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Liu J, Li Y, Chen T, Zhang F, Xu F. Machine Learning for Single-Molecule Localization Microscopy: From Data Analysis to Quantification. Anal Chem 2024; 96:11103-11114. [PMID: 38946062 DOI: 10.1021/acs.analchem.3c05857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Single-molecule localization microscopy (SMLM) is a versatile tool for realizing nanoscale imaging with visible light and providing unprecedented opportunities to observe bioprocesses. The integration of machine learning with SMLM enhances data analysis by improving efficiency and accuracy. This tutorial aims to provide a comprehensive overview of the data analysis process and theoretical aspects of SMLM, while also highlighting the typical applications of machine learning in this field. By leveraging advanced analytical techniques, SMLM is becoming a powerful quantitative analysis tool for biological research.
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Affiliation(s)
- Jianli Liu
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Yumian Li
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Tailong Chen
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Fa Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Fan Xu
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
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2
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Adler J, Bernhem K, Parmryd I. Membrane topography and the overestimation of protein clustering in single molecule localisation microscopy - identification and correction. Commun Biol 2024; 7:791. [PMID: 38951588 PMCID: PMC11217499 DOI: 10.1038/s42003-024-06472-3] [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: 01/16/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
According to single-molecule localisation microscopy almost all plasma membrane proteins are clustered. We demonstrate that clusters can arise from variations in membrane topography where the local density of a randomly distributed membrane molecule to a degree matches the variations in the local amount of membrane. Further, we demonstrate that this false clustering can be differentiated from genuine clustering by using a membrane marker to report on local variations in the amount of membrane. In dual colour live cell single molecule localisation microscopy using the membrane probe DiI alongside either the transferrin receptor or the GPI-anchored protein CD59, we found that pair correlation analysis reported both proteins and DiI as being clustered, as did its derivative pair correlation-photoactivation localisation microscopy and nearest neighbour analyses. After converting the localisations into images and using the DiI image to factor out topography variations, no CD59 clusters were visible, suggesting that the clustering reported by the other methods is an artefact. However, the TfR clusters persisted after topography variations were factored out. We demonstrate that membrane topography variations can make membrane molecules appear clustered and present a straightforward remedy suitable as the first step in the cluster analysis pipeline.
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Affiliation(s)
- Jeremy Adler
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kristoffer Bernhem
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Ingela Parmryd
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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3
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Chen H, Yan G, Wen MH, Brooks KN, Zhang Y, Huang PS, Chen TY. Advancements and Practical Considerations for Biophysical Research: Navigating the Challenges and Future of Super-resolution Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:331-344. [PMID: 38817319 PMCID: PMC11134610 DOI: 10.1021/cbmi.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 06/01/2024]
Abstract
The introduction of super-resolution microscopy (SRM) has significantly advanced our understanding of cellular and molecular dynamics, offering a detailed view previously beyond our reach. Implementing SRM in biophysical research, however, presents numerous challenges. This review addresses the crucial aspects of utilizing SRM effectively, from selecting appropriate fluorophores and preparing samples to analyzing complex data sets. We explore recent technological advancements and methodological improvements that enhance the capabilities of SRM. Emphasizing the integration of SRM with other analytical methods, we aim to overcome inherent limitations and expand the scope of biological insights achievable. By providing a comprehensive guide for choosing the most suitable SRM methods based on specific research objectives, we aim to empower researchers to explore complex biological processes with enhanced precision and clarity, thereby advancing the frontiers of biophysical research.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Guangjie Yan
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Meng-Hsuan Wen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Kameron N. Brooks
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Yuteng Zhang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Pei-San Huang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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4
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Lebreton S, Paladino S, Lelek M, Tramier M, Zimmer C, Zurzolo C. Actin cytoskeleton differently regulates cell surface organization of GPI-anchored proteins in polarized epithelial cells and fibroblasts. Front Mol Biosci 2024; 11:1360142. [PMID: 38774234 PMCID: PMC11106487 DOI: 10.3389/fmolb.2024.1360142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/11/2024] [Indexed: 05/24/2024] Open
Abstract
The spatiotemporal compartmentalization of membrane-associated glycosylphosphatidylinositol-anchored proteins (GPI-APs) on the cell surface regulates their biological activities. These GPI-APs occupy distinct cellular functions such as enzymes, receptors, and adhesion molecules, and they are implicated in several vital cellular processes. Thus, unraveling the mechanisms and regulators of their membrane organization is essential. In polarized epithelial cells, GPI-APs are enriched at the apical surface, where they form small cholesterol-independent homoclusters and larger heteroclusters accommodating multiple GPI-AP species, all confined within areas of approximately 65-70 nm in diameter. Notably, GPI-AP homoclustering occurs in the Golgi apparatus through a cholesterol- and calcium-dependent mechanism that drives their apical sorting. Despite the critical role of Golgi GPI-AP clustering in their cell surface organization and the importance of cholesterol in heterocluster formation, the regulatory mechanisms governing GPI-AP surface organization, particularly in the context of epithelial polarity, remain elusive. Given that the actin cytoskeleton undergoes substantial remodeling during polarity establishment, this study explores whether the actin cytoskeleton regulates the spatiotemporal apical organization of GPI-APs in MDCK cells. Utilizing various imaging techniques (number and brightness, FRET/FLIM, and dSTORM coupled to pair correlation analysis), we demonstrate that the apical organization of GPI-APs, at different scales, does not rely on the actin cytoskeleton, unlike in fibroblastic cells. Interestingly, calcium chelation disrupts the organization of GPI-APs at the apical surface by impairing Golgi GPI-AP clustering, emphasizing the existence of an interplay among Golgi clustering, apical sorting, and surface organization in epithelial cells. In summary, our findings unveil distinct mechanisms regulating the organization of GPI-APs in cell types of different origins, plausibly allowing them to adapt to different external signals and different cellular environments in order to achieve specialized functions.
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Affiliation(s)
- Stéphanie Lebreton
- Institut Pasteur, Unité de Trafic Membranaire et Pathogenèse, Paris, France
| | - Simona Paladino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational Biology, Institut Pasteur, Paris, France
| | - Marc Tramier
- Université Rennes, Centre National de la recherche scientifique, IGDR (Genetics and Development Institute of Rennes), Unité mixte de receherche 6290, Rennes, France
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational Biology, Institut Pasteur, Paris, France
- Rudolf Virchow Center, University of Würzburg, Würzburg, Germany
| | - Chiara Zurzolo
- Institut Pasteur, Unité de Trafic Membranaire et Pathogenèse, Paris, France
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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5
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Lin X, Gupta D, Vaitsiankova A, Bhandari SK, Leung KSK, Menolfi D, Lee BJ, Russell HR, Gershik S, Gu W, McKinnon PJ, Dantzer F, Rothenberg E, Tomkinson AE, Zha S. Inactive Parp2 causes Tp53-dependent lethal anemia by blocking replication-associated nick ligation in erythroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584665. [PMID: 38559022 PMCID: PMC10980059 DOI: 10.1101/2024.03.12.584665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
PARP1&2 enzymatic inhibitors (PARPi) are promising cancer treatments. But recently, their use has been hindered by unexplained severe anemia and treatment-related leukemia. In addition to enzymatic inhibition, PARPi also trap PARP1&2 at DNA lesions. Here, we report that unlike Parp2 -/- mice, which develop normally, mice expressing catalytically-inactive Parp2 (E534A, Parp2 EA/EA ) succumb to Tp53- and Chk2 -dependent erythropoietic failure in utero , mirroring Lig1 -/- mice. While DNA damage mainly activates PARP1, we demonstrate that DNA replication activates PARP2 robustly. PARP2 is selectively recruited and activated by 5'-phosphorylated nicks (5'p-nicks) between Okazaki fragments, typically resolved by Lig1. Inactive PARP2, but not its active form or absence, impedes Lig1- and Lig3-mediated ligation, causing dose-dependent replication fork collapse, particularly harmful to erythroblasts with ultra-fast forks. This PARylation-dependent structural function of PARP2 at 5'p-nicks explains the detrimental effects of PARP2 inhibition on erythropoiesis, revealing the mechanism behind the PARPi-induced anemia and leukemia, especially those with TP53/CHK2 loss. Significance This work shows that the hematological toxicities associated with PARP inhibitors stem not from impaired PARP1 or PARP2 enzymatic activity but rather from the presence of inactive PARP2 protein. Mechanistically, these toxicities reflect a unique role of PARP2 at 5'-phosphorylated DNA nicks during DNA replication in erythroblasts.
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6
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Zhu X, Chen Q, Zhao H, Yang Q, Goudappagouda, Gelléri M, Ritz S, Ng D, Koynov K, Parekh SH, Chetty VK, Thakur BK, Cremer C, Landfester K, Müllen K, Terenzio M, Bonn M, Narita A, Liu X. Intrinsic Burst-Blinking Nanographenes for Super-Resolution Bioimaging. J Am Chem Soc 2024; 146:5195-5203. [PMID: 38275287 PMCID: PMC10910517 DOI: 10.1021/jacs.3c11152] [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: 10/09/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
Single-molecule localization microscopy (SMLM) is a powerful technique to achieve super-resolution imaging beyond the diffraction limit. Although various types of blinking fluorophores are currently considered for SMLM, intrinsic blinking fluorophores remain rare at the single-molecule level. Here, we report the synthesis of nanographene-based intrinsic burst-blinking fluorophores for highly versatile SMLM. We image amyloid fibrils in air and in various pH solutions without any additive and lysosome dynamics in live mammalian cells under physiological conditions. In addition, the single-molecule labeling of nascent proteins in primary sensory neurons was achieved with azide-functionalized nanographenes via click chemistry. SMLM imaging reveals higher local translation at axonal branching with unprecedented detail, while the size of translation foci remained similar throughout the entire network. These various results demonstrate the potential of nanographene-based fluorophores to drastically expand the applicability of super-resolution imaging.
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Affiliation(s)
- Xingfu Zhu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Qiang Chen
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Hao Zhao
- Organic
and Carbon Nanomaterials Unit, Okinawa Institute
of Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Qiqi Yang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Goudappagouda
- Organic
and Carbon Nanomaterials Unit, Okinawa Institute
of Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Márton Gelléri
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Sandra Ritz
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| | - David Ng
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kaloian Koynov
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | | | - Basant Kumar Thakur
- Department
of Pediatrics III, University Hospital Essen, 45147 Essen, Germany
| | - Christoph Cremer
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Katharina Landfester
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Klaus Müllen
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Marco Terenzio
- Molecular
Neuroscience Unit, Okinawa Institute of
Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Akimitsu Narita
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Organic
and Carbon Nanomaterials Unit, Okinawa Institute
of Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Xiaomin Liu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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7
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Ying Y, Yang Y, Chen AK. Roles of RNA scaffolding in nanoscale Gag multimerization and selective protein sorting at HIV membranes. SCIENCE ADVANCES 2024; 10:eadk8297. [PMID: 38394201 PMCID: PMC10889351 DOI: 10.1126/sciadv.adk8297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/19/2024] [Indexed: 02/25/2024]
Abstract
HIV-1 Gag proteins can multimerize upon the viral genomic RNA or multiple random cellular messenger RNAs to form a virus particle or a virus-like particle, respectively. To date, whether the two types of particles form via the same Gag multimerization process has remained unclarified. Using photoactivated localization microscopy to illuminate Gag organizations and dynamics at the nanoscale, here, we showed that genomic RNA mediates Gag multimerization in a more cluster-centric, cooperative, and spatiotemporally coordinated fashion, with the ability to drive dense Gag clustering dependent on its ability to act as a long-stranded scaffold not easily attainable by cellular messenger RNAs. These differences in Gag multimerization were further shown to affect downstream selective protein sorting into HIV membranes, indicating that the choice of RNA for packaging can modulate viral membrane compositions. These findings should advance the understanding of HIV assembly and further benefit the development of virus-like particle-based therapeutics.
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Affiliation(s)
- Yachen Ying
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
- National Biomedical Imaging Center, Peking University, Beijing 100871, China
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8
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Obara CJ, Nixon-Abell J, Moore AS, Riccio F, Hoffman DP, Shtengel G, Xu CS, Schaefer K, Pasolli HA, Masson JB, Hess HF, Calderon CP, Blackstone C, Lippincott-Schwartz J. Motion of VAPB molecules reveals ER-mitochondria contact site subdomains. Nature 2024; 626:169-176. [PMID: 38267577 PMCID: PMC10830423 DOI: 10.1038/s41586-023-06956-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/08/2023] [Indexed: 01/26/2024]
Abstract
To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites1,2. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signalling molecules, lipids and metabolites3,4. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle5,6. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation7,8, a clear understanding of their nanoscale organization and regulation is still lacking. Here we combine three-dimensional electron microscopy with high-speed molecular tracking of a model organelle tether, Vesicle-associated membrane protein (VAMP)-associated protein B (VAPB), to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodelling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis-associated mutation in VAPB perturbs these subdomains, likely impairing their remodelling capacity and resulting in impaired interorganelle communication. These results establish high-speed single-molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.
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Affiliation(s)
| | - Jonathon Nixon-Abell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
- Cambridge Institute for Medical Research (CIMR), Cambridge, UK
| | - Andrew S Moore
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Federica Riccio
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
- Centre for Gene Therapy & Regenerative Medicine, King's College London, London, UK
| | - David P Hoffman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- 10x Genomics, Pleasanton, CA, USA
| | - Gleb Shtengel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Kathy Schaefer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - H Amalia Pasolli
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jean-Baptiste Masson
- Decision and Bayesian Computation, Neuroscience, & Computational Biology Departments, CNRS UMR 3751, Institut Pasteur, Université de Paris, Paris, France
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Christopher P Calderon
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
- Ursa Analytics, Inc., Denver, CO, USA
| | - Craig Blackstone
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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9
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Mukund K, Alva-Ornelas JA, Maddox AL, Murali D, Veraksa D, Saftics A, Tomsic J, Frankhouser D, Razo M, Jovanovic-Talisman T, Seewaldt VL, Subramaniam S. Molecular Atlas of HER2+ Breast Cancer Cells Treated with Endogenous Ligands: Temporal Insights into Mechanisms of Trastuzumab Resistance. Cancers (Basel) 2024; 16:553. [PMID: 38339304 PMCID: PMC10854992 DOI: 10.3390/cancers16030553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Trastuzumab therapy in HER2+ breast cancer patients has mixed success owing to acquired resistance to therapy. A detailed understanding of downstream molecular cascades resulting from trastuzumab resistance is yet to emerge. In this study, we investigate the cellular mechanisms underlying acquired resistance using trastuzumab-sensitive and -resistant cancer cells (BT474 and BT474R) treated with endogenous ligands EGF and HRG across time. We probe early receptor organization through microscopy and signaling events through multiomics measurements and assess the bioenergetic state through mitochondrial measurements. Integrative analyses of our measurements reveal significant alterations in EGF-treated BT474 HER2 membrane dynamics and robust downstream activation of PI3K/AKT/mTORC1 signaling. EGF-treated BT474R shows a sustained interferon-independent activation of the IRF1/STAT1 cascade, potentially contributing to trastuzumab resistance. Both cell lines exhibit temporally divergent metabolic demands and HIF1A-mediated stress responses. BT474R demonstrates inherently increased mitochondrial activity. HRG treatment in BT474R leads to a pronounced reduction in AR expression, affecting downstream lipid metabolism with implications for treatment response. Our results provide novel insights into mechanistic changes underlying ligand treatment in BT474 and BT474R and emphasize the pivotal role of endogenous ligands. These results can serve as a framework for furthering the understanding of trastuzumab resistance, with therapeutic implications for women with acquired resistance.
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Affiliation(s)
- Kavitha Mukund
- Department of Bioengineering, UC San Diego, Gilman Drive, La Jolla, CA 92093, USA; (K.M.); (D.M.); (D.V.)
| | - Jackelyn A. Alva-Ornelas
- City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, USA; (J.A.A.-O.); (J.T.); (D.F.); (M.R.)
| | - Adam L. Maddox
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA; (A.L.M.); (A.S.); (T.J.-T.)
| | - Divya Murali
- Department of Bioengineering, UC San Diego, Gilman Drive, La Jolla, CA 92093, USA; (K.M.); (D.M.); (D.V.)
| | - Darya Veraksa
- Department of Bioengineering, UC San Diego, Gilman Drive, La Jolla, CA 92093, USA; (K.M.); (D.M.); (D.V.)
| | - Andras Saftics
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA; (A.L.M.); (A.S.); (T.J.-T.)
| | - Jerneja Tomsic
- City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, USA; (J.A.A.-O.); (J.T.); (D.F.); (M.R.)
| | - David Frankhouser
- City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, USA; (J.A.A.-O.); (J.T.); (D.F.); (M.R.)
| | - Meagan Razo
- City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, USA; (J.A.A.-O.); (J.T.); (D.F.); (M.R.)
| | - Tijana Jovanovic-Talisman
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA; (A.L.M.); (A.S.); (T.J.-T.)
| | - Victoria L. Seewaldt
- City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, USA; (J.A.A.-O.); (J.T.); (D.F.); (M.R.)
| | - Shankar Subramaniam
- Department of Bioengineering, UC San Diego, Gilman Drive, La Jolla, CA 92093, USA; (K.M.); (D.M.); (D.V.)
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10
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Shimokawa N, Takagi M. Biomimetic Lipid Raft: Domain Stability and Interaction with Physiologically Active Molecules. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1461:15-32. [PMID: 39289271 DOI: 10.1007/978-981-97-4584-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
The cell membrane, also called the plasma membrane, is the membrane on the cytoplasmic surface that separates the extracellular from the intracellular. It is thin, about 10 nm thick when viewed with an electron microscope, and is composed of two monolayers of phospholipid membranes (lipid bilayers) containing many types of proteins. It is now known that this cell membrane not only separates the extracellular from the intracellular, but is also involved in sensory stimuli such as pain, itching, sedation, and excitement. Since the "Fluid mosaic model" was proposed for cell membranes, molecules have been thought to be homogeneously distributed on the membrane surface. Later, at the end of the twentieth century, the existence of "Phase-separated microdomain structures" consisting of ordered phases rich in saturated lipids and cholesterol was suggested, and these were termed "Lipid rafts." A model in which lipid rafts regulate cell signaling has been proposed and is the subject of active research.This chapter first outlines the physicochemical properties and thermodynamic models of membrane phase separation (lipid rafts), which play an important role in cell signaling. Next, how physiologically active molecules such as local anesthetics, cooling agents (menthol), and warming agents (capsaicin) interact with artificial cell membranes will be presented.It is undeniable that the plasma membrane contains many channels and receptors that are involved in the propagation of sensory stimuli. At the same time, however, it is important to understand that the membrane exerts a significant influence on the intensity and propagation of these stimuli.
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Affiliation(s)
- Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan
| | - Masahiro Takagi
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan.
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11
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Li R, Zhao R, Yang M, Zhang X, Lin J. Membrane microdomains: Structural and signaling platforms for establishing membrane polarity. PLANT PHYSIOLOGY 2023; 193:2260-2277. [PMID: 37549378 DOI: 10.1093/plphys/kiad444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/16/2023] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
Abstract
Cell polarity results from the asymmetric distribution of cellular structures, molecules, and functions. Polarity is a fundamental cellular trait that can determine the orientation of cell division, the formation of particular cell shapes, and ultimately the development of a multicellular body. To maintain the distinct asymmetric distribution of proteins and lipids in cellular membranes, plant cells have developed complex trafficking and regulatory mechanisms. Major advances have been made in our understanding of how membrane microdomains influence the asymmetric distribution of proteins and lipids. In this review, we first give an overview of cell polarity. Next, we discuss current knowledge concerning membrane microdomains and their roles as structural and signaling platforms to establish and maintain membrane polarity, with a special focus on the asymmetric distribution of proteins and lipids, and advanced microscopy techniques to observe and characterize membrane microdomains. Finally, we review recent advances regarding membrane trafficking in cell polarity establishment and how the balance between exocytosis and endocytosis affects membrane polarity.
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Affiliation(s)
- Ruili Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Ran Zhao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Mei Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Xi Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Jinxing Lin
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
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12
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Platzer R, Hellmeier J, Göhring J, Perez ID, Schatzlmaier P, Bodner C, Focke‐Tejkl M, Schütz GJ, Sevcsik E, Stockinger H, Brameshuber M, Huppa JB. Monomeric agonist peptide/MHCII complexes activate T-cells in an autonomous fashion. EMBO Rep 2023; 24:e57842. [PMID: 37768718 PMCID: PMC10626418 DOI: 10.15252/embr.202357842] [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: 07/19/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Molecular crowding of agonist peptide/MHC class II complexes (pMHCIIs) with structurally similar, yet per se non-stimulatory endogenous pMHCIIs is postulated to sensitize T-cells for the recognition of single antigens on the surface of dendritic cells and B-cells. When testing this premise with the use of advanced live cell microscopy, we observe pMHCIIs as monomeric, randomly distributed entities diffusing rapidly after entering the APC surface. Synaptic TCR engagement of highly abundant endogenous pMHCIIs is low or non-existent and affects neither TCR engagement of rare agonist pMHCII in early and advanced synapses nor agonist-induced TCR-proximal signaling. Our findings highlight the capacity of single freely diffusing agonist pMHCIIs to elicit the full T-cell response in an autonomous and peptide-specific fashion with consequences for adaptive immunity and immunotherapeutic approaches.
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Affiliation(s)
- René Platzer
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Joschka Hellmeier
- TU Wien, Institute of Applied PhysicsViennaAustria
- Present address:
Max Planck Institute of Biochemistry, Molecular Imaging and BionanotechnologyMartinsriedGermany
| | - Janett Göhring
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Iago Doel Perez
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
- Present address:
Takeda Manufacturing Austria AGViennaAustria
| | - Philipp Schatzlmaier
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Clara Bodner
- TU Wien, Institute of Applied PhysicsViennaAustria
| | - Margarete Focke‐Tejkl
- Center for Pathophysiology, Infectiology, Immunology, Institute for Pathophysiology and Allergy ResearchMedical University of ViennaViennaAustria
| | | | - Eva Sevcsik
- TU Wien, Institute of Applied PhysicsViennaAustria
| | - Hannes Stockinger
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | | | - Johannes B Huppa
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
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13
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Stroik S, Carvajal-Garcia J, Gupta D, Edwards A, Luthman A, Wyatt DW, Dannenberg RL, Feng W, Kunkel TA, Gupta GP, Hedglin M, Wood R, Doublié S, Rothenberg E, Ramsden DA. Stepwise requirements for polymerases δ and θ in theta-mediated end joining. Nature 2023; 623:836-841. [PMID: 37968395 PMCID: PMC10959172 DOI: 10.1038/s41586-023-06729-7] [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: 09/12/2022] [Accepted: 10/06/2023] [Indexed: 11/17/2023]
Abstract
Timely repair of chromosomal double-strand breaks is required for genome integrity and cellular viability. The polymerase theta-mediated end joining pathway has an important role in resolving these breaks and is essential in cancers defective in other DNA repair pathways, thus making it an emerging therapeutic target1. It requires annealing of 2-6 nucleotides of complementary sequence, microhomologies, that are adjacent to the broken ends, followed by initiation of end-bridging DNA synthesis by polymerase θ. However, the other pathway steps remain inadequately defined, and the enzymes required for them are unknown. Here we demonstrate requirements for exonucleolytic digestion of unpaired 3' tails before polymerase θ can initiate synthesis, then a switch to a more accurate, processive and strand-displacing polymerase to complete repair. We show the replicative polymerase, polymerase δ, is required for both steps; its 3' to 5' exonuclease activity for flap trimming, then its polymerase activity for extension and completion of repair. The enzymatic steps that are essential and specific to this pathway are mediated by two separate, sequential engagements of the two polymerases. The requisite coupling of these steps together is likely to be facilitated by physical association of the two polymerases. This pairing of polymerase δ with a polymerase capable of end-bridging synthesis, polymerase θ, may help to explain why the normally high-fidelity polymerase δ participates in genome destabilizing processes such as mitotic DNA synthesis2 and microhomology-mediated break-induced replication3.
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Affiliation(s)
- Susanna Stroik
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Alyssa Edwards
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam Luthman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David W Wyatt
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Wanjuan Feng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Richard Wood
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center and The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Dale A Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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14
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Park J, Ahn Y, Lee WJ, Jin S, Jeong S, Kim J, Lee YS, Lee JC, Seo D. Analysis of Phase Heterogeneity in Lipid Membranes Using Single-Molecule Tracking in Live Cells. Anal Chem 2023; 95:15924-15932. [PMID: 37774148 DOI: 10.1021/acs.analchem.3c02655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
In live cells, the plasma membrane is composed of lipid domains separated by hundreds of nanometers in dynamic equilibrium. Lipid phase separation regulates the trafficking and spatiotemporal organization of membrane molecules that promote signal transduction. However, visualizing domains with adequate spatiotemporal accuracy remains challenging because of their subdiffraction limit size and highly dynamic properties. Here, we present a single lipid-molecular motion analysis pipeline (lipid-MAP) for analyzing the phase heterogeneity of lipid membranes by detecting the instantaneous velocity change of a single lipid molecule using the excellent optical properties of nanoparticles, high spatial localization accuracy of single-molecule localization microscopy, and separation capability of the diffusion state of the hidden Markov model algorithm. Using lipid-MAP, individual lipid molecules were found to be in dynamic equilibrium between two statistically distinguishable phases, leading to the formation of small (∼170 nm), viscous (2.5× more viscous than surrounding areas), and transient domains in live cells. Moreover, our findings provide an understanding of how membrane compositional changes, i.e., cholesterol and phospholipids, affect domain formation. This imaging method can contribute to an improved understanding of spatiotemporal-controlled membrane dynamics at the molecular level.
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Affiliation(s)
- Jiseong Park
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Yongdeok Ahn
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Wonhee John Lee
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Siwoo Jin
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Sejoo Jeong
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Jaeyong Kim
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Young-Sam Lee
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Jong-Chan Lee
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Daeha Seo
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
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15
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Mayor S, Bhat A, Kusumi A. A Survey of Models of Cell Membranes: Toward a New Understanding of Membrane Organization. Cold Spring Harb Perspect Biol 2023; 15:a041394. [PMID: 37643877 PMCID: PMC10547391 DOI: 10.1101/cshperspect.a041394] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The cell membrane, the boundary that separates living cells from their environment, has been the subject of study for over a century. The fluid-mosaic model of Singer and Nicolson in 1972 proposed the plasma membrane as a two-dimensional fluid composed of lipids and proteins. Fifty years hence, advances in biophysical and biochemical tools, particularly optical imaging techniques, have allowed for a better understanding of the physical nature, organization, and composition of cell membranes. This has been made possible by visualizing membrane heterogeneities and their dynamics and appreciating the asymmetrical arrangement of lipids in living cell membranes. Despite these advances, mechanisms underlying the local spatiotemporal organization of membrane components remain unclear. This review surveys various models of membrane organization, culminating in a new model that incorporates nonequilibrium processes and forces exerted by interactions with extramembrane elements such as the actin cytoskeleton. The proposed model provides a comprehensive understanding of membrane organization, taking into account the dynamic nature of the cell membrane and its interactions with its immediate environment.
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Affiliation(s)
- Satyajit Mayor
- National Centre for Biological Science, TIFR, Bangalore 560065, India
| | - Abrar Bhat
- National Centre for Biological Science, TIFR, Bangalore 560065, India
| | - Akihiro Kusumi
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
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16
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Banerjee C, Mehra D, Song D, Mancebo A, Park JM, Kim DH, Puchner EM. ULK1 forms distinct oligomeric states and nanoscopic structures during autophagy initiation. SCIENCE ADVANCES 2023; 9:eadh4094. [PMID: 37774021 PMCID: PMC10541014 DOI: 10.1126/sciadv.adh4094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Autophagy induction involves extensive molecular and membrane reorganization. Despite substantial progress, the mechanism underlying autophagy initiation remains poorly understood. Here, we used quantitative photoactivated localization microscopy with single-molecule sensitivity to analyze the nanoscopic distribution of endogenous ULK1, the kinase that triggers autophagy. Under amino acid starvation, ULK1 formed large clusters containing up to 161 molecules at the endoplasmic reticulum. Cross-correlation analysis revealed that ULK1 clusters engaging in autophagosome formation require 30 or more molecules. The ULK1 structures with more than the threshold number contained varying levels of Atg13, Atg14, Atg16, LC3B, GEC1, and WIPI2. We found that ULK1 activity is dispensable for the initial clustering of ULK1, but necessary for the subsequent expansion of the clusters, which involves interaction with Atg14, Atg16, and LC3B and relies on Vps34 activity. This quantitative analysis at the single-molecule level has provided unprecedented insights into the behavior of ULK1 during autophagy initiation.
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Affiliation(s)
- Chiranjib Banerjee
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Dushyant Mehra
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
- Department of Biomedical Engineering and Physiology, Mayo Clinic, Rochester, MN, USA
| | - Daihyun Song
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Angel Mancebo
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Ji-Man Park
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Do-Hyung Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Elias M. Puchner
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
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17
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Barr VA, Piao J, Balagopalan L, McIntire KM, Schoenberg FP, Samelson LE. Heterogeneity of Signaling Complex Nanostructure in T Cells Activated Via the T Cell Antigen Receptor. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1503-1522. [PMID: 37488826 PMCID: PMC11230849 DOI: 10.1093/micmic/ozad072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/08/2023] [Accepted: 06/18/2023] [Indexed: 07/26/2023]
Abstract
Activation of the T cell antigen receptor (TCR) is a key step in initiating the adaptive immune response. Single-molecule localization techniques have been used to investigate the arrangement of proteins within the signaling complexes formed around activated TCRs, but a clear picture of nanoscale organization in stimulated T cells has not emerged. Here, we have improved the examination of T cell nanostructure by visualizing individual molecules of six different proteins in a single sample of activated Jurkat T cells using the multiplexed antibody-size limited direct stochastic optical reconstruction microscopy (madSTORM) technique. We formally define irregularly shaped regions of interest, compare areas where signaling complexes are concentrated with other areas, and improve the statistical analyses of the locations of molecules. We show that nanoscale organization of proteins is mainly confined to the areas with dense concentrations of TCR-based signaling complexes. However, randomly distributed molecules are also found in some areas containing concentrated signaling complexes. These results are consistent with the view that the proteins within signaling complexes are connected by numerous weak interactions, leading to flexible, dynamic, and mutable structures which produce large variations in the nanostructure found in activated T cells.
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Affiliation(s)
- Valarie A Barr
- Laboratory of Cellular & Molecular Biology, Building 37 Room 2066, 37 Convent Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892-4256, USA
| | - Juan Piao
- Department of Statistics, University of California at Los Angeles, 8965 Math Sciences Building, Los Angeles, CA 90095-1554, USA
| | - Lakshmi Balagopalan
- Laboratory of Cellular & Molecular Biology, Building 37 Room 2066, 37 Convent Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892-4256, USA
| | - Katherine M McIntire
- Laboratory of Cellular & Molecular Biology, Building 37 Room 2066, 37 Convent Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892-4256, USA
| | - Frederic P Schoenberg
- Department of Statistics, University of California at Los Angeles, 8965 Math Sciences Building, Los Angeles, CA 90095-1554, USA
| | - Lawrence E Samelson
- Laboratory of Cellular & Molecular Biology, Building 37 Room 2066, 37 Convent Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892-4256, USA
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18
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Tan HL, Bungert-Plümke S, Kortzak D, Fahlke C, Stölting G. Dual-color Colocalization in Single-molecule Localization Microscopy to Determine the Oligomeric State of Proteins in the Plasma Membrane. Bio Protoc 2023; 13:e4749. [PMID: 37456335 PMCID: PMC10339340 DOI: 10.21769/bioprotoc.4749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/15/2023] [Accepted: 05/21/2023] [Indexed: 07/18/2023] Open
Abstract
Determining the oligomeric state of membrane proteins is critical for understanding their function. However, traditional ex situ methods like clear native gel electrophoresis can disrupt protein subunit interactions during sample preparation. In situ methods such as stepwise photobleaching have limitations due to high expression levels and limitations of optical resolution in microscopy. Super-resolution microscopy techniques such as single-molecule localization microscopy (SMLM) have the potential to overcome these limitations, but the stochastic nature of signals can lead to miscounting due to over-expression, background noise, and temporal separation of signals. Additionally, this technique has limited application due to the limited selection of fluorescent labels and the demanding control of laser power. To address these issues, we developed a dual color colocalization (DCC) strategy that offers higher tolerance to background noise and simplifies data acquisition and processing for high-throughput and reliable counting. The DCC strategy was used to determine the oligomeric states of membrane proteins of the SLC17 and SLC26 family with SMLM, providing a robust and efficient method for studying protein interactions.
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Affiliation(s)
- Hua Leonhard Tan
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Stefanie Bungert-Plümke
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Daniel Kortzak
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Christoph Fahlke
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Gabriel Stölting
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Center of Functional Genomics, Hypertension and Molecular Biology of Endocrine Tumors, Berlin, Germany
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19
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Müller GA, Müller TD. (Patho)Physiology of Glycosylphosphatidylinositol-Anchored Proteins I: Localization at Plasma Membranes and Extracellular Compartments. Biomolecules 2023; 13:biom13050855. [PMID: 37238725 DOI: 10.3390/biom13050855] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
Glycosylphosphatidylinositol (GPI)-anchored proteins (APs) are anchored at the outer leaflet of plasma membranes (PMs) of all eukaryotic organisms studied so far by covalent linkage to a highly conserved glycolipid rather than a transmembrane domain. Since their first description, experimental data have been accumulating for the capability of GPI-APs to be released from PMs into the surrounding milieu. It became evident that this release results in distinct arrangements of GPI-APs which are compatible with the aqueous milieu upon loss of their GPI anchor by (proteolytic or lipolytic) cleavage or in the course of shielding of the full-length GPI anchor by incorporation into extracellular vesicles, lipoprotein-like particles and (lyso)phospholipid- and cholesterol-harboring micelle-like complexes or by association with GPI-binding proteins or/and other full-length GPI-APs. In mammalian organisms, the (patho)physiological roles of the released GPI-APs in the extracellular environment, such as blood and tissue cells, depend on the molecular mechanisms of their release as well as the cell types and tissues involved, and are controlled by their removal from circulation. This is accomplished by endocytic uptake by liver cells and/or degradation by GPI-specific phospholipase D in order to bypass potential unwanted effects of the released GPI-APs or their transfer from the releasing donor to acceptor cells (which will be reviewed in a forthcoming manuscript).
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Affiliation(s)
- Günter A Müller
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC) at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Oberschleissheim, Germany
- German Center for Diabetes Research (DZD), 85764 Oberschleissheim, Germany
| | - Timo D Müller
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC) at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Oberschleissheim, Germany
- German Center for Diabetes Research (DZD), 85764 Oberschleissheim, Germany
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20
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Wakefield DL, Golfetto O, Jorand R, Biswas S, Meyer K, Avery KN, Zer C, Cacao EE, Tobin SJ, Talisman IJ, Williams JC, Jovanovic-Talisman T. Using quantitative single molecule localization microscopy to optimize multivalent HER2-targeting ligands. Front Med (Lausanne) 2023; 10:1064242. [PMID: 37138747 PMCID: PMC10149953 DOI: 10.3389/fmed.2023.1064242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 03/30/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction The progression-free survival of patients with HER2-positive metastatic breast cancer is significantly extended by a combination of two monoclonal antibodies, trastuzumab and pertuzumab, which target independent epitopes of the extracellular domain of HER2. The improved efficacy of the combination over individual antibody therapies targeting HER2 is still being investigated, and several molecular mechanisms may be in play: the combination downregulates HER2, improves antibody-dependent cell mediated cytotoxicity, and/or affects the organization of surface-expressed antigens, which may attenuate downstream signaling. Methods By combining protein engineering and quantitative single molecule localization microscopy (qSMLM), here we both assessed and optimized clustering of HER2 in cultured breast cancer cells. Results We detected marked changes to the cellular membrane organization of HER2 when cells were treated with therapeutic antibodies. When we compared untreated samples to four treatment scenarios, we observed the following HER2 membrane features: (1) the monovalent Fab domain of trastuzumab did not significantly affect HER2 clustering; (2) individual therapy with either trastuzumab or (3) pertuzumab produced significantly higher levels of HER2 clustering; (4) a combination of trastuzumab plus pertuzumab produced the highest level of HER2 clustering. To further enhance this last effect, we created multivalent ligands using meditope technology. Treatment with a tetravalent meditope ligand combined with meditope-enabled trastuzumab resulted in pronounced HER2 clustering. Moreover, compared to pertuzumab plus trastuzumab, at early time points this meditope-based combination was more effective at inhibiting epidermal growth factor (EGF) dependent activation of several downstream protein kinases. Discussion Collectively, mAbs and multivalent ligands can efficiently alter the organization and activation of the HER2 receptors. We expect this approach could be used in the future to develop new therapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - John C. Williams
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, Duarte, CA, United States
| | - Tijana Jovanovic-Talisman
- Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, Duarte, CA, United States
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21
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Scalisi S, Pisignano D, Cella Zanacchi F. Single-molecule localization microscopy goes quantitative. Microsc Res Tech 2023; 86:494-504. [PMID: 36601697 DOI: 10.1002/jemt.24281] [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: 11/15/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023]
Abstract
In the last few years, single-molecule localization (SMLM) techniques have been used to address biological questions in different research fields. More recently, super-resolution has also been proposed as a quantitative tool for quantifying protein copy numbers at the nanoscale level. In this scenario, quantitative approaches, mainly based on stepwise photobleaching and quantitative SMLM assisted by calibration standards, offer an exquisite tool for investigating protein complexes. This primer focuses on the basic concepts behind quantitative super-resolution microscopy, also providing strategies to overcome the technical hurdles that could limit their application.
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Affiliation(s)
- Silvia Scalisi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Dario Pisignano
- Dipartimento di Fisica "E. Fermi", Università di Pisa, Pisa, Italy
| | - Francesca Cella Zanacchi
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Fisica "E. Fermi", Università di Pisa, Pisa, Italy
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22
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Shemonti AS, Plebani E, Biscola NP, Jaffey DM, Havton LA, Keast JR, Pothen A, Dundar MM, Powley TL, Rajwa B. A novel statistical methodology for quantifying the spatial arrangements of axons in peripheral nerves. Front Neurosci 2023; 17:1072779. [PMID: 36968498 PMCID: PMC10034020 DOI: 10.3389/fnins.2023.1072779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/09/2023] [Indexed: 03/11/2023] Open
Abstract
A thorough understanding of the neuroanatomy of peripheral nerves is required for a better insight into their function and the development of neuromodulation tools and strategies. In biophysical modeling, it is commonly assumed that the complex spatial arrangement of myelinated and unmyelinated axons in peripheral nerves is random, however, in reality the axonal organization is inhomogeneous and anisotropic. Present quantitative neuroanatomy methods analyze peripheral nerves in terms of the number of axons and the morphometric characteristics of the axons, such as area and diameter. In this study, we employed spatial statistics and point process models to describe the spatial arrangement of axons and Sinkhorn distances to compute the similarities between these arrangements (in terms of first- and second-order statistics) in various vagus and pelvic nerve cross-sections. We utilized high-resolution transmission electron microscopy (TEM) images that have been segmented using a custom-built high-throughput deep learning system based on a highly modified U-Net architecture. Our findings show a novel and innovative approach to quantifying similarities between spatial point patterns using metrics derived from the solution to the optimal transport problem. We also present a generalizable pipeline for quantitative analysis of peripheral nerve architecture. Our data demonstrate differences between male- and female-originating samples and similarities between the pelvic and abdominal vagus nerves.
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Affiliation(s)
| | - Emanuele Plebani
- Department of Computer & Information Sciences, Indiana University - Purdue University Indianapolis, Indianapolis, IN, United States
| | - Natalia P. Biscola
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Deborah M. Jaffey
- Department of Psychological Sciences, Purdue University, West Lafayette, IN, United States
| | - Leif A. Havton
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- James J. Peters Department of Veterans Affairs Medical Center, Bronx, NY, United States
| | - Janet R. Keast
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Alex Pothen
- Department of Computer Science, Purdue University, West Lafayette, IN, United States
| | - M. Murat Dundar
- Department of Computer & Information Sciences, Indiana University - Purdue University Indianapolis, Indianapolis, IN, United States
| | - Terry L. Powley
- Department of Psychological Sciences, Purdue University, West Lafayette, IN, United States
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, United States
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23
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Ball ML, Koestler SA, Muresan L, Rehman SA, O’Holleran K, White R. The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy. PLoS Genet 2023; 19:e1010654. [PMID: 36867662 PMCID: PMC10016678 DOI: 10.1371/journal.pgen.1010654] [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: 10/20/2022] [Revised: 03/15/2023] [Accepted: 02/04/2023] [Indexed: 03/04/2023] Open
Abstract
While the biochemistry of gene transcription has been well studied, our understanding of how this process is organised in 3D within the intact nucleus is less well understood. Here we investigate the structure of actively transcribed chromatin and the architecture of its interaction with active RNA polymerase. For this analysis, we have used super-resolution microscopy to image the Drosophila melanogaster Y loops which represent huge, several megabases long, single transcription units. The Y loops provide a particularly amenable model system for transcriptionally active chromatin. We find that, although these transcribed loops are decondensed they are not organised as extended 10nm fibres, but rather they largely consist of chains of nucleosome clusters. The average width of each cluster is around 50nm. We find that foci of active RNA polymerase are generally located off the main fibre axis on the periphery of the nucleosome clusters. Foci of RNA polymerase and nascent transcripts are distributed around the Y loops rather than being clustered in individual transcription factories. However, as the RNA polymerase foci are considerably less prevalent than the nucleosome clusters, the organisation of this active chromatin into chains of nucleosome clusters is unlikely to be determined by the activity of the polymerases transcribing the Y loops. These results provide a foundation for understanding the topological relationship between chromatin and the process of gene transcription.
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Affiliation(s)
- Madeleine L. Ball
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, United Kingdom
| | - Stefan A. Koestler
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, United Kingdom
| | - Leila Muresan
- Cambridge Advanced Imaging Centre, University of Cambridge, Downing Site, Cambridge, United Kingdom
| | - Sohaib Abdul Rehman
- Cambridge Advanced Imaging Centre, University of Cambridge, Downing Site, Cambridge, United Kingdom
| | - Kevin O’Holleran
- Cambridge Advanced Imaging Centre, University of Cambridge, Downing Site, Cambridge, United Kingdom
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, United Kingdom
- * E-mail:
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24
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Refinement of Singer-Nicolson fluid-mosaic model by microscopy imaging: Lipid rafts and actin-induced membrane compartmentalization. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184093. [PMID: 36423676 DOI: 10.1016/j.bbamem.2022.184093] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
This year celebrates the 50th anniversary of the Singer-Nicolson fluid mosaic model for biological membranes. The next level of sophistication we have achieved for understanding plasma membrane (PM) structures, dynamics, and functions during these 50 years includes the PM interactions with cortical actin filaments and the partial demixing of membrane constituent molecules in the PM, particularly raft domains. Here, first, we summarize our current knowledge of these two structures and emphasize that they are interrelated. Second, we review the structure, molecular dynamics, and function of raft domains, with main focuses on raftophilic glycosylphosphatidylinositol-anchored proteins (GPI-APs) and their signal transduction mechanisms. We pay special attention to the results obtained by single-molecule imaging techniques and other advanced microscopy methods. We also clarify the limitations of present optical microscopy methods for visualizing raft domains, but emphasize that single-molecule imaging techniques can "detect" raft domains associated with molecules of interest in the PM.
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25
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Mao J, Xue M, Guan X, Wang Q, Wang Z, Qin G, He H. Near-Infrared Blinking Carbon Dots Designed for Quantitative Nanoscopy. NANO LETTERS 2023; 23:124-131. [PMID: 36579734 DOI: 10.1021/acs.nanolett.2c03711] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Blinking carbon dots (CDs) have attracted attention as a probe for single molecule localization microscopy (SMLM), yet quantitative analysis is limited because of inept blinking and low signal-to-noise ratio (SNR). Here we report the design and synthesis of near-infrared (NIR) blinking CDs with a maximum emission of around 750 nm by weaving a nitrogen-doped aromatic backbone with surplus carboxyl groups on the surface. The NIR-CDs allow conjugation to monovalent antibody fragments for labeling and imaging of cellular receptors as well as afford increases of 52% in SNR and 33% in localization precision over visible CDs. Analysis of fluorescent bursts allows for accurate counting of cellular receptors at the nanoscale resolution. Using NIR-CDs-based SMLM, we demonstrate oligomerization and internalization of programmed cell death-ligand 1 by a small molecule inhibitor for checkpoint blockade. Our NIR-CDs can become a generally applicable probe for quantitative nanoscopy in chemistry and biology.
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Affiliation(s)
- Jian Mao
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Minmin Xue
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xin Guan
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Qian Wang
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Zhirui Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Guangyong Qin
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Hua He
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
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26
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Hyun Y, Kim D. Recent development of computational cluster analysis methods for single-molecule localization microscopy images. Comput Struct Biotechnol J 2023; 21:879-888. [PMID: 36698968 PMCID: PMC9860261 DOI: 10.1016/j.csbj.2023.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/07/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
With the development of super-resolution imaging techniques, it is crucial to understand protein structure at the nanoscale in terms of clustering and organization in a cell. However, cluster analysis from single-molecule localization microscopy (SMLM) images remains challenging because the classical computational cluster analysis methods developed for conventional microscopy images do not apply to pointillism SMLM data, necessitating the development of distinct methods for cluster analysis from SMLM images. In this review, we discuss the development of computational cluster analysis methods for SMLM images by categorizing them into classical and machine-learning-based methods. Finally, we address possible future directions for machine learning-based cluster analysis methods for SMLM data.
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Affiliation(s)
- Yoonsuk Hyun
- Department of Mathematics, Inha University, Republic of Korea
| | - Doory Kim
- Department of Chemistry, Hanyang University, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Republic of Korea
- Institute of Nano Science and Technology, Hanyang University, Republic of Korea
- Research Institute for Natural Sciences, Hanyang University, Republic of Korea
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27
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Isik OA, Cizmecioglu O. Rafting on the Plasma Membrane: Lipid Rafts in Signaling and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1436:87-108. [PMID: 36648750 DOI: 10.1007/5584_2022_759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The plasma membrane is not a uniform phospholipid bilayer; it has specialized membrane nano- or microdomains called lipid rafts. Lipid rafts are small cholesterol and sphingolipid-rich plasma membrane islands. Although their existence was long debated, their presence in the plasma membrane of living cells is now well accepted with the advent of super-resolution imaging techniques. It is interesting to note that lipid rafts function to compartmentalize receptors and their regulators and substantially modulate cellular signaling. In this review, we will examine the role of lipid rafts and caveolae-lipid raft-like microdomains with a distinct 3D morphology-in cellular signaling. Moreover, we will investigate how raft compartmentalized signaling regulates diverse physiological processes such as proliferation, apoptosis, immune signaling, and development. Also, the deregulation of lipid raft-mediated signaling during tumorigenesis and metastasis will be explored.
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Affiliation(s)
- Ozlem Aybuke Isik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Onur Cizmecioglu
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.
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28
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Shelby SA, Shaw TR, Veatch SL. Measuring the Co-Localization and Dynamics of Mobile Proteins in Live Cells Undergoing Signaling Responses. Methods Mol Biol 2023; 2654:1-23. [PMID: 37106172 PMCID: PMC10758997 DOI: 10.1007/978-1-0716-3135-5_1] [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] [Indexed: 04/29/2023]
Abstract
Single molecule imaging in live cells enables the study of protein interactions and dynamics as they participate in signaling processes. When combined with fluorophores that stochastically transition between fluorescent and reversible dark states, as in super-resolution localization imaging, labeled molecules can be visualized in single cells over time. This improvement in sampling enables the study of extended cellular responses at the resolution of single molecule localization. This chapter provides optimized experimental and analytical methods used to quantify protein interactions and dynamics within the membranes of adhered live cells. Importantly, the use of pair-correlation functions resolved in both space and time allows researchers to probe interactions between proteins on biologically relevant distance and timescales, even though fluorescence localization methods typically require long times to assemble well-sampled reconstructed images. We describe an application of this approach to measure protein interactions in B cell receptor signaling and include sample analysis code for post-processing of imaging data. These methods are quantitative, sensitive, and broadly applicable to a range of signaling systems.
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Affiliation(s)
- Sarah A Shelby
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Thomas R Shaw
- Program in Applied Physics, University of Michigan, Ann Arbor, MI, USA
| | - Sarah L Veatch
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA.
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29
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Scalisi S, Ahmad A, D'Annunzio S, Rousseau D, Zippo A. Quantitative Analysis of PcG-Associated Condensates by Stochastic Optical Reconstruction Microscopy (STORM). Methods Mol Biol 2023; 2655:183-200. [PMID: 37212997 DOI: 10.1007/978-1-0716-3143-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The polycomb group (PcG) proteins play a central role in the maintenance of a repressive state of gene expression. Recent findings demonstrate that PcG components are organized into nuclear condensates, contributing to the reshaping of chromatin architecture in physiological and pathological conditions, thus affecting the nuclear mechanics. In this context, direct stochastic optical reconstruction microscopy (dSTORM) provides an effective tool to achieve a detailed characterization of PcG condensates by visualizing them at a nanometric level. Furthermore, by analyzing dSTORM datasets with cluster analysis algorithms, quantitative information can be yielded regarding protein numbers, grouping, and spatial organization. Here, we describe how to set up a dSTORM experiment and perform the data analysis to study PcG complexes' components in adhesion cells quantitatively.
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Affiliation(s)
- Silvia Scalisi
- Chromatin Biology & Epigenetics Lab, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Ali Ahmad
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes, UMR INRAE IRHS, Université d'Angers, Angers, France
| | - Sarah D'Annunzio
- Chromatin Biology & Epigenetics Lab, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - David Rousseau
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes, UMR INRAE IRHS, Université d'Angers, Angers, France
| | - Alessio Zippo
- Chromatin Biology & Epigenetics Lab, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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30
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Wu YL, Hoess P, Tschanz A, Matti U, Mund M, Ries J. Maximum-likelihood model fitting for quantitative analysis of SMLM data. Nat Methods 2023; 20:139-148. [PMID: 36522500 PMCID: PMC9834062 DOI: 10.1038/s41592-022-01676-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 10/14/2022] [Indexed: 12/23/2022]
Abstract
Quantitative data analysis is important for any single-molecule localization microscopy (SMLM) workflow to extract biological insights from the coordinates of the single fluorophores. However, current approaches are restricted to simple geometries or require identical structures. Here, we present LocMoFit (Localization Model Fit), an open-source framework to fit an arbitrary model to localization coordinates. It extracts meaningful parameters from individual structures and can select the most suitable model. In addition to analyzing complex, heterogeneous and dynamic structures for in situ structural biology, we demonstrate how LocMoFit can assemble multi-protein distribution maps of six nuclear pore components, calculate single-particle averages without any assumption about geometry or symmetry, and perform a time-resolved reconstruction of the highly dynamic endocytic process from static snapshots. We provide extensive simulation and visualization routines to validate the robustness of LocMoFit and tutorials to enable any user to increase the information content they can extract from their SMLM data.
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Affiliation(s)
- Yu-Le Wu
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Philipp Hoess
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Ulf Matti
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Markus Mund
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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31
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Embacher PA, Germanova TE, Roscioli E, McAinsh AD, Burroughs NJ. Bayesian inference of multi-point macromolecular architecture mixtures at nanometre resolution. PLoS Comput Biol 2022; 18:e1010765. [PMID: 36574448 PMCID: PMC9829179 DOI: 10.1371/journal.pcbi.1010765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/09/2023] [Accepted: 11/28/2022] [Indexed: 12/29/2022] Open
Abstract
Gaussian spot fitting methods have significantly extended the spatial range where fluorescent microscopy can be used, with recent techniques approaching nanometre (nm) resolutions. However, small inter-fluorophore distances are systematically over-estimated for typical molecular scales. This bias can be corrected computationally, but current algorithms are limited to correcting distances between pairs of fluorophores. Here we present a flexible Bayesian computational approach that infers the distances and angles between multiple fluorophores and has several advantages over these previous methods. Specifically it improves confidence intervals for small lengths, estimates measurement errors of each fluorophore individually and infers the correlations between polygon lengths. The latter is essential for determining the full multi-fluorophore 3D architecture. We further developed the algorithm to infer the mixture composition of a heterogeneous population of multiple polygon states. We use our algorithm to analyse the 3D architecture of the human kinetochore, a macro-molecular complex that is essential for high fidelity chromosome segregation during cell division. Using triple fluorophore image data we unravel the mixture of kinetochore states during human mitosis, inferring the conformation of microtubule attached and unattached kinetochores and their proportions across mitosis. We demonstrate that the attachment conformation correlates with intersister tension and sister alignment to the metaphase plate.
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Affiliation(s)
- Peter A. Embacher
- Department of Medical Physics & Biomedical Engineering, University College London, London, United Kingdom
| | - Tsvetelina E. Germanova
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Emanuele Roscioli
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Andrew D. McAinsh
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Nigel J. Burroughs
- Mathematics Institute and Zeeman Institute, University of Warwick, Coventry, United Kingdom
- * E-mail:
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32
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Vipat S, Gupta D, Jonchhe S, Anderspuk H, Rothenberg E, Moiseeva TN. The non-catalytic role of DNA polymerase epsilon in replication initiation in human cells. Nat Commun 2022; 13:7099. [PMID: 36402816 PMCID: PMC9675812 DOI: 10.1038/s41467-022-34911-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
DNA polymerase epsilon (PolE) in an enzyme essential for DNA replication. Deficiencies and mutations in PolE cause severe developmental abnormalities and cancers. Paradoxically, the catalytic domain of yeast PolE catalytic subunit is dispensable for survival, and its non-catalytic essential function is linked with replicative helicase (CMG) assembly. Less is known about the PolE role in replication initiation in human cells. Here we use an auxin-inducible degron system to study the effect of POLE1 depletion on replication initiation in U2OS cells. POLE1-depleted cells were able to assemble CMG helicase and initiate DNA synthesis that failed shortly after. Expression of POLE1 non-catalytic domain rescued this defect resulting in slow, but continuous DNA synthesis. We propose a model where in human U2OS cells POLE1/POLE2 are dispensable for CMG assembly, but essential during later steps of replication initiation. Our study provides some insights into the role of PolE in replication initiation in human cells.
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Affiliation(s)
- Sameera Vipat
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Sagun Jonchhe
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Hele Anderspuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Tatiana N Moiseeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia.
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33
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Application of Lacunarity for Quantification of Single Molecule Localization Microscopy Images. Cells 2022; 11:cells11193105. [PMID: 36231067 PMCID: PMC9562870 DOI: 10.3390/cells11193105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
The quantitative analysis of datasets achieved by single molecule localization microscopy is vital for studying the structure of subcellular organizations. Cluster analysis has emerged as a multi-faceted tool in the structural analysis of localization datasets. However, the results it produces greatly depend on the set parameters, and the process can be computationally intensive. Here we present a new approach for structural analysis using lacunarity. Unlike cluster analysis, lacunarity can be calculated quickly while providing definitive information about the structure of the localizations. Using simulated data, we demonstrate how lacunarity results can be interpreted. We use these interpretations to compare our lacunarity analysis with our previous cluster analysis-based results in the field of DNA repair, showing the new algorithm’s efficiency.
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34
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Etheridge TJ, Carr AM, Herbert AD. GDSC SMLM: Single-molecule localisation microscopy software for ImageJ. Wellcome Open Res 2022; 7:241. [PMID: 37351368 PMCID: PMC10282564 DOI: 10.12688/wellcomeopenres.18327.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 08/03/2023] Open
Abstract
Single-molecule localisation microscopy (SMLM) uses software to extract super-resolved positions from microscope images of fluorescent molecules. These localisations can then be used to render super-resolution images or analysed to extract information about molecular behaviour. The GDSC SMLM software provides a set of tools for analysing SMLM data in a single cross-platform environment. The software identifies fluorescent molecules in raw microscope images and localises their positions using stages of spot detection, spot fitting and spot rejection. The resulting localisation data set can then be visualised, cropped and filtered. A suite of downstream analysis tools enable the user to perform single-particle tracking, cluster analysis and drift correction. In addition, GDSC SMLM also provides utility tools that enable modelling of EM-CCD and sCMOS cameras as well as point spread functions (PSFs) for data simulation. The software is written in Java and runs as a collection of plugins for the ImageJ software.
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Affiliation(s)
- Thomas J. Etheridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
| | - Antony M. Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
| | - Alex D. Herbert
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
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35
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Milstein JN, Nino DF, Zhou X, Gradinaru CC. Single-molecule counting applied to the study of GPCR oligomerization. Biophys J 2022; 121:3175-3187. [PMID: 35927960 PMCID: PMC9463696 DOI: 10.1016/j.bpj.2022.07.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/29/2022] [Accepted: 07/28/2022] [Indexed: 11/24/2022] Open
Abstract
Single-molecule counting techniques enable a precise determination of the intracellular abundance and stoichiometry of proteins and macromolecular complexes. These details are often challenging to quantitatively assess yet are essential for our understanding of cellular function. Consider G-protein-coupled receptors-an expansive class of transmembrane signaling proteins that participate in many vital physiological functions making them a popular target for drug development. While early evidence for the role of oligomerization in receptor signaling came from ensemble biochemical and biophysical assays, innovations in single-molecule measurements are now driving a paradigm shift in our understanding of its relevance. Here, we review recent developments in single-molecule counting with a focus on photobleaching step counting and the emerging technique of quantitative single-molecule localization microscopy-with a particular emphasis on the potential for these techniques to advance our understanding of the role of oligomerization in G-protein-coupled receptor signaling.
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Affiliation(s)
- Joshua N Milstein
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.
| | - Daniel F Nino
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Xiaohan Zhou
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Claudiu C Gradinaru
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.
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36
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Correlated STORM-homoFRET imaging reveals highly heterogeneous membrane receptor structures. J Biol Chem 2022; 298:102448. [PMID: 36063991 PMCID: PMC9539790 DOI: 10.1016/j.jbc.2022.102448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Mapping the self-organization and spatial distribution of membrane proteins is key to understanding their function. Developing methods that can provide insight into correlations between membrane protein co-localization and interactions is challenging. We report here on a correlated stochastic optical reconstruction microscopy (STORM)/homoFRET imaging approach for resolving the nanoscale distribution and oligomeric state of membrane proteins. Using live cell homoFRET imaging of carcinoembryonic antigen-related cellular adhesion molecule (CEACAM1), a cell-surface receptor known to exist in a complex equilibrium between monomer and dimer/oligomer states, we revealed highly heterogeneous diffraction-limited structures on the surface of HeLa cells. Furthermore, correlated super-resolved STORM imaging showed that these structures comprised a complex mixture and spatial distribution of self-associated CEACAM1 molecules. In conclusion, this correlated approach provides a compelling strategy for addressing challenging questions about the interplay between membrane protein concentration, distribution, interaction, clustering, and function.
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37
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Jensen LG, Williamson DJ, Hahn U. Semiparametric point process modeling of blinking artifacts in PALM. Ann Appl Stat 2022. [DOI: 10.1214/21-aoas1553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | | | - Ute Hahn
- Department of Mathematics, Aarhus University
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Active emulsions in living cell membranes driven by contractile stresses and transbilayer coupling. Proc Natl Acad Sci U S A 2022; 119:e2123056119. [PMID: 35867835 PMCID: PMC9335261 DOI: 10.1073/pnas.2123056119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The spatiotemporal organization of proteins and lipids on the cell surface has direct functional consequences for signaling, sorting, and endocytosis. Earlier studies have shown that multiple types of membrane proteins, including transmembrane proteins that have cytoplasmic actin binding capacity and lipid-tethered glycosylphosphatidylinositol-anchored proteins (GPI-APs), form nanoscale clusters driven by active contractile flows generated by the actin cortex. To gain insight into the role of lipids in organizing membrane domains in living cells, we study the molecular interactions that promote the actively generated nanoclusters of GPI-APs and transmembrane proteins. This motivates a theoretical description, wherein a combination of active contractile stresses and transbilayer coupling drives the creation of active emulsions, mesoscale liquid order (lo) domains of the GPI-APs and lipids, at temperatures greater than equilibrium lipid phase segregation. To test these ideas, we use spatial imaging of molecular clustering combined with local membrane order, and we demonstrate that mesoscopic domains enriched in nanoclusters of GPI-APs are maintained by cortical actin activity and transbilayer interactions and exhibit significant lipid order, consistent with predictions of the active composite model.
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39
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Nishimura T, Suetsugu S. Super-resolution analysis of PACSIN2 and EHD2 at caveolae. PLoS One 2022; 17:e0271003. [PMID: 35834519 PMCID: PMC9282494 DOI: 10.1371/journal.pone.0271003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
Caveolae are plasma membrane invaginations that play important roles in both endocytosis and membrane tension buffering. Typical caveolae have invaginated structures with a high-density caveolin assembly. Membrane sculpting proteins, including PACSIN2 and EHD2, are involved in caveolar biogenesis. PACSIN2 is an F-BAR domain-containing protein with a membrane sculpting ability that is essential for caveolar shaping. EHD2 is also localized at caveolae and involved in their stability. However, the spatial relationship between PACSIN2, EHD2, and caveolin has not yet been investigated. We observed the single-molecule localizations of PACSIN2 and EHD2 relative to caveolin-1 in three-dimensional space. The single-molecule localizations were grouped by their proximity localizations into the geometric structures of blobs. In caveolin-1 blobs, PACSIN2, EHD2, and caveolin-1 had overlapped spatial localizations. Interestingly, the mean centroid of the PACSIN2 F-BAR domain at the caveolin-1 blobs was closer to the plasma membrane than those of EHD2 and caveolin-1, suggesting that PACSIN2 is involved in connecting caveolae to the plasma membrane. Most of the blobs with volumes typical of caveolae had PACSIN2 and EHD2, in contrast to those with smaller volumes. Therefore, PACSIN2 and EHD2 are apparently localized at typically sized caveolae.
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Affiliation(s)
- Tamako Nishimura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shiro Suetsugu
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- Data Science Center, Nara Institute of Science and Technology, Ikoma, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Japan
- * E-mail:
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40
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Frazzette N, Cruz AC, Wu X, Hammer JA, Lippincott-Schwartz J, Siegel RM, Sengupta P. Super-Resolution Imaging of Fas/CD95 Reorganization Induced by Membrane-Bound Fas Ligand Reveals Nanoscale Clustering Upstream of FADD Recruitment. Cells 2022; 11:cells11121908. [PMID: 35741037 PMCID: PMC9221696 DOI: 10.3390/cells11121908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
Signaling through the TNF-family receptor Fas/CD95 can trigger apoptosis or non-apoptotic cellular responses and is essential for protection from autoimmunity. Receptor clustering has been observed following interaction with Fas ligand (FasL), but the stoichiometry of Fas, particularly when triggered by membrane-bound FasL, the only form of FasL competent at inducing programmed cell death, is not known. Here we used super-resolution microscopy to study the behavior of single molecules of Fas/CD95 on the plasma membrane after interaction of Fas with FasL on planar lipid bilayers. We observed rapid formation of Fas protein superclusters containing more than 20 receptors after interactions with membrane-bound FasL. Fluorescence correlation imaging demonstrated recruitment of FADD dependent on an intact Fas death domain, with lipid raft association playing a secondary role. Flow-cytometric FRET analysis confirmed these results, and also showed that some Fas clustering can occur in the absence of FADD and caspase-8. Point mutations in the Fas death domain associated with autoimmune lymphoproliferative syndrome (ALPS) completely disrupted Fas reorganization and FADD recruitment, confirming structure-based predictions of the critical role that these residues play in Fas–Fas and Fas–FADD interactions. Finally, we showed that induction of apoptosis correlated with the ability to form superclusters and recruit FADD.
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Affiliation(s)
- Nicholas Frazzette
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD 20892, USA; (N.F.); (A.C.C.)
| | - Anthony C. Cruz
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD 20892, USA; (N.F.); (A.C.C.)
| | - Xufeng Wu
- Cell and Developmental Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (X.W.); (J.A.H.)
| | - John A. Hammer
- Cell and Developmental Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (X.W.); (J.A.H.)
| | | | - Richard M. Siegel
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD 20892, USA; (N.F.); (A.C.C.)
- Correspondence: (R.M.S.); (P.S.)
| | - Prabuddha Sengupta
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA;
- Correspondence: (R.M.S.); (P.S.)
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41
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Maddox AL, Brehove MS, Eliato KR, Saftics A, Romano E, Press MF, Mortimer J, Jones V, Schmolze D, Seewaldt VL, Jovanovic-Talisman T. Molecular Assessment of HER2 to Identify Signatures Associated with Therapy Response in HER2-Positive Breast Cancer. Cancers (Basel) 2022; 14:2795. [PMID: 35681773 PMCID: PMC9179327 DOI: 10.3390/cancers14112795] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022] Open
Abstract
Trastuzumab, the prototype HER2-directed therapy, has markedly improved survival for women with HER2-positive breast cancers. However, only 40-60% of women with HER2-positive breast cancers achieve a complete pathological response to chemotherapy combined with HER2-directed therapy. The current diagnostic assays have poor positive-predictive accuracy in identifying therapy-responsive breast cancers. Here, we deployed quantitative single molecule localization microscopy to assess the molecular features of HER2 in a therapy-responsive setting. Using fluorescently labeled trastuzumab as a probe, we first compared the molecular features of HER2 in trastuzumab-sensitive (BT-474 and SK-BR-3) and trastuzumab-resistant (BT-474R and JIMT-1) cultured cell lines. Trastuzumab-sensitive cells had significantly higher detected HER2 densities and clustering. We then evaluated HER2 in pre-treatment core biopsies from women with breast cancer undergoing neoadjuvant therapy. A complete pathological response was associated with a high detected HER2 density and significant HER2 clustering. These results established the nano-organization of HER2 as a potential signature of therapy-responsive disease.
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Affiliation(s)
- Adam L. Maddox
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
| | - Matthew S. Brehove
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
| | - Kiarash R. Eliato
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
| | - Andras Saftics
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
| | - Eugenia Romano
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
| | - Michael F. Press
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA;
| | - Joanne Mortimer
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Veronica Jones
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Daniel Schmolze
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Victoria L. Seewaldt
- Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Tijana Jovanovic-Talisman
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
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42
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Li H, Zhang J, Shi Y, Zhao G, Xu H, Cai M, Gao J, Wang H. Mechanism of INSR clustering with insulin activation and resistance revealed by super-resolution imaging. NANOSCALE 2022; 14:7747-7755. [PMID: 35579582 DOI: 10.1039/d2nr01051h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Insulin receptor (INSR) is a key protein in the INSR signaling pathway and plays a critical role in biological processes, especially in the regulation of glucose homeostasis. Many metabolic diseases are often accompanied by abnormal INSR signaling. However, the specific effector mechanisms regulating insulin resistance and the distribution patterns of INSR during cell membrane activation remain unclear. Here, we investigated the changes in the distribution of INSR during activation using super-resolution imaging. By observing the connection between INSR activation and its distribution, we found that insulin resistance inhibits its receptor clustering. More importantly, we found that INSR has a highly co-localized relationship with the skeletal protein βII-spectrin. Specific knockout of βII-spectrin inhibited the interaction of INSR with GLUT4 and affected the normal metabolism of glucose. Our work elucidates the effects of insulin activation and insulin resistance on INSR distribution and reveals a potential relationship between INSR and cytoskeleton at the single molecule level, which promotes a deeper understanding of the roles associated with insulin signaling and insulin resistance.
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Affiliation(s)
- Hongru Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Jinrui Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.
| | - Yan Shi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.
| | - Guanfang Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Haijiao Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.
| | - Mingjun Cai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Jing Gao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
- Laboratory for Marine Biology and Biotechnology, Qing dao National Laboratory for Marine Science and Technology, Wenhai Road, Aoshanwei, Jimo, Qingdao, Shandong 266237, China
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43
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Jensen LG, Hoh TY, Williamson DJ, Griffié J, Sage D, Rubin-Delanchy P, Owen DM. Correction of multiple-blinking artifacts in photoactivated localization microscopy. Nat Methods 2022; 19:594-602. [PMID: 35545712 DOI: 10.1038/s41592-022-01463-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022]
Abstract
Photoactivated localization microscopy (PALM) produces an array of localization coordinates by means of photoactivatable fluorescent proteins. However, observations are subject to fluorophore multiple blinking and each protein is included in the dataset an unknown number of times at different positions, due to localization error. This causes artificial clustering to be observed in the data. We present a 'model-based correction' (MBC) workflow using calibration-free estimation of blinking dynamics and model-based clustering to produce a corrected set of localization coordinates representing the true underlying fluorophore locations with enhanced localization precision, outperforming the state of the art. The corrected data can be reliably tested for spatial randomness or analyzed by other clustering approaches, and descriptors such as the absolute number of fluorophores per cluster are now quantifiable, which we validate with simulated data and experimental data with known ground truth. Using MBC, we confirm that the adapter protein, the linker for activation of T cells, is clustered at the T cell immunological synapse.
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Affiliation(s)
- Louis G Jensen
- Department of Mathematics, Aarhus University, Aarhus, Denmark.
| | - Tjun Yee Hoh
- Institute for Statistical Science, School of Mathematics, University of Bristol, Bristol, UK
| | - David J Williamson
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Daniel Sage
- Biomedical Imaging Group, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Patrick Rubin-Delanchy
- Institute for Statistical Science, School of Mathematics, University of Bristol, Bristol, UK.
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, School of Mathematics and Centre of Membrane Proteins and Receptors, University of Birmingham, Birmingham, UK.
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44
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Schönfeldová T, Okur HI, Vezočnik V, Iacovache I, Cao C, Dal Peraro M, Maček P, Zuber B, Roke S. Ultrasensitive Label-Free Detection of Protein-Membrane Interaction Exemplified by Toxin-Liposome Insertion. J Phys Chem Lett 2022; 13:3197-3201. [PMID: 35377651 PMCID: PMC9014461 DOI: 10.1021/acs.jpclett.1c04011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Measuring the high-affinity binding of proteins to liposome membranes remains a challenge. Here, we show an ultrasensitive and direct detection of protein binding to liposome membranes using high throughput second harmonic scattering (SHS). Perfringolysin O (PFO), a pore-forming toxin, with a highly membrane selective insertion into cholesterol-rich membranes is used. PFO inserts only into liposomes with a cholesterol concentration >30%. Twenty mole-percent cholesterol results in neither SHS-signal deviation nor pore formation as seen by cryo-electron microscopy of PFO and liposomes. PFO inserts into cholesterol-rich membranes of large unilamellar vesicles in an aqueous solution with Kd = (1.5 ± 0.2) × 10-12 M. Our results demonstrate a promising approach to probe protein-membrane interactions below sub-picomolar concentrations in a label-free and noninvasive manner on 3D systems. More importantly, the volume of protein sample is ultrasmall (<10 μL). These findings enable the detection of low-abundance proteins and their interaction with membranes.
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Affiliation(s)
- T. Schönfeldová
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bio-engineering (IBI),
School of Engineering (STI), École
Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - H. I. Okur
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bio-engineering (IBI),
School of Engineering (STI), École
Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Department
of Chemistry and National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey
| | - V. Vezočnik
- Department
of Biology, Biotechnical Faculty, University
of Ljubljana, Jamnikarjeva 101, Ljubljana 1000, Slovenia
| | - I. Iacovache
- Institute
of Anatomy, University of Bern, Baltzerstrasse 2, 3012 Bern, Switzerland
| | - C. Cao
- Institute
of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - M. Dal Peraro
- Institute
of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - P. Maček
- Department
of Biology, Biotechnical Faculty, University
of Ljubljana, Jamnikarjeva 101, Ljubljana 1000, Slovenia
| | - B. Zuber
- Institute
of Anatomy, University of Bern, Baltzerstrasse 2, 3012 Bern, Switzerland
| | - S. Roke
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bio-engineering (IBI),
School of Engineering (STI), École
Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Institute
of Materials Science (IMX) and Lausanne Centre for Ultrafast Science
(LACUS), École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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45
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Jäger J, Patra P, Sanchez CP, Lanzer M, Schwarz US. A particle-based computational model to analyse remodelling of the red blood cell cytoskeleton during malaria infections. PLoS Comput Biol 2022; 18:e1009509. [PMID: 35394995 PMCID: PMC9020725 DOI: 10.1371/journal.pcbi.1009509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/20/2022] [Accepted: 03/21/2022] [Indexed: 11/18/2022] Open
Abstract
Red blood cells can withstand the harsh mechanical conditions in the vasculature only because the bending rigidity of their plasma membrane is complemented by the shear elasticity of the underlying spectrin-actin network. During an infection by the malaria parasite Plasmodium falciparum, the parasite mines host actin from the junctional complexes and establishes a system of adhesive knobs, whose main structural component is the knob-associated histidine rich protein (KAHRP) secreted by the parasite. Here we aim at a mechanistic understanding of this dramatic transformation process. We have developed a particle-based computational model for the cytoskeleton of red blood cells and simulated it with Brownian dynamics to predict the mechanical changes resulting from actin mining and KAHRP-clustering. Our simulations include the three-dimensional conformations of the semi-flexible spectrin chains, the capping of the actin protofilaments and several established binding sites for KAHRP. For the healthy red blood cell, we find that incorporation of actin protofilaments leads to two regimes in the shear response. Actin mining decreases the shear modulus, but knob formation increases it. We show that dynamical changes in KAHRP binding affinities can explain the experimentally observed relocalization of KAHRP from ankyrin to actin complexes and demonstrate good qualitative agreement with experiments by measuring pair cross-correlations both in the computer simulations and in super-resolution imaging experiments. Malaria is one of the deadliest infectious diseases and its symptoms are related to the blood stage, when the parasite multiplies within red blood cells. In order to avoid clearance by the spleen, the parasite produces specific factors like the adhesion receptor PfEMP1 and the multifunctional protein KAHRP that lead to the formation of adhesive knobs on the surface of the red blood cells and thus increase residence time in the vasculature. We have developed a computational model for the parasite-induced remodelling of the actin-spectrin network to quantitatively predict the dynamical changes in the mechanical properties of the infected red blood cells and the spatial distribution of the different protein components of the membrane skeleton. Our simulations show that KAHRP can relocate to actin junctions due to dynamical changes in binding affinities, in good qualitative agreement with super-resolution imaging experiments. In the future, our simulation framework can be used to gain further mechanistic insight into the way malaria parasites attack the red blood cell cytoskeleton.
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Affiliation(s)
- Julia Jäger
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| | - Pintu Patra
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| | - Cecilia P. Sanchez
- Center of Infectious Diseases, Parasitology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Lanzer
- Center of Infectious Diseases, Parasitology, University Hospital Heidelberg, Heidelberg, Germany
- * E-mail: (ML); (USS)
| | - Ulrich S. Schwarz
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
- * E-mail: (ML); (USS)
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A coordinate-based co-localization index to quantify and visualize spatial associations in single-molecule localization microscopy. Sci Rep 2022; 12:4676. [PMID: 35304545 PMCID: PMC8933590 DOI: 10.1038/s41598-022-08746-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/07/2022] [Indexed: 11/09/2022] Open
Abstract
Visualizing the subcellular distribution of proteins and determining whether specific proteins co-localize is one of the main strategies in determining the organization and potential interactions of protein complexes in biological samples. The development of super-resolution microscopy techniques such as single-molecule localization microscopy (SMLM) has tremendously increased the ability to resolve protein distribution at nanometer resolution. As super-resolution imaging techniques are becoming instrumental in revealing novel biological insights, new quantitative approaches that exploit the unique nature of SMLM datasets are required. Here, we present a new, local density-based algorithm to quantify co-localization in dual-color SMLM datasets. We show that this method is broadly applicable and only requires molecular coordinates and their localization precision as inputs. Using simulated point patterns, we show that this method robustly measures the co-localization in dual-color SMLM datasets, independent of localization density, but with high sensitivity towards local enrichments. We further validated our method using SMLM imaging of the microtubule network in epithelial cells and used it to study the spatial association between proteins at neuronal synapses. Together, we present a simple and easy-to-use, but powerful method to analyze the spatial association of molecules in dual-color SMLM datasets.
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47
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Schneider MC, Schütz GJ. Don’t Be Fooled by Randomness: Valid p-Values for Single Molecule Microscopy. FRONTIERS IN BIOINFORMATICS 2022; 2:811053. [PMID: 36304307 PMCID: PMC9580918 DOI: 10.3389/fbinf.2022.811053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/12/2022] [Indexed: 12/04/2022] Open
Abstract
The human mind shows extraordinary capability at recognizing patterns, while at the same time tending to underestimate the natural scope of random processes. Taken together, this easily misleads researchers in judging whether the observed characteristics of their data are of significance or just the outcome of random effects. One of the best tools to assess whether observed features fall into the scope of pure randomness is statistical significance testing, which quantifies the probability to falsely reject a chosen null hypothesis. The central parameter in this context is the p-value, which can be calculated from the recorded data sets. In case of p-values smaller than the level of significance, the null hypothesis is rejected, otherwise not. While significance testing has found widespread application in many sciences including the life sciences, it is hardly used in (bio-)physics. We propose here that significance testing provides an important and valid addendum to the toolbox of quantitative (single molecule) biology. It allows to support a quantitative judgement (the hypothesis) about the data set with a probabilistic assessment. In this manuscript we describe ways for obtaining valid p-values in two selected applications of single molecule microscopy: (i) Nanoclustering in single molecule localization microscopy. Previously, we developed a method termed 2-CLASTA, which allows to calculate a valid p-value for the null hypothesis of an underlying random distribution of molecules of interest while circumventing overcounting issues. Here, we present an extension to this approach, yielding a single overall p-value for data pooled from multiple cells or experiments. (ii) Single molecule trajectories. Data from a single molecule trajectory are inherently correlated, thus prohibiting a direct analysis via conventional statistical tools. Here, we introduce a block permutation test, which yields a valid p-value for the analysis and comparison of single molecule trajectory data. We exemplify the approach based on FRET trajectories.
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48
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Balcioglu HE, Harkes R, Danen EHJ, Schmidt T. Substrate rigidity modulates traction forces and stoichiometry of cell–matrix adhesions. J Chem Phys 2022; 156:085101. [DOI: 10.1063/5.0077004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In cell–matrix adhesions, integrin receptors and associated proteins provide a dynamic coupling of the extracellular matrix (ECM) to the cytoskeleton. This allows bidirectional transmission of forces between the ECM and the cytoskeleton, which tunes intracellular signaling cascades that control survival, proliferation, differentiation, and motility. The quantitative relationships between recruitment of distinct cell–matrix adhesion proteins and local cellular traction forces are not known. Here, we applied quantitative super-resolution microscopy to cell–matrix adhesions formed on fibronectin-stamped elastomeric pillars and developed an approach to relate the number of talin, vinculin, paxillin, and focal adhesion kinase (FAK) molecules to the local cellular traction force. We find that FAK recruitment does not show an association with traction-force application, whereas a ∼60 pN force increase is associated with the recruitment of one talin, two vinculin, and two paxillin molecules on a substrate with an effective stiffness of 47 kPa. On a substrate with a fourfold lower effective stiffness, the stoichiometry of talin:vinculin:paxillin changes to 2:12:6 for the same ∼60 pN traction force. The relative change in force-related vinculin recruitment indicates a stiffness-dependent switch in vinculin function in cell–matrix adhesions. Our results reveal a substrate-stiffness-dependent modulation of the relationship between cellular traction-force and the molecular stoichiometry of cell–matrix adhesions.
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Affiliation(s)
- Hayri E. Balcioglu
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Rolf Harkes
- Physics of Life Processes, Kamerlingh Onnes-Huygens Laboratory, Leiden University, Leiden, The Netherlands
| | - Erik H. J. Danen
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Thomas Schmidt
- Physics of Life Processes, Kamerlingh Onnes-Huygens Laboratory, Leiden University, Leiden, The Netherlands
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Fernandez A, Bautista M, Wu L, Pinaud F. Emerin self-assembly and nucleoskeletal coupling regulate nuclear envelope mechanics against stress. J Cell Sci 2022; 135:274432. [PMID: 35178558 PMCID: PMC8995096 DOI: 10.1242/jcs.258969] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/14/2022] [Indexed: 11/20/2022] Open
Abstract
Emerin is an integral nuclear envelope protein participating in the maintenance of nuclear shape. When mutated or absent, emerin causes X-linked Emery-Dreifuss muscular dystrophy (EDMD). To define how emerin takes parts in molecular scaffolding at the nuclear envelope and helps protect the nucleus against mechanical stress, we established its nanoscale organization using single molecule tracking and super-resolution microscopy. We show that emerin monomers form localized oligomeric nanoclusters stabilized by both lamin A/C and SUN1 LINC complex. Interactions of emerin with nuclear actin and BAF additionally modulate its membrane mobility and its ability to oligomerize. In nuclei subjected to mechanical challenges, the mechanotransducing functions of emerin are coupled to changes in its oligomeric state, and the incremental self-assembly of emerin determines nuclear shape adaptation against forces. We also show that the abnormal nuclear envelope deformations induced by EDMD emerin mutants stem from an improper formation of lamin A/C and LINC complex-stabilized emerin oligomers. These findings place emerin at the center of the molecular processes that regulate nuclear shape remodeling in response to mechanical challenges.
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Affiliation(s)
- Anthony Fernandez
- Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA
| | - Markville Bautista
- Department of Chemistry, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA
| | - Liying Wu
- Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA
| | - Fabien Pinaud
- Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA.,Department of Chemistry, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA.,Department of Physics and Astronomy, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA
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50
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Vermaas JV, Mayne CG, Shinn E, Tajkhorshid E. Assembly and Analysis of Cell-Scale Membrane Envelopes. J Chem Inf Model 2022; 62:602-617. [PMID: 34910495 PMCID: PMC8903035 DOI: 10.1021/acs.jcim.1c01050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms─a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.
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Affiliation(s)
- Josh V. Vermaas
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401
| | - Christopher G. Mayne
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Eric Shinn
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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