteins, and our methodology has great potential for further exploration of the interface between the protein and nucleic acid realms.
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Borgdorff V, Rix U, Winter GE, Gridling M, Müller AC, Breitwieser FP, Wagner C, Colinge J, Bennett KL, Superti-Furga G, Wagner SN. A chemical biology approach identifies AMPK as a modulator of melanoma oncogene MITF. Oncogene 2013; 33:2531-9. [DOI: 10.1038/onc.2013.185] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 01/29/2013] [Accepted: 04/12/2013] [Indexed: 12/12/2022]
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Pfannenberg C, Schwenzer NF, Schraml C, Brendle C, Werner M, Reimold M, Claussen CD, Müller AC. Stellenwert der C-11-Cholin-PET/CT für das LK-Staging bei Patienten mit high-risk Prostata-Karzinom bzw. Rezidiv - eine histologisch kontrollierte retrospektive Studie. ROFO-FORTSCHR RONTG 2013. [DOI: 10.1055/s-0033-1346363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Rudashevskaya EL, Breitwieser FP, Huber ML, Colinge J, Müller AC, Bennett KL. Multiple and Sequential Data Acquisition Method: An Improved Method for Fragmentation and Detection of Cross-Linked Peptides on a Hybrid Linear Trap Quadrupole Orbitrap Velos Mass Spectrometer. Anal Chem 2013; 85:1454-61. [DOI: 10.1021/ac302251f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Elena L. Rudashevskaya
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Florian P. Breitwieser
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marie L. Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department
of Dermatology, Division
of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Maurer M, Müller AC, Wagner C, Huber ML, Rudashevskaya EL, Wagner SN, Bennett KL. Combining Filter-Aided Sample Preparation and Pseudoshotgun Technology To Profile the Proteome of a Low Number of Early Passage Human Melanoma Cells. J Proteome Res 2012; 12:1040-8. [DOI: 10.1021/pr301009u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Margarita Maurer
- Division of Immunology, Allergy
and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090
Vienna, Austria
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH Building BT 25.3, A-1090 Vienna, Austria
| | - Christine Wagner
- Division of Immunology, Allergy
and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090
Vienna, Austria
| | - Marie L. Huber
- Division of Immunology, Allergy
and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090
Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH Building BT 25.3, A-1090 Vienna, Austria
| | - Elena L. Rudashevskaya
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH Building BT 25.3, A-1090 Vienna, Austria
| | - Stephan N. Wagner
- Division of Immunology, Allergy
and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090
Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH Building BT 25.3, A-1090 Vienna, Austria
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Pichlmair A, Kandasamy K, Alvisi G, Mulhern O, Sacco R, Habjan M, Binder M, Stefanovic A, Eberle CA, Goncalves A, Bürckstümmer T, Müller AC, Fauster A, Holze C, Lindsten K, Goodbourn S, Kochs G, Weber F, Bartenschlager R, Bowie AG, Bennett KL, Colinge J, Superti-Furga G. Viral immune modulators perturb the human molecular network by common and unique strategies. Nature 2012; 487:486-90. [PMID: 22810585 DOI: 10.1038/nature11289] [Citation(s) in RCA: 198] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 06/07/2012] [Indexed: 12/24/2022]
Abstract
Viruses must enter host cells to replicate, assemble and propagate. Because of the restricted size of their genomes, viruses have had to evolve efficient ways of exploiting host cell processes to promote their own life cycles and also to escape host immune defence mechanisms. Many viral open reading frames (viORFs) with immune-modulating functions essential for productive viral growth have been identified across a range of viral classes. However, there has been no comprehensive study to identify the host factors with which these viORFs interact for a global perspective of viral perturbation strategies. Here we show that different viral perturbation patterns of the host molecular defence network can be deduced from a mass-spectrometry-based host-factor survey in a defined human cellular system by using 70 innate immune-modulating viORFs from 30 viral species. The 579 host proteins targeted by the viORFs mapped to an unexpectedly large number of signalling pathways and cellular processes, suggesting yet unknown mechanisms of antiviral immunity. We further experimentally verified the targets heterogeneous nuclear ribonucleoprotein U, phosphatidylinositol-3-OH kinase, the WNK (with-no-lysine) kinase family and USP19 (ubiquitin-specific peptidase 19) as vulnerable nodes in the host cellular defence system. Evaluation of the impact of viral immune modulators on the host molecular network revealed perturbation strategies used by individual viruses and by viral classes. Our data are also valuable for the design of broad and specific antiviral therapies.
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Affiliation(s)
- Andreas Pichlmair
- CeMMResearch Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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Müller AC, Gani C, Weinmann M, Mayer F, Sipos B, Bamberg M, Eckert F. Limited disease of extra-pulmonary small cell carcinoma. Impact of local treatment and nodal status, role of cranial irradiation. Strahlenther Onkol 2012; 188:269-73. [PMID: 22314576 DOI: 10.1007/s00066-011-0045-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 10/04/2011] [Indexed: 01/12/2023]
Abstract
PURPOSE As extra-pulmonary small cell carcinoma (EPSCC) is a rare entity of tumors, the available treatment recommendations are mainly based on retrospective analyses and deduction from treatment of small cell lung cancer. The aim of this study was to provide a detailed analysis concerning prognostic factors and treatment modalities. PATIENTS AND METHODS A total of 20 patients with limited disease (LD) of EPSCC treated at our institution from 1999–2009 were retrospectively analyzed. Data were gathered from chart review. Localization, lymph node involvement, as well as local and systemic treatment were documented and their impact on pattern of failure and survival times statistically evaluated. RESULTS With a median follow-up of 21 months, the estimated median overall- and disease-free survival were 59 and 25 months, respectively. Local control was excellent with 100% at 2 years. Nodal involvement was observed in 74% (n = 14/19) of evaluable patients. However, outcome was not altered by this parameter. Local treatment consisted of surgery in 10 cases, radiotherapy in 7 cases, and a combination of both in 3 cases. Only 3 patients (15%) developed hematogenous central nervous system metastases, while none of the patients received prophylactic cranial irradiation. CONCLUSION Nodal involvement did not worsen prognosis. Local control was excellent irrespective of local treatment modality and the leading cause of failure was distant metastasis. Therefore, systemic treatment should not be omitted. Prophylactic cranial irradiation might be dispensable but discussed for head and neck malignancies.
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Affiliation(s)
- A C Müller
- Department of Radiooncology, Eberhard-Karls-University Tübingen, Tuebingen
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Haura EB, Sacco R, Li J, Müller AC, Grebien F, Superti-Furga G, Bennett KL. Optimisation of Downscaled Tandem Affinity Purifications to Identify Core Protein Complexes. ACTA ACUST UNITED AC 2012; 2:55-68. [PMID: 24077984 DOI: 10.5584/jiomics.v2i1.81] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this study we show that via stable, retroviral-expression of tagged EGFR del (L747-S752 deletion mutant) in the PC9 lung cancer cell line and stable doxycycline-inducible expression of tagged Grb2 using a Flp-mediated recombination HEK293 cell system, the SH-TAP can be downscaled to 5 to 12.5 mg total protein input (equivalent to 0.5 - 1 × 15 cm culture plate or 4 - 8 × 106 cells). The major constituents of the EGFR del complex (USB3B, GRB2, ERRFI, HSP7C, GRP78, HSP71) and the Grb2 complex (ARHG5, SOS1, ARG35, CBL, CBLB, PTPRA, SOS2, DYN2, WIPF2, IRS4) were identified. Adjustment of the quantity of digested protein injected into the mass spectrometer reveals that optimisation is required as high quantities of material led to a decrease in protein sequence coverage and the loss of some interacting proteins. This investigation should aid other researchers in performing tandem affinity purifications in general, and in particular, from low quantities of input material.
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Affiliation(s)
- Eric B Haura
- Department of Thoracic Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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Müller AC, Breitwieser FP, Fischer H, Schuster C, Brandt O, Colinge J, Superti-Furga G, Stingl G, Elbe-Bürger A, Bennett KL. A comparative proteomic study of human skin suction blister fluid from healthy individuals using immunodepletion and iTRAQ labeling. J Proteome Res 2012; 11:3715-27. [PMID: 22578099 DOI: 10.1021/pr3002035] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [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]
Abstract
Aberrations in skin morphology and functionality can cause acute and chronic skin-related diseases that are the focus of dermatological research. Mechanically induced skin suction blister fluid may serve as a potential, alternative human body fluid for quantitative mass spectrometry (MS)-based proteomics in order to assist in the understanding of the mechanisms and causes underlying skin-related diseases. The combination of abundant-protein removal with iTRAQ technology and multidimensional fractionation techniques improved the number of identified protein groups. A relative comparison of a cohort of 8 healthy volunteers was thus recruited in order to assess the net variability encountered in a healthy scenario. The technology enabled the identification, to date, of the highest number of reported protein groups (739) with concomitant relative quantitative data for over 90% of all proteins with high reproducibility and accuracy. The use of iTRAQ 8-plex resulted in a 66% decrease in protein identifications but, despite this, provided valuable insight into interindividual differences of the healthy control samples. The geometric mean ratio was close to 1 with 95% of all ratios ranging between 0.45 and 2.05 and a calculated mean coefficient of variation of 15.8%, indicating a lower biological variance than that reported for plasma or urine. By applying a multistep sample processing, the obtained sensitivity and accuracy of quantitative MS analysis demonstrates the prospective value of the approach in future research into skin diseases.
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Affiliation(s)
- André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Pfannenberg C, Schwenzer N, Henke G, Müller AC, Reimold M, Claussen CD, Thorwarth D. Simultane [68Ga]DOTATOC PET/MR für die IMRT Bestrahlungsplanung von Meningeomen - erste Ergebnisse. ROFO-FORTSCHR RONTG 2012. [DOI: 10.1055/s-0032-1311117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abstract
AIDS-related encephalopathy, including AIDS dementia complex (ADC) and the opportunistic disease, herpes simplex encephalitis (HSE), are postulated to arise due to the release of neurotoxic products, such as quinolinic acid (QUIN), by activated microglial cells in the brain. QUIN causes a cascade of events to occur, which leads to the production of reactive oxygen species (ROS), these being ultimately responsible for oxidative neurotoxicity. The antiherpes antiviral aciclovir has been reported to protect against neuron loss in HSE, but the mechanism for this neuroprotection is unknown. Therefore, this study was conducted to investigate whether aciclovir has the ability to inhibit QUIN-induced lipid peroxidation in rat brain homogenates, after in-vitro and in-vivo exposure to QUIN and aciclovir. The thiobarbituric acid (TBA) assay was the method used to analyse lipid peroxidation. Rat brains were also examined histologically after in-vivo exposure to visually assess whether neuron loss was suppressed. The results show that aciclovir inhibits the QUIN-induced lipid peroxidation, in a dose-dependent manner. Furthermore, aciclovir reduced necrosis of hippocampal neurons and retained the characteristic morphology, integrity and arrangement of these cells. Thus, it appears that aciclovir has neuroprotective properties, which could possibly be useful in the treatment of AIDS-related encephalopathy.
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Affiliation(s)
- A C Müller
- Division of Pharmacology, Faculty of Pharmacy, Rhodes University, Grahamstown, 6140, South Africa
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Abstract
Graves' ophthalmopathy (GO) is the most frequent extrathyroidal manifestation of Graves' disease, an autoimmune disorder of the thyroid, whereas the precise pathogenesis still remains unclear. In Hashimoto's thyroiditis the occurrence of proptosis is an extremely rare event. The therapy for middle and severe courses of GO shows in partly disappointing results, although several therapy modalities are possible (glucocorticoid therapy, radiotherapy, antithyroid drug treatment, surgery). All these therapies lead in only 40 - 70 % to an improvement of the pathogenic symptoms. An intensive interdisciplinary cooperation is necessary to satisfy the requirements for the treatment of Graves' ophthalmopathy. As a consequence of the very different results of the few of clinical studies that were accomplished with reference to this topic, treatment by radiotherapy in the management of the disease is presently controversially discussed. In the German-speaking countries the radiotherapy is, however, firmly established as a therapy option in the treatment of the moderate disease classes (class 2-5 according to NO SPECS), especially if diplopia is present. This article describes the sequences, dosages and fractionation schemes as well as the risks and side effects of the radiotherapy. Altogether, radiotherapy is assessed as an effective and sure method. The administration of glucocorticoids can take place before the beginning of or during the radiotherapy. For the success of treatment the correct selection of patients who may possibly profit from a radiotherapy is absolutely essential. By realising that GO proceeds normally over a period of 2-5 years, which is followed by a period of fibrotic alteration, the application of the radiotherapy in the early, active phase is indispensable. A precise explanation for the effects of radiotherapy in treatment of the GO does not exist at present. The determination of the most effective irradiation doses was made from retrospectively evaluated collectives. Recently the results of a national survey of all German RT departments were published, initiated by the working group of the DEGRO (German Society of Radiooncology). In the most of the German radiooncology departments irradiation with 8 to 10 x 1.8-2.0 Gy 5 x weekly to 16 or 20 Gy is standard. Two recently published prospective German studies pointed out the equivalence of the effectiveness of a short therapy in low dose ranges up to 2.4 Gy as well as of a low proportioned irradiation during a longer period in relation to a standard therapy with 20 Gy. That is why at the moment it is not possible to give a definite recommendation with reference to dosages or the fractionation schemes. In 2003 the first European group (European Group on Graves ' Orbitopathy Experience -- EUGOGO) was founded for pursuing investigations of GO in multi-centric studies, mainly to improve therapy results.
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Affiliation(s)
- T Kuhnt
- Martin-Luther-Universität Halle-Wittenberg, Universitätsklinik und Poliklinik für Strahlentherapie.
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Dunst J, Semlin S, Pigorsch S, Müller AC, Reese T. Intermittent use of amifostine during postoperative radiochemotherapy and acute toxicity in rectal cancer patients. Strahlenther Onkol 2000; 176:416-21. [PMID: 11050915 DOI: 10.1007/pl00002350] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PURPOSE Amifostine has been shown to be able to reduce acute radiation toxicity if administered daily prior to radiation during a course of a conventionally fractionated radiotherapy. A disadvantage is the necessity of daily intravenous injection. We have used amifostin in patients undergoing adjuvant radiochemotherapy for rectal cancer. Amifostine was administered only in the first and fifth week of radiotherapy together with 5-FU chemotherapy. The objective was to determine whether the intermittent use of amifostine may be effective in reducing acute radiation toxicity. PATIENTS AND METHODS From September 1997 through October 1998, 30 patients with stage II/III rectal cancer underwent postoperative radiochemotherapy at our department. All patients had undergone curative (R0) resection and received 50.4 Gy to the pelvis with a 3-field technique using a belly board followed by a boost of 5.4 Gy to the presacral space in conventional fractionation with 1.8 Gy per fraction. 5-FU chemotherapy was administered as 120-hours continuous infusion in the first and fifth radiation week via a central venous catheter in a daily dosage of 1,000 mg/m2. All patients were offered to participate in a phase-II study using additional amifostine. Fifteen patients participated and received 500 mg amifostine daily on chemotherapy days (days 1 to 5 and 29 to 33) immediately prior to the daily radiation fraction. Fifteen patients did not participate and served as non-randomized control. The study was approved by the ethical committee of the Martin-Luther-University and informed consent was obtained from all patients. RESULTS The distribution of patients' characteristics and prognostic parameters was comparable in both groups. Side effects of amifostine were mild and included hypotension (53% grade I, 7% grade II) and nausea (47% grade I, 13% grade II). Antiemetics were not routinely used. All patients completed radiochemotherapy plus amifostine without unplanned breaks or dose reductions. One patient developed a cerebral infarction which was considered to be not related to the use of amifostine. As compared to the non-randomized control group, patients with additional amifostine had less acute skin and bowel toxicity (maximum erythema score 1.47 +/- 0.64 without vs 0.87 +/- 0.52 with amifostine, p = 0.009 and maximum diarrhea score 1.07 +/- 1.03 vs 0.40 +/- 0.63, p = 0.044). Oral 5-FU-related mucositis and hematological toxicity were not significantly different. CONCLUSIONS In this phase-II study, amifostine significantly reduced acute skin and bowel toxicity of adjuvant chemoradiation in patients with rectal cancer even if the drug was administered only intermittently and not during the whole course of radiotherapy. This finding might be important with regard to intense combined regimes and should be further investigated.
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Affiliation(s)
- J Dunst
- Department of Radiotherapy, Martin-Luther-University Halle-Wittenberg, Germany.
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