1
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Peschke JC, Bergmann R, Mehnert M, Gonzalez Soto KE, Loureiro LR, Mitwasi N, Kegler A, Altmann H, Wobus M, Máthé D, Szigeti K, Feldmann A, Bornhäuser M, Bachmann M, Fasslrinner F, Arndt C. FLT3-directed UniCAR T-cell therapy of acute myeloid leukaemia. Br J Haematol 2023; 202:1137-1150. [PMID: 37460273 DOI: 10.1111/bjh.18971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 09/12/2023]
Abstract
Adaptor chimeric antigen receptor (CAR) T-cell therapy offers solutions for improved safety and antigen escape, which represent main obstacles for the clinical translation of CAR T-cell therapy in myeloid malignancies. The adaptor CAR T-cell platform 'UniCAR' is currently under early clinical investigation. Recently, the first proof of concept of a well-tolerated, rapidly switchable, CD123-directed UniCAR T-cell product treating patients with acute myeloid leukaemia (AML) was reported. Relapsed and refractory AML is prone to high plasticity under therapy pressure targeting one single tumour antigen. Thus, targeting of multiple tumour antigens seems to be required to achieve durable anti-tumour responses, underlining the need to further design alternative AML-specific target modules (TM) for the UniCAR platform. We here present the preclinical development of a novel FMS-like tyrosine kinase 3 (FLT3)-directed UniCAR T-cell therapy, which is highly effective for in vitro killing of both AML cell lines and primary AML samples. Furthermore, we show in vivo functionality in a murine xenograft model. PET analyses further demonstrate a short serum half-life of FLT3 TMs, which will enable a rapid on/off switch of UniCAR T cells. Overall, the presented preclinical data encourage the further development and clinical translation of FLT3-specific UniCAR T cells for the therapy of AML.
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Affiliation(s)
- J C Peschke
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
- Mildred Scheel Early Career Center, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC): German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Partner Site, Dresden, Germany
| | - R Bergmann
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - M Mehnert
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
- Mildred Scheel Early Career Center, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - K E Gonzalez Soto
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - L R Loureiro
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - N Mitwasi
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - A Kegler
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - H Altmann
- National Center for Tumor Diseases Dresden (NCT/UCC): German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Partner Site, Dresden, Germany
- Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Wobus
- Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - D Máthé
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- Hungarian Centre of Excellence for Molecular Medicine, In Vivo Imaging Advanced Core Facility, Szeged, Hungary
| | - K Szigeti
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - A Feldmann
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC): German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Partner Site, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Bornhäuser
- National Center for Tumor Diseases Dresden (NCT/UCC): German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Partner Site, Dresden, Germany
- Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- School of Cancer and Pharmaceutical Science, King's College, London, UK
| | - M Bachmann
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC): German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Partner Site, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - F Fasslrinner
- Mildred Scheel Early Career Center, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - C Arndt
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
- Mildred Scheel Early Career Center, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
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2
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Naschberger E, Flierl C, Huang J, Erkert L, Gamez-Belmonte R, Gonzalez-Acera M, Bober M, Mehnert M, Becker C, Schellerer VS, Britzen-Laurent N, Stürzl M. Analysis of the interferon-γ-induced secretome of intestinal endothelial cells: putative impact on epithelial barrier dysfunction in IBD. Front Cell Dev Biol 2023; 11:1213383. [PMID: 37645250 PMCID: PMC10460912 DOI: 10.3389/fcell.2023.1213383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023] Open
Abstract
The development of inflammatory bowel diseases (IBD) involves the breakdown of two barriers: the epithelial barrier and the gut-vascular barrier (GVB). The destabilization of each barrier can promote initiation and progression of the disease. Interestingly, first evidence is available that both barriers are communicating through secreted factors that may accordingly serve as targets for therapeutic modulation of barrier functions. Interferon (IFN)-γ is among the major pathogenesis factors in IBD and can severely impair both barriers. In order to identify factors transmitting signals from the GVB to the epithelial cell barrier, we analyzed the secretome of IFN-γ-treated human intestinal endothelial cells (HIEC). To this goal, HIEC were isolated in high purity from normal colon tissues. HIEC were either untreated or stimulated with IFN-γ (10 U/mL). After 48 h, conditioned media (CM) were harvested and subjected to comparative hyper reaction monitoring mass spectrometry (HRM™ MS). In total, 1,084 human proteins were detected in the HIEC-CM. Among these, 43 proteins were present in significantly different concentrations between the CM of IFN-γ- and control-stimulated HIEC. Several of these proteins were also differentially expressed in various murine colitis models as compared to healthy animals supporting the relevance of these proteins secreted by inflammatory activated HIEC in the inter-barrier communication in IBD. The angiocrine pathogenic impact of these differentially secreted HIEC proteins on the epithelial cell barrier and their perspectives as targets to treat IBD by modulation of trans-barrier communication is discussed in detail.
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Affiliation(s)
- Elisabeth Naschberger
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christian Flierl
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jinghao Huang
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Lena Erkert
- Department of Medicine I, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Reyes Gamez-Belmonte
- Department of Medicine I, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Miguel Gonzalez-Acera
- Department of Medicine I, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | | | | | - Christoph Becker
- Department of Medicine I, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Vera S. Schellerer
- Department of Pediatric Surgery, University Medicine Greifswald, Greifswald, Germany
| | - Nathalie Britzen-Laurent
- Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, Erlangen, Germany
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3
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Au YW, Satijn D, Mehnert M, Lachaud A, Feng Y, Vowinckel J, Bon H. Abstract 3974: Discovery and validation of therapeutic targets in immune cells by mass spectrometry-based proteomics. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3974] [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: 04/07/2023]
Abstract
Abstract
Immuno-oncology (IO) has substantially improved the survival of cancer patients over the past several years encouraging the discovery of novel IO targets which are typically proteins expressed on the surface of immune cells. Sensitive quantification of proteins in complex biological samples is routinely achieved by immunoassays that use antibodies specific to target proteins. Such approaches can be a limitation in IO drug discovery and development as de novo development of antibodies is associated with long lead times, high costs, and high failure rates.
Protein quantification using mass spectrometry (MS) is agnostic to species and matrices and removes the barriers of availability or specificity of antibody-based assay. Further, MS proteomics workflows can support both large scale discovery studies but also represent an attractive alternative to targeted quantitative studies.
The main purpose of this work is to assess the performance of the TrueDiscovery™ and TrueSignature™ MS-proteomics platforms for the deep proteome and surfaceome profiling of human primary and immortalized immune cells compared to flow cytometry solutions. We assess the number of quantified proteins and specifically the coverage of immune cell marker proteins in primary human immune cells across cell count groups from 2 million down to 2500 immune cells. In addition, we compared the quantification of a multiplexed surface antigens panel using TrueSignature™ and QIFI® flow cytometry platforms.
We found that the applied MS-based proteomics workflows achieve high sensitivity and robustness in detection and quantification of immune cell markers down to 2500 primary immune cells. Additionally, we observed a strong correlation of the quantitative data derived from our MS-based proteomics workflows with flow cytometry supporting the substitution of immunoassays by MS-based proteomics workflows in target discovery and validation.
Citation Format: Yu-Wah Au, David Satijn, Martin Mehnert, Amaury Lachaud, Yuehan Feng, Jakob Vowinckel, Hélène Bon. Discovery and validation of therapeutic targets in immune cells by mass spectrometry-based proteomics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3974.
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4
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Eichhoff OM, Stoffel CI, Käsler J, Briker L, Turko P, Karsai G, Zila N, Paulitschke V, Cheng PF, Leitner A, Bileck A, Zamboni N, Irmisch A, Balazs Z, Tastanova A, Pascoal S, Johansen P, Wegmann R, Mena J, Othman A, Viswanathan VS, Wenzina J, Aloia A, Saltari A, Dzung A, Aebersold R, Ak M, Al-Quaddoomi FS, Albert SI, Albinus J, Alborelli I, Andani S, Attinger PO, Bacac M, Baumhoer D, Beck-Schimmer B, Beerenwinkel N, Beisel C, Bernasconi L, Bertolini A, Bodenmiller B, Bonilla X, Bosshard L, Calgua B, Casanova R, Chevrier S, Chicherova N, Coelho R, D'Costa M, Danenberg E, Davidson N, Drãgan MA, Dummer R, Engler S, Erkens M, Eschbach K, Esposito C, Fedier A, Ferreira P, Ficek J, Frei AL, Frey B, Goetze S, Grob L, Gut G, Günther D, Haberecker M, Haeuptle P, Heinzelmann-Schwarz V, Herter S, Holtackers R, Huesser T, Immer A, Irmisch A, Jacob F, Jacobs A, Jaeger TM, Jahn K, James AR, Jermann PM, Kahles A, Kahraman A, Koelzer VH, Kuebler W, Kuipers J, Kunze CP, Kurzeder C, Lehmann KV, Levesque M, Lischetti U, Lugert S, Maass G, Manz MG, Markolin P, Mehnert M, Mena J, Metzler JM, Miglino N, Milani ES, Moch H, Muenst S, Murri R, Ng CK, Nicolet S, Nowak M, Lopez MN, Pedrioli PG, Pelkmans L, Piscuoglio S, Prummer M, Rimmer N, Ritter M, Rommel C, Rosano-González ML, Rätsch G, Santacroce N, Del Castillo JS, Schlenker R, Schwalie PC, Schwan S, Schär T, Senti G, Shao W, Singer F, Sivapatham S, Snijder B, Sobottka B, Sreedharan VT, Stark S, Stekhoven DJ, Tanna T, Theocharides AP, Thomas TM, Tolnay M, Tosevski V, Toussaint NC, Tuncel MA, Tusup M, Van Drogen A, Vetter M, Vlajnic T, Weber S, Weber WP, Wegmann R, Weller M, Wendt F, Wey N, Wicki A, Wildschut MH, Wollscheid B, Yu S, Ziegler J, Zimmermann M, Zoche M, Zuend G, Krauthammer M, Schreiber SL, Hornemann T, Distel M, Snijder B, Dummer R, Levesque MP. ROS Induction Targets Persister Cancer Cells with Low Metabolic Activity in NRAS-Mutated Melanoma. Cancer Res 2023; 83:1128-1146. [PMID: 36946761 DOI: 10.1158/0008-5472.can-22-1826] [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] [Received: 06/03/2022] [Revised: 10/04/2022] [Accepted: 01/24/2023] [Indexed: 03/23/2023]
Abstract
Clinical management of melanomas with NRAS mutations is challenging. Targeting MAPK signaling is only beneficial to a small subset of patients due to resistance that arises through genetic, transcriptional, and metabolic adaptation. Identification of targetable vulnerabilities in NRAS-mutated melanoma could help improve patient treatment. Here, we used multiomics analyses to reveal that NRAS-mutated melanoma cells adopt a mesenchymal phenotype with a quiescent metabolic program to resist cellular stress induced by MEK inhibition. The metabolic alterations elevated baseline reactive oxygen species (ROS) levels, leading these cells to become highly sensitive to ROS induction. In vivo xenograft experiments and single-cell RNA sequencing demonstrated that intratumor heterogeneity necessitates the combination of a ROS inducer and a MEK inhibitor to inhibit both tumor growth and metastasis. Ex vivo pharmacoscopy of 62 human metastatic melanomas confirmed that MEK inhibitor-resistant tumors significantly benefited from the combination therapy. Finally, oxidative stress response and translational suppression corresponded with ROS-inducer sensitivity in 486 cancer cell lines, independent of cancer type. These findings link transcriptional plasticity to a metabolic phenotype that can be inhibited by ROS inducers in melanoma and other cancers. SIGNIFICANCE Metabolic reprogramming in drug-resistant NRAS-mutated melanoma cells confers sensitivity to ROS induction, which suppresses tumor growth and metastasis in combination with MAPK pathway inhibitors.
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Affiliation(s)
- Ossia M Eichhoff
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Corinne I Stoffel
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Jan Käsler
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Luzia Briker
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Patrick Turko
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Gergely Karsai
- Institute for Clinical Chemistry, University Hospital Zurich, Zurich, Switzerland; Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Nina Zila
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Verena Paulitschke
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Phil F Cheng
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | | | - Andrea Bileck
- Joint Metabolome Facility, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Nicola Zamboni
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | - Anja Irmisch
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Zsolt Balazs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Biomedical Informatics, University Hospital of Zurich, Zurich, Switzerland
| | - Aizhan Tastanova
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Susana Pascoal
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Pål Johansen
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Rebekka Wegmann
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | - Julien Mena
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | - Alaa Othman
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | | | - Judith Wenzina
- Skin and Endothelium Research Division, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Andrea Aloia
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | - Annalisa Saltari
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Andreas Dzung
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michael Krauthammer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Biomedical Informatics, University Hospital of Zurich, Zurich, Switzerland
| | | | - Thorsten Hornemann
- Institute for Clinical Chemistry, University Hospital Zurich, Zurich, Switzerland; Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Martin Distel
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Berend Snijder
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
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5
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Uliana F, Ciuffa R, Mishra R, Fossati A, Frommelt F, Keller S, Mehnert M, Birkeland ES, van Drogen F, Srejic N, Peter M, Tapon N, Aebersold R, Gstaiger M. Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration. Mol Syst Biol 2023; 19:e11024. [PMID: 36896621 PMCID: PMC10090947 DOI: 10.15252/msb.202211024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
While several computational methods have been developed to predict the functional relevance of phosphorylation sites, experimental analysis of the interdependency between protein phosphorylation and Protein-Protein Interactions (PPIs) remains challenging. Here, we describe an experimental strategy to establish interdependencies between protein phosphorylation and complex formation. This strategy is based on three main steps: (i) systematically charting the phosphorylation landscape of a target protein; (ii) assigning distinct proteoforms of the target protein to different protein complexes by native complex separation (AP-BNPAGE) and protein correlation profiling; and (iii) analyzing proteoforms and complexes in cells lacking regulators of the target protein. We applied this strategy to YAP1, a transcriptional co-activator for the control of organ size and tissue homeostasis that is highly phosphorylated and among the most connected proteins in human cells. We identified multiple YAP1 phosphosites associated with distinct complexes and inferred how both are controlled by Hippo pathway members. We detected a PTPN14/LATS1/YAP1 complex and suggest a model how PTPN14 inhibits YAP1 via augmenting WW domain-dependent complex formation and phosphorylation by LATS1/2.
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Affiliation(s)
- Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ranjan Mishra
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Andrea Fossati
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sabrina Keller
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Frank van Drogen
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Nevena Srejic
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Nicolas Tapon
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, London, UK
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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6
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Ciuffa R, Uliana F, Mannion J, Mehnert M, Tenev T, Marulli C, Satanowski A, Keller LML, Rodilla Ramírez PN, Ori A, Gstaiger M, Meier P, Aebersold R. Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics. Proc Natl Acad Sci U S A 2022; 119:e2117175119. [PMID: 36179048 PMCID: PMC9546619 DOI: 10.1073/pnas.2117175119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 07/28/2022] [Indexed: 12/03/2022] Open
Abstract
Protein-protein interactions (PPIs) represent the main mode of the proteome organization in the cell. In the last decade, several large-scale representations of PPI networks have captured generic aspects of the functional organization of network components but mostly lack the context of cellular states. However, the generation of context-dependent PPI networks is essential for structural and systems-level modeling of biological processes-a goal that remains an unsolved challenge. Here we describe an experimental/computational strategy to achieve a modeling of PPIs that considers contextual information. This strategy defines the composition, stoichiometry, temporal organization, and cellular requirements for the formation of target assemblies. We used this approach to generate an integrated model of the formation principles and architecture of a large signalosome, the TNF-receptor signaling complex (TNF-RSC). Overall, we show that the integration of systems- and structure-level information provides a generic, largely unexplored link between the modular proteome and cellular function.
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Affiliation(s)
- Rodolfo Ciuffa
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Federico Uliana
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jonathan Mannion
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, SW3 6JB London, United Kingdom
| | - Martin Mehnert
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tencho Tenev
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, SW3 6JB London, United Kingdom
| | - Cathy Marulli
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ari Satanowski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | | | | | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, SW3 6JB London, United Kingdom
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
- Faculty of Science, University of Zurich, 8093 Zurich, Switzerland
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7
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Buljan M, Ciuffa R, van Drogen A, Vichalkovski A, Mehnert M, Rosenberger G, Lee S, Varjosalo M, Pernas LE, Spegg V, Snijder B, Aebersold R, Gstaiger M. Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. Mol Cell 2020; 79:504-520.e9. [PMID: 32707033 PMCID: PMC7427327 DOI: 10.1016/j.molcel.2020.07.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 02/14/2020] [Accepted: 06/30/2020] [Indexed: 12/30/2022]
Abstract
Protein kinases are essential for signal transduction and control of most cellular processes, including metabolism, membrane transport, motility, and cell cycle. Despite the critical role of kinases in cells and their strong association with diseases, good coverage of their interactions is available for only a fraction of the 535 human kinases. Here, we present a comprehensive mass-spectrometry-based analysis of a human kinase interaction network covering more than 300 kinases. The interaction dataset is a high-quality resource with more than 5,000 previously unreported interactions. We extensively characterized the obtained network and were able to identify previously described, as well as predict new, kinase functional associations, including those of the less well-studied kinases PIM3 and protein O-mannose kinase (POMK). Importantly, the presented interaction map is a valuable resource for assisting biomedical studies. We uncover dozens of kinase-disease associations spanning from genetic disorders to complex diseases, including cancer.
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Affiliation(s)
- Marija Buljan
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Empa, Swiss Federal Laboratories for Materials Science and Technology, 9014 St. Gallen, Switzerland
| | - Rodolfo Ciuffa
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Audrey van Drogen
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Anton Vichalkovski
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Martin Mehnert
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - George Rosenberger
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Columbia University Department of Systems Biology, New York, NY 10032, USA
| | - Sohyon Lee
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Lucia Espona Pernas
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Berend Snijder
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
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8
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Mehnert M, Ciuffa R, Frommelt F, Uliana F, van Drogen A, Ruminski K, Gstaiger M, Aebersold R. Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes. Nat Commun 2020; 11:3563. [PMID: 32678104 PMCID: PMC7366679 DOI: 10.1038/s41467-020-17387-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/26/2020] [Indexed: 01/09/2023] Open
Abstract
Rapidly increasing availability of genomic data and ensuing identification of disease associated mutations allows for an unbiased insight into genetic drivers of disease development. However, determination of molecular mechanisms by which individual genomic changes affect biochemical processes remains a major challenge. Here, we develop a multilayered proteomic workflow to explore how genetic lesions modulate the proteome and are translated into molecular phenotypes. Using this workflow we determine how expression of a panel of disease-associated mutations in the Dyrk2 protein kinase alter the composition, topology and activity of this kinase complex as well as the phosphoproteomic state of the cell. The data show that altered protein-protein interactions caused by the mutations are associated with topological changes and affected phosphorylation of known cancer driver proteins, thus linking Dyrk2 mutations with cancer-related biochemical processes. Overall, we discover multiple mutation-specific functionally relevant changes, thus highlighting the extensive plasticity of molecular responses to genetic lesions.
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Affiliation(s)
- Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Audrey van Drogen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Kilian Ruminski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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9
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Mehnert M, Li W, Wu C, Salovska B, Liu Y. Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics 2019; 19:e1800438. [PMID: 30901150 DOI: 10.1002/pmic.201800438] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/24/2019] [Indexed: 12/21/2022]
Abstract
CRISPR-Cas gene editing holds substantial promise in many biomedical disciplines and basic research. Due to the important functional implications of non-histone chromosomal protein HMG-14 (HMGN1) in regulating chromatin structure and tumor immunity, gene knockout of HMGN1 is performed by CRISPR in cancer cells and the following proteomic regulation events are studied. In particular, DIA mass spectrometry (DIA-MS) is utilized, and more than 6200 proteins (protein- FDR 1%) and more than 82 000 peptide precursors are reproducibly measured in the single MS shots of 2 h. HMGN1 protein deletion is confidently verified by DIA-MS in all of the clone- and dish- replicates following CRISPR. Statistical analysis reveals 147 proteins change their expressions significantly after HMGN1 knockout. Functional annotation and enrichment analysis indicate the deletion of HMGN1 induces histone inactivation, various stress pathways, remodeling of extracellular proteomes, cell proliferation, as well as immune regulation processes such as complement and coagulation cascade and interferon alpha/ gamma response in cancer cells. These results shed new lights on the cellular functions of HMGN1. It is suggested that DIA-MS can be reliably used as a rapid, robust, and cost-effective proteomic-screening tool to assess the outcome of the CRISPR experiments.
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Affiliation(s)
- Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Chongde Wu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
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10
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Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt WD, Aebersold R. Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nat Biotechnol 2019; 37:314-322. [PMID: 30778230 DOI: 10.1038/s41587-019-0037-y] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 11/21/2018] [Indexed: 11/09/2022]
Abstract
Reproducibility in research can be compromised by both biological and technical variation, but most of the focus is on removing the latter. Here we investigate the effects of biological variation in HeLa cell lines using a systems-wide approach. We determine the degree of molecular and phenotypic variability across 14 stock HeLa samples from 13 international laboratories. We cultured cells in uniform conditions and profiled genome-wide copy numbers, mRNAs, proteins and protein turnover rates in each cell line. We discovered substantial heterogeneity between HeLa variants, especially between lines of the CCL2 and Kyoto varieties, and observed progressive divergence within a specific cell line over 50 successive passages. Genomic variability has a complex, nonlinear effect on transcriptome, proteome and protein turnover profiles, and proteotype patterns explain the varying phenotypic response of different cell lines to Salmonella infection. These findings have implications for the interpretation and reproducibility of research results obtained from human cultured cells.
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Affiliation(s)
- Yansheng Liu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA. .,Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.
| | - Yang Mi
- Heidelberg University, Faculty of Biosciences, Heidelberg, Germany.,Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Torsten Mueller
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Evan G Williams
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Audrey Van Drogen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, and University Hospitals of Geneva, Geneva, Switzerland
| | - Max Frank
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Michael Seifert
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases, Dresden, Germany
| | | | - Isabel Sorg
- Biozentrum, University of Basel, Basel, Switzerland
| | - Fedor Bezrukov
- Department of Genetic Medicine and Development, University of Geneva Medical School, and University Hospitals of Geneva, Geneva, Switzerland
| | | | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | | | - Giuseppe Testa
- IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Julio Saez-Rodriguez
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, Aachen, Germany.,Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Bioquant Heidelberg, Germany
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, and University Hospitals of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | | | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. .,Faculty of Science, University of Zurich, Zurich, Switzerland.
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11
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Mehnert M, Sommermeyer F, Berger M, Kumar Lakshmipathy S, Gauss R, Aebi M, Jarosch E, Sommer T. The interplay of Hrd3 and the molecular chaperone system ensures efficient degradation of malfolded secretory proteins. Mol Biol Cell 2014; 26:185-94. [PMID: 25428985 PMCID: PMC4294667 DOI: 10.1091/mbc.e14-07-1202] [Citation(s) in RCA: 26] [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: 11/11/2022] Open
Abstract
A central ubiquitin ligase involved in endoplasmic reticulum (ER)–associated protein degradation is the HRD-ligase. The ER-luminal subunit Hrd3 cooperates with the cochaperone Scj1 in clearing misfolded proteins from the ER. Misfolded proteins of the secretory pathway are extracted from the endoplasmic reticulum (ER), polyubiquitylated by a protein complex termed the Hmg-CoA reductase degradation ligase (HRD-ligase), and degraded by cytosolic 26S proteasomes. This process is termed ER-associated protein degradation (ERAD). We previously showed that the membrane protein Der1, which is a subunit of the HRD-ligase, is involved in the export of aberrant polypeptides from the ER. Unexpectedly, we also uncovered a close spatial proximity of Der1 and the substrate receptor Hrd3 in the ER lumen. We report here on a mutant Hrd3KR that is selectively defective for ERAD of soluble proteins. Hrd3KR displays subtle structural changes that affect its positioning toward Der1. Furthermore, increased quantities of the ER-resident Hsp70-type chaperone Kar2 and the Hsp40-type cochaperone Scj1 bind to Hrd3KR. Of note, deletion of SCJ1 impairs ERAD of model substrates and causes the accumulation of client proteins at Hrd3. Our data imply a function of Scj1 in the removal of malfolded proteins from the receptor Hrd3, which facilitates their delivery to downstream-acting components like Der1.
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Affiliation(s)
- Martin Mehnert
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Maren Berger
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Robert Gauss
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, 8093 Zurich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, 8093 Zurich, Switzerland
| | - Ernst Jarosch
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Thomas Sommer
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany Institute of Biology, Humboldt Universität zu Berlin, 10115 Berlin, Germany
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12
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Mehnert M, Sommer T, Jarosch E. ERAD ubiquitin ligases: multifunctional tools for protein quality control and waste disposal in the endoplasmic reticulum. Bioessays 2010; 32:905-13. [PMID: 20806269 DOI: 10.1002/bies.201000046] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In eukaryotic cells terminally misfolded proteins of the secretory pathway are retarded in the endoplasmic reticulum (ER) and subsequently degraded in a ubiquitin-proteasome-dependent manner. This highly conserved process termed ER-associated protein degradation (ERAD) ensures homeostasis in the secretory pathway by disposing faulty polypeptides and preventing their deleterious accumulation and eventual aggregation in the cell. The focus of this paper is the functional description of membrane-bound ubiquitin ligases, which are involved in all critical steps of ERAD. In the end we want to speculate on how the modular architecture of these entities ensures the specificity of substrate selection and possibly accomplishes the transport of misfolded polypeptides from the ER into the cytoplasm.
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Affiliation(s)
- Martin Mehnert
- Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Str., Berlin, Germany
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13
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Mehnert M, Ulbricht J, Baumann B, Engel S. [Frequency and significance of mycoplasma in male partners of infertile couples (author's transl)]. Dermatol Monatsschr 1979; 165:598-602. [PMID: 510644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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