1
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Guzman NA, Guzman DE, Blanc T. Advancements in portable instruments based on affinity-capture-migration and affinity-capture-separation for use in clinical testing and life science applications. J Chromatogr A 2023; 1704:464109. [PMID: 37315445 DOI: 10.1016/j.chroma.2023.464109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/16/2023]
Abstract
The shift from testing at centralized diagnostic laboratories to remote locations is being driven by the development of point-of-care (POC) instruments and represents a transformative moment in medicine. POC instruments address the need for rapid results that can inform faster therapeutic decisions and interventions. These instruments are especially valuable in the field, such as in an ambulance, or in remote and rural locations. The development of telehealth, enabled by advancements in digital technologies like smartphones and cloud computing, is also aiding in this evolution, allowing medical professionals to provide care remotely, potentially reducing healthcare costs and improving patient longevity. One notable POC device is the lateral flow immunoassay (LFIA), which played a major role in addressing the COVID-19 pandemic due to its ease of use, rapid analysis time, and low cost. However, LFIA tests exhibit relatively low analytical sensitivity and provide semi-quantitative information, indicating either a positive, negative, or inconclusive result, which can be attributed to its one-dimensional format. Immunoaffinity capillary electrophoresis (IACE), on the other hand, offers a two-dimensional format that includes an affinity-capture step of one or more matrix constituents followed by release and electrophoretic separation. The method provides greater analytical sensitivity, and quantitative information, thereby reducing the rate of false positives, false negatives, and inconclusive results. Combining LFIA and IACE technologies can thus provide an effective and economical solution for screening, confirming results, and monitoring patient progress, representing a key strategy in advancing diagnostics in healthcare.
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Affiliation(s)
- Norberto A Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08543, United States of America.
| | - Daniel E Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08543, United States of America; Columbia University Irving Medical Center, New York, NY 10032, United States of America
| | - Timothy Blanc
- Eli Lilly and Company, Branchburg, NJ 08876, United States of America
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2
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Malkusch S, Rahm JV, Dietz MS, Heilemann M, Sibarita JB, Lötsch J. Receptor tyrosine kinase MET ligand-interaction classified via machine learning from single-particle tracking data. Mol Biol Cell 2022; 33:ar60. [PMID: 35171646 PMCID: PMC9265154 DOI: 10.1091/mbc.e21-10-0496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Internalin B–mediated activation of the membrane-bound receptor tyrosine kinase MET is accompanied by a change in receptor mobility. Conversely, it should be possible to infer from receptor mobility whether a cell has been treated with internalin B. Here, we propose a method based on hidden Markov modeling and explainable artificial intelligence that machine-learns the key differences in MET mobility between internalin B–treated and –untreated cells from single-particle tracking data. Our method assigns receptor mobility to three diffusion modes (immobile, slow, and fast). It discriminates between internalin B–treated and –untreated cells with a balanced accuracy of >99% and identifies three parameters that are most affected by internalin B treatment: a decrease in the mobility of slow molecules (1) and a depopulation of the fast mode (2) caused by an increased transition of fast molecules to the slow mode (3). Our approach is based entirely on free software and is readily applicable to the analysis of other membrane receptors.
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Affiliation(s)
- Sebastian Malkusch
- Institute of Clinical Pharmacology, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Johanna V Rahm
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Marina S Dietz
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Jean-Baptiste Sibarita
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France
| | - Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
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3
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Stapornwongkul KS, Vincent JP. Generation of extracellular morphogen gradients: the case for diffusion. Nat Rev Genet 2021; 22:393-411. [PMID: 33767424 DOI: 10.1038/s41576-021-00342-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Cells within developing tissues rely on morphogens to assess positional information. Passive diffusion is the most parsimonious transport model for long-range morphogen gradient formation but does not, on its own, readily explain scaling, robustness and planar transport. Here, we argue that diffusion is sufficient to ensure robust morphogen gradient formation in a variety of tissues if the interactions between morphogens and their extracellular binders are considered. A current challenge is to assess how the affinity for extracellular binders, as well as other biophysical and cell biological parameters, determines gradient dynamics and shape in a diffusion-based transport system. Technological advances in genome editing, tissue engineering, live imaging and in vivo biophysics are now facilitating measurement of these parameters, paving the way for mathematical modelling and a quantitative understanding of morphogen gradient formation and modulation.
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4
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A quantitative view on multivalent nanomedicine targeting. Adv Drug Deliv Rev 2021; 169:1-21. [PMID: 33264593 DOI: 10.1016/j.addr.2020.11.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/11/2020] [Accepted: 11/21/2020] [Indexed: 12/17/2022]
Abstract
Although the concept of selective delivery has been postulated over 100 years ago, no targeted nanomedicine has been clinically approved so far. Nanoparticles modified with targeting ligands to promote the selective delivery of therapeutics towards a specific cell population have been extensively reported. However, the rational design of selective particles is still challenging. One of the main reasons for this is the lack of quantitative theoretical and experimental understanding of the interactions involved in cell targeting. In this review, we discuss new theoretical models and experimental methods that provide a quantitative view of targeting. We show the new advancements in multivalency theory enabling the rational design of super-selective nanoparticles. Furthermore, we present the innovative approaches to obtain key targeting parameters at the single-cell and single molecule level and their role in the design of targeting nanoparticles. We believe that the combination of new theoretical multivalent design and experimental methods to quantify receptors and ligands aids in the rational design and clinical translation of targeted nanomedicines.
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5
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Dietz MS, Wehrheim SS, Harwardt MLIE, Niemann HH, Heilemann M. Competitive Binding Study Revealing the Influence of Fluorophore Labels on Biomolecular Interactions. NANO LETTERS 2019; 19:8245-8249. [PMID: 31621335 DOI: 10.1021/acs.nanolett.9b03736] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fluorescence methods are important tools in modern biology. Direct labeling of biomolecules with a fluorophore might, however, change interaction surfaces. Here, we introduce a competitive binding assay in combination with fluorescence correlation spectroscopy that reports binding affinities of both labeled and unlabeled biomolecules to their binding target. We investigated how fluorophore labels at different positions of a DNA oligonucleotide affect hybridization to a complementary oligonucleotide and found dissociation constants varying within 2 orders of magnitude. We next demonstrated that placing a fluorophore label at position Leu280 in the protein ligand internalin B does not alter the binding affinity to the MET receptor tyrosine kinase, compared to unlabeled internalin B. Our approach is simple to implement and can be applied to investigate the influence of fluorophore labels in a large variety of biomolecular interactions.
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Affiliation(s)
- Marina S Dietz
- Single-Molecule Biophysics, Institute of Physical and Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Straße 7 , 60438 Frankfurt/Main , Germany
| | - S Sophia Wehrheim
- Single-Molecule Biophysics, Institute of Physical and Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Straße 7 , 60438 Frankfurt/Main , Germany
| | - Marie-Lena I E Harwardt
- Single-Molecule Biophysics, Institute of Physical and Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Straße 7 , 60438 Frankfurt/Main , Germany
| | - Hartmut H Niemann
- Structural Biochemistry, Department of Chemistry , Bielefeld University , Universitätsstraße 25 , 33615 Bielefeld , Germany
| | - Mike Heilemann
- Single-Molecule Biophysics, Institute of Physical and Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Straße 7 , 60438 Frankfurt/Main , Germany
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6
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Dietz MS, Heilemann M. Optical super-resolution microscopy unravels the molecular composition of functional protein complexes. NANOSCALE 2019; 11:17981-17991. [PMID: 31573593 DOI: 10.1039/c9nr06364a] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Optical super-resolution microscopy has revolutionized our understanding of cell biology. Next to visualizing cellular structures with near-molecular spatial resolution, an additional benefit is the molecular characterization of biomolecular complexes directly in an intact cell. Single-molecule localization microscopy, as one technology out of the toolbox of super-resolution methods, generates images by detecting the position of single fluorophore labels and is particularly suited for molecular quantification. We review imaging and analysis methods employing single-molecule localization microscopy and extract molecule numbers.
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Affiliation(s)
- Marina S Dietz
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany.
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7
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Matveeva A, Fichtner M, McAllister K, McCann C, Sturrock M, Longley DB, Prehn JHM. Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform. PLoS Comput Biol 2019; 15:e1007374. [PMID: 31553717 PMCID: PMC6779275 DOI: 10.1371/journal.pcbi.1007374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 10/07/2019] [Accepted: 09/03/2019] [Indexed: 01/29/2023] Open
Abstract
Ligand binding to death receptors activates apoptosis in cancer cells. Stimulation of death receptors results in the formation of intracellular multiprotein platforms that either activate the apoptotic initiator Caspase-8 to trigger cell death, or signal through kinases to initiate inflammatory and cell survival signalling. Two of these platforms, the Death-Inducing Signalling Complex (DISC) and the RIPoptosome, also initiate necroptosis by building filamentous scaffolds that lead to the activation of mixed lineage kinase domain-like pseudokinase. To explain cell decision making downstream of death receptor activation, we developed a semi-stochastic model of DISC/RIPoptosome formation. The model is a hybrid of a direct Gillespie stochastic simulation algorithm for slow assembly of the RIPoptosome and a deterministic model of downstream caspase activation. The model explains how alterations in the level of death receptor-ligand complexes, their clustering properties and intrinsic molecular fluctuations in RIPoptosome assembly drive heterogeneous dynamics of Caspase-8 activation. The model highlights how kinetic proofreading leads to heterogeneous cell responses and results in fractional cell killing at low levels of receptor stimulation. It reveals that the noise in Caspase-8 activation-exclusively caused by the stochastic molecular assembly of the DISC/RIPoptosome platform-has a key function in extrinsic apoptotic stimuli recognition.
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Affiliation(s)
- Anna Matveeva
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Michael Fichtner
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Katherine McAllister
- Centre for Cancer Research and Cell Biology, Queen’s University, Belfast, United Kingdom
| | - Christopher McCann
- Centre for Cancer Research and Cell Biology, Queen’s University, Belfast, United Kingdom
| | - Marc Sturrock
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Daniel B. Longley
- Centre for Cancer Research and Cell Biology, Queen’s University, Belfast, United Kingdom
| | - Jochen H. M. Prehn
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- * E-mail:
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8
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Golfetto O, Wakefield DL, Cacao EE, Avery KN, Kenyon V, Jorand R, Tobin SJ, Biswas S, Gutierrez J, Clinton R, Ma Y, Horne DA, Williams JC, Jovanović-Talisman T. A Platform To Enhance Quantitative Single Molecule Localization Microscopy. J Am Chem Soc 2018; 140:12785-12797. [PMID: 30256630 PMCID: PMC6187371 DOI: 10.1021/jacs.8b04939] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Quantitative single molecule localization microscopy (qSMLM) is a powerful approach to study in situ protein organization. However, uncertainty regarding the photophysical properties of fluorescent reporters can bias the interpretation of detected localizations and subsequent quantification. Furthermore, strategies to efficiently detect endogenous proteins are often constrained by label heterogeneity and reporter size. Here, a new surface assay for molecular isolation (SAMI) was developed for qSMLM and used to characterize photophysical properties of fluorescent proteins and dyes. SAMI-qSMLM afforded robust quantification. To efficiently detect endogenous proteins, we used fluorescent ligands that bind to a specific site on engineered antibody fragments. Both the density and nano-organization of membrane-bound epidermal growth factor receptors (EGFR, HER2, and HER3) were determined by a combination of SAMI, antibody engineering, and pair-correlation analysis. In breast cancer cell lines, we detected distinct differences in receptor density and nano-organization upon treatment with therapeutic agents. This new platform can improve molecular quantification and can be developed to study the local protein environment of intact cells.
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Affiliation(s)
- Ottavia Golfetto
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Devin L Wakefield
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Eliedonna E Cacao
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Kendra N Avery
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Victor Kenyon
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Raphael Jorand
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Steven J Tobin
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Sunetra Biswas
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Jennifer Gutierrez
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Ronald Clinton
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Yuelong Ma
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - David A Horne
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - John C Williams
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Tijana Jovanović-Talisman
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
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9
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Oppelt A, Kaschek D, Huppelschoten S, Sison-Young R, Zhang F, Buck-Wiese M, Herrmann F, Malkusch S, Krüger CL, Meub M, Merkt B, Zimmermann L, Schofield A, Jones RP, Malik H, Schilling M, Heilemann M, van de Water B, Goldring CE, Park BK, Timmer J, Klingmüller U. Model-based identification of TNFα-induced IKKβ-mediated and IκBα-mediated regulation of NFκB signal transduction as a tool to quantify the impact of drug-induced liver injury compounds. NPJ Syst Biol Appl 2018; 4:23. [PMID: 29900006 PMCID: PMC5995845 DOI: 10.1038/s41540-018-0058-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 04/16/2018] [Accepted: 05/04/2018] [Indexed: 02/07/2023] Open
Abstract
Drug-induced liver injury (DILI) has become a major problem for patients and for clinicians, academics and the pharmaceutical industry. To date, existing hepatotoxicity test systems are only poorly predictive and the underlying mechanisms are still unclear. One of the factors known to amplify hepatotoxicity is the tumor necrosis factor alpha (TNFα), especially due to its synergy with commonly used drugs such as diclofenac. However, the exact mechanism of how diclofenac in combination with TNFα induces liver injury remains elusive. Here, we combined time-resolved immunoblotting and live-cell imaging data of HepG2 cells and primary human hepatocytes (PHH) with dynamic pathway modeling using ordinary differential equations (ODEs) to describe the complex structure of TNFα-induced NFκB signal transduction and integrated the perturbations of the pathway caused by diclofenac. The resulting mathematical model was used to systematically identify parameters affected by diclofenac. These analyses showed that more than one regulatory module of TNFα-induced NFκB signal transduction is affected by diclofenac, suggesting that hepatotoxicity is the integrated consequence of multiple changes in hepatocytes and that multiple factors define toxicity thresholds. Applying our mathematical modeling approach to other DILI-causing compounds representing different putative DILI mechanism classes enabled us to quantify their impact on pathway activation, highlighting the potential of the dynamic pathway model as a quantitative tool for the analysis of DILI compounds.
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Affiliation(s)
- Angela Oppelt
- 1Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Kaschek
- 2Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Suzanna Huppelschoten
- 3Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Rowena Sison-Young
- 4MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Fang Zhang
- 4MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Marie Buck-Wiese
- 1Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Franziska Herrmann
- 1Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Malkusch
- 5Institute of Physical and Theoretical Chemistry, Single Molecule Biophysics, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Carmen L Krüger
- 5Institute of Physical and Theoretical Chemistry, Single Molecule Biophysics, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Mara Meub
- 5Institute of Physical and Theoretical Chemistry, Single Molecule Biophysics, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Benjamin Merkt
- 2Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Lea Zimmermann
- 1Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amy Schofield
- 4MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Robert P Jones
- 4MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK.,6North Western Hepatobiliary Unit, Aintree University Hospital NHS Foundation Trust, Liverpool, UK
| | - Hassan Malik
- 6North Western Hepatobiliary Unit, Aintree University Hospital NHS Foundation Trust, Liverpool, UK
| | - Marcel Schilling
- 1Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mike Heilemann
- 5Institute of Physical and Theoretical Chemistry, Single Molecule Biophysics, Johann Wolfgang Goethe-University, Frankfurt, Germany.,7Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Bob van de Water
- 3Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Christopher E Goldring
- 4MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - B Kevin Park
- 4MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Jens Timmer
- 2Institute of Physics, University of Freiburg, Freiburg, Germany.,8BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Ursula Klingmüller
- 1Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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Roch T, Hahne S, Kratz K, Ma N, Lendlein A. Transparent Substrates Prepared From Different Amorphous Polymers Can Directly Modulate Primary Human B cell functions. Biotechnol J 2017; 12. [PMID: 28857458 DOI: 10.1002/biot.201700334] [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: 05/05/2017] [Revised: 08/17/2017] [Indexed: 11/08/2022]
Abstract
Manipulation of B cell functions such as antibody and cytokine secretion, is of clinical and biotechnological interest and can be achieved by soluble ligands activating cell surface receptors. Alternatively, the exposure to suitable solid substrates would offer the possibility to transiently induced cell signaling, since the signaling is interrupted when the cells are removed from the substrate. Cell/substrate interactions are mediated by physical valences such as, hydrogen bonds or hydrophobic forces on the substrate surface. Therefore, in this study B cells were cultivated on polymeric substrates, differing in their chemical composition and thus their capacity to undergo physical interactions. Activated B cells cultivated on polystyrene (PS) showed an altered cytokine response indicated by increased IL-10 and decreased IL-6 secretion. Interestingly, B cells cultivated on polyetherurethane (PEU), which has among all tested polymers the highest potential to form strong hydrogen bonds showed an impaired activation, which could be restored by re-cultivation on tissue culture polystyrene. The results indicate that B cell behavior can transiently be manipulated solely by interacting with polymeric surface, which could be explained by receptor activation mediated by physical interaction with the substrate or by altering the availability of the soluble stimulatory reagents by adsorption processes.
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Affiliation(s)
- Toralf Roch
- Institute of Biomaterial Science and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Helmholtz-Zentrum Geesthacht, Kantstraße 55, 14513 Teltow, Germany.,Helmholtz Virtual Institute - Multifunctional Biomaterials for Medicine, Kantstr. 55, 14513 Teltow, Germany
| | - Stefanie Hahne
- Institute of Biomaterial Science and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Helmholtz-Zentrum Geesthacht, Kantstraße 55, 14513 Teltow, Germany
| | - Karl Kratz
- Institute of Biomaterial Science and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Helmholtz-Zentrum Geesthacht, Kantstraße 55, 14513 Teltow, Germany.,Helmholtz Virtual Institute - Multifunctional Biomaterials for Medicine, Kantstr. 55, 14513 Teltow, Germany
| | - Nan Ma
- Institute of Biomaterial Science and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Helmholtz-Zentrum Geesthacht, Kantstraße 55, 14513 Teltow, Germany.,Helmholtz Virtual Institute - Multifunctional Biomaterials for Medicine, Kantstr. 55, 14513 Teltow, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Andreas Lendlein
- Institute of Biomaterial Science and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Helmholtz-Zentrum Geesthacht, Kantstraße 55, 14513 Teltow, Germany.,Helmholtz Virtual Institute - Multifunctional Biomaterials for Medicine, Kantstr. 55, 14513 Teltow, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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11
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Lesitha Jeeva Kumari J, Jesu Jaya Sudan R, Sudandiradoss C. Evaluation of peptide designing strategy against subunit reassociation in mucin 1: A steered molecular dynamics approach. PLoS One 2017; 12:e0183041. [PMID: 28817726 PMCID: PMC5560680 DOI: 10.1371/journal.pone.0183041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/30/2017] [Indexed: 12/20/2022] Open
Abstract
Subunit reassociation in mucin 1, a breast cancer tumor marker, is reported as one of the critical factors for its cytoplasmic activation. Inhibition of its heterodimeric association would therefore result in loss of its function and alter disease progression. The present study aimed at evaluating peptide inhibitor designing strategies that may serve as antagonist against this receptor-ligand alliance. Several peptides and their derivatives were designed based on native residues, subunit interface, hydrogen bonding and secondary structure. Docking studies with the peptides were carried on the receptor subunit and their binding affinities were evaluated using steered molecular dynamics simulation and umbrella sampling. Our results showed that among all the different classes of peptides evaluated, the receptor based peptide showed the highest binding affinity. This result was concurrent with the experimental observation that the receptor-ligand alliance in mucin 1 is highly specific. Our results also show that peptide ligand against this subunit association is only stabilized through native residue inter-protein interaction irrespective of the peptide structure, peptide length and number of hydrogen bonds. Consistency in binding affinity, pull force and free energy barrier was observed with only the receptor derived peptides which resulted in favorable interprotein interactions at the interface. Several observations were made and discussed which will eventually lead to designing efficient peptide inhibitors against mucin 1 heterodimeric subunit reassociation.
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Affiliation(s)
- J. Lesitha Jeeva Kumari
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore, India
| | - R. Jesu Jaya Sudan
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore, India
| | - C. Sudandiradoss
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore, India
- * E-mail:
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12
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Polajnar M, Dietz MS, Heilemann M, Behrends C. Expanding the host cell ubiquitylation machinery targeting cytosolic Salmonella. EMBO Rep 2017; 18:1572-1585. [PMID: 28784601 DOI: 10.15252/embr.201643851] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 06/26/2017] [Accepted: 06/30/2017] [Indexed: 12/16/2022] Open
Abstract
Ubiquitylation is one of the cardinal post-translational modifications in the cell, balancing several distinct biological processes and acting as a pathogen recognition receptor during bacterial pathogen invasion. A dense layer of polyubiquitin chains marks invading bacteria that gain access to the host cytosol for their selective clearance via xenophagy. However, the enzymes that mediate recognition of cytosolic bacteria and generate this ubiquitin (Ub) coat remain largely elusive. To address this, we employed an image-based RNAi screening approach to monitor the loss of Ub on Salmonella upon depletion of human Ub E3 ligases in cells. Using this approach, we identified ARIH1 as one of the ligases involved in the formation of Ub coat on cytosolic bacteria. In addition, we provide evidence that the RING-between-RING ligase ARIH1, together with LRSAM1 and HOIP, forms part of a network of ligases that orchestrates recognition of intracellular Salmonella and participates in the activation of the host cell immune response.
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Affiliation(s)
- Mira Polajnar
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Munich Cluster for Systems Neurology (SyNergy), Medical Faculty, Ludwig-Maximilians-University München, München, Germany
| | - Marina S Dietz
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Christian Behrends
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany .,Munich Cluster for Systems Neurology (SyNergy), Medical Faculty, Ludwig-Maximilians-University München, München, Germany
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13
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Abstract
Imaging is widely used in anticancer drug development, typically for whole-body tracking of labelled drugs to different organs or to assess drug efficacy through volumetric measurements. However, increasing attention has been drawn to pharmacology at the single-cell level. Diverse cell types, including cancer-associated immune cells, physicochemical features of the tumour microenvironment and heterogeneous cell behaviour all affect drug delivery, response and resistance. This Review summarizes developments in the imaging of in vivo anticancer drug action, with a focus on microscopy approaches at the single-cell level and translational lessons for the clinic.
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Affiliation(s)
- Miles A. Miller
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA
- Department of Systems Biology, Harvard Medical School, Boston, MA
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14
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Linear ubiquitination of cytosolic Salmonella Typhimurium activates NF-κB and restricts bacterial proliferation. Nat Microbiol 2017; 2:17066. [DOI: 10.1038/nmicrobiol.2017.66] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/28/2017] [Indexed: 12/11/2022]
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15
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Beuke K, Schildberg FA, Pinna F, Albrecht U, Liebe R, Bissinger M, Schirmacher P, Dooley S, Bode JG, Knolle PA, Kummer U, Breuhahn K, Sahle S. Quantitative and integrative analysis of paracrine hepatocyte activation by nonparenchymal cells upon lipopolysaccharide induction. FEBS J 2017; 284:796-813. [PMID: 28109179 DOI: 10.1111/febs.14022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 12/02/2016] [Accepted: 01/18/2017] [Indexed: 12/14/2022]
Abstract
Gut-derived bacterial lipopolysaccharides (LPS) stimulate the secretion of tumour necrosis factor (TNF) from liver macrophages (MCs), liver sinusoidal endothelial cells (LSECs) and hepatic stellate cells (HSCs), which control the acute phase response in hepatocytes through activation of the NF-κB pathway. The individual and cooperative impact of nonparenchymal cells on this clinically relevant response has not been analysed in detail due to technical limitations. To gain an integrative view on this complex inter- and intracellular communication, we combined a multiscale mathematical model with quantitative, time-resolved experimental data of different primary murine liver cell types. We established a computational model for TNF-induced NF-κB signalling in hepatocytes, accurately describing dose-responsiveness for physiologically relevant cytokine concentrations. TNF secretion profiles were quantitatively measured for all nonparenchymal cell types upon LPS stimulation. This novel approach allowed the analysis of individual and collective paracrine TNF-mediated NF-κB induction in hepatocytes, revealing strongest effects of MCs and LSECs on hepatocellular NF-κB signalling. Simulations suggest that both cell types act together to maximize the NF-κB pathway response induced by low LPS concentrations (0.1 and 1 ng/mL). Higher LPS concentrations (≥ 5 ng/mL) induced sufficient TNF levels from MCs or LSECs to induce a strong and nonadjustable pathway response. Importantly, these simulations also revealed that the initial cytokine secretion (1-2 h after stimulation) rather than final TNF level (10 h after stimulation) defines the hepatocellular NF-κB response. This raises the question whether the current experimental standard of single high-dose cytokine administration is suitable to mimic in vivo cytokine exposure. DATABASE The computational models described in this manuscript are available in the JWS database via the following link: https://jjj.bio.vu.nl/database/beuke.
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Affiliation(s)
- Katharina Beuke
- Department of Modeling of Biological Processes, COS Heidelberg/BIOQUANT, Heidelberg University, Germany
| | - Frank A Schildberg
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Federico Pinna
- Institute of Pathology, University Hospital of Heidelberg, Germany
| | - Ute Albrecht
- Clinic for Gastroenterology, Heinrich-Heine-University of Düsseldorf, Germany
| | - Roman Liebe
- Molecular Hepatology, Department of Medicine II, Medical Faculty at Mannheim, Heidelberg University, Germany
| | | | | | - Steven Dooley
- Molecular Hepatology, Department of Medicine II, Medical Faculty at Mannheim, Heidelberg University, Germany
| | - Johannes G Bode
- Clinic for Gastroenterology, Heinrich-Heine-University of Düsseldorf, Germany
| | - Percy A Knolle
- Institute of Molecular Immunology and Experimental Oncology, München Rechts der Isar, Technische Universität München, Germany
| | - Ursula Kummer
- Department of Modeling of Biological Processes, COS Heidelberg/BIOQUANT, Heidelberg University, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital of Heidelberg, Germany
| | - Sven Sahle
- Department of Modeling of Biological Processes, COS Heidelberg/BIOQUANT, Heidelberg University, Germany
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16
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Zeuner MT, Krüger CL, Volk K, Bieback K, Cottrell GS, Heilemann M, Widera D. Biased signalling is an essential feature of TLR4 in glioma cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:3084-3095. [PMID: 27669113 DOI: 10.1016/j.bbamcr.2016.09.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 01/19/2023]
Abstract
A distinct feature of the Toll-like receptor 4 (TLR4) is its ability to trigger both MyD88-dependent and MyD88-independent signalling, culminating in activation of pro-inflammatory NF-κB and/or the antiviral IRF3. Although TLR4 agonists (lipopolysaccharides; LPSs) derived from different bacterial species have different endotoxic activity, the impact of LPS chemotype on the downstream signalling is not fully understood. Notably, different TLR4 agonists exhibit anti-tumoural activity in animal models of glioma, but the underlying molecular mechanisms are largely unknown. Thus, we investigated the impact of LPS chemotype on the signalling events in the human glioma cell line U251. We found that LPS of Escherichia coli origin (LPSEC) leads to NF-κB-biased downstream signalling compared to Salmonella minnesota-derived LPS (LPSSM). Exposure of U251 cells to LPSEC resulted in faster nuclear translocation of the NF-κB subunit p65, higher NF-κB-activity and expression of its targets genes, and higher amount of secreted IL-6 compared to LPSSM. Using super-resolution microscopy we showed that the biased agonism of TLR4 in glioma cells is neither a result of differential regulation of receptor density nor of formation of higher order oligomers. Consistent with previous reports, LPSEC-mediated NF-κB activation led to significantly increased U251 proliferation, whereas LPSSM-induced IRF3 activity negatively influenced their invasiveness. Finally, treatment with methyl-β-cyclodextrin (MCD) selectively increased LPSSM-induced nuclear translocation of p65 and NF-κB activity without affecting IRF3. Our data may explain how TLR4 agonists differently affect glioma cell proliferation and migration.
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Affiliation(s)
- Marie-Theres Zeuner
- Stem Cell Biology and Regenerative Medicine, School of Pharmacy, University of Reading, Reading, United Kingdom
| | - Carmen L Krüger
- Institute of Physical and Theoretical Chemistry, Goethe-University, Frankfurt, Germany
| | - Katharina Volk
- Department of Cell Biology, University of Bielefeld, Bielefeld, Germany
| | - Karen Bieback
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Graeme S Cottrell
- Cellular and Molecular Neuroscience, School of Pharmacy, University of Reading, Reading, United Kingdom
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University, Frankfurt, Germany
| | - Darius Widera
- Stem Cell Biology and Regenerative Medicine, School of Pharmacy, University of Reading, Reading, United Kingdom.
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17
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Xiao L, Wang H, Schultz ZD. Selective Detection of RGD-Integrin Binding in Cancer Cells Using Tip Enhanced Raman Scattering Microscopy. Anal Chem 2016; 88:6547-53. [PMID: 27189228 DOI: 10.1021/acs.analchem.6b01344] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ligand-receptor interactions play important roles in many biological processes. Cyclic arginine-glycine-aspartic acid (RGD) containing peptides are known to mimic the binding domain of extracellular matrix protein fibronectin and selectively bind to a subset of integrin receptors. Here we report the tip enhanced Raman scattering (TERS) detection of RGD-functionalized nanoparticles bound to integrins produces a Raman scattering signal specific to the bound protein. These results demonstrate that this method can detect and differentiate between two different integrins (α5β1 and αvβ3) bound to RGD-conjugated gold nanoparticles both on surfaces and in a cancer cell membrane. In situ measurements of RGD nanoparticles bound to purified α5β1 and αvβ3 receptors attached to a glass surface provide reference spectra for a multivariate regression model. The TERS spectra observed from nanoparticles bound to cell membranes are analyzed using this regression model and the identity of the receptor can be determined. The ability to distinguish between receptors in the cell membrane provides a new tool to chemically characterize ligand-receptor recognition at molecular level and provide chemical perspective on the molecular recognition of membrane receptors.
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Affiliation(s)
- Lifu Xiao
- Department of Chemistry & Biochemistry, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Hao Wang
- Department of Chemistry & Biochemistry, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Zachary D Schultz
- Department of Chemistry & Biochemistry, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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18
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Kollmannsperger A, Sharei A, Raulf A, Heilemann M, Langer R, Jensen KF, Wieneke R, Tampé R. Live-cell protein labelling with nanometre precision by cell squeezing. Nat Commun 2016; 7:10372. [PMID: 26822409 PMCID: PMC4740111 DOI: 10.1038/ncomms10372] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/30/2015] [Indexed: 11/08/2022] Open
Abstract
Live-cell labelling techniques to visualize proteins with minimal disturbance are important; however, the currently available methods are limited in their labelling efficiency, specificity and cell permeability. We describe high-throughput protein labelling facilitated by minimalistic probes delivered to mammalian cells by microfluidic cell squeezing. High-affinity and target-specific tracing of proteins in various subcellular compartments is demonstrated, culminating in photoinduced labelling within live cells. Both the fine-tuned delivery of subnanomolar concentrations and the minimal size of the probe allow for live-cell super-resolution imaging with very low background and nanometre precision. This method is fast in probe delivery (∼ 1,000,000 cells per second), versatile across cell types and can be readily transferred to a multitude of proteins. Moreover, the technique succeeds in combination with well-established methods to gain multiplexed labelling and has demonstrated potential to precisely trace target proteins, in live mammalian cells, by super-resolution microscopy.
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Affiliation(s)
- Alina Kollmannsperger
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt/Main, Germany
| | - Armon Sharei
- Department of Chemical Engineering, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), 500 Main Street, Building 76-661, Cambridge, Massachusetts 02139, USA
| | - Anika Raulf
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Robert Langer
- Department of Chemical Engineering, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), 500 Main Street, Building 76-661, Cambridge, Massachusetts 02139, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), 500 Main Street, Building 76-661, Cambridge, Massachusetts 02139, USA
| | - Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt/Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt/Main, Germany
- Cluster of Excellence—Macromolecular Complexes, Goethe-University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt/Main, Germany
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19
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Zessin PJM, Sporbert A, Heilemann M. PCNA appears in two populations of slow and fast diffusion with a constant ratio throughout S-phase in replicating mammalian cells. Sci Rep 2016; 6:18779. [PMID: 26758689 PMCID: PMC4725372 DOI: 10.1038/srep18779] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/26/2015] [Indexed: 01/14/2023] Open
Abstract
DNA replication is a fundamental cellular process that precedes cell division. Proliferating cell nuclear antigen (PCNA) is a central scaffold protein that orchestrates DNA replication by recruiting many factors essential for the replication machinery. We studied the mobility of PCNA in live mammalian cells using single-particle tracking in combination with photoactivated-localization microscopy (sptPALM) and found two populations. The first population which is only present in cells with active DNA replication, showed slow diffusion and was found to be located in replication foci. The second population showed fast diffusion, and represents the nucleoplasmic pool of unbound PCNA not involved in DNA replication. The ratio of these two populations remained constant throughout different stages of S-phase. A fraction of molecules in both populations showed spatially constrained mobility. We determined an exploration radius of ~100 nm for 13% of the slow-diffusing PCNA molecules, and of ~600 nm for 46% of the fast-diffusing PCNA molecules.
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Affiliation(s)
- Patrick J M Zessin
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt/Main, Germany
| | - Anje Sporbert
- Advanced Light Microscopy, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt/Main, Germany
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20
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Kim DH, Zhou K, Kim DK, Park S, Noh J, Kwon Y, Kim D, Song NW, Lee JB, Suh PG, Lee NK, Ryu SH. Analysis of Interactions between the Epidermal Growth Factor Receptor and Soluble Ligands on the Basis of Single-Molecule Diffusivity in the Membrane of Living Cells. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Kim DH, Zhou K, Kim DK, Park S, Noh J, Kwon Y, Kim D, Song NW, Lee JB, Suh PG, Lee NK, Ryu SH. Analysis of Interactions between the Epidermal Growth Factor Receptor and Soluble Ligands on the Basis of Single-Molecule Diffusivity in the Membrane of Living Cells. Angew Chem Int Ed Engl 2015; 54:7028-32. [DOI: 10.1002/anie.201500871] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/01/2015] [Indexed: 11/06/2022]
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22
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Fricke F, Dietz MS, Heilemann M. Single-Molecule Methods to Study Membrane Receptor Oligomerization. Chemphyschem 2014; 16:713-21. [DOI: 10.1002/cphc.201402765] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Indexed: 11/06/2022]
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23
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Coltharp C, Yang X, Xiao J. Quantitative analysis of single-molecule superresolution images. Curr Opin Struct Biol 2014; 28:112-21. [PMID: 25179006 DOI: 10.1016/j.sbi.2014.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/14/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022]
Abstract
This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10-50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images.
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Affiliation(s)
- Carla Coltharp
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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24
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Fricke F, Malkusch S, Wangorsch G, Greiner JF, Kaltschmidt B, Kaltschmidt C, Widera D, Dandekar T, Heilemann M. Quantitative single-molecule localization microscopy combined with rule-based modeling reveals ligand-induced TNF-R1 reorganization toward higher-order oligomers. Histochem Cell Biol 2014; 142:91-101. [DOI: 10.1007/s00418-014-1195-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2014] [Indexed: 11/27/2022]
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