1
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Zhang Y, Naguro I, Ryuno H, Herr A. Contact Blot: Microfluidic Control and Measurement of Cell-Cell Contact State to Assess Contact-Inhibited ERK Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.06.565857. [PMID: 37986875 PMCID: PMC10659358 DOI: 10.1101/2023.11.06.565857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Extracellular signal-regulated kinase (ERK) signaling is essential to regulated cell behaviors, including cell proliferation, differentiation, and apoptosis. The influence of cell-cell contacts on ERK signaling is central to epithelial cells, yet few studies have sought to understand the same in cancer cells, particularly with single-cell resolution. To acquire same-cell measurements of both phenotypic (cell-contact state) and targeted-protein profile (ERK phosphorylation), we prepend high-content, whole-cell imaging prior to endpoint cellular-resolution western blot analyses for each of hundreds of individual HeLa cancer cells cultured on that same chip, which we call contact Blot. By indexing the phosphorylation level of ERK in each cell or cell-cluster to the imaged cell-contact state, we compare ERK signaling between isolated and in-contact cells. We observe attenuated (~2×) ERK signaling in HeLa cells which are in-contact versus isolated. Attenuation is sustained when the HeLa cells are challenged with hyperosmotic stress. Our findings show the impact of cell-cell contacts on ERK activation with isolated and in-contact cells, while introducing a multi omics tool for control and scrutiny of cell-cell interactions.
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2
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Bestsennaia E, Maslov I, Balandin T, Alekseev A, Yudenko A, Abu Shamseye A, Zabelskii D, Baumann A, Catapano C, Karathanasis C, Gordeliy V, Heilemann M, Gensch T, Borshchevskiy V. Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy. Angew Chem Int Ed Engl 2024; 63:e202307555. [PMID: 38226794 DOI: 10.1002/anie.202307555] [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: 06/06/2023] [Revised: 01/03/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
Microbial rhodopsins are retinal membrane proteins that found a broad application in optogenetics. The oligomeric state of rhodopsins is important for their functionality and stability. Of particular interest is the oligomeric state in the cellular native membrane environment. Fluorescence microscopy provides powerful tools to determine the oligomeric state of membrane proteins directly in cells. Among these methods is quantitative photoactivated localization microscopy (qPALM) allowing the investigation of molecular organization at the level of single protein clusters. Here, we apply qPALM to investigate the oligomeric state of the first and most used optogenetic tool Channelrhodopsin-2 (ChR2) in the plasma membrane of eukaryotic cells. ChR2 appeared predominantly as a dimer in the cell membrane and did not form higher oligomers. The disulfide bonds between Cys34 and Cys36 of adjacent ChR2 monomers were not required for dimer formation and mutations disrupting these bonds resulted in only partial monomerization of ChR2. The monomeric fraction increased when the total concentration of mutant ChR2 in the membrane was low. The dissociation constant was estimated for this partially monomerized mutant ChR2 as 2.2±0.9 proteins/μm2 . Our findings are important for understanding the mechanistic basis of ChR2 activity as well as for improving existing and developing future optogenetic tools.
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Affiliation(s)
- Ekaterina Bestsennaia
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Ivan Maslov
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and the Biomedical Research Institute, Hasselt University, B3590, Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001, Leuven, Belgium
| | - Taras Balandin
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alexey Alekseev
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Anna Yudenko
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Assalla Abu Shamseye
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Dmitrii Zabelskii
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
- European XFEL, 22869, Schenefeld, Germany
| | - Arnd Baumann
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Claudia Catapano
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Christos Karathanasis
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Valentin Gordeliy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Thomas Gensch
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Valentin Borshchevskiy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
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3
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Mudumbi KC, Burns EA, Schodt DJ, Petrova ZO, Kiyatkin A, Kim LW, Mangiacapre EM, Ortiz-Caraveo I, Rivera Ortiz H, Hu C, Ashtekar KD, Lidke KA, Lidke DS, Lemmon MA. Distinct interactions stabilize EGFR dimers and higher-order oligomers in cell membranes. Cell Rep 2024; 43:113603. [PMID: 38117650 PMCID: PMC10835193 DOI: 10.1016/j.celrep.2023.113603] [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: 06/23/2023] [Revised: 09/23/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase with important roles in many cellular processes as well as in cancer and other diseases. EGF binding promotes EGFR dimerization and autophosphorylation through interactions that are well understood structurally. How these dimers relate to higher-order EGFR oligomers seen in cell membranes, however, remains unclear. Here, we used single-particle tracking (SPT) and Förster resonance energy transfer imaging to examine how each domain of EGFR contributes to receptor oligomerization and the rate of receptor diffusion in the cell membrane. Although the extracellular region of EGFR is sufficient to drive receptor dimerization, we find that the EGF-induced EGFR slowdown seen by SPT requires higher-order oligomerization-mediated in part by the intracellular tyrosine kinase domain when it adopts an active conformation. Our data thus provide important insight into the interactions required for higher-order EGFR assemblies involved in EGF signaling.
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Affiliation(s)
- Krishna C Mudumbi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA.
| | - Eric A Burns
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - David J Schodt
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87106, USA
| | - Zaritza O Petrova
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Anatoly Kiyatkin
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Lucy W Kim
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Emma M Mangiacapre
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Irais Ortiz-Caraveo
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Hector Rivera Ortiz
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Chun Hu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Kumar D Ashtekar
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Keith A Lidke
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87106, USA
| | - Diane S Lidke
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA.
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4
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Martin‐Fernandez ML. A perspective of fluorescence microscopy for cellular structural biology with EGFR as witness. J Microsc 2023; 291:73-91. [PMID: 36282005 PMCID: PMC10952613 DOI: 10.1111/jmi.13151] [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: 09/20/2022] [Revised: 09/20/2022] [Accepted: 10/11/2022] [Indexed: 10/31/2022]
Abstract
The epidermal growth factor receptor (EGFR) is a poster child for the understanding of receptor behaviour, and of paramount importance to cell function and human health. Cloned almost forty years ago, the interest in EGFR's structure/function relationships remains unabated, not least because changes in oncogenic EGFR mutants are key drivers of the formation of lung and brain tumours. The structure of the assemblies formed by EGFR have been comprehensibly investigated by techniques such as high-resolution X-ray crystallography, NMR and all-atom molecular dynamics (MD) simulations. However, the complexity embedded in the portfolio of EGFR states that are only possible in the physiological environment of cells has often proved refractory to cell-free structural methods. Conversely, some key inroads made by quantitative fluorescence microscopy and super-resolution have depended on exploiting the wealth of structures available. Here, a brief personal perspective is provided on how quantitative fluorescence microscopy and super-resolution methods have cross-fertilised with cell-free-derived EGFR structural information. I primarily discuss areas in which my research group has made a contribution to fill gaps in EGFR's cellular structural biology and towards developing new tools to investigate macromolecular assemblies in cells.
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Affiliation(s)
- M. L. Martin‐Fernandez
- Central Laser FacilityScience and Technology Facilities Council, Rutherford Appleton LaboratoryDidcotUK
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5
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Mudumbi KC, Burns EA, Schodt DJ, Petrova ZO, Kiyatkin A, Kim LW, Mangiacapre EM, Ortiz-Caraveo I, Ortiz HR, Hu C, Ashtekar KD, Lidke KA, Lidke DS, Lemmon MA. Distinct interactions stabilize EGFR dimers and higher-order oligomers in cell membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536273. [PMID: 37090557 PMCID: PMC10120646 DOI: 10.1101/2023.04.10.536273] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase (RTK) with important roles in many cellular processes as well as cancer and other diseases. EGF binding promotes EGFR dimerization and autophosphorylation through interactions that are well understood structurally. However, it is not clear how these dimers relate to higher-order EGFR oligomers detected at the cell surface. We used single-particle tracking (SPT) and Förster resonance energy transfer (FRET) imaging to examine how each domain within EGFR contributes to receptor dimerization and the rate of its diffusion in the cell membrane. We show that the EGFR extracellular region is sufficient to drive receptor dimerization, but that the EGF-induced EGFR slow-down seen by SPT requires formation of higher order oligomers, mediated in part by the intracellular tyrosine kinase domain - but only when in its active conformation. Our data thus provide important insight into higher-order EGFR interactions required for EGF signaling.
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6
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Balasubramanian H, Sankaran J, Pandey S, Goh CJH, Wohland T. The dependence of EGFR oligomerization on environment and structure: A camera-based N&B study. Biophys J 2022; 121:4452-4466. [PMID: 36335429 PMCID: PMC9748371 DOI: 10.1016/j.bpj.2022.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Number and brightness (N&B) analysis is a fluorescence spectroscopy technique to quantify oligomerization of the mobile fraction of proteins. Accurate results, however, rely on a good knowledge of nonfluorescent states of the fluorescent labels, especially of fluorescent proteins, which are widely used in biology. Fluorescent proteins have been characterized for confocal, but not camera-based, N&B, which allows, in principle, faster measurements over larger areas. Here, we calibrate camera-based N&B implemented on a total internal reflection fluorescence microscope for various fluorescent proteins by determining their propensity to be fluorescent. We then apply camera-based N&B in live CHO-K1 cells to determine the oligomerization state of the epidermal growth factor receptor (EGFR), a transmembrane receptor tyrosine kinase that is a crucial regulator of cell proliferation and survival with implications in many cancers. EGFR oligomerization in resting cells and its regulation by the plasma membrane microenvironment are still under debate. Therefore, we investigate the effects of extrinsic factors, including membrane organization, cytoskeletal structure, and ligand stimulation, and intrinsic factors, including mutations in various EGFR domains, on the receptor's oligomerization. Our results demonstrate that EGFR oligomerization increases with removal of cholesterol or sphingolipids or the disruption of GM3-EGFR interactions, indicating raft association. However, oligomerization is not significantly influenced by the cytoskeleton. Mutations in either I706/V948 residues or E685/E687/E690 residues in the kinase and juxtamembrane domains, respectively, lead to a decrease in oligomerization, indicating their necessity for EGFR dimerization. Finally, EGFR phosphorylation is oligomerization dependent, involving the extracellular domain (550-580 residues). Coupled with biochemical investigations, camera-based N&B indicates that EGFR oligomerization and phosphorylation are the outcomes of several molecular interactions involving the lipid content and structure of the cell membrane and multiple residues in the kinase, juxtamembrane, and extracellular domains.
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Affiliation(s)
- Harikrushnan Balasubramanian
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Jagadish Sankaran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Shambhavi Pandey
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Corinna Jie Hui Goh
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore.
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7
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Zapata-Mercado E, Biener G, McKenzie DM, Wimley WC, Pasquale EB, Raicu V, Hristova K. The efficacy of receptor tyrosine kinase EphA2 autophosphorylation increases with EphA2 oligomer size. J Biol Chem 2022; 298:102370. [PMID: 35970390 PMCID: PMC9512837 DOI: 10.1016/j.jbc.2022.102370] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/30/2022] Open
Abstract
The receptor tyrosine kinase (RTK) EphA2 is expressed in epithelial and endothelial cells and controls the assembly of cell-cell junctions. EphA2 has also been implicated in many diseases, including cancer. Unlike most RTKs, which signal predominantly as dimers, EphA2 readily forms high-order oligomers upon ligand binding. Here, we investigated if a correlation exists between EphA2 signaling properties and the size of the EphA2 oligomers induced by multiple ligands, including the widely used ephrinA1-Fc ligand, the soluble monomeric m-ephrinA1, and novel engineered peptide ligands. We used fluorescence intensity fluctuation (FIF) spectrometry to characterize the EphA2 oligomer populations induced by the different ligands. Interestingly, we found that different monomeric and dimeric ligands induce EphA2 oligomers with widely different size distributions. Our comparison of FIF brightness distribution parameters and EphA2 signaling parameters reveals that the efficacy of EphA2 phosphorylation on tyrosine 588, an autophosphorylation response contributing to EphA2 activation, correlates with EphA2 mean oligomer size. However, we found that other characteristics, such as the efficacy of AKT inhibition and ligand bias coefficients, appear to be independent of EphA2 oligomer size. Taken together, this work highlights the utility of FIF in RTK signaling research and demonstrates a quantitative correlation between the architecture of EphA2 signaling complexes and signaling features.
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Affiliation(s)
- Elmer Zapata-Mercado
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gabriel Biener
- Department of Physics, University of Wisconsin, Milwaukee, Wisconsin, USA
| | - Daniel M McKenzie
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - William C Wimley
- Tulane University School of Medicine, Department of Biochemistry and Molecular Biology, New Orleans, Louisiana, USA
| | - Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
| | - Valerica Raicu
- Department of Physics, University of Wisconsin, Milwaukee, Wisconsin, USA; Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, USA.
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
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8
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Wollman AJM, Fournier C, Llorente-Garcia I, Harriman O, Payne-Dwyer AL, Shashkova S, Zhou P, Liu TC, Ouaret D, Wilding J, Kusumi A, Bodmer W, Leake MC. Critical roles for EGFR and EGFR-HER2 clusters in EGF binding of SW620 human carcinoma cells. J R Soc Interface 2022; 19:20220088. [PMID: 35612280 PMCID: PMC9131850 DOI: 10.1098/rsif.2022.0088] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Epidermal growth factor (EGF) signalling regulates normal epithelial and other cell growth, with EGF receptor (EGFR) overexpression reported in many cancers. However, the role of EGFR clusters in cancer and their dependence on EGF binding is unclear. We present novel single-molecule total internal reflection fluorescence microscopy of (i) EGF and EGFR in living cancer cells, (ii) the action of anti-cancer drugs that separately target EGFR and human EGFR2 (HER2) on these cells and (iii) EGFR–HER2 interactions. We selected human epithelial SW620 carcinoma cells for their low level of native EGFR expression, for stable transfection with fluorescent protein labelled EGFR, and imaged these using single-molecule localization microscopy to quantify receptor architectures and dynamics upon EGF binding. Prior to EGF binding, we observe pre-formed EGFR clusters. Unexpectedly, clusters likely contain both EGFR and HER2, consistent with co-diffusion of EGFR and HER2 observed in a different model CHO-K1 cell line, whose stoichiometry increases following EGF binding. We observe a mean EGFR : EGF stoichiometry of approximately 4 : 1 for plasma membrane-colocalized EGFR–EGF that we can explain using novel time-dependent kinetics modelling, indicating preferential ligand binding to monomers. Our results may inform future cancer drug developments.
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Affiliation(s)
- Adam J M Wollman
- Department of Physics, University of York, York, UK.,Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Charlotte Fournier
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, UK.,Science and Technology Group, Okinawa Institute of Science and Technology Graduate University (OIST), 1919 Tancha, Onna-son, Okinawa 904-0495, Japan
| | | | - Oliver Harriman
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, UK
| | | | | | - Peng Zhou
- Membrane Cooperativity Unit, OIST, 1919 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Ta-Chun Liu
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Djamila Ouaret
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Jenny Wilding
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Akihiro Kusumi
- Membrane Cooperativity Unit, OIST, 1919 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Walter Bodmer
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Mark C Leake
- Department of Physics, University of York, York, UK.,Department of Biology, University of York, York, UK.,Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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9
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Litsios A, Goswami P, Terpstra HM, Coffin C, Vuillemenot LA, Rovetta M, Ghazal G, Guerra P, Buczak K, Schmidt A, Tollis S, Tyers M, Royer CA, Milias-Argeitis A, Heinemann M. The timing of Start is determined primarily by increased synthesis of the Cln3 activator rather than dilution of the Whi5 inhibitor. Mol Biol Cell 2022; 33:rp2. [PMID: 35482514 PMCID: PMC9282015 DOI: 10.1091/mbc.e21-07-0349] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Athanasios Litsios
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Pooja Goswami
- Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Hanna M Terpstra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Carleton Coffin
- Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Luc-Alban Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Mattia Rovetta
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Ghada Ghazal
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, H3T 1J4 QC, Canada
| | - Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Sylvain Tollis
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, H3T 1J4 QC, Canada.,Institute of Biomedicine, University of Eastern Finland, FI-70210 Kuopio, Finland
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, H3T 1J4 QC, Canada
| | - Catherine A Royer
- Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
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10
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Killeen TD, Rahman S, Badu DN, Biener G, Stoneman MR, Raicu V. Fluorescence Intensity Fluctuation Analysis of Protein Oligomerization in Cell Membranes. Curr Protoc 2022; 2:e384. [PMID: 35312215 DOI: 10.1002/cpz1.384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Fluorescence fluctuation spectroscopy (FFS) encompasses a bevy of techniques that involve analyzing fluorescence intensity fluctuations occurring due to fluorescently labeled molecules diffusing in and out of a microscope's focal region. Statistical analysis of these fluctuations may reveal the oligomerization (i.e., association) state of said molecules. We have recently developed a new FFS-based method, termed Two-Dimensional Fluorescence Intensity Fluctuation (2D FIF) spectrometry, which provides quantitative information on the size and stability of protein oligomers as a function of receptor concentration. This article describes protocols for employing FIF spectrometry to quantify the oligomerization of a membrane protein of interest, with specific instructions regarding cell preparation, image acquisition, and analysis of images given in detail. Application of the FIF Spectrometry Suite, a software package designed for applying FIF analysis on fluorescence images, is emphasized in the protocol. Also discussed in detail is the identification, removal, and/or analysis of inhomogeneous regions of the membrane that appear as bright spots. The 2D FIF approach is particularly suited to assess the effects of agonists and antagonists on the oligomeric size of membrane receptors of interest. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of live cells expressing protein constructs Basic Protocol 2: Image acquisition and noise correction Basic Protocol 3: Drawing and segmenting regions of interest Basic Protocol 4: Calculating the molecular brightness and concentration of individual image segments Basic Protocol 5: Combining data subsets using a manual procedure (Optional) Alternate Protocol 1: Combining data subsets using the advanced FIF spectrometry suite (Optional; alternative to Basic Protocol 5) Basic Protocol 6: Performing meta-analysis of brightness spectrograms Alternate Protocol 2: Performing meta-analysis of brightness spectrograms (alternative to Basic Protocol 6) Basic Protocol 7: Spot extraction and analysis using a manual procedure or by writing a program (Optional) Alternate Protocol 3: Automated spot extraction and analysis (Optional; alternative to Protocol 7) Support Protocol: Monomeric brightness determination.
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Affiliation(s)
- Tom D Killeen
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Sadia Rahman
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Dammar N Badu
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Gabriel Biener
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Michael R Stoneman
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Valerică Raicu
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin.,Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
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11
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It Takes More than Two to Tango: Complex, Hierarchal, and Membrane-Modulated Interactions in the Regulation of Receptor Tyrosine Kinases. Cancers (Basel) 2022; 14:cancers14040944. [PMID: 35205690 PMCID: PMC8869822 DOI: 10.3390/cancers14040944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 12/18/2022] Open
Abstract
The search for an understanding of how cell fate and motility are regulated is not a purely scientific undertaking, but it can also lead to rationally designed therapies against cancer. The discovery of tyrosine kinases about half a century ago, the subsequent characterization of certain transmembrane receptors harboring tyrosine kinase activity, and their connection to the development of human cancer ushered in a new age with the hope of finding a treatment for malignant diseases in the foreseeable future. However, painstaking efforts were required to uncover the principles of how these receptors with intrinsic tyrosine kinase activity are regulated. Developments in molecular and structural biology and biophysical approaches paved the way towards better understanding of these pathways. Discoveries in the past twenty years first resulted in the formulation of textbook dogmas, such as dimerization-driven receptor association, which were followed by fine-tuning the model. In this review, the role of molecular interactions taking place during the activation of receptor tyrosine kinases, with special attention to the epidermal growth factor receptor family, will be discussed. The fact that these receptors are anchored in the membrane provides ample opportunities for modulatory lipid-protein interactions that will be considered in detail in the second part of the manuscript. Although qualitative and quantitative alterations in lipids in cancer are not sufficient in their own right to drive the malignant transformation, they both contribute to tumor formation and also provide ways to treat cancer. The review will be concluded with a summary of these medical aspects of lipid-protein interactions.
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12
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Distinct mechanisms orchestrate the contra-polarity of IRK and KOIN, two LRR-receptor-kinases controlling root cell division. Nat Commun 2022; 13:235. [PMID: 35017541 PMCID: PMC8752632 DOI: 10.1038/s41467-021-27913-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 12/22/2021] [Indexed: 11/24/2022] Open
Abstract
In plants, cell polarity plays key roles in coordinating developmental processes. Despite the characterization of several polarly localized plasma membrane proteins, the mechanisms connecting protein dynamics with cellular functions often remain unclear. Here, we introduce a polarized receptor, KOIN, that restricts cell divisions in the Arabidopsis root meristem. In the endodermis, KOIN polarity is opposite to IRK, a receptor that represses endodermal cell divisions. Their contra-polar localization facilitates dissection of polarity mechanisms and the links between polarity and function. We find that IRK and KOIN are recognized, sorted, and secreted through distinct pathways. IRK extracellular domains determine its polarity and partially rescue the mutant phenotype, whereas KOIN’s extracellular domains are insufficient for polar sorting and function. Endodermal expression of an IRK/KOIN chimera generates non-cell-autonomous misregulation of root cell divisions that impacts patterning. Altogether, we reveal two contrasting mechanisms determining these receptors’ polarity and link their polarity to cell divisions in root tissue patterning. Protein polarization coordinates many plant developmental processes. Here the authors show that IRK and KOIN, two LRR-receptor-kinases polarized to opposite sides of cells in the root meristem, rely on distinct mechanisms to achieve polarity.
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13
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Yang Q, Shang J, Chen Y, Tang D, Ouyang Y, Xiong B, Zhang X. Plasmonic Imaging of Dynamic Interactions between Membrane Receptor Clusters beyond the Diffraction Limit in Live Cells. Anal Chem 2021; 93:16571-16580. [PMID: 34847664 DOI: 10.1021/acs.analchem.1c03843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As a general mechanism, ligand-induced receptor clustering on cell membrane plays determinative roles in pattern recognition and transmembrane signaling. Nevertheless, probing the dynamic characteristics for the complicated interactions between receptor clusters remains difficult because of the lack of strategy for receptor cluster labeling and long-term monitoring in live cells. Herein, we proposed a data-mining-integrated plasmon coupling microscopy to study the dynamic cluster-cluster interactions on cell surface. The receptor clusters were activated and labeled with multivalent plasmonic nanoprobes, which enables the real-time monitoring of individual receptor clusters and the measurement of cluster-cluster interactions from the analysis of plasmonic coupling for the nanoprobe pairs beyond the diffraction limit. Using this method, we found that the protease-activated receptor 1 (PAR1) clusters would experience an initial contact and then form a weakly bound cluster-cluster complex, followed by cluster fusion to generate large-sized signaling complexes. The underlying state transitions for the cluster-cluster fusion process were uncovered using a data-mining technique named the K-means-based hidden Markov model with the scattering intensity of coupled nanoprobe pairs as observations. All of the findings from single-particle analysis and bulk measurements suggested that the allosteric inhibitors could suppress the dynamic transitions from the weakly bound cluster-cluster complexes to fused signaling complexes, leading to the subsequent downregulation of intracellular calcium signaling pathways. We believe that this strategy is promising for imaging and monitoring receptor clustering as well as protein phase separation on the cell surface in various biological and physiological processes.
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Affiliation(s)
- Qian Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082 Changsha, P. R. China
| | - Jinhui Shang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082 Changsha, P. R. China
| | - Yancao Chen
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082 Changsha, P. R. China
| | - Decui Tang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082 Changsha, P. R. China
| | - Yuzhi Ouyang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082 Changsha, P. R. China
| | - Bin Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082 Changsha, P. R. China
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082 Changsha, P. R. China
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14
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Faure C, Djerbi-Bouillié R, Domingot A, Bouzinba-Segard H, Taouji S, Saidi Y, Bernard S, Carallis F, Rothe-Walther R, Lenormand JL, Chevet E, Bourdoulous S. Allosteric Inhibition of HER2 by Moesin-Mimicking Compounds Targets HER2-Positive Cancers and Brain Metastases. Cancer Res 2021; 81:5464-5476. [PMID: 34493594 DOI: 10.1158/0008-5472.can-21-0162] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 07/27/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022]
Abstract
Therapies targeting the tyrosine kinase receptor HER2 have significantly improved survival of patients with HER2+ cancer. However, both de novo and acquired resistance remain a challenge, particularly in the brain metastatic setting. Here we report that, unlike other HER tyrosine kinase receptors, HER2 possesses a binding motif in its cytosolic juxtamembrane region that allows interaction with members of the Ezrin/Radixin/Moesin (ERM) family. Under physiologic conditions, this interaction controls the localization of HER2 in ERM-enriched domains and stabilizes HER2 in a catalytically repressed state. In HER2+ breast cancers, low expression of Moesin correlated with increased HER2 expression. Restoring expression of ERM proteins in HER2+ breast cancer cells was sufficient to revert HER2 activation and inhibit HER2-dependent proliferation. A high-throughput assay recapitulating the HER2-ERM interaction allowed for screening of about 1,500 approved drugs. From this screen, we found Zuclopenthixol, an antipsychotic drug that behaved as a Moesin-mimicking compound, because it directly binds the juxtamembrane region of HER2 and specifically inhibits HER2 activation in HER2+ cancers, as well as activation of oncogenic mutated and truncated forms of HER2. Zuclopenthixol efficiently inhibited HER2+ breast tumor progression in vitro and in vivo and, more importantly, showed significant activity on HER2+ brain tumor progression. Collectively, these data reveal a novel class of allosteric HER2 inhibitors, increasing the number of approaches to consider for intervention on HER2+ breast cancers and brain metastases. SIGNIFICANCE: This study demonstrates the functional role of Moesin in maintaining HER2 in a catalytically repressed state and provides novel therapeutic approaches targeting HER2+ breast cancers and brain metastasis using Moesin-mimicking compounds.
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Affiliation(s)
- Camille Faure
- Université de Paris, Institut Cochin, Inserm, CNRS, Paris, France.
| | | | - Anaïs Domingot
- Université de Paris, Institut Cochin, Inserm, CNRS, Paris, France
| | | | - Saïd Taouji
- Inserm, Université de Bordeaux, Institut Bergonié, Bordeaux, France
| | - Yanis Saidi
- Université de Paris, Institut Cochin, Inserm, CNRS, Paris, France
| | - Sandra Bernard
- Université de Paris, Institut Cochin, Inserm, CNRS, Paris, France
| | | | - Romy Rothe-Walther
- TIMC-IMAG Laboratory, CNRS, Université Joseph Fourier, UFR de Médecine, La Tronche, France
| | - Jean-Luc Lenormand
- TIMC-IMAG Laboratory, CNRS, Université Joseph Fourier, UFR de Médecine, La Tronche, France
| | - Eric Chevet
- Inserm, Université de Bordeaux, Institut Bergonié, Bordeaux, France
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15
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Ramachandran A, Mehić M, Wasim L, Malinova D, Gori I, Blaszczyk BK, Carvalho DM, Shore EM, Jones C, Hyvönen M, Tolar P, Hill CS. Pathogenic ACVR1 R206H activation by Activin A-induced receptor clustering and autophosphorylation. EMBO J 2021; 40:e106317. [PMID: 34003511 PMCID: PMC8280795 DOI: 10.15252/embj.2020106317] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 11/23/2022] Open
Abstract
Fibrodysplasia ossificans progressiva (FOP) and diffuse intrinsic pontine glioma (DIPG) are debilitating diseases that share causal mutations in ACVR1, a TGF-β family type I receptor. ACVR1R206H is a frequent mutation in both diseases. Pathogenic signaling via the SMAD1/5 pathway is mediated by Activin A, but how the mutation triggers aberrant signaling is not known. We show that ACVR1 is essential for Activin A-mediated SMAD1/5 phosphorylation and is activated by two distinct mechanisms. Wild-type ACVR1 is activated by the Activin type I receptors, ACVR1B/C. In contrast, ACVR1R206H activation does not require upstream kinases, but is predominantly activated via Activin A-dependent receptor clustering, which induces its auto-activation. We use optogenetics and live-imaging approaches to demonstrate Activin A-induced receptor clustering and show it requires the type II receptors ACVR2A/B. Our data provide molecular mechanistic insight into the pathogenesis of FOP and DIPG by linking the causal activating genetic mutation to disrupted signaling.
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Affiliation(s)
- Anassuya Ramachandran
- Developmental Signalling LaboratoryThe Francis Crick InstituteLondonUK
- Present address:
Department of Molecular Medicine and PathologyUniversity of AucklandAucklandNew Zealand
| | - Merima Mehić
- Developmental Signalling LaboratoryThe Francis Crick InstituteLondonUK
| | - Laabiah Wasim
- Immune Receptor Activation LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Ilaria Gori
- Developmental Signalling LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Diana M Carvalho
- Division of Molecular PathologyThe Institute of Cancer ResearchSuttonUK
| | - Eileen M Shore
- Departments of Orthopaedic Surgery and GeneticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Chris Jones
- Division of Molecular PathologyThe Institute of Cancer ResearchSuttonUK
| | - Marko Hyvönen
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Pavel Tolar
- Immune Receptor Activation LaboratoryThe Francis Crick InstituteLondonUK
- Present address:
Division of Infection and ImmunityInstitute of Immunity and TransplantationUniversity CollegeLondonUK
| | - Caroline S Hill
- Developmental Signalling LaboratoryThe Francis Crick InstituteLondonUK
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16
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Nederveen-Schippers LM, Pathak P, Keizer-Gunnink I, Westphal AH, van Haastert PJM, Borst JW, Kortholt A, Skakun V. Combined FCS and PCH Analysis to Quantify Protein Dimerization in Living Cells. Int J Mol Sci 2021; 22:ijms22147300. [PMID: 34298920 PMCID: PMC8307594 DOI: 10.3390/ijms22147300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 11/29/2022] Open
Abstract
Protein dimerization plays a crucial role in the regulation of numerous biological processes. However, detecting protein dimers in a cellular environment is still a challenge. Here we present a methodology to measure the extent of dimerization of GFP-tagged proteins in living cells, using a combination of fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analysis of single-color fluorescence fluctuation data. We named this analysis method brightness and diffusion global analysis (BDGA) and adapted it for biological purposes. Using cell lysates containing different ratios of GFP and tandem-dimer GFP (diGFP), we show that the average brightness per particle is proportional to the fraction of dimer present. We further adapted this methodology for its application in living cells, and we were able to distinguish GFP, diGFP, as well as ligand-induced dimerization of FKBP12 (FK506 binding protein 12)-GFP. While other analysis methods have only sporadically been used to study dimerization in living cells and may be prone to errors, this paper provides a robust approach for the investigation of any cytosolic protein using single-color fluorescence fluctuation spectroscopy.
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Affiliation(s)
- Laura M. Nederveen-Schippers
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Pragya Pathak
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Ineke Keizer-Gunnink
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Adrie H. Westphal
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (A.H.W.); (J.W.B.)
| | - Peter J. M. van Haastert
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (A.H.W.); (J.W.B.)
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
- Correspondence: (A.K.); (V.S.)
| | - Victor Skakun
- Department of Systems Analysis and Computer Simulation, Belarusian State University, 220030 Minsk, Belarus
- Correspondence: (A.K.); (V.S.)
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17
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Kim DH, Triet HM, Ryu SH. Regulation of EGFR activation and signaling by lipids on the plasma membrane. Prog Lipid Res 2021; 83:101115. [PMID: 34242725 DOI: 10.1016/j.plipres.2021.101115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/02/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022]
Abstract
Lipids on the plasma membrane are not only components of the membrane biophysical structures but also regulators of receptor functions. Recently, the critical roles of lipid-protein interactions have been intensively highlighted. Epidermal growth factor receptor (EGFR) is one of the most extensively studied receptors exhibiting various lipid interactions, including interactions with phosphatidylcholine, phosphatidylserine, phosphatidylinositol phosphate, cholesterol, gangliosides, and palmitate. Here, we review recent findings on how direct interaction with these lipids regulates EGFR activation and signaling, providing unprecedented insight into the comprehensive roles of various lipids in the control of EGFR functions. Finally, the current limitations in investigating lipid-protein interactions and novel technologies to potentially overcome these limitations are discussed.
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Affiliation(s)
- Do-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Hong Minh Triet
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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18
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Light TP, Gomez-Soler M, Wang Z, Karl K, Zapata-Mercado E, Gehring MP, Lechtenberg BC, Pogorelov TV, Hristova K, Pasquale EB. A cancer mutation promotes EphA4 oligomerization and signaling by altering the conformation of the SAM domain. J Biol Chem 2021; 297:100876. [PMID: 34139238 PMCID: PMC8260879 DOI: 10.1016/j.jbc.2021.100876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/20/2021] [Accepted: 06/13/2021] [Indexed: 12/24/2022] Open
Abstract
The Eph receptor tyrosine kinases and their ephrin ligands regulate many physiological and pathological processes. EphA4 plays important roles in nervous system development and adult homeostasis, while aberrant EphA4 signaling has been implicated in neurodegeneration. EphA4 may also affect cancer malignancy, but the regulation and effects of EphA4 signaling in cancer are poorly understood. A correlation between decreased patient survival and high EphA4 mRNA expression in melanoma tumors that also highly express ephrinA ligands suggests that enhanced EphA4 signaling may contribute to melanoma progression. A search for EphA4 gain-of-function mutations in melanoma uncovered a mutation of the highly conserved leucine 920 in the EphA4 sterile alpha motif (SAM) domain. We found that mutation of L920 to phenylalanine (L920F) potentiates EphA4 autophosphorylation and signaling, making it the first documented EphA4 cancer mutation that increases kinase activity. Quantitative Föster resonance energy transfer and fluorescence intensity fluctuation (FIF) analyses revealed that the L920F mutation induces a switch in EphA4 oligomer size, from a dimer to a trimer. We propose this switch in oligomer size as a novel mechanism underlying EphA4-linked tumorigenesis. Molecular dynamics simulations suggest that the L920F mutation alters EphA4 SAM domain conformation, leading to the formation of EphA4 trimers that assemble through two aberrant SAM domain interfaces. Accordingly, EphA4 wild-type and the L920F mutant are affected differently by the SAM domain and are differentially regulated by ephrin ligand stimulation. The increased EphA4 activation induced by the L920F mutation, through the novel mechanism we uncovered, supports a functional role for EphA4 in promoting pathogenesis.
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Affiliation(s)
- Taylor P Light
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maricel Gomez-Soler
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Zichen Wang
- Department of Chemistry, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, and National Center for Supercomputing Applications, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kelly Karl
- Program in Molecular Biophysics, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Elmer Zapata-Mercado
- Program in Molecular Biophysics, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Marina P Gehring
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Bernhard C Lechtenberg
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Taras V Pogorelov
- Department of Chemistry, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, and National Center for Supercomputing Applications, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA; Program in Molecular Biophysics, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA.
| | - Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
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19
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Wirth D, McCall A, Hristova K. Neural network strategies for plasma membrane selection in fluorescence microscopy images. Biophys J 2021; 120:2374-2385. [PMID: 33961865 PMCID: PMC8390876 DOI: 10.1016/j.bpj.2021.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 10/21/2022] Open
Abstract
In recent years, there has been an explosion of fluorescence microscopy studies of live cells in the literature. The analysis of the images obtained in these studies often requires labor-intensive manual annotation to extract meaningful information. In this study, we explore the utility of a neural network approach to recognize, classify, and select plasma membranes in high-resolution images, thus greatly speeding up data analysis and reducing the need for personnel training for highly repetitive tasks. Two different strategies are tested: 1) a semantic segmentation strategy, and 2) a sequential application of an object detector followed by a semantic segmentation network. Multiple network architectures are evaluated for each strategy, and the best performing solutions are combined and implemented in the Recognition Of Cellular Membranes software. We show that images annotated manually and with the Recognition Of Cellular Membranes software yield identical results by comparing Förster resonance energy transfer binding curves for the membrane protein fibroblast growth factor receptor 3. The approach that we describe in this work can be applied to other image selection tasks in cell biology.
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Affiliation(s)
- Daniel Wirth
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - Alec McCall
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.
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20
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Characterization of clostridium botulinum neurotoxin serotype A (BoNT/A) and fibroblast growth factor receptor interactions using novel receptor dimerization assay. Sci Rep 2021; 11:7832. [PMID: 33837264 PMCID: PMC8035261 DOI: 10.1038/s41598-021-87331-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 03/24/2021] [Indexed: 01/03/2023] Open
Abstract
Clostridium botulinum neurotoxin serotype A (BoNT/A) is a potent neurotoxin that serves as an effective therapeutic for several neuromuscular disorders via induction of temporary muscular paralysis. Specific binding and internalization of BoNT/A into neuronal cells is mediated by its binding domain (HC/A), which binds to gangliosides, including GT1b, and protein cell surface receptors, including SV2. Previously, recombinant HC/A was also shown to bind to FGFR3. As FGFR dimerization is an indirect measure of ligand-receptor binding, an FCS & TIRF receptor dimerization assay was developed to measure rHC/A-induced dimerization of fluorescently tagged FGFR subtypes (FGFR1-3) in cells. rHC/A dimerized FGFR subtypes in the rank order FGFR3c (EC50 ≈ 27 nM) > FGFR2b (EC50 ≈ 70 nM) > FGFR1c (EC50 ≈ 163 nM); rHC/A dimerized FGFR3c with similar potency as the native FGFR3c ligand, FGF9 (EC50 ≈ 18 nM). Mutating the ganglioside binding site in HC/A, or removal of GT1b from the media, resulted in decreased dimerization. Interestingly, reduced dimerization was also observed with an SV2 mutant variant of HC/A. Overall, the results suggest that the FCS & TIRF receptor dimerization assay can assess FGFR dimerization with known and novel ligands and support a model wherein HC/A, either directly or indirectly, interacts with FGFRs and induces receptor dimerization.
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21
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Paul MD, Rainwater R, Zuo Y, Gu L, Hristova K. Probing Membrane Protein Association Using Concentration‐Dependent Number and Brightness. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael D. Paul
- Program in Molecular Biophysics Johns Hopkins University Baltimore MD 21218 USA
| | - Randall Rainwater
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
| | - Yi Zuo
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
| | - Luo Gu
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
| | - Kalina Hristova
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
- Program in Molecular Biophysics Johns Hopkins University Baltimore MD 21218 USA
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22
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Işbilir A, Serfling R, Möller J, Thomas R, De Faveri C, Zabel U, Scarselli M, Beck-Sickinger AG, Bock A, Coin I, Lohse MJ, Annibale P. Determination of G-protein-coupled receptor oligomerization by molecular brightness analyses in single cells. Nat Protoc 2021; 16:1419-1451. [PMID: 33514946 DOI: 10.1038/s41596-020-00458-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023]
Abstract
Oligomerization of membrane proteins has received intense research interest because of their importance in cellular signaling and the large pharmacological and clinical potential this offers. Fluorescence imaging methods are emerging as a valid tool to quantify membrane protein oligomerization at high spatial and temporal resolution. Here, we provide a detailed protocol for an image-based method to determine the number and oligomerization state of fluorescently labeled prototypical G-protein-coupled receptors (GPCRs) on the basis of small out-of-equilibrium fluctuations in fluorescence (i.e., molecular brightness) in single cells. The protocol provides a step-by-step procedure that includes instructions for (i) a flexible labeling strategy for the protein of interest (using fluorescent proteins, small self-labeling tags or bio-orthogonal labeling) and the appropriate controls, (ii) performing temporal and spatial brightness image acquisition on a confocal microscope and (iii) analyzing and interpreting the data, excluding clusters and intensity hot-spots commonly observed in receptor distributions. Although specifically tailored for GPCRs, this protocol can be applied to diverse classes of membrane proteins of interest. The complete protocol can be implemented in 1 month.
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Affiliation(s)
- Ali Işbilir
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Robert Serfling
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Jan Möller
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Romy Thomas
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Chiara De Faveri
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Ulrike Zabel
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Marco Scarselli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Andreas Bock
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Martin J Lohse
- Max Delbrück Center for Molecular Medicine, Berlin, Germany. .,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany. .,ISAR Bioscience Institute, Munich, Germany.
| | - Paolo Annibale
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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23
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Paul MD, Rainwater R, Zuo Y, Gu L, Hristova K. Probing Membrane Protein Association Using Concentration-Dependent Number and Brightness. Angew Chem Int Ed Engl 2021; 60:6503-6508. [PMID: 33351993 DOI: 10.1002/anie.202010049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/11/2020] [Indexed: 01/13/2023]
Abstract
We introduce concentration-dependent number and brightness (cdN&B), a fluorescence fluctuation technique that can be implemented on a standard confocal microscope and can report on the thermodynamics of membrane protein association in the native plasma membrane. It uses transient transfection to enable measurements of oligomer size as a function of receptor concentration over a broad range, yielding the association constant. We discuss artifacts in cdN&B that are concentration-dependent and can distort the oligomerization curves, and we outline procedures that can correct for them. Using cdN&B, we characterize the association of neuropilin 1 (NRP1), a protein that plays a critical role in the development of the embryonic cardiovascular and nervous systems. We show that NRP1 associates into a tetramer in a concentration-dependent manner, and we quantify the strength of the association. This work demonstrates the utility of cdN&B as a powerful tool in biophysical chemistry.
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Affiliation(s)
- Michael D Paul
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Randall Rainwater
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Yi Zuo
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Luo Gu
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA.,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
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24
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Ahmed F, Zapata-Mercado E, Rahman S, Hristova K. The Biased Ligands NGF and NT-3 Differentially Stabilize Trk-A Dimers. Biophys J 2020; 120:55-63. [PMID: 33285113 DOI: 10.1016/j.bpj.2020.11.2262] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/14/2020] [Accepted: 11/23/2020] [Indexed: 12/23/2022] Open
Abstract
Trk-A is a receptor tyrosine kinase (RTK) that plays an essential role in the development and functioning of the nervous system. Trk-A is expressed in neurons and signals in response to two ligands, NGF and neurotrophin-3 (NT-3), with very different functional consequences. Thus, NGF and NT-3 are "biased" ligands for Trk-A. Because it has been hypothesized that biased RTK ligands induce differential stabilization of RTK dimers, here, we seek to test this hypothesis for NGF and NT-3. In particular, we use Förster resonance energy transfer (FRET) and fluorescence intensity fluctuation spectroscopy to assess the strength of Trk-A interactions and Trk-A oligomer size in the presence of the two ligands. Although the difference in Trk-A behavior in response to the two ligands has been previously attributed to differences in their binding to Trk-A in the endosomes at low pH, here, we further show differences in the stabilities of the NGF- and NT-3-bound Trk-A dimers in the plasma membrane and at neutral pH. We discuss the biological significance of these new findings and their implications for the design of Trk-A ligands with novel functionalities.
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Affiliation(s)
- Fozia Ahmed
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - Elmer Zapata-Mercado
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
| | - Sanim Rahman
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.
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25
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Conserved roles for receptor tyrosine kinase extracellular regions in regulating receptor and pathway activity. Biochem J 2020; 477:4207-4220. [PMID: 33043983 DOI: 10.1042/bcj20200702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 11/17/2022]
Abstract
Receptor Tyrosine Kinases (RTKs) comprise a diverse group of cell-surface receptors that mediate key signaling events during animal development and are frequently activated in cancer. We show here that deletion of the extracellular regions of 10 RTKs representing 7 RTK classes or their substitution with the dimeric immunoglobulin Fc region results in constitutive receptor phosphorylation but fails to result in phosphorylation of downstream signaling effectors Erk or Akt. Conversely, substitution of RTK extracellular regions with the extracellular region of the Epidermal Growth Factor Receptor (EGFR) results in increases in effector phosphorylation in response to EGF. These results indicate that the activation signal generated by the EGFR extracellular region is capable of activating at least seven different RTK classes. Failure of phosphorylated Fc-RTK chimeras or RTKs with deleted extracellular regions to stimulate phosphorylation of downstream effectors indicates that either dimerization and receptor phosphorylation per se are insufficient to activate signaling or constitutive dimerization leads to pathway inhibition.
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26
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Hajdu T, Váradi T, Rebenku I, Kovács T, Szöllösi J, Nagy P. Comprehensive Model for Epidermal Growth Factor Receptor Ligand Binding Involving Conformational States of the Extracellular and the Kinase Domains. Front Cell Dev Biol 2020; 8:776. [PMID: 32850868 PMCID: PMC7431817 DOI: 10.3389/fcell.2020.00776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/23/2020] [Indexed: 12/03/2022] Open
Abstract
The epidermal growth factor (EGF) receptor (EGFR) undergoes ligand-dependent dimerization to initiate transmembrane signaling. Although crystallographic structures of the extracellular and kinase domains are available, ligand binding has not been quantitatively analyzed taking the influence of both domains into account. Here, we developed a model explicitly accounting for conformational changes of the kinase and extracellular domains, their dimerizations and ligand binding to monomeric and dimeric receptor species. The model was fitted to ligand binding data of suspended cells expressing receptors with active or inactive kinase conformations. Receptor dimers with inactive, symmetric configuration of the kinase domains exhibit positive cooperativity and very weak binding affinity for the first ligand, whereas dimers with active, asymmetric kinase dimers are characterized by negative cooperativity and subnanomolar binding affinity for the first ligand. The homodimerization propensity of EGFR monomers with active kinase domains is ∼100-times higher than that of dimers with inactive kinase domains. Despite this fact, constitutive, ligand-independent dimers are mainly generated from monomers with inactive kinase domains due to the excess of such monomers in the membrane. The experimental finding of increased positive cooperativity at high expression levels of EGFR was recapitulated by the model. Quantitative prediction of ligand binding to different receptor species revealed that EGF binds to receptor monomers and dimers in an expression-level dependent manner without significant recruitment of monomers to dimers upon EGF stimulation below the phase transition temperature of the membrane. Results of the fitting offer unique insight into the workings of the EGFR.
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Affiliation(s)
- Tímea Hajdu
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tímea Váradi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - István Rebenku
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tamás Kovács
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - János Szöllösi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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27
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Byrne PO, Hristova K, Leahy DJ. EGFR forms ligand-independent oligomers that are distinct from the active state. J Biol Chem 2020; 295:13353-13362. [PMID: 32727847 DOI: 10.1074/jbc.ra120.012852] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/27/2020] [Indexed: 01/15/2023] Open
Abstract
The human epidermal growth factor receptor (EGFR/ERBB1) is a receptor tyrosine kinase (RTK) that forms activated oligomers in response to ligand. Much evidence indicates that EGFR/ERBB1 also forms oligomers in the absence of ligand, but the structure and physiological role of these ligand-independent oligomers remain unclear. To examine these features, we use fluorescence microscopy to measure the oligomer stability and FRET efficiency for homo- and hetero-oligomers of fluorescent protein-labeled forms of EGFR and its paralog, human epidermal growth factor receptor 2 (HER2/ERBB2) in vesicles derived from mammalian cell membranes. We observe that both receptors form ligand-independent oligomers at physiological plasma membrane concentrations. Mutations introduced in the kinase region at the active state asymmetric kinase dimer interface do not affect the stability of ligand-independent EGFR oligomers. These results indicate that ligand-independent EGFR oligomers form using interactions that are distinct from the EGFR active state.
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Affiliation(s)
- Patrick O Byrne
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Daniel J Leahy
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, USA.
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28
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Influenza A viruses use multivalent sialic acid clusters for cell binding and receptor activation. PLoS Pathog 2020; 16:e1008656. [PMID: 32639985 PMCID: PMC7371231 DOI: 10.1371/journal.ppat.1008656] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/20/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022] Open
Abstract
Influenza A virus (IAV) binds its host cell using the major viral surface protein hemagglutinin (HA). HA recognizes sialic acid, a plasma membrane glycan that functions as the specific primary attachment factor (AF). Since sialic acid alone cannot fulfill a signaling function, the virus needs to activate downstream factors to trigger endocytic uptake. Recently, the epidermal growth factor receptor (EGFR), a member of the receptor-tyrosine kinase family, was shown to be activated by IAV and transmit cell entry signals. However, how IAV’s binding to sialic acid leads to engagement and activation of EGFR remains largely unclear. We used multicolor super-resolution microscopy to study the lateral organization of both IAV’s AFs and its functional receptor EGFR at the scale of the IAV particle. Intriguingly, quantitative cluster analysis revealed that AFs and EGFR are organized in partially overlapping submicrometer clusters in the plasma membrane of A549 cells. Within AF domains, the local AF concentration reaches on average 10-fold the background concentration and tends to increase towards the cluster center, thereby representing a multivalent virus-binding platform. Using our experimentally measured cluster characteristics, we simulated virus diffusion on a flat membrane. The results predict that the local AF concentration strongly influences the distinct mobility pattern of IAVs, in a manner consistent with live-cell single-virus tracking data. In contrast to AFs, EGFR resides in smaller clusters. Virus binding activates EGFR, but interestingly, this process occurs without a major lateral EGFR redistribution, indicating the activation of pre-formed clusters, which we show are long-lived. Taken together, our results provide a quantitative understanding of the initial steps of influenza virus infection. Co-clustering of AF and EGFR permit a cooperative effect of binding and signaling at specific platforms, thus linking their spatial organization to their functional role during virus-cell binding and receptor activation. The plasma membrane is the major interface between a cell and its environment. This complex and dynamic organelle needs to protect, as a barrier, but also transmit subtle signals into and out of the cell. For the enveloped virus IAV, the plasma membrane represents both a major obstacle to overcome during infection, and the site for the assembly of progeny virus particles. However, the organisation of the plasma membrane–a key to understanding how viral entry works—at the scale of an infecting particle (length scales < 100 nm) remains largely unknown. Sialylated glycans serve as IAV attachment factors but are not able to transmit signals across the plasma membrane. Receptor tyrosine kinases were identified to be activated upon virus binding and serve as functional receptors. How IAV engages and activates its functional receptors while initially binding glycans still remains speculative. Here, we use super resolution microscopy to study the lateral organization of plasma membrane-bound molecules involved in IAV infection, as well as their functional relationship. We find that molecules are organized in submicrometer nanodomains and, in combination with virus diffusion simulations, present a mechanistic model for how IAV first engages with AFs in the plasma membrane to subsequently engage and trigger entry-associated membrane receptors.
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29
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Clark NM, Van den Broeck L, Guichard M, Stager A, Tanner HG, Blilou I, Grossmann G, Iyer-Pascuzzi AS, Maizel A, Sparks EE, Sozzani R. Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:789-816. [PMID: 32119794 DOI: 10.1146/annurev-arplant-050718-100038] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale.
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Affiliation(s)
- Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50010, USA;
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
| | - Marjorie Guichard
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
- CellNetworks Cluster of Excellence, Heidelberg University, 69120 Heidelberg, Germany
| | - Adam Stager
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware 19711, USA; ,
| | - Herbert G Tanner
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware 19711, USA; ,
| | - Ikram Blilou
- Department of Plant Cell and Developmental Biology, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
| | - Guido Grossmann
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
- CellNetworks Cluster of Excellence, Heidelberg University, 69120 Heidelberg, Germany
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA;
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany; , ,
| | - Erin E Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA;
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA; ,
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30
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Wang J, Min J, Eghtesadi SA, Kane RS, Chilkoti A. Quantitative Study of the Interaction of Multivalent Ligand-Modified Nanoparticles with Breast Cancer Cells with Tunable Receptor Density. ACS NANO 2020; 14:372-383. [PMID: 31899613 DOI: 10.1021/acsnano.9b05689] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Multivalent nanoparticles that target a cell surface receptor that is overexpressed by cancer cells are a promising delivery system for cancer therapy. However, the impact of the receptor density and nanoparticle ligand valency on the cell uptake has not been studied in a system where both variables can be systematically tuned over a wide range. To address this lacuna, we report cell-uptake studies on a genetically engineered breast cancer cell line with tunable ErbB2 expression by a polypeptide micelle with tunable ligand valency. We examined the uptake of ErbB2-targeting micelles at 5 ligand densities and 11 receptor densities. We identified a matching pattern between receptors and ligands in which a receptor-to-ligand density ratio of 0.7-4.5 and a minimum of ∼1.6 bonds are required to initiate receptor-mediated endocytosis. Lower and upper limits of receptor density in the cell-uptake profile suggested a standard by which to categorize breast cancer patients as ErbB2-low, ErbB2-medium, and ErbB2-high, with each group expected to respond differently to multivalent therapeutic nanoparticles. At ErbB2-medium and ErbB2-high levels, increasing the ligand valency to 40-valent ErbB2-targeting peptides for a 20 nm radius nanoparticle accelerated the cell uptake, suggesting that the use of nanoparticles with high ligand valency for drug delivery will greatly benefit patients in these two groups. This study advances our understanding of how to rationally optimize nanotechnology for targeted drug delivery.
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Affiliation(s)
- Jing Wang
- Department of Biomedical Engineering , Duke University , Durham , North Carolina 27708 , United States
| | - Junseon Min
- Department of Biomedical Engineering , Duke University , Durham , North Carolina 27708 , United States
| | - Seyed Ali Eghtesadi
- Department of Biomedical Engineering , Duke University , Durham , North Carolina 27708 , United States
| | - Ravi S Kane
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering , Duke University , Durham , North Carolina 27708 , United States
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31
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Indira Chandran V, Månsson AS, Barbachowska M, Cerezo-Magaña M, Nodin B, Joshi B, Koppada N, Saad OM, Gluz O, Isaksson K, Borgquist S, Jirström K, Nabi IR, Jernström H, Belting M. Hypoxia Attenuates Trastuzumab Uptake and Trastuzumab-Emtansine (T-DM1) Cytotoxicity through Redistribution of Phosphorylated Caveolin-1. Mol Cancer Res 2020; 18:644-656. [PMID: 31900313 DOI: 10.1158/1541-7786.mcr-19-0856] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/28/2019] [Accepted: 12/20/2019] [Indexed: 11/16/2022]
Abstract
The antibody-drug conjugate trastuzumab-emtansine (T-DM1) offers an additional treatment option for patients with HER2-amplified tumors. However, primary and acquired resistance is a limiting factor in a significant subset of patients. Hypoxia, a hallmark of cancer, regulates the trafficking of several receptor proteins with potential implications for tumor targeting. Here, we have investigated how hypoxic conditions may regulate T-DM1 treatment efficacy in breast cancer. The therapeutic effect of T-DM1 and its metabolites was evaluated in conjunction with biochemical, flow cytometry, and high-resolution imaging studies to elucidate the functional and mechanistic aspects of hypoxic regulation. HER2 and caveolin-1 expression was investigated in a well-annotated breast cancer cohort. We find that hypoxia fosters relative resistance to T-DM1 in HER2+ cells (SKBR3 and BT474). This effect was not a result of deregulated HER2 expression or resistance to emtansine and its metabolites. Instead, we show that hypoxia-induced translocation of caveolin-1 from cytoplasmic vesicles to the plasma membrane contributes to deficient trastuzumab internalization and T-DM1 chemosensitivity. Caveolin-1 depletion mimicked the hypoxic situation, indicating that vesicular caveolin-1 is indispensable for trastuzumab uptake and T-DM1 cytotoxicity. In vitro studies suggested that HER2 and caveolin-1 are not coregulated, which was supported by IHC analysis in patient tumors. We find that phosphorylation-deficient caveolin-1 inhibits trastuzumab internalization and T-DM1 cytotoxicity, suggesting a specific role for caveolin-1 phosphorylation in HER2 trafficking. IMPLICATIONS: Together, our data for the first time identify hypoxic regulation of caveolin-1 as a resistance mechanism to T-DM1 with potential implications for individualized treatment of breast cancer.
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Affiliation(s)
- Vineesh Indira Chandran
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Lund, Sweden.
| | - Ann-Sofie Månsson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Lund, Sweden
| | - Magdalena Barbachowska
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Lund, Sweden
| | - Myriam Cerezo-Magaña
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Lund, Sweden
| | - Björn Nodin
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Lund, Sweden
| | - Bharat Joshi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Neelima Koppada
- BioAnalytical Sciences-ADT, gRED, Genentech, South San Francisco, California
| | - Ola M Saad
- BioAnalytical Sciences-ADT, gRED, Genentech, South San Francisco, California
| | - Oleg Gluz
- West German Study Group, Moenchengladbach, Germany
| | - Karolin Isaksson
- Division of Surgery, Lund University, Skåne University Hospital, Lund, Central Hospital, Kristianstad, Sweden
| | - Signe Borgquist
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Lund, Sweden
- Department of Oncology, Aarhus University Hospital, Aarhus University, Aarhus, Denmark
| | - Karin Jirström
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Lund, Sweden
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Helena Jernström
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Lund, Sweden
| | - Mattias Belting
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Lund, Sweden.
- Department of Hematology, Oncology and Radiophysics, Skåne University Hospital, Lund, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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32
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Petazzi RA, Aji AK, Chiantia S. Fluorescence microscopy methods for the study of protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:1-41. [DOI: 10.1016/bs.pmbts.2019.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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33
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Caballero-Díaz D, Bertran E, Peñuelas-Haro I, Moreno-Càceres J, Malfettone A, López-Luque J, Addante A, Herrera B, Sánchez A, Alay A, Solé X, Serrano T, Ramos E, Fabregat I. Clathrin switches transforming growth factor-β role to pro-tumorigenic in liver cancer. J Hepatol 2020; 72:125-134. [PMID: 31562907 DOI: 10.1016/j.jhep.2019.09.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS Upon ligand binding, tyrosine kinase receptors, such as epidermal growth factor receptor (EGFR), are recruited into clathrin-coated pits for internalization by endocytosis, which is relevant for signalling and/or receptor degradation. In liver cells, transforming growth factor-β (TGF-β) induces both pro- and anti-apoptotic signals; the latter are mediated by the EGFR pathway. Since EGFR mainly traffics via clathrin-coated vesicles, we aimed to analyse the potential role of clathrin in TGF-β-induced signalling in liver cells and its relevance in liver cancer. METHODS Real-Time PCR and immunohistochemistry were used to analyse clathrin heavy-chain expression in human (CLTC) and mice (Cltc) liver tumours. Transient knockdown (siRNA) or overexpression of CLTC were used to analyse its role on TGF-β and EGFR signalling in vitro. Bioinformatic analysis was used to determine the effect of CLTC and TGFB1 expression on prognosis and overall survival in patients with hepatocellular carcinoma (HCC). RESULTS Clathrin expression increased during liver tumorigenesis in humans and mice. CLTC knockdown cells responded to TGF-β phosphorylating SMADs (canonical signalling) but showed impairment in the anti-apoptotic signals (EGFR transactivation). Experiments of loss or gain of function in HCC cells reveal an essential role for clathrin in inhibiting TGF-β-induced apoptosis and upregulation of its pro-apoptotic target NOX4. Autocrine TGF-β signalling in invasive HCC cells upregulates CLTC expression, switching its role to pro-tumorigenic. A positive correlation between TGFB1 and CLTC was found in HCC cells and patients. Patients expressing high levels of TGFB1 and CLTC had a worse prognosis and lower overall survival. CONCLUSIONS This work describes a novel role for clathrin in liver tumorigenesis, favouring non-canonical pro-tumorigenic TGF-β pathways. CLTC expression in human HCC samples could help select patients that would benefit from TGF-β-targeted therapy. LAY SUMMARY Clathrin heavy-chain expression increases during liver tumorigenesis in humans (CLTC) and mice (Cltc), altering the cellular response to TGF-β in favour of anti-apoptotic/pro-tumorigenic signals. A positive correlation between TGFB1 and CLTC was found in HCC cells and patients. Patients expressing high levels of TGFB1 and CLTC had a worse prognosis and lower overall survival. CLTC expression in HCC human samples could help select patients that would benefit from therapies targeting TGF-β.
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Affiliation(s)
- Daniel Caballero-Díaz
- Oncology Program, CIBEREHD, National Biomedical Research Institute on Liver and Gastrointestinal Diseases, Instituto de Salud Carlos III, 28029 Madrid, Spain; TGF-β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Gran Via de L'Hospitalet, 199, 08908 Barcelona, Spain.
| | - Esther Bertran
- Oncology Program, CIBEREHD, National Biomedical Research Institute on Liver and Gastrointestinal Diseases, Instituto de Salud Carlos III, 28029 Madrid, Spain; TGF-β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Gran Via de L'Hospitalet, 199, 08908 Barcelona, Spain
| | - Irene Peñuelas-Haro
- Oncology Program, CIBEREHD, National Biomedical Research Institute on Liver and Gastrointestinal Diseases, Instituto de Salud Carlos III, 28029 Madrid, Spain; TGF-β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Gran Via de L'Hospitalet, 199, 08908 Barcelona, Spain
| | - Joaquim Moreno-Càceres
- TGF-β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Gran Via de L'Hospitalet, 199, 08908 Barcelona, Spain
| | - Andrea Malfettone
- TGF-β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Gran Via de L'Hospitalet, 199, 08908 Barcelona, Spain
| | - Judit López-Luque
- Oncology Program, CIBEREHD, National Biomedical Research Institute on Liver and Gastrointestinal Diseases, Instituto de Salud Carlos III, 28029 Madrid, Spain; TGF-β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Gran Via de L'Hospitalet, 199, 08908 Barcelona, Spain
| | - Annalisa Addante
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University of Madrid, Health Research Institute of the Hospital Clínico San Carlos, Madrid, Spain
| | - Blanca Herrera
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University of Madrid, Health Research Institute of the Hospital Clínico San Carlos, Madrid, Spain
| | - Aránzazu Sánchez
- Dept. Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University of Madrid, Health Research Institute of the Hospital Clínico San Carlos, Madrid, Spain
| | - Ania Alay
- Oncology Data Analytics Program, Bellvitge Biomedical Research Institute (IDIBELL), CIBER Epidemiología y Salud Pública (CIBERESP), L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Xavier Solé
- Oncology Data Analytics Program, Bellvitge Biomedical Research Institute (IDIBELL), CIBER Epidemiología y Salud Pública (CIBERESP), L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Teresa Serrano
- Oncology Program, CIBEREHD, National Biomedical Research Institute on Liver and Gastrointestinal Diseases, Instituto de Salud Carlos III, 28029 Madrid, Spain; TGF-β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Gran Via de L'Hospitalet, 199, 08908 Barcelona, Spain; Pathological Anatomy Service, University Hospital of Bellvitge, Barcelona, Spain; Faculty of Medicine and Health Sciences, University of Barcelona, L'Hospitalet, 08907 Barcelona, Spain
| | - Emilio Ramos
- Oncology Program, CIBEREHD, National Biomedical Research Institute on Liver and Gastrointestinal Diseases, Instituto de Salud Carlos III, 28029 Madrid, Spain; TGF-β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Gran Via de L'Hospitalet, 199, 08908 Barcelona, Spain; Department of Surgery, Liver Transplant Unit, University Hospital of Bellvitge, Barcelona, Spain; Faculty of Medicine and Health Sciences, University of Barcelona, L'Hospitalet, 08907 Barcelona, Spain
| | - Isabel Fabregat
- Oncology Program, CIBEREHD, National Biomedical Research Institute on Liver and Gastrointestinal Diseases, Instituto de Salud Carlos III, 28029 Madrid, Spain; TGF-β and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Gran Via de L'Hospitalet, 199, 08908 Barcelona, Spain; Faculty of Medicine and Health Sciences, University of Barcelona, L'Hospitalet, 08907 Barcelona, Spain.
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34
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Westerfield JM, Barrera FN. Membrane receptor activation mechanisms and transmembrane peptide tools to elucidate them. J Biol Chem 2019; 295:1792-1814. [PMID: 31879273 DOI: 10.1074/jbc.rev119.009457] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Single-pass membrane receptors contain extracellular domains that respond to external stimuli and transmit information to intracellular domains through a single transmembrane (TM) α-helix. Because membrane receptors have various roles in homeostasis, signaling malfunctions of these receptors can cause disease. Despite their importance, there is still much to be understood mechanistically about how single-pass receptors are activated. In general, single-pass receptors respond to extracellular stimuli via alterations in their oligomeric state. The details of this process are still the focus of intense study, and several lines of evidence indicate that the TM domain (TMD) of the receptor plays a central role. We discuss three major mechanistic hypotheses for receptor activation: ligand-induced dimerization, ligand-induced rotation, and receptor clustering. Recent observations suggest that receptors can use a combination of these activation mechanisms and that technical limitations can bias interpretation. Short peptides derived from receptor TMDs, which can be identified by screening or rationally developed on the basis of the structure or sequence of their targets, have provided critical insights into receptor function. Here, we explore recent evidence that, depending on the target receptor, TMD peptides cannot only inhibit but also activate target receptors and can accommodate novel, bifunctional designs. Furthermore, we call for more sharing of negative results to inform the TMD peptide field, which is rapidly transforming into a suite of unique tools with the potential for future therapeutics.
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Affiliation(s)
- Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996.
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35
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Martin EW, Chakraborty S, Presman DM, Tomassoni Ardori F, Oh KS, Kaileh M, Tessarollo L, Sung MH. Assaying Homodimers of NF-κB in Live Single Cells. Front Immunol 2019; 10:2609. [PMID: 31787981 PMCID: PMC6853996 DOI: 10.3389/fimmu.2019.02609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/21/2019] [Indexed: 11/25/2022] Open
Abstract
NF-κB is a family of heterodimers and homodimers which are generated from subunits encoded by five genes. The predominant classical dimer RelA:p50 is presumed to operate as “NF-κB” in many contexts. However, there are several other dimer species which exist and may even be more functionally relevant in specific cell types. Accurate characterization of stimulus-specific and tissue-specific dimer repertoires is fundamentally important for understanding the downstream gene regulation by NF-κB proteins. In vitro assays such as immunoprecipitation have been widely used to analyze subunit composition, but these methods do not provide information about dimerization status within the natural intracellular environment of intact live cells. Here we apply a live single cell microscopy technique termed Number and Brightness to examine dimers translocating to the nucleus in fibroblasts after pro-inflammatory stimulation. This quantitative assay suggests that RelA:RelA homodimers are more prevalent than might be expected. We also found that the relative proportion of RelA:RelA homodimers can be perturbed by small molecule inhibitors known to disrupt the NF-κB pathway. Our findings show that Number and Brightness is a useful method for investigating NF-κB dimer species in live cells. This approach may help identify the relevant targets in pathophysiological contexts where the dimer specificity of NF-κB intervention is desired.
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Affiliation(s)
- Erik W Martin
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Sayantan Chakraborty
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Francesco Tomassoni Ardori
- Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Kyu-Seon Oh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Mary Kaileh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
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36
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Paul MD, Hristova K. The transition model of RTK activation: A quantitative framework for understanding RTK signaling and RTK modulator activity. Cytokine Growth Factor Rev 2019; 49:23-31. [PMID: 31711797 DOI: 10.1016/j.cytogfr.2019.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/10/2019] [Indexed: 01/15/2023]
Abstract
Here, we discuss the transition model of receptor tyrosine kinase (RTK) activation, which is derived from biophysical investigations of RTK interactions and signaling. The model postulates that (1) RTKs can interact laterally to form dimers even in the absence of ligand, (2) different unliganded RTK dimers have different stabilities, (3) ligand binding stabilizes the RTK dimers, and (4) ligand binding causes structural changes in the RTK dimer. The model is grounded in the principles of physical chemistry and provides a framework to understand RTK activity and to make predictions in quantitative terms. It can guide basic research aimed at uncovering the mechanism of RTK activation and, in the long run, can empower the search for modulators of RTK function.
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Affiliation(s)
- Michael D Paul
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, United States.
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37
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EGF Receptor Stalls upon Activation as Evidenced by Complementary Fluorescence Correlation Spectroscopy and Fluorescence Recovery after Photobleaching Measurements. Int J Mol Sci 2019; 20:ijms20133370. [PMID: 31323980 PMCID: PMC6650801 DOI: 10.3390/ijms20133370] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 12/28/2022] Open
Abstract
To elucidate the molecular details of the activation-associated clustering of epidermal growth factor receptors (EGFRs), the time course of the mobility and aggregation states of eGFP tagged EGFR in the membranes of Chinese hamster ovary (CHO) cells was assessed by in situ mobility assays. Fluorescence correlation spectroscopy (FCS) was used to probe molecular movements of small ensembles of molecules over short distances and time scales, and to report on the state of aggregation. The diffusion of larger ensembles of molecules over longer distances (and time scales) was investigated by fluorescence recovery after photobleaching (FRAP). Autocorrelation functions could be best fitted by a two-component diffusion model corrected for triplet formation and blinking. The slow, 100–1000 ms component was attributed to membrane localized receptors moving with free Brownian diffusion, whereas the fast, ms component was assigned to cytosolic receptors or their fragments. Upon stimulation with 50 nM EGF, a significant decrease from 0.11 to 0.07 μm2/s in the diffusion coefficient of membrane-localized receptors was observed, followed by recovery to the original value in ~20 min. In contrast, the apparent brightness of diffusing species remained the same. Stripe FRAP experiments yielded a decrease in long-range molecular mobility directly after stimulation, evidenced by an increase in the recovery time of the slow component from 13 to 21.9 s. Our observations are best explained by the transient attachment of ligand-bound EGFRs to immobile or slowly moving structures such as the cytoskeleton or large, previously photobleached receptor aggregates.
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Serfling R, Seidel L, Bock A, Lohse MJ, Annibale P, Coin I. Quantitative Single-Residue Bioorthogonal Labeling of G Protein-Coupled Receptors in Live Cells. ACS Chem Biol 2019; 14:1141-1149. [PMID: 31074969 DOI: 10.1021/acschembio.8b01115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
High-end microscopy studies of G protein-coupled receptors (GPCRs) require installing onto the receptors bright and photostable dyes. Labeling must occur in quantitative yields, to allow stoichiometric data analysis, and in a minimally invasive fashion, to avoid perturbing GPCR function. We demonstrate here that the genetic incorporation of trans-cyclooct-2-ene lysine (TCO*) allows achieving quantitative single-residue labeling of the extracellular loops of the β2-adrenergic and the muscarinic M2 class A GPCRs, as well as of the corticotropin releasing factor class B GPCR. Labeling occurs within a few minutes by reaction with dye-tetrazine conjugates on the surface of live cells and preserves the functionality of the receptors. To precisely quantify the labeling yields, we devise a method based on fluorescence fluctuation microscopy that extracts the number of labeling sites at the single-cell level. Further, we show that single-residue labeling is better suited for studies of GPCR diffusion than fluorescent-protein tags, since the latter can affect the mobility of the receptor. Finally, by performing dual-color competitive labeling on a single TCO* site, we devise a method to estimate the oligomerization state of a GPCR without the need for a biological monomeric reference, which facilitates the application of fluorescence methods to oligomerization studies. As TCO* and the dye-tetrazines used in this study are commercially available and the described microscopy techniques can be performed on a commercial microscope, we expect our approach to be widely applicable to fluorescence microscopy studies of membrane proteins in general.
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Affiliation(s)
- Robert Serfling
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
| | - Lisa Seidel
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
| | - Andreas Bock
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Martin J. Lohse
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Paolo Annibale
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Irene Coin
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
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Zhang S, Reinhard BM. Characterizing Large-Scale Receptor Clustering on the Single Cell Level: A Comparative Plasmon Coupling and Fluorescence Superresolution Microscopy Study. J Phys Chem B 2019; 123:5494-5505. [PMID: 31244098 DOI: 10.1021/acs.jpcb.9b05176] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Spatial clustering of cell membrane receptors has been indicated to play a regulatory role in signal initiation, and the distribution of receptors on the cell surface may represent a potential biomarker. To realize its potential for diagnostic purposes, scalable assays capable of mapping spatial receptor heterogeneity with high throughput are needed. In this work, we use gold nanoparticle (NP) labels with an average diameter of 72.17 ± 2.16 nm as bright markers for large-scale epidermal growth factor receptor (EGFR) clustering in hyperspectral plasmon coupling microscopy and compare the obtained clustering maps with those obtained through fluorescence superresolution microscopy (direct stochastic optical reconstruction microscopy, dSTORM). Our dSTORM experiments reveal average EGFR cluster sizes of 172 ± 99 and 150 ± 90 nm for MDA-MB-468 and HeLa, respectively. The cluster sizes decrease after EGFR activation. Hyperspectral imaging of the NP labels shows that differences in the EGFR cluster sizes are accompanied by differences in the average separations between electromagnetically coupled NPs. Because of the distance dependence of plasmon coupling, changes in the average interparticle separation result in significant spectral shifts. For the experimental conditions investigated in this work, hyperspectral plasmon coupling microscopy of NP labels identified the same trends in large-scale EGFR clustering as dSTORM, but the NP imaging approach provided the information in a fraction of the time. Both dSTORM and hyperspectral plasmon coupling microscopy confirm the cortical actin network as one structural component that determines the average size of EGFR clusters.
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Affiliation(s)
- Sandy Zhang
- Department of Chemistry and The Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Björn M Reinhard
- Department of Chemistry and The Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
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40
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Resolving the conformational dynamics of ErbB growth factor receptor dimers. J Struct Biol 2019; 207:225-233. [PMID: 31163211 DOI: 10.1016/j.jsb.2019.05.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/20/2019] [Accepted: 05/31/2019] [Indexed: 12/30/2022]
Abstract
The combinatorial dimerization of the ErbB growth factor receptors (ErbB1- ErbB4) are critical for their function. Here, we have characterized the conformational dynamics of ErbB transmembrane homo-dimers and hetero-dimers by using a coarse-grain simulation framework. All dimers, except ErbB4-4 and ErbB1-4, exhibit at least two conformations. The reported NMR structures correspond to one of these conformations, representing the N-terminal active state in ErbB1-1 (RH2), ErbB2-2 (RH1) and ErbB4-4 (RH) homo-dimers and the LH dimer in ErbB3-3 homo-dimer, validating the computational approach. Further, we predict a right-handed ErbB3-3 dimer conformer that warrants experimental testing. The five hetero-dimers that have not yet been experimentally resolved display prominent right-handed dimers associating by the SmXXXSm motif. Our results provide insights into the constitutive signaling of ErbB4 after cleavage of the extracellular region. The presence of the inactive-like dimer conformers leading to symmetric kinase domains gives clues on the autoinhibition of the receptor dimers. The dimer states characterized here represent an important step towards understanding the combinatorial cross associations in the ErbB family.
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41
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Diwanji D, Thaker T, Jura N. More than the sum of the parts: Toward full-length receptor tyrosine kinase structures. IUBMB Life 2019; 71:706-720. [PMID: 31046201 DOI: 10.1002/iub.2060] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/20/2019] [Indexed: 01/01/2023]
Abstract
Intercellular communication governs complex physiological processes ranging from growth and development to the maintenance of cellular and organ homeostasis. In nearly all metazoans, receptor tyrosine kinases (RTKs) are central players in these diverse and fundamental signaling processes. Aberrant RTK signaling is at the root of many developmental diseases and cancers and it remains a key focus of targeted therapies, several of which have achieved considerable success in patients. These therapeutic advances in targeting RTKs have been propelled by numerous genetic, biochemical, and structural studies detailing the functions and molecular mechanisms of regulation and activation of RTKs. The latter in particular have proven to be instrumental for the development of new drugs, selective targeting of mutant forms of RTKs found in disease, and counteracting ensuing drug resistance. However, to this day, such studies have not yet yielded high-resolution structures of intact RTKs that encompass the extracellular and intracellular domains and the connecting membrane-spanning transmembrane domain. Technically challenging to obtain, these structures are instrumental to complete our understanding of the mechanisms by which RTKs are activated by extracellular ligands and of the effect of pathological mutations that do not directly reside in the catalytic sites of tyrosine kinase domains. In this review, we focus on the recent progress toward obtaining such structures and the insights already gained by structural studies of the subdomains of the receptors that belong to the epidermal growth factor receptor, insulin receptor, and platelet-derived growth factor receptor RTK families. © 2019 IUBMB Life, 71(6):706-720, 2019.
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Affiliation(s)
- Devan Diwanji
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Tarjani Thaker
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.,Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
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42
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Clarke DT, Martin-Fernandez ML. A Brief History of Single-Particle Tracking of the Epidermal Growth Factor Receptor. Methods Protoc 2019; 2:mps2010012. [PMID: 31164594 PMCID: PMC6481046 DOI: 10.3390/mps2010012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Single-particle tracking (SPT) has been used and developed over the last 25 years as a method to investigate molecular dynamics, structure, interactions, and function in the cellular context. SPT is able to show how fast and how far individual molecules move, identify different dynamic populations, measure the duration and strength of intermolecular interactions, and map out structures on the nanoscale in cells. In combination with other techniques such as macromolecular crystallography and molecular dynamics simulation, it allows us to build models of complex structures, and develop and test hypotheses of how these complexes perform their biological roles in health as well as in disease states. Here, we use the example of the epidermal growth factor receptor (EGFR), which has been studied extensively by SPT, demonstrating how the method has been used to increase our understanding of the receptor’s organization and function, including its interaction with the plasma membrane, its activation, clustering, and oligomerization, and the role of other receptors and endocytosis. The examples shown demonstrate how SPT might be employed in the investigation of other biomolecules and systems.
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Affiliation(s)
- David T Clarke
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK.
| | - Marisa L Martin-Fernandez
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK.
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43
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Cutrale F, Rodriguez D, Hortigüela V, Chiu CL, Otterstrom J, Mieruszynski S, Seriola A, Larrañaga E, Raya A, Lakadamyali M, Fraser SE, Martinez E, Ojosnegros S. Using enhanced number and brightness to measure protein oligomerization dynamics in live cells. Nat Protoc 2019; 14:616-638. [DOI: 10.1038/s41596-018-0111-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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44
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Zamai M, Trullo A, Giordano M, Corti V, Arza Cuesta E, Francavilla C, Cavallaro U, Caiolfa VR. Number and brightness analysis reveals that NCAM and FGF2 elicit different assembly and dynamics of FGFR1 in live cells. J Cell Sci 2019; 132:jcs.220624. [PMID: 30478195 DOI: 10.1242/jcs.220624] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/15/2018] [Indexed: 12/31/2022] Open
Abstract
Both fibroblast growth factor-2 (FGF2) and neural cell adhesion molecule (NCAM) trigger FGF receptor 1 (FGFR1) signaling; however, they induce remarkably distinct receptor trafficking and cellular responses. The molecular basis of such a dichotomy and the role of distinct types of ligand-receptor interaction remain elusive. Number of molecules and brightness (N&B) analysis revealed that FGF2 and NCAM promote different FGFR1 assembly and dynamics at the plasma membrane. NCAM stimulation elicits long-lasting cycles of short-lived FGFR1 monomers and multimers, a behavior that might reflect a rapid FGFR1 internalization and recycling. FGF2, instead, induces stable dimerization at the dose that stimulates cell proliferation. Reducing the occupancy of FGFR1 in response to low FGF2 doses causes a switch towards cyclically exposed and unstable receptor dimers, consistently with previously reported biphasic response to FGF2 and with the divergent signaling elicited by different ligand concentrations. Similar instability was observed upon altering the endocytic pathway. Thus, FGF2 and NCAM induce differential FGFR1 clustering at the cell surface, which might account for the distinct intracellular fate of the receptor and, hence, for the different signaling cascades and cellular responses.
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Affiliation(s)
- Moreno Zamai
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy.,Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Antonio Trullo
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy
| | - Marco Giordano
- Unit of Gynecological Oncology Research, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Valeria Corti
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy
| | - Elvira Arza Cuesta
- Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Chiara Francavilla
- Division of Molecular and Cellular Functions, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Ugo Cavallaro
- Unit of Gynecological Oncology Research, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Valeria R Caiolfa
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy .,Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
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45
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Dunsing V, Luckner M, Zühlke B, Petazzi RA, Herrmann A, Chiantia S. Optimal fluorescent protein tags for quantifying protein oligomerization in living cells. Sci Rep 2018; 8:10634. [PMID: 30006597 PMCID: PMC6045628 DOI: 10.1038/s41598-018-28858-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/02/2018] [Indexed: 11/30/2022] Open
Abstract
Fluorescence fluctuation spectroscopy has become a popular toolbox for non-disruptive analysis of molecular interactions in living cells. The quantification of protein oligomerization in the native cellular environment is highly relevant for a detailed understanding of complex biological processes. An important parameter in this context is the molecular brightness, which serves as a direct measure of oligomerization and can be easily extracted from temporal or spatial fluorescence fluctuations. However, fluorescent proteins (FPs) typically used in such studies suffer from complex photophysical transitions and limited maturation, inducing non-fluorescent states. Here, we show how these processes strongly affect molecular brightness measurements. We perform a systematic characterization of non-fluorescent states for commonly used FPs and provide a simple guideline for accurate, unbiased oligomerization measurements in living cells. Further, we focus on novel red FPs and demonstrate that mCherry2, an mCherry variant, possesses superior properties with regards to precise quantification of oligomerization.
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Affiliation(s)
- Valentin Dunsing
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Madlen Luckner
- Institute for Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Boris Zühlke
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Roberto A Petazzi
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Andreas Herrmann
- Institute for Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Salvatore Chiantia
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
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46
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Palau VE, Chakraborty K, Wann D, Lightner J, Hilton K, Brannon M, Stone W, Krishnan K. γ-Tocotrienol induces apoptosis in pancreatic cancer cells by upregulation of ceramide synthesis and modulation of sphingolipid transport. BMC Cancer 2018; 18:564. [PMID: 29769046 PMCID: PMC5956825 DOI: 10.1186/s12885-018-4462-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/30/2018] [Indexed: 11/27/2022] Open
Abstract
Background Ceramide synthesis and metabolism is a promising target in cancer drug development. γ-tocotrienol (GT3), a member of the vitamin E family, orchestrates multiple effects that ensure the induction of apoptosis in both, wild-type and RAS-mutated pancreatic cancer cells. Here, we investigated whether these effects involve changes in ceramide synthesis and transport. Methods The effects of GT3 on the synthesis of ceramide via the de novo pathway, and the hydrolysis of sphingomyelin were analyzed by the expression levels of the enzymes serine palmitoyl transferase, ceramide synthase-6, and dihydroceramide desaturase, and acid sphingomyelinase in wild-type RAS BxPC3, and RAS-mutated MIA PaCa-2 and Panc 1 pancreatic cancer cells. Quantitative changes in ceramides, dihydroceramides, and sphingomyelin at the cell membrane were detected by LCMS. Modulation of ceramide transport by GT3 was studied by immunochemistry of CERT and ARV-1, and the subsequent effects at the cell membrane was analyzed via immunofluorescence of ceramide, caveolin, and DR5. Results GT3 favors the upregulation of ceramide by stimulating synthesis at the ER and the plasma membrane. Additionally, the conversion of newly synthesized ceramide to sphingomyelin and glucosylceramide at the Golgi is prevented by the inhibition of CERT. Modulation ARV1 and previously observed inhibition of the HMG-CoA pathway, contribute to changes in membrane structure and signaling functions, allows the clustering of DR5, effectively initiating apoptosis. Conclusions Our results suggest that GT3 targets ceramide synthesis and transport, and that the upregulation of ceramide and modulation of transporters CERT and ARV1 are important contributors to the apoptotic properties demonstrated by GT3 in pancreatic cancer cells.
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Affiliation(s)
- Victoria E Palau
- Division of Hematology-Oncology, Department of Internal Medicine, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA.,Department of Pharmaceutical Sciences, Gatton College of Pharmacy, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Kanishka Chakraborty
- Division of Hematology-Oncology, Department of Internal Medicine, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Daniel Wann
- Department of Internal Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Janet Lightner
- Division of Hematology-Oncology, Department of Internal Medicine, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Keely Hilton
- Division of Hematology-Oncology, Department of Internal Medicine, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Marianne Brannon
- Department of Pediatrics, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
| | - William Stone
- Department of Pediatrics, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Koyamangalath Krishnan
- Division of Hematology-Oncology, Department of Internal Medicine, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA.
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47
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Claus J, Patel G, Autore F, Colomba A, Weitsman G, Soliman TN, Roberts S, Zanetti-Domingues LC, Hirsch M, Collu F, George R, Ortiz-Zapater E, Barber PR, Vojnovic B, Yarden Y, Martin-Fernandez ML, Cameron A, Fraternali F, Ng T, Parker PJ. Inhibitor-induced HER2-HER3 heterodimerisation promotes proliferation through a novel dimer interface. eLife 2018; 7:e32271. [PMID: 29712619 PMCID: PMC5929906 DOI: 10.7554/elife.32271] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 03/21/2018] [Indexed: 12/13/2022] Open
Abstract
While targeted therapy against HER2 is an effective first-line treatment in HER2+ breast cancer, acquired resistance remains a clinical challenge. The pseudokinase HER3, heterodimerisation partner of HER2, is widely implicated in the resistance to HER2-mediated therapy. Here, we show that lapatinib, an ATP-competitive inhibitor of HER2, is able to induce proliferation cooperatively with the HER3 ligand neuregulin. This counterintuitive synergy between inhibitor and growth factor depends on their ability to promote atypical HER2-HER3 heterodimerisation. By stabilising a particular HER2 conformer, lapatinib drives HER2-HER3 kinase domain heterocomplex formation. This dimer exists in a head-to-head orientation distinct from the canonical asymmetric active dimer. The associated clustering observed for these dimers predisposes to neuregulin responses, affording a proliferative outcome. Our findings provide mechanistic insights into the liabilities involved in targeting kinases with ATP-competitive inhibitors and highlight the complex role of protein conformation in acquired resistance.
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Affiliation(s)
- Jeroen Claus
- Protein Phosphorylation LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
| | - Gargi Patel
- Richard Dimbleby Department of Cancer Research, Randall Division and Division of Cancer StudiesKings College LondonLondonUnited Kingdom
- Sussex Cancer CentreBrighton and Sussex University HospitalsBrightonUnited States
| | - Flavia Autore
- Randall Division of Cell & Molecular BiophysicsKings College LondonLondonUnited Kingdom
| | - Audrey Colomba
- Protein Phosphorylation LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
| | - Gregory Weitsman
- Richard Dimbleby Department of Cancer Research, Randall Division and Division of Cancer StudiesKings College LondonLondonUnited Kingdom
| | - Tanya N Soliman
- Protein Phosphorylation LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
| | - Selene Roberts
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities CouncilRutherford Appleton LaboratoryDidcotUnited Kingdom
| | - Laura C Zanetti-Domingues
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities CouncilRutherford Appleton LaboratoryDidcotUnited Kingdom
| | - Michael Hirsch
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities CouncilRutherford Appleton LaboratoryDidcotUnited Kingdom
| | - Francesca Collu
- Randall Division of Cell & Molecular BiophysicsKings College LondonLondonUnited Kingdom
| | - Roger George
- The Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Elena Ortiz-Zapater
- Department of Asthma, Allergy and Respiratory ScienceKing’s College London, Guy’s HospitalLondonUnited Kingdom
| | - Paul R Barber
- Randall Division of Cell & Molecular BiophysicsKings College LondonLondonUnited Kingdom
- UCL Cancer InstituteUniversity College LondonLondonUnited Kingdom
| | - Boris Vojnovic
- Randall Division of Cell & Molecular BiophysicsKings College LondonLondonUnited Kingdom
- Department of OncologyCancer Research UK and Medical Research Council Oxford Institute for Radiation OncologyOxfordUnited Kingdom
| | - Yosef Yarden
- Department of Biological RegulationWeizmann Institute of ScienceRehovotIsrael
| | - Marisa L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities CouncilRutherford Appleton LaboratoryDidcotUnited Kingdom
| | - Angus Cameron
- Protein Phosphorylation LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
- Barts Cancer InstituteQueen Mary University of LondonLondonUnited Kingdom
| | - Franca Fraternali
- Randall Division of Cell & Molecular BiophysicsKings College LondonLondonUnited Kingdom
| | - Tony Ng
- Richard Dimbleby Department of Cancer Research, Randall Division and Division of Cancer StudiesKings College LondonLondonUnited Kingdom
- UCL Cancer InstituteUniversity College LondonLondonUnited Kingdom
- Breast Cancer Now Research Unit, Department of Research OncologyGuy’s Hospital King’s College London School of MedicineLondonUnited Kingdom
| | - Peter J Parker
- Protein Phosphorylation LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
- School of Cancer and Pharmaceutical SciencesKing’s College London, Guy’s CampusLondonUnited Kingdom
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48
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Fukushima R, Yamamoto J, Ishikawa H, Kinjo M. Two-detector number and brightness analysis reveals spatio-temporal oligomerization of proteins in living cells. Methods 2018; 140-141:161-171. [PMID: 29572069 DOI: 10.1016/j.ymeth.2018.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/06/2018] [Accepted: 03/16/2018] [Indexed: 01/10/2023] Open
Abstract
Number and brightness analysis (N&B) is a useful tool for the simultaneous visualization of protein oligomers and their localization, with single-molecule sensitivity. N&B determines particle brightness (fluorescence intensity per particle) and maps the spatial distribution of fluorescently labeled proteins by performing statistical analyses of the image series obtained using laser scanning microscopy. The brightness map reveals presence of the oligomers of the targeted protein and their distribution in living cells. However, even when corrections are applied, conventional N&B is affected by afterpulsing, shot noise, thermal noise, dead time, and overestimation of particle brightness when the concentration of the fluorescent particles changes during measurement. The drawbacks of conventional N&B can be circumvented by using two detectors, a novel approach that we henceforth call two-detector number and brightness analysis (TD-N&B), and introducing a linear regression of fluorescence intensity. This statistically eliminates the effect of noise from the detectors, and ensures that the correct particle brightness is obtained. Our method was theoretically assessed by numerical simulations and experimentally validated using a dilution series of purified enhanced green fluorescent protein (EGFP), EGFP tandem oligomers in cell lysate, and EGFP tandem oligomers in living cells. Furthermore, this method was used to characterize the complex process of ligand-induced glucocorticoid receptor dimerization and their translocation to the cell nucleus in live cells. Our method can be applied to other oligomer-forming proteins in cell signaling, or to aggregations of proteins such as those that cause neurodegenerative diseases.
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Affiliation(s)
- Ryosuke Fukushima
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Johtaro Yamamoto
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Hideto Ishikawa
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
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49
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Papini C, Royer CA. Scanning number and brightness yields absolute protein concentrations in live cells: a crucial parameter controlling functional bio-molecular interaction networks. Biophys Rev 2018; 10:87-96. [PMID: 29383593 DOI: 10.1007/s12551-017-0394-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/29/2017] [Indexed: 12/27/2022] Open
Abstract
Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation. Clearly, a mechanistic understanding of any given high level biological function requires a quantitative characterization of the principal bio-molecular interactions involved and how these may change dynamically. Such information can be obtained using fluctation analysis, in particular scanning number and brightness, and used to build and test mechanistic models of the functional network to define which characteristics are the most important for its regulation.
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Affiliation(s)
- Christina Papini
- Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Catherine A Royer
- Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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50
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Pawar AB, Sengupta D. Effect of Membrane Composition on Receptor Association: Implications of Cancer Lipidomics on ErbB Receptors. J Membr Biol 2018; 251:359-368. [DOI: 10.1007/s00232-018-0015-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
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