1
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Winkelmann H, Richter CP, Eising J, Piehler J, Kurre R. Correlative single-molecule and structured illumination microscopy of fast dynamics at the plasma membrane. Nat Commun 2024; 15:5813. [PMID: 38987559 PMCID: PMC11236984 DOI: 10.1038/s41467-024-49876-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/21/2024] [Indexed: 07/12/2024] Open
Abstract
Total internal reflection fluorescence (TIRF) microscopy offers powerful means to uncover the functional organization of proteins in the plasma membrane with very high spatial and temporal resolution. Traditional TIRF illumination, however, shows a Gaussian intensity profile, which is typically deteriorated by overlaying interference fringes hampering precise quantification of intensities-an important requisite for quantitative analyses in single-molecule localization microscopy (SMLM). Here, we combine flat-field illumination by using a standard πShaper with multi-angular TIR illumination by incorporating a spatial light modulator compatible with fast super-resolution structured illumination microscopy (SIM). This distinct combination enables quantitative multi-color SMLM with a highly homogenous illumination. By using a dual camera setup with optimized image splitting optics, we achieve a versatile combination of SMLM and SIM with up to three channels. We deploy this setup for establishing robust detection of receptor stoichiometries based on single-molecule intensity analysis and single-molecule Förster resonance energy transfer (smFRET). Homogeneous illumination furthermore enables long-term tracking and localization microscopy (TALM) of cell surface receptors identifying spatial heterogeneity of mobility and accessibility in the plasma membrane. By combination of TALM and SIM, spatially and molecularly heterogenous diffusion properties can be correlated with nanoscale cytoskeletal organization and dynamics.
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Affiliation(s)
- Hauke Winkelmann
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Christian P Richter
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Jasper Eising
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Jacob Piehler
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Center for Cellular Nanoanalytics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
| | - Rainer Kurre
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Center for Cellular Nanoanalytics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Integrated Bioimaging Facility iBiOs, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
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2
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Caveney NA, Rodriguez GE, Pollmann C, Meyer T, Borowska MT, Wilson SC, Wang N, Xiang X, Householder KD, Tao P, Su LL, Saxton RA, Piehler J, Garcia KC. Structure of the interleukin-5 receptor complex exemplifies the organizing principle of common beta cytokine signaling. Mol Cell 2024; 84:1995-2005.e7. [PMID: 38614096 PMCID: PMC11102305 DOI: 10.1016/j.molcel.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/20/2024] [Accepted: 03/22/2024] [Indexed: 04/15/2024]
Abstract
Cytokines regulate immune responses by binding to cell surface receptors, including the common subunit beta (βc), which mediates signaling for GM-CSF, IL-3, and IL-5. Despite known roles in inflammation, the structural basis of IL-5 receptor activation remains unclear. We present the cryo-EM structure of the human IL-5 ternary receptor complex, revealing architectural principles for IL-5, GM-CSF, and IL-3. In mammalian cell culture, single-molecule imaging confirms hexameric IL-5 complex formation on cell surfaces. Engineered chimeric receptors show that IL-5 signaling, as well as IL-3 and GM-CSF, can occur through receptor heterodimerization, obviating the need for higher-order assemblies of βc dimers. These findings provide insights into IL-5 and βc receptor family signaling mechanisms, aiding in the development of therapies for diseases involving deranged βc signaling.
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Affiliation(s)
- Nathanael A Caveney
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.
| | - Grayson E Rodriguez
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christoph Pollmann
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Thomas Meyer
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Marta T Borowska
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven C Wilson
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nan Wang
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinyu Xiang
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Biophysics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karsten D Householder
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pingdong Tao
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leon L Su
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert A Saxton
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - K Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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3
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Tsutsumi N, Masoumi Z, James SC, Tucker JA, Winkelmann H, Grey W, Picton LK, Moss L, Wilson SC, Caveney NA, Jude KM, Gati C, Piehler J, Hitchcock IS, Garcia KC. Structure of the thrombopoietin-MPL receptor complex is a blueprint for biasing hematopoiesis. Cell 2023; 186:4189-4203.e22. [PMID: 37633268 PMCID: PMC10528194 DOI: 10.1016/j.cell.2023.07.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
Thrombopoietin (THPO or TPO) is an essential cytokine for hematopoietic stem cell (HSC) maintenance and megakaryocyte differentiation. Here, we report the 3.4 Å resolution cryoelectron microscopy structure of the extracellular TPO-TPO receptor (TpoR or MPL) signaling complex, revealing the basis for homodimeric MPL activation and providing a structural rationalization for genetic loss-of-function thrombocytopenia mutations. The structure guided the engineering of TPO variants (TPOmod) with a spectrum of signaling activities, from neutral antagonists to partial- and super-agonists. Partial agonist TPOmod decoupled JAK/STAT from ERK/AKT/CREB activation, driving a bias for megakaryopoiesis and platelet production without causing significant HSC expansion in mice and showing superior maintenance of human HSCs in vitro. These data demonstrate the functional uncoupling of the two primary roles of TPO, highlighting the potential utility of TPOmod in hematology research and clinical HSC transplantation.
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Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan.
| | - Zahra Masoumi
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Sophie C James
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Julie A Tucker
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hauke Winkelmann
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - William Grey
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Lora K Picton
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lucie Moss
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Steven C Wilson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nathanael A Caveney
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cornelius Gati
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jacob Piehler
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - Ian S Hitchcock
- York Biomedical Research Institute, Department of Biology, University of York, Heslington, York YO10 5DD, UK.
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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4
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Tsirigotaki A, Dansercoer A, Verschueren KHG, Marković I, Pollmann C, Hafer M, Felix J, Birck C, Van Putte W, Catteeuw D, Tavernier J, Fernando Bazan J, Piehler J, Savvides SN, Verstraete K. Mechanism of receptor assembly via the pleiotropic adipokine Leptin. Nat Struct Mol Biol 2023; 30:551-563. [PMID: 36959263 DOI: 10.1038/s41594-023-00941-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/06/2023] [Indexed: 03/25/2023]
Abstract
The adipokine Leptin activates its receptor LEP-R in the hypothalamus to regulate body weight and exerts additional pleiotropic functions in immunity, fertility and cancer. However, the structure and mechanism of Leptin-mediated LEP-R assemblies has remained unclear. Intriguingly, the signaling-competent isoform of LEP-R is only lowly abundant amid several inactive short LEP-R isoforms contributing to a mechanistic conundrum. Here we show by X-ray crystallography and cryo-EM that, in contrast to long-standing paradigms, Leptin induces type I cytokine receptor assemblies featuring 3:3 stoichiometry and demonstrate such Leptin-induced trimerization of LEP-R on living cells via single-molecule microscopy. In mediating these assemblies, Leptin undergoes drastic restructuring that activates its site III for binding to the Ig domain of an adjacent LEP-R. These interactions are abolished by mutations linked to obesity. Collectively, our study provides the structural and mechanistic framework for how evolutionarily conserved Leptin:LEP-R assemblies with 3:3 stoichiometry can engage distinct LEP-R isoforms to achieve signaling.
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Affiliation(s)
- Alexandra Tsirigotaki
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Ann Dansercoer
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Koen H G Verschueren
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Iva Marković
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Christoph Pollmann
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Maximillian Hafer
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Jan Felix
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Catherine Birck
- Integrated Structural Biology Platform, Centre for Integrative Biology (CBI), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U1258, University of Strasbourg, Illkirch, France
| | | | - Dominiek Catteeuw
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Orionis Biosciences, Ghent, Belgium
| | - J Fernando Bazan
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- ħ Bioconsulting llc, Stillwater, MN, USA
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
| | - Kenneth Verstraete
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
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5
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Gaggero S, Martinez-Fabregas J, Cozzani A, Fyfe PK, Leprohon M, Yang J, Thomasen FE, Winkelmann H, Magnez R, Conti AG, Wilmes S, Pohler E, van Gijsel Bonnello M, Thuru X, Quesnel B, Soncin F, Piehler J, Lindorff-Larsen K, Roychoudhuri R, Moraga I, Mitra S. IL-2 is inactivated by the acidic pH environment of tumors enabling engineering of a pH-selective mutein. Sci Immunol 2022; 7:eade5686. [PMID: 36459543 DOI: 10.1126/sciimmunol.ade5686] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Cytokines interact with their receptors in the extracellular space to control immune responses. How the physicochemical properties of the extracellular space influence cytokine signaling is incompletely elucidated. Here, we show that the activity of interleukin-2 (IL-2), a cytokine critical to T cell immunity, is profoundly affected by pH, limiting IL-2 signaling within the acidic environment of tumors. Generation of lactic acid by tumors limits STAT5 activation, effector differentiation, and antitumor immunity by CD8+ T cells and renders high-dose IL-2 therapy poorly effective. Directed evolution enabled selection of a pH-selective IL-2 mutein (Switch-2). Switch-2 binds the IL-2 receptor subunit IL-2Rα with higher affinity, triggers STAT5 activation, and drives CD8+ T cell effector function more potently at acidic pH than at neutral pH. Consequently, high-dose Switch-2 therapy induces potent immune activation and tumor rejection with reduced on-target toxicity in normal tissues. Last, we show that sensitivity to pH is a generalizable property of a diverse range of cytokines with broad relevance to immunity and immunotherapy in healthy and diseased tissues.
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Affiliation(s)
- Silvia Gaggero
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
| | | | - Adeline Cozzani
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
| | - Paul K Fyfe
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Malo Leprohon
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Jie Yang
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - F Emil Thomasen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Hauke Winkelmann
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Romain Magnez
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
| | - Alberto G Conti
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Stephan Wilmes
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Elizabeth Pohler
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Xavier Thuru
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
| | - Bruno Quesnel
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
| | - Fabrice Soncin
- CNRS/IIS/Centre Oscar Lambret/Lille University SMMiL-E Project, CNRS Délégation Hauts-de-France, Lille, France
- CNRS IRL 2820; Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Rahul Roychoudhuri
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Ignacio Moraga
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Suman Mitra
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
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6
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Ma X, Zhang MJ, Wang J, Zhang T, Xue P, Kang Y, Sun ZJ, Xu Z. Emerging Biomaterials Imaging Antitumor Immune Response. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2204034. [PMID: 35728795 DOI: 10.1002/adma.202204034] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Immunotherapy is one of the most promising clinical modalities for the treatment of malignant tumors and has shown excellent therapeutic outcomes in clinical settings. However, it continues to face several challenges, including long treatment cycles, high costs, immune-related adverse events, and low response rates. Thus, it is critical to predict the response rate to immunotherapy by using imaging technology in the preoperative and intraoperative. Here, the latest advances in nanosystem-based biomaterials used for predicting responses to immunotherapy via the imaging of immune cells and signaling molecules in the immune microenvironment are comprehensively summarized. Several imaging methods, such as fluorescence imaging, magnetic resonance imaging, positron emission tomography imaging, ultrasound imaging, and photoacoustic imaging, used in immune predictive imaging, are discussed to show the potential of nanosystems for distinguishing immunotherapy responders from nonresponders. Nanosystem-based biomaterials aided by various imaging technologies are expected to enable the effective prediction and diagnosis in cases of tumors, inflammation, and other public diseases.
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Affiliation(s)
- Xianbin Ma
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Materials and Energy and Chongqing Engineering Research Center for Micro-Nano Biomedical Materials and Devices, Southwest University, Chongqing, 400715, P. R. China
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Meng-Jie Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, P. R. China
| | - Jingting Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Materials and Energy and Chongqing Engineering Research Center for Micro-Nano Biomedical Materials and Devices, Southwest University, Chongqing, 400715, P. R. China
| | - Tian Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Materials and Energy and Chongqing Engineering Research Center for Micro-Nano Biomedical Materials and Devices, Southwest University, Chongqing, 400715, P. R. China
| | - Peng Xue
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Materials and Energy and Chongqing Engineering Research Center for Micro-Nano Biomedical Materials and Devices, Southwest University, Chongqing, 400715, P. R. China
| | - Yuejun Kang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Materials and Energy and Chongqing Engineering Research Center for Micro-Nano Biomedical Materials and Devices, Southwest University, Chongqing, 400715, P. R. China
| | - Zhi-Jun Sun
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, P. R. China
| | - Zhigang Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Materials and Energy and Chongqing Engineering Research Center for Micro-Nano Biomedical Materials and Devices, Southwest University, Chongqing, 400715, P. R. China
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7
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Malkusch S, Rahm JV, Dietz MS, Heilemann M, Sibarita JB, Lötsch J. Receptor tyrosine kinase MET ligand-interaction classified via machine learning from single-particle tracking data. Mol Biol Cell 2022; 33:ar60. [PMID: 35171646 PMCID: PMC9265154 DOI: 10.1091/mbc.e21-10-0496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 11/11/2022] Open
Abstract
Internalin B-mediated activation of the membrane-bound receptor tyrosine kinase MET is accompanied by a change in receptor mobility. Conversely, it should be possible to infer from receptor mobility whether a cell has been treated with internalin B. Here, we propose a method based on hidden Markov modeling and explainable artificial intelligence that machine-learns the key differences in MET mobility between internalin B-treated and -untreated cells from single-particle tracking data. Our method assigns receptor mobility to three diffusion modes (immobile, slow, and fast). It discriminates between internalin B-treated and -untreated cells with a balanced accuracy of >99% and identifies three parameters that are most affected by internalin B treatment: a decrease in the mobility of slow molecules (1) and a depopulation of the fast mode (2) caused by an increased transition of fast molecules to the slow mode (3). Our approach is based entirely on free software and is readily applicable to the analysis of other membrane receptors.
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Affiliation(s)
- Sebastian Malkusch
- Institute of Clinical Pharmacology, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Johanna V. Rahm
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Marina S. Dietz
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Jean-Baptiste Sibarita
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France
| | - Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
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8
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Kuchler O, Gerlach J, Vomhof T, Hettich J, Steinmetz J, Gebhardt JCM, Michaelis J, Knöll B. Single-molecule tracking (SMT) and localization of SRF and MRTF transcription factors during neuronal stimulation and differentiation. Open Biol 2022; 12:210383. [PMID: 35537478 PMCID: PMC9090491 DOI: 10.1098/rsob.210383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In cells, proteins encoded by the same gene do not all behave uniformly but engage in functional subpopulations induced by spatial or temporal segregation. While conventional microscopy has limitations in revealing such spatial and temporal diversity, single-molecule tracking (SMT) microscopy circumvented this problem and allows for high-resolution imaging and quantification of dynamic single-molecule properties. Particularly in the nucleus, SMT has identified specific DNA residence times of transcription factors (TFs), DNA-bound TF fractions and positions of transcriptional hot-spots upon cell stimulation. By contrast to cell stimulation, SMT has not been employed to follow dynamic TF changes along stages of cell differentiation. Herein, we analysed the serum response factor (SRF), a TF involved in the differentiation of many cell types to study nuclear single-molecule dynamics in neuronal differentiation. Our data in living mouse hippocampal neurons show dynamic changes in SRF DNA residence time and SRF DNA-bound fraction between the stages of adhesion, neurite growth and neurite differentiation in axon and dendrites. Using TALM (tracking and localization microscopy), we identified nuclear positions of SRF clusters and observed changes in their numbers and size during differentiation. Furthermore, we show that the SRF cofactor MRTF-A (myocardin-related TF or MKL1) responds to cell activation by enhancing the long-bound DNA fraction. Finally, a first SMT colocalization study of two proteins was performed in living cells showing enhanced SRF/MRTF-A colocalization upon stimulation. In summary, SMT revealed modulation of dynamic TF properties during cell stimulation and differentiation.
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Affiliation(s)
- Oliver Kuchler
- Institute of Neurobiochemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany,Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Jule Gerlach
- Institute of Neurobiochemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany,Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Thomas Vomhof
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Johannes Hettich
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Julia Steinmetz
- Department of Statistics, TU Dortmund University, August-Schmidt Straße 1, 44227 Dortmund, Germany
| | | | - Jens Michaelis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Bernd Knöll
- Institute of Neurobiochemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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9
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Dirscherl C, Löchte S, Hein Z, Kopicki JD, Harders AR, Linden N, Karner A, Preiner J, Weghuber J, Garcia-Alai M, Uetrecht C, Zacharias M, Piehler J, Lanzerstorfer P, Springer S. Dissociation of β2m from MHC class I Triggers formation of Noncovalent, transient heavy chain dimers. J Cell Sci 2022; 135:274997. [PMID: 35393611 DOI: 10.1242/jcs.259498] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/30/2022] [Indexed: 11/20/2022] Open
Abstract
At the plasma membrane of mammalian cells, major histocompatibility complex class I molecules (MHC-I) present antigenic peptides to cytotoxic T cells. Following the loss of the peptide and the light chain beta-2 microglobulin (β2m), the resulting free heavy chains (FHCs) can associate into homotypic complexes in the plasma membrane. Here, we investigate the stoichiometry and dynamics of MHC-I FHCs assemblies by combining a micropattern assay with fluorescence recovery after photobleaching (FRAP) and with single molecule co-tracking. We identify non-covalent MHC-I FHC dimers mediated by the α3 domain as the prevalent species at the plasma membrane, leading a moderate decrease in the diffusion coefficient. MHC-I FHC dimers show increased tendency to cluster into higher order oligomers as concluded from an increased immobile fraction with higher single molecule co-localization. In vitro studies with isolated proteins in conjunction with molecular docking and dynamics simulations suggest that in the complexes, the α3 domain of one FHC binds to another FHC in a manner similar to the β2m light chain.
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Affiliation(s)
- Cindy Dirscherl
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Sara Löchte
- Department of Biology and Center for Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - Zeynep Hein
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Noemi Linden
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Andreas Karner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Johannes Preiner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Julian Weghuber
- University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany.,Centre for Structural Systems Biology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.,European XFEL, Schenefeld, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, Garching, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | | | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
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10
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Sotolongo Bellón J, Birkholz O, Richter CP, Eull F, Kenneweg H, Wilmes S, Rothbauer U, You C, Walter MR, Kurre R, Piehler J. Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane. CELL REPORTS METHODS 2022; 2:100165. [PMID: 35474965 PMCID: PMC9017138 DOI: 10.1016/j.crmeth.2022.100165] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/19/2021] [Accepted: 01/13/2022] [Indexed: 12/22/2022]
Abstract
Localization and tracking of individual receptors by single-molecule imaging opens unique possibilities to unravel the assembly and dynamics of signaling complexes in the plasma membrane. We present a comprehensive workflow for imaging and analyzing receptor diffusion and interaction in live cells at single molecule level with up to four colors. Two engineered, monomeric GFP variants, which are orthogonally recognized by anti-GFP nanobodies, are employed for efficient and selective labeling of target proteins in the plasma membrane with photostable fluorescence dyes. This labeling technique enables us to quantitatively resolve the stoichiometry and dynamics of the interferon-γ (IFNγ) receptor signaling complex in the plasma membrane of living cells by multicolor single-molecule imaging. Based on versatile spatial and spatiotemporal correlation analyses, we identify ligand-induced receptor homo- and heterodimerization. Multicolor single-molecule co-tracking and quantitative single-molecule Förster resonance energy transfer moreover reveals transient assembly of IFNγ receptor heterotetramers and confirms its structural architecture.
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Affiliation(s)
- Junel Sotolongo Bellón
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Oliver Birkholz
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Christian P. Richter
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Florian Eull
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Hella Kenneweg
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Stephan Wilmes
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
- Division of Cell Signalling and Immunology, University of Dundee, School of Life Sciences, Dundee, UK
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard-Karls-University, Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Changjiang You
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Mark R. Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rainer Kurre
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
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11
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Stüber JC, Richter CP, Bellón JS, Schwill M, König I, Schuler B, Piehler J, Plückthun A. Apoptosis-inducing anti-HER2 agents operate through oligomerization-induced receptor immobilization. Commun Biol 2021; 4:762. [PMID: 34155320 PMCID: PMC8217238 DOI: 10.1038/s42003-021-02253-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/21/2021] [Indexed: 01/08/2023] Open
Abstract
Overexpression of the receptor tyrosine kinase HER2 plays a critical role in the development of various tumors. Biparatopic designed ankyrin repeat proteins (bipDARPins) potently induce apoptosis in HER2-addicted breast cancer cell lines. Here, we have investigated how the spatiotemporal receptor organization at the cell surface is modulated by these agents and is distinguished from other molecules, which do not elicit apoptosis. Binding of conventional antibodies is accompanied by moderate reduction of receptor mobility, in agreement with HER2 being dimerized by the bivalent IgG. In contrast, the most potent apoptosis-inducing bipDARPins lead to a dramatic arrest of HER2. Dual-color single-molecule tracking revealed that the HER2 "lockdown" by these bipDARPins is caused by the formation of HER2-DARPin oligomer chains, which are trapped in nanoscopic membrane domains. Our findings establish that efficient neutralization of receptor tyrosine kinase signaling can be achieved through intermolecular bipDARPin crosslinking alone, resulting in inactivated, locked-down bipDARPin-HER2 complexes.
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Affiliation(s)
- Jakob C Stüber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.,Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Christian P Richter
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Junel Sotolongo Bellón
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Martin Schwill
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Iwo König
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.,Roche Diagnostics Int. AG, Rotkreuz, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany.
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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12
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Glassman CR, Su L, Majri-Morrison SS, Winkelmann H, Mo F, Li P, Pérez-Cruz M, Ho PP, Koliesnik I, Nagy N, Hnizdilova T, Picton LK, Kovar M, Bollyky P, Steinman L, Meyer E, Piehler J, Leonard WJ, Garcia KC. Calibration of cell-intrinsic interleukin-2 response thresholds guides design of a regulatory T cell biased agonist. eLife 2021; 10:e65777. [PMID: 34003116 PMCID: PMC8131104 DOI: 10.7554/elife.65777] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
Interleukin-2 is a pleiotropic cytokine that mediates both pro- and anti-inflammatory functions. Immune cells naturally differ in their sensitivity to IL-2 due to cell type and activation state-dependent expression of receptors and signaling pathway components. To probe differences in IL-2 signaling across cell types, we used structure-based design to create and profile a series of IL-2 variants with the capacity to titrate maximum signal strength in fine increments. One of these partial agonists, IL-2-REH, specifically expanded Foxp3+ regulatory T cells with reduced activity on CD8+ T cells due to cell type-intrinsic differences in IL-2 signaling. IL-2-REH elicited cell type-dependent differences in gene expression and provided mixed therapeutic results: showing benefit in the in vivo mouse dextran sulfate sodium (DSS) model of colitis, but no therapeutic efficacy in a transfer colitis model. Our findings show that cytokine partial agonists can be used to calibrate intrinsic differences in response thresholds across responding cell types to narrow pleiotropic actions, which may be generalizable to other cytokine and growth factor systems.
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Affiliation(s)
- Caleb R Glassman
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Immunology Graduate Program, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | - Leon Su
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | - Sonia S Majri-Morrison
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | | | - Fei Mo
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, NIHBethesdaUnited States
| | - Peng Li
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, NIHBethesdaUnited States
| | - Magdiel Pérez-Cruz
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of MedicineStanfordUnited States
| | - Peggy P Ho
- Department of Neurology and Neurological Sciences, Stanford UniversityStanfordUnited States
| | - Ievgen Koliesnik
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford UniversityStanfordUnited States
| | - Nadine Nagy
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford UniversityStanfordUnited States
| | - Tereza Hnizdilova
- Laboratory of Tumor Immunology, Institute of Microbiology of Czech Academy of SciencesPragueCzech Republic
| | - Lora K Picton
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | - Marek Kovar
- Laboratory of Tumor Immunology, Institute of Microbiology of Czech Academy of SciencesPragueCzech Republic
| | - Paul Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford UniversityStanfordUnited States
| | - Lawrence Steinman
- Department of Neurology and Neurological Sciences, Stanford UniversityStanfordUnited States
- Department of Pediatrics, Stanford UniversityStanfordUnited States
| | - Everett Meyer
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of MedicineStanfordUnited States
| | - Jacob Piehler
- Department of Biology, University of OsnabrückOsnabrückGermany
| | - Warren J Leonard
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, NIHBethesdaUnited States
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
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13
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Zanin N, Viaris de Lesegno C, Lamaze C, Blouin CM. Interferon Receptor Trafficking and Signaling: Journey to the Cross Roads. Front Immunol 2021; 11:615603. [PMID: 33552080 PMCID: PMC7855707 DOI: 10.3389/fimmu.2020.615603] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
Like most plasma membrane proteins, type I interferon (IFN) receptor (IFNAR) traffics from the outer surface to the inner compartments of the cell. Long considered as a passive means to simply control subunits availability at the plasma membrane, an array of new evidence establishes IFNAR endocytosis as an active contributor to the regulation of signal transduction triggered by IFN binding to IFNAR. During its complex journey initiated at the plasma membrane, the internalized IFNAR complex, i.e. IFNAR1 and IFNAR2 subunits, will experience post-translational modifications and recruit specific effectors. These finely tuned interactions will determine not only IFNAR subunits destiny (lysosomal degradation vs. plasma membrane recycling) but also the control of IFN-induced signal transduction. Finally, the IFNAR system perfectly illustrates the paradigm of the crosstalk between membrane trafficking and intracellular signaling. Investigating the complexity of IFN receptor intracellular routes is therefore necessary to reveal new insight into the role of IFNAR membrane dynamics in type I IFNs signaling selectivity and biological activity.
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Affiliation(s)
- Natacha Zanin
- NDORMS, The Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Christine Viaris de Lesegno
- Institut Curie-Centre de Recherche, PSL Research University, Membrane Dynamics and Mechanics of Intracellular Signalling Laboratory, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 3666, Paris, France
| | - Christophe Lamaze
- Institut Curie-Centre de Recherche, PSL Research University, Membrane Dynamics and Mechanics of Intracellular Signalling Laboratory, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 3666, Paris, France
| | - Cedric M Blouin
- Institut Curie-Centre de Recherche, PSL Research University, Membrane Dynamics and Mechanics of Intracellular Signalling Laboratory, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 3666, Paris, France
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14
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Wilmes S, Hafer M, Vuorio J, Tucker JA, Winkelmann H, Löchte S, Stanly TA, Pulgar Prieto KD, Poojari C, Sharma V, Richter CP, Kurre R, Hubbard SR, Garcia KC, Moraga I, Vattulainen I, Hitchcock IS, Piehler J. Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations. Science 2020; 367:643-652. [PMID: 32029621 PMCID: PMC8117407 DOI: 10.1126/science.aaw3242] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 10/08/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022]
Abstract
Homodimeric class I cytokine receptors are assumed to exist as preformed dimers that are activated by ligand-induced conformational changes. We quantified the dimerization of three prototypic class I cytokine receptors in the plasma membrane of living cells by single-molecule fluorescence microscopy. Spatial and spatiotemporal correlation of individual receptor subunits showed ligand-induced dimerization and revealed that the associated Janus kinase 2 (JAK2) dimerizes through its pseudokinase domain. Oncogenic receptor and hyperactive JAK2 mutants promoted ligand-independent dimerization, highlighting the formation of receptor dimers as the switch responsible for signal activation. Atomistic modeling and molecular dynamics simulations based on a detailed energetic analysis of the interactions involved in dimerization yielded a mechanistic blueprint for homodimeric class I cytokine receptor activation and its dysregulation by individual mutations.
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Affiliation(s)
- Stephan Wilmes
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Maximillian Hafer
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Joni Vuorio
- Department of Physics, University of Helsinki, Helsinki, Finland
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Julie A Tucker
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hauke Winkelmann
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sara Löchte
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Tess A Stanly
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Katiuska D Pulgar Prieto
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Chetan Poojari
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Christian P Richter
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Rainer Kurre
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Stevan R Hubbard
- Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ignacio Moraga
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland.
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Ian S Hitchcock
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK.
| | - Jacob Piehler
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany.
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15
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Zanin N, Blouin CM. [Endosomal control of intracellular signaling]. Biol Aujourdhui 2018; 212:45-51. [PMID: 30362455 DOI: 10.1051/jbio/2018023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Indexed: 11/14/2022]
Abstract
Membrane receptors control essential processes such as cell growth, adhesion, differentiation and metabolism through the activation of specific signaling pathways. Nowadays, these receptors are not only known to signal from the plasma membrane but also from intracellular compartments. Indeed, after being internalized with their ligands via different endocytic pathways, some membrane receptors can initiate signal only after reaching the sorting endosome where they associate with specific protein partners. This review illustrates how this spatio-temporal regulation of signal transduction can occur, with several examples, including interferon receptors which activate JAK/STAT signaling pathways. The literature presented here explains why this control of signaling pathways occuring at the endosomal level creates a higher degree of tuning for the affected cellular processes.
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Affiliation(s)
- Natacha Zanin
- The Kennedy Institute of Rheumatology, University of Oxford, OX3 7FY, Oxford, UK
| | - Cedric M Blouin
- Institut Curie - Centre de Recherche, PSL Research University, Membrane Dynamics and Mechanics of Intracellular Signaling Laboratory, 75248 Paris Cedex 05, France - Institut National de la Santé et de la Recherche Médicale (INSERM), U1143, Paris, France - Centre National de la Recherche Scientifique (CNRS), UMR 3666, Paris, France
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16
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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17
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Niewidok B, Igaev M, Pereira da Graca A, Strassner A, Lenzen C, Richter CP, Piehler J, Kurre R, Brandt R. Single-molecule imaging reveals dynamic biphasic partition of RNA-binding proteins in stress granules. J Cell Biol 2018; 217:1303-1318. [PMID: 29463567 PMCID: PMC5881506 DOI: 10.1083/jcb.201709007] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/25/2017] [Accepted: 01/23/2018] [Indexed: 11/22/2022] Open
Abstract
Niewidok et al. analyze the distribution and dynamics of RNA-binding proteins (RBPs) with single-molecule resolution in living neuronal cells, providing direct support for liquid droplet behavior of stress granules in living cells and revealing transient binding of RBPs in nanocores. Stress granules (SGs) are cytosolic, nonmembranous RNA–protein complexes. In vitro experiments suggested that they are formed by liquid–liquid phase separation; however, their properties in mammalian cells remain unclear. We analyzed the distribution and dynamics of two paradigmatic RNA-binding proteins (RBPs), Ras GTPase-activating protein SH3-domain–binding protein (G3BP1) and insulin-like growth factor II mRNA-binding protein 1 (IMP1), with single-molecule resolution in living neuronal cells. Both RBPs exhibited different exchange kinetics between SGs. Within SGs, single-molecule localization microscopy revealed distributed hotspots of immobilized G3BP1 and IMP1 that reflect the presence of relatively immobile nanometer-sized nanocores. We demonstrate alternating binding in nanocores and anomalous diffusion in the liquid phase with similar characteristics for both RBPs. Reduction of low-complexity regions in G3BP1 resulted in less detectable mobile molecules in the liquid phase without change in binding in nanocores. The data provide direct support for liquid droplet behavior of SGs in living cells and reveal transient binding of RBPs in nanocores. Our study uncovers a surprising disconnect between SG partitioning and internal diffusion and interactions of RBPs.
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Affiliation(s)
- Benedikt Niewidok
- Department of Neurobiology, University of Osnabrück, Osnabrück, Germany
| | - Maxim Igaev
- Department of Neurobiology, University of Osnabrück, Osnabrück, Germany
| | | | - Andre Strassner
- Department of Neurobiology, University of Osnabrück, Osnabrück, Germany
| | - Christine Lenzen
- Department of Neurobiology, University of Osnabrück, Osnabrück, Germany
| | | | - Jacob Piehler
- Department of Biophysics, University of Osnabrück, Osnabrück, Germany
| | - Rainer Kurre
- Center of Cellular Nanoanalytics, Integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
| | - Roland Brandt
- Department of Neurobiology, University of Osnabrück, Osnabrück, Germany
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18
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Functional Selectivity in Cytokine Signaling Revealed Through a Pathogenic EPO Mutation. Cell 2017; 168:1053-1064.e15. [PMID: 28283061 DOI: 10.1016/j.cell.2017.02.026] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/30/2016] [Accepted: 02/15/2017] [Indexed: 12/16/2022]
Abstract
Cytokines are classically thought to stimulate downstream signaling pathways through monotonic activation of receptors. We describe a severe anemia resulting from a homozygous mutation (R150Q) in the cytokine erythropoietin (EPO). Surprisingly, the EPO R150Q mutant shows only a mild reduction in affinity for its receptor but has altered binding kinetics. The EPO mutant is less effective at stimulating erythroid cell proliferation and differentiation, even at maximally potent concentrations. While the EPO mutant can stimulate effectors such as STAT5 to a similar extent as the wild-type ligand, there is reduced JAK2-mediated phosphorylation of select downstream targets. This impairment in downstream signaling mechanistically arises from altered receptor dimerization dynamics due to extracellular binding changes. These results demonstrate how variation in a single cytokine can lead to biased downstream signaling and can thereby cause human disease. Moreover, we have defined a distinct treatable form of anemia through mutation identification and functional studies.
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19
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Ho CCM, Chhabra A, Starkl P, Schnorr PJ, Wilmes S, Moraga I, Kwon HS, Gaudenzio N, Sibilano R, Wehrman TS, Gakovic M, Sockolosky JT, Tiffany MR, Ring AM, Piehler J, Weissman IL, Galli SJ, Shizuru JA, Garcia KC. Decoupling the Functional Pleiotropy of Stem Cell Factor by Tuning c-Kit Signaling. Cell 2017; 168:1041-1052.e18. [PMID: 28283060 DOI: 10.1016/j.cell.2017.02.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/20/2016] [Accepted: 02/06/2017] [Indexed: 12/20/2022]
Abstract
Most secreted growth factors and cytokines are functionally pleiotropic because their receptors are expressed on diverse cell types. While important for normal mammalian physiology, pleiotropy limits the efficacy of cytokines and growth factors as therapeutics. Stem cell factor (SCF) is a growth factor that acts through the c-Kit receptor tyrosine kinase to elicit hematopoietic progenitor expansion but can be toxic when administered in vivo because it concurrently activates mast cells. We engineered a mechanism-based SCF partial agonist that impaired c-Kit dimerization, truncating downstream signaling amplitude. This SCF variant elicited biased activation of hematopoietic progenitors over mast cells in vitro and in vivo. Mouse models of SCF-mediated anaphylaxis, radioprotection, and hematopoietic expansion revealed that this SCF partial agonist retained therapeutic efficacy while exhibiting virtually no anaphylactic off-target effects. The approach of biasing cell activation by tuning signaling thresholds and outputs has applications to many dimeric receptor-ligand systems.
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Affiliation(s)
- Chia Chi M Ho
- Department of Bioengineering, Stanford University School of Engineering, 443 Via Ortega, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Akanksha Chhabra
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Philipp Starkl
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine I, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Peter-John Schnorr
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Stephan Wilmes
- Department of Biology, University of Osnabruck, Barbarastr. 11, 49076 Osnabruck, Germany
| | - Ignacio Moraga
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Hye-Sook Kwon
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Nicolas Gaudenzio
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Riccardo Sibilano
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Tom S Wehrman
- Primity Bio, 48383 Fremont Blvd, Suite 118, Fremont, CA 94538, USA
| | - Milica Gakovic
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Jonathan T Sockolosky
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Matthew R Tiffany
- Department of Pediatrics and Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Aaron M Ring
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA
| | - Jacob Piehler
- Department of Biology, University of Osnabruck, Barbarastr. 11, 49076 Osnabruck, Germany
| | - Irving L Weissman
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA; Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Stephen J Galli
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA
| | - Judith A Shizuru
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA.
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20
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You C, Marquez-Lago TT, Richter CP, Wilmes S, Moraga I, Garcia KC, Leier A, Piehler J. Receptor dimer stabilization by hierarchical plasma membrane microcompartments regulates cytokine signaling. SCIENCE ADVANCES 2016; 2:e1600452. [PMID: 27957535 PMCID: PMC5135388 DOI: 10.1126/sciadv.1600452] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 10/26/2016] [Indexed: 06/06/2023]
Abstract
The interaction dynamics of signaling complexes is emerging as a key determinant that regulates the specificity of cellular responses. We present a combined experimental and computational study that quantifies the consequences of plasma membrane microcompartmentalization for the dynamics of type I interferon receptor complexes. By using long-term dual-color quantum dot (QD) tracking, we found that the lifetime of individual ligand-induced receptor heterodimers depends on the integrity of the membrane skeleton (MSK), which also proved important for efficient downstream signaling. By pair correlation tracking and localization microscopy as well as by fast QD tracking, we identified a secondary confinement within ~300-nm-sized zones. A quantitative spatial stochastic diffusion-reaction model, entirely parameterized on the basis of experimental data, predicts that transient receptor confinement by the MSK meshwork allows for rapid reassociation of dissociated receptor dimers. Moreover, the experimentally observed apparent stabilization of receptor dimers in the plasma membrane was reproduced by simulations of a refined, hierarchical compartment model. Our simulations further revealed that the two-dimensional association rate constant is a key parameter for controlling the extent of MSK-mediated stabilization of protein complexes, thus ensuring the specificity of this effect. Together, experimental evidence and simulations support the hypothesis that passive receptor confinement by MSK-based microcompartmentalization promotes maintenance of signaling complexes in the plasma membrane.
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Affiliation(s)
- Changjiang You
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | | | | | - Stephan Wilmes
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - K. Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - André Leier
- Isaac Newton Institute for Mathematical Sciences, University of Cambridge, Cambridge, U.K
- Okinawa Institute of Science and Technology, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
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21
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Quantum Dot-Based Nanotools for Bioimaging, Diagnostics, and Drug Delivery. Chembiochem 2016; 17:2103-2114. [DOI: 10.1002/cbic.201600357] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Indexed: 12/12/2022]
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22
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Barlag B, Beutel O, Janning D, Czarniak F, Richter CP, Kommnick C, Göser V, Kurre R, Fabiani F, Erhardt M, Piehler J, Hensel M. Single molecule super-resolution imaging of proteins in living Salmonella enterica using self-labelling enzymes. Sci Rep 2016; 6:31601. [PMID: 27534893 PMCID: PMC4989173 DOI: 10.1038/srep31601] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 07/20/2016] [Indexed: 12/23/2022] Open
Abstract
The investigation of the subcellular localization, dynamics and interaction of proteins and protein complexes in prokaryotes is complicated by the small size of the cells. Super-resolution microscopy (SRM) comprise various new techniques that allow light microscopy with a resolution that can be up to ten-fold higher than conventional light microscopy. Application of SRM techniques to living prokaryotes demands the introduction of suitable fluorescent probes, usually by fusion of proteins of interest to fluorescent proteins with properties compatible to SRM. Here we describe an approach that is based on the genetically encoded self-labelling enzymes HaloTag and SNAP-tag. Proteins of interest are fused to HaloTag or SNAP-tag and cell permeable substrates can be labelled with various SRM-compatible fluorochromes. Fusions of the enzyme tags to subunits of a type I secretion system (T1SS), a T3SS, the flagellar rotor and a transcription factor were generated and analysed in living Salmonella enterica. The new approach is versatile in tagging proteins of interest in bacterial cells and allows to determine the number, relative subcellular localization and dynamics of protein complexes in living cells.
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Affiliation(s)
- Britta Barlag
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Oliver Beutel
- Abt. Biophysik, Universität Osnabrück, Osnabrück, Germany
| | - Dennis Janning
- Abt. Neurobiologie, Universität Osnabrück, Osnabrück, Germany
| | | | | | - Carina Kommnick
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Vera Göser
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Rainer Kurre
- CALMOS, Universität Osnabrück, Osnabrück, Germany
| | - Florian Fabiani
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marc Erhardt
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jacob Piehler
- Abt. Biophysik, Universität Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
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23
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Shivanandan A, Unnikrishnan J, Radenovic A. On characterizing protein spatial clusters with correlation approaches. Sci Rep 2016; 6:31164. [PMID: 27507257 PMCID: PMC4979030 DOI: 10.1038/srep31164] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/15/2016] [Indexed: 12/31/2022] Open
Abstract
Spatial aggregation of proteins might have functional importance, e.g., in signaling, and nano-imaging can be used to study them. Such studies require accurate characterization of clusters based on noisy data. A set of spatial correlation approaches free of underlying cluster processes and input parameters have been widely used for this purpose. They include the radius of maximal aggregation ra obtained from Ripley’s L(r) − r function as an estimator of cluster size, and the estimation of various cluster parameters based on an exponential model of the Pair Correlation Function(PCF). While convenient, the accuracy of these methods is not clear: e.g., does it depend on how the molecules are distributed within the clusters, or on cluster parameters? We analyze these methods for a variety of cluster models. We find that ra relates to true cluster size by a factor that is nonlinearly dependent on parameters and that can be arbitrarily large. For the PCF method, for the models analyzed, we obtain linear relationships between the estimators and true parameters, and the estimators were found to be within ±100% of true parameters, depending on the model. Our results, based on an extendable general framework, point to the need for caution in applying these methods.
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Affiliation(s)
- Arun Shivanandan
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Jayakrishnan Unnikrishnan
- Audiovisual Communications Laboratory, School of Computer and Communication Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
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24
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Wedeking T, Löchte S, Birkholz O, Wallenstein A, Trahe J, Klingauf J, Piehler J, You C. Spatiotemporally Controlled Reorganization of Signaling Complexes in the Plasma Membrane of Living Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:5912-5918. [PMID: 26421417 DOI: 10.1002/smll.201502132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/18/2015] [Indexed: 06/05/2023]
Abstract
Triggered immobilization of proteins in the plasma membrane of living cells into functional micropatterns is established by using an adaptor protein, which is comprised of an antiGFP nanobody fused to the HaloTag protein. Efficient in situ reorganization of the type I interferon receptor subunits as well as intact, fully functional signaling complexes in living cells are achieved by this method.
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Affiliation(s)
- Tim Wedeking
- Department of BiologyUniversity of Osnabrück, Barbarastr. 11, Osnabrück, 49076, Germany
| | - Sara Löchte
- Department of BiologyUniversity of Osnabrück, Barbarastr. 11, Osnabrück, 49076, Germany
| | - Oliver Birkholz
- Department of BiologyUniversity of Osnabrück, Barbarastr. 11, Osnabrück, 49076, Germany
| | - Alexander Wallenstein
- Department of BiologyUniversity of Osnabrück, Barbarastr. 11, Osnabrück, 49076, Germany
| | - Julia Trahe
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Str. 31, Münster, 48149, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003-CiM), University of Münster, Münster, 48149, Germany
| | - Jürgen Klingauf
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Str. 31, Münster, 48149, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003-CiM), University of Münster, Münster, 48149, Germany
| | - Jacob Piehler
- Department of BiologyUniversity of Osnabrück, Barbarastr. 11, Osnabrück, 49076, Germany
| | - Changjiang You
- Department of BiologyUniversity of Osnabrück, Barbarastr. 11, Osnabrück, 49076, Germany
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25
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Beinlich FRM, Drees C, Piehler J, Busch KB. Shuttling of PINK1 between Mitochondrial Microcompartments Resolved by Triple-Color Superresolution Microscopy. ACS Chem Biol 2015; 10:1970-6. [PMID: 26046594 DOI: 10.1021/acschembio.5b00295] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cytosolic phosphatase and tensin homologue Pten-kinase PINK1 involved in mitochondrial quality control undergoes a proteolytic process inside mitochondria. It has been suggested that the protein is not fully imported into mitochondria during this maturation. Here, we have established live cell triple-color super-resolution microscopy by combining FPALM and tracking and localization microscopy (TALM) in order to unravel the spatiotemporal organization of the C-terminal kinase domain of PINK1 during this process. We find that the kinase domain is imported into active mitochondria and colocalizes with respiratory complex I at the inner mitochondrial membrane. When the processing step inside mitochondria is inhibited or mitochondria are de-energized, full length PINK1 distributes between the outer and the inner mitochondrial membranes, indicating a holdup of import. These findings give the molecular base for a dual role of PINK1-inside energized mitochondria and outside of de-energized mitochondria.
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Affiliation(s)
- Felix R. M. Beinlich
- Mitochondrial Dynamics Group
and Biophysics Group, School of Biology, University of Osnabrück, 49076 Osnabrück, Lower
Saxony, Germany
| | - Christoph Drees
- Mitochondrial Dynamics Group
and Biophysics Group, School of Biology, University of Osnabrück, 49076 Osnabrück, Lower
Saxony, Germany
| | - Jacob Piehler
- Mitochondrial Dynamics Group
and Biophysics Group, School of Biology, University of Osnabrück, 49076 Osnabrück, Lower
Saxony, Germany
| | - Karin B. Busch
- Mitochondrial Dynamics Group
and Biophysics Group, School of Biology, University of Osnabrück, 49076 Osnabrück, Lower
Saxony, Germany
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26
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Blaszczyk M, Harmer NJ, Chirgadze DY, Ascher DB, Blundell TL. Achieving high signal-to-noise in cell regulatory systems: Spatial organization of multiprotein transmembrane assemblies of FGFR and MET receptors. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 118:103-11. [PMID: 25957048 PMCID: PMC4832006 DOI: 10.1016/j.pbiomolbio.2015.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 01/12/2023]
Abstract
How is information communicated both within and between cells of living systems with high signal to noise? We discuss transmembrane signaling models involving two receptor tyrosine kinases: the fibroblast growth factor receptor (FGFR) and the MET receptor. We suggest that simple dimerization models might occur opportunistically giving rise to noise but cooperative clustering of the receptor tyrosine kinases observed in these systems is likely to be important for signal transduction. We propose that this may be a more general prerequisite for high signal to noise in transmembrane receptor signaling.
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Affiliation(s)
- Michal Blaszczyk
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Nicholas J Harmer
- The Henry Wellcome Building for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Dimitri Y Chirgadze
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - David B Ascher
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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27
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Moraga I, Wernig G, Wilmes S, Gryshkova V, Richter CP, Hong WJ, Sinha R, Guo F, Fabionar H, Wehrman TS, Krutzik P, Demharter S, Plo I, Weissman IL, Minary P, Majeti R, Constantinescu SN, Piehler J, Garcia KC. Tuning cytokine receptor signaling by re-orienting dimer geometry with surrogate ligands. Cell 2015; 160:1196-208. [PMID: 25728669 PMCID: PMC4766813 DOI: 10.1016/j.cell.2015.02.011] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/22/2015] [Accepted: 02/03/2015] [Indexed: 01/07/2023]
Abstract
Most cell-surface receptors for cytokines and growth factors signal as dimers, but it is unclear whether remodeling receptor dimer topology is a viable strategy to "tune" signaling output. We utilized diabodies (DA) as surrogate ligands in a prototypical dimeric receptor-ligand system, the cytokine Erythropoietin (EPO) and its receptor (EpoR), to dimerize EpoR ectodomains in non-native architectures. Diabody-induced signaling amplitudes varied from full to minimal agonism, and structures of these DA/EpoR complexes differed in EpoR dimer orientation and proximity. Diabodies also elicited biased or differential activation of signaling pathways and gene expression profiles compared to EPO. Non-signaling diabodies inhibited proliferation of erythroid precursors from patients with a myeloproliferative neoplasm due to a constitutively active JAK2V617F mutation. Thus, intracellular oncogenic mutations causing ligand-independent receptor activation can be counteracted by extracellular ligands that re-orient receptors into inactive dimer topologies. This approach has broad applications for tuning signaling output for many dimeric receptor systems.
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Affiliation(s)
- Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Gerlinde Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Pathology, Division of Hematopathology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Stephan Wilmes
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076, Germany
| | - Vitalina Gryshkova
- Ludwig Institute For Cancer Research and de Duve Institute, Université catholique de Louvain, B-1200 Brussels, Belgium
| | | | - Wan-Jen Hong
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Internal Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Feng Guo
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Hyna Fabionar
- DiscoveRx, 42501 Albrae St, Fremont, California, 94538, USA
| | - Tom S. Wehrman
- Primity Bio, 3350 Scott blvd ste 6101, Santa Clara, CA 95054
| | - Peter Krutzik
- Primity Bio, 3350 Scott blvd ste 6101, Santa Clara, CA 95054
| | - Samuel Demharter
- Department of Computer Science Wolfson Building, University of Oxford, Oxford OX1 3QD, United Kingdom
| | - Isabelle Plo
- Institut Gustave Roussy, INSERM U1009, 94805, Villejuif, France
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Peter Minary
- Department of Computer Science Wolfson Building, University of Oxford, Oxford OX1 3QD, United Kingdom
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Internal Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Stefan N. Constantinescu
- Ludwig Institute For Cancer Research and de Duve Institute, Université catholique de Louvain, B-1200 Brussels, Belgium
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076, Germany
| | - K. Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Correspondence to:
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28
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The molecular basis for functional plasticity in type I interferon signaling. Trends Immunol 2015; 36:139-49. [DOI: 10.1016/j.it.2015.01.002] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 01/16/2023]
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29
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Vu TQ, Lam WY, Hatch EW, Lidke DS. Quantum dots for quantitative imaging: from single molecules to tissue. Cell Tissue Res 2015; 360:71-86. [PMID: 25620410 DOI: 10.1007/s00441-014-2087-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
Abstract
Since their introduction to biological imaging, quantum dots (QDs) have progressed from a little known, but attractive, technology to one that has gained broad application in many areas of biology. The versatile properties of these fluorescent nanoparticles have allowed investigators to conduct biological studies with extended spatiotemporal capabilities that were previously not possible. In this review, we focus on QD applications that provide enhanced quantitative information concerning protein dynamics and localization, including single particle tracking and immunohistochemistry, and finish by examining the prospects of upcoming applications, such as correlative light and electron microscopy and super-resolution. Advances in single molecule imaging, including multi-color and three-dimensional QD tracking, have provided new insights into the mechanisms of cell signaling and protein trafficking. New forms of QD tracking in vivo have allowed the observation of biological processes at molecular level resolution in the physiological context of the whole animal. Further methodological development of multiplexed QD-based immunohistochemistry assays should enable more quantitative analysis of key proteins in tissue samples. These advances highlight the unique quantitative data sets that QDs can provide to further our understanding of biological and disease processes.
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Affiliation(s)
- Tania Q Vu
- Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, Ore., USA,
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30
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Fricke F, Dietz MS, Heilemann M. Single-Molecule Methods to Study Membrane Receptor Oligomerization. Chemphyschem 2014; 16:713-21. [DOI: 10.1002/cphc.201402765] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Indexed: 11/06/2022]
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