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Drexhage LZ, Zhang S, Dupont M, Ragaller F, Sjule E, Cabezas-Caballero J, Deimel LP, Robertson H, Russell RA, Dushek O, Sezgin E, Karaji N, Sattentau QJ. Apoptosis-mediated ADAM10 activation removes a mucin barrier promoting T cell efferocytosis. Nat Commun 2024; 15:541. [PMID: 38225245 PMCID: PMC10789802 DOI: 10.1038/s41467-023-44619-8] [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: 04/19/2023] [Accepted: 12/22/2023] [Indexed: 01/17/2024] Open
Abstract
Efferocytic clearance of apoptotic cells in general, and T cells in particular, is required for tissue and immune homeostasis. Transmembrane mucins are extended glycoproteins highly expressed in the cell glycocalyx that function as a barrier to phagocytosis. Whether and how mucins may be regulated during cell death to facilitate efferocytic corpse clearance is not well understood. Here we show that normal and transformed human T cells express a subset of mucins which are rapidly and selectively removed from the cell surface during apoptosis. This process is mediated by the ADAM10 sheddase, the activity of which is associated with XKR8-catalyzed flipping of phosphatidylserine to the outer leaflet of the plasma membrane. Mucin clearance enhances uptake of apoptotic T cells by macrophages, confirming mucins as an enzymatically-modulatable barrier to efferocytosis. Together these findings demonstrate a glycocalyx regulatory pathway with implications for therapeutic intervention in the clearance of normal and transformed apoptotic T cells.
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Affiliation(s)
- Linnea Z Drexhage
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, OX13RE, UK
| | - Shengpan Zhang
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, OX13RE, UK
| | - Maeva Dupont
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, OX13RE, UK
- Immunocore Ltd., 92 Park Dr, Milton, Abingdon, OX14 4RY, UK
| | - Franziska Ragaller
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165, Solna, Sweden
| | - Ellen Sjule
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165, Solna, Sweden
| | | | - Lachlan P Deimel
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, OX13RE, UK
| | - Helen Robertson
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, OX13RE, UK
| | - Rebecca A Russell
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, OX13RE, UK
- SpyBiotech Ltd.; 7600 Quorum, Oxford Business Park North, Oxford, OX4 2JZ, UK
| | - Omer Dushek
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, OX13RE, UK
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165, Solna, Sweden
| | - Niloofar Karaji
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, OX13RE, UK.
- Oxford Biomedica plc.; Windrush Court, Transport Way, Oxford, OX4 6LT, UK.
| | - Quentin J Sattentau
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, OX13RE, UK.
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association; Berlin-Buch, 13125, Berlin, Germany.
- Experimental and Clinical Research Center (ECRC), Charité Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany.
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2
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Rice LJ, Ecroyd H, van Oijen AM. Illuminating amyloid fibrils: Fluorescence-based single-molecule approaches. Comput Struct Biotechnol J 2021; 19:4711-4724. [PMID: 34504664 PMCID: PMC8405898 DOI: 10.1016/j.csbj.2021.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022] Open
Abstract
The aggregation of proteins into insoluble filamentous amyloid fibrils is a pathological hallmark of neurodegenerative diseases that include Parkinson's disease and Alzheimer's disease. Since the identification of amyloid fibrils and their association with disease, there has been much work to describe the process by which fibrils form and interact with other proteins. However, due to the dynamic nature of fibril formation and the transient and heterogeneous nature of the intermediates produced, it can be challenging to examine these processes using techniques that rely on traditional ensemble-based measurements. Single-molecule approaches overcome these limitations as rare and short-lived species within a population can be individually studied. Fluorescence-based single-molecule methods have proven to be particularly useful for the study of amyloid fibril formation. In this review, we discuss the use of different experimental single-molecule fluorescence microscopy approaches to study amyloid fibrils and their interaction with other proteins, in particular molecular chaperones. We highlight the mechanistic insights these single-molecule techniques have already provided in our understanding of how fibrils form, and comment on their potential future use in studying amyloid fibrils and their intermediates.
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Affiliation(s)
- Lauren J. Rice
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Antoine M. van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
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3
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Williams ND, Landajuela A, Kasula RK, Zhou W, Powell JT, Xi Z, Isaacs FJ, Berro J, Toomre D, Karatekin E, Lin C. DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells. NANO LETTERS 2020; 20:8890-8896. [PMID: 33164530 PMCID: PMC7726105 DOI: 10.1021/acs.nanolett.0c03925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fluorescence microscopy has been one of the most discovery-rich methods in biology. In the digital age, the discipline is becoming increasingly quantitative. Virtually all biological laboratories have access to fluorescence microscopes, but abilities to quantify biomolecule copy numbers are limited by the complexity and sophistication associated with current quantification methods. Here, we present DNA-origami-based fluorescence brightness standards for counting 5-300 copies of proteins in bacterial and mammalian cells, tagged with fluorescent proteins or membrane-permeable organic dyes. Compared to conventional quantification techniques, our brightness standards are robust, straightforward to use, and compatible with nearly all fluorescence imaging applications, thereby providing a practical and versatile tool to quantify biomolecules via fluorescence microscopy.
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Affiliation(s)
- Nathan D. Williams
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
| | - Ane Landajuela
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
- Department of Cellular and Molecular Physiology, Yale
University School of Medicine, New Haven, CT 06520, USA
| | - Ravi Kiran Kasula
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
| | - Wenjiao Zhou
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
| | - John T. Powell
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
| | - Zhiqun Xi
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
| | - Farren J. Isaacs
- Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, CT 06520, USA
- Department of Biomedical Engineering, Yale University, New
Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT
06516, USA
| | - Julien Berro
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
- Department of Molecular Biophysics and Biochemistry, New
Haven, CT 06520, USA
| | - Derek Toomre
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
| | - Erdem Karatekin
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
- Department of Cellular and Molecular Physiology, Yale
University School of Medicine, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, New
Haven, CT 06520, USA
- Université de Paris, SPPIN –
Saints-Pères Paris Institute for the Neurosciences, Centre National de la
Recherche Scientifique (CNRS), F-75006 Paris, France
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
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4
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Su D, Huang X, Dong C, Ren J. Quantitative Determination of Telomerase Activity by Combining Fluorescence Correlation Spectroscopy with Telomerase Repeat Amplification Protocol. Anal Chem 2017; 90:1006-1013. [PMID: 29211436 DOI: 10.1021/acs.analchem.7b04256] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Telomerase is a key enzyme for maintaining the telomere length and is regarded as a versatile cancer biomarker and a potential drug target due to its important role in cancer and aging. It is necessary to develop a sensitive and reliable method for detection of telomerase activity due to its very low level in cells. In this Article, we propose an ultrasensitive and robust method for quantitative determination of telomerase activity by combining single molecule fluorescence correlation spectroscopy (FCS) with telomerase repeat amplification protocol (TRAP). The principle of this new method (FCS-TRAP) is based on measurement of the change in characteristic diffusion time and molecule number of TRAP products by FCS. The characteristic diffusion time is related to the length of TRAP products, and the molecule number represents the concentration of TRAP products. We optimized the conditions of TRAP procedure and FCS measurements. We observed that the telomerase activities are positively correlated to characteristic diffusion time and molecule number of TRAP products at optimal conditions. This method was successfully used for determination of telomerase activity of different cells, and detection of a single cell was realized. Meanwhile, this method was used to evaluate the inhibition efficiency of inhibitors, and the IC50 values obtained were in good agreement with the references. Compared to current TRAP methods, this method shows reliable quantification, ultrahigh sensitivity, and short detection time and is without separation. We believe that the FCS-TRAP method has a potential application in clinical diagnosis and screening of telomerase inhibitors.
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Affiliation(s)
- Di Su
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Xiangyi Huang
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, P. R. China
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5
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Goulet DR, Zwolak A, Chiu ML, Nath A, Atkins WM. Diffusion of Soluble Aggregates of THIOMABs and Bispecific Antibodies in Serum. Biochemistry 2017; 56:2251-2260. [PMID: 28394577 DOI: 10.1021/acs.biochem.6b01097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Submicrometer aggregates are frequently present at low levels in antibody-based therapeutics. Although intuition suggests that the fraction of the aggregate or the size of the aggregate present might correlate with deleterious clinical properties or formulation difficulties, it has been challenging to demonstrate which aggregate states, if any, trigger specific biological effects. One source of uncertainty about the putative linkage between aggregation and safety or efficacy lies in the likelihood that noncovalent aggregation differs in ideal buffers versus in serum and biological tissues; self-association or association with other proteins may vary widely with environment. Therefore, methods for monitoring aggregation and aggregate behavior in biologically relevant matrices could provide a tool for better predicting aggregate-dependent clinical outcomes and provide a basis for antibody engineering prior to clinical studies. Here, we generate models for soluble aggregates of THIOMABs and a bispecific antibody (bsAb) of defined size and exploit fluorescence correlation spectroscopy to monitor their diffusion properties in serum and viscosity-matched buffers. The monomers, dimers, and trimers of both THIOMABs and a bsAb reveal a modest increase in diffusion time in serum greater than expected for an increase in viscosity alone. A mixture of larger aggregates containing mostly bsAb pentamers exhibits a marked increase in diffusion time in serum and much greater intrasample variability, consistent with significant aggregation or interactions with serum components. The results indicate that small aggregates of several IgG platforms are not likely to aggregate with serum components, but nanometer-scale aggregates larger than trimers can interact with the serum in an Ab-dependent manner.
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Affiliation(s)
- Dennis R Goulet
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195-7631, United States
| | - Adam Zwolak
- Biologics Research, Janssen Research & Development, LLC , Spring House, Pennsylvania 19477, United States
| | - Mark L Chiu
- Biologics Research, Janssen Research & Development, LLC , Spring House, Pennsylvania 19477, United States
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195-7631, United States
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195-7631, United States
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6
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Spatial dynamics of SIRT1 and the subnuclear distribution of NADH species. Proc Natl Acad Sci U S A 2016; 113:12715-12720. [PMID: 27791113 DOI: 10.1073/pnas.1609227113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Sirtuin 1 (SIRT1) is an NAD+-dependent deacetylase that functions as metabolic sensor of cellular energy and modulates biochemical pathways in the adaptation to changes in the environment. SIRT1 substrates include histones and proteins related to enhancement of mitochondrial function as well as antioxidant protection. Fluctuations in intracellular NAD+ levels regulate SIRT1 activity, but how SIRT1 enzymatic activity impacts on NAD+ levels and its intracellular distribution remains unclear. Here, we show that SIRT1 determines the nuclear organization of protein-bound NADH. Using multiphoton microscopy in live cells, we show that free and bound NADH are compartmentalized inside of the nucleus, and its subnuclear distribution depends on SIRT1. Importantly, SIRT6, a chromatin-bound deacetylase of the same class, does not influence NADH nuclear localization. In addition, using fluorescence fluctuation spectroscopy in single living cells, we reveal that NAD+ metabolism in the nucleus is linked to subnuclear dynamics of active SIRT1. These results reveal a connection between NAD+ metabolism, NADH distribution, and SIRT1 activity in the nucleus of live cells and pave the way to decipher links between nuclear organization and metabolism.
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7
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Abstract
Cytokinesis, a model cell shape change event, is controlled by an integrated system that coordinates the mitotic spindle signals with a mechanoresponsive cytoskeletal network that drives contractility and furrow ingression. Quantitative methods that measure cell mechanics, mechanoresponse (mechanical stress-induced protein accumulation), protein dynamics, and molecular interactions are necessary to provide insight into both the mechanical and biochemical components involved in cytokinesis and cell shape regulation. Micropipette aspiration, fluorescence correlation and cross-correlation spectroscopy, and fluorescence recovery after photobleaching are valuable methods for measuring cell mechanics and protein dynamics in vivo that occur on nanometer to micron length-scales, and microsecond to minute timescales. Collectively, these methods provide the ability to quantify the molecular interactions that control the cell's ability to change shape and undergo cytokinesis.
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8
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Wohlgemuth I, Lenz C, Urlaub H. Studying macromolecular complex stoichiometries by peptide-based mass spectrometry. Proteomics 2015; 15:862-79. [PMID: 25546807 PMCID: PMC5024058 DOI: 10.1002/pmic.201400466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/22/2014] [Indexed: 11/11/2022]
Abstract
A majority of cellular functions are carried out by macromolecular complexes. A host of biochemical and spectroscopic methods exists to characterize especially protein/protein complexes, however there has been a lack of a universal method to determine protein stoichiometries. Peptide‐based MS, especially as a complementary method to the MS analysis of intact protein complexes, has now been developed to a point where it can be employed to assay protein stoichiometries in a routine manner. While the experimental demands are still significant, peptide‐based MS has been successfully applied to analyze stoichiometries for a variety of protein complexes from very different biological backgrounds. In this review, we discuss the requirements especially for targeted MS acquisition strategies to be used in this context, with a special focus on the interconnected experimental aspects of sample preparation, protein digestion, and peptide stability. In addition, different strategies for the introduction of quantitative peptide standards and their suitability for different scenarios are compared.
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Affiliation(s)
- Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
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9
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Abstract
Biological questions are increasingly being addressed using a wide range of quantitative analytical tools to examine protein complex composition. Knowledge of the absolute number of proteins present provides insights into organization, function, and maintenance and is used in mathematical modeling of complex cellular dynamics. In this chapter, we outline and describe three microscopy-based methods for determining absolute protein numbers--fluorescence correlation spectroscopy, stepwise photobleaching, and ratiometric comparison of fluorescence intensity to known standards. In addition, we discuss the various fluorescently labeled proteins that have been used as standards for both stepwise photobleaching and ratiometric comparison analysis. A detailed procedure for determining absolute protein number by ratiometric comparison is outlined in the second half of this chapter. Counting proteins by quantitative microscopy is a relatively simple yet very powerful analytical tool that will increase our understanding of protein complex composition.
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