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Kapitany V, Fatima A, Zickus V, Whitelaw J, McGhee E, Insall R, Machesky L, Faccio D. Single-sample image-fusion upsampling of fluorescence lifetime images. SCIENCE ADVANCES 2024; 10:eadn0139. [PMID: 38781345 PMCID: PMC11114222 DOI: 10.1126/sciadv.adn0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) provides detailed information about molecular interactions and biological processes. A major bottleneck for FLIM is image resolution at high acquisition speeds due to the engineering and signal-processing limitations of time-resolved imaging technology. Here, we present single-sample image-fusion upsampling, a data-fusion approach to computational FLIM super-resolution that combines measurements from a low-resolution time-resolved detector (that measures photon arrival time) and a high-resolution camera (that measures intensity only). To solve this otherwise ill-posed inverse retrieval problem, we introduce statistically informed priors that encode local and global correlations between the two "single-sample" measurements. This bypasses the risk of out-of-distribution hallucination as in traditional data-driven approaches and delivers enhanced images compared, for example, to standard bilinear interpolation. The general approach laid out by single-sample image-fusion upsampling can be applied to other image super-resolution problems where two different datasets are available.
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Affiliation(s)
- Valentin Kapitany
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
| | - Areeba Fatima
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
| | - Vytautas Zickus
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
- Department of Laser Technologies, Center for Physical Sciences and Technology, LT-10257 Vilnius, Lithuania
| | | | - Ewan McGhee
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
- Cancer Research UK, Beatson Institute, Glasgow, UK
| | | | | | - Daniele Faccio
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
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2
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Santalla Méndez R, Rodgers Furones A, Classens R, Fedorova K, Haverdil M, Canela Capdevila M, van Duffelen A, Spruijt CG, Vermeulen M, Ter Beest M, van Spriel AB, Querol Cano L. Galectin-9 interacts with Vamp-3 to regulate cytokine secretion in dendritic cells. Cell Mol Life Sci 2023; 80:306. [PMID: 37755527 PMCID: PMC10533640 DOI: 10.1007/s00018-023-04954-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/20/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023]
Abstract
Intracellular vesicle transport is essential for cellular homeostasis and is partially mediated by SNARE proteins. Endosomal trafficking to the plasma membrane ensures cytokine secretion in dendritic cells (DCs) and the initiation of immune responses. Despite its critical importance, the specific molecular components that regulate DC cytokine secretion are poorly characterised. Galectin-9, a ß-galactoside-binding protein, has emerged as a novel cellular modulator although its exact intracellular roles in regulating (immune) cell homeostasis and vesicle transport are virtually unknown. We investigated galectin-9 function in primary human DCs and report that galectin-9 is essential for intracellular cytokine trafficking to the cell surface. Galectin-9-depleted DCs accumulate cytokine-containing vesicles in the Golgi complex that eventually undergo lysosomal degradation. We observed galectin-9 to molecularly interact with Vamp-3 using immunoprecipitation-mass-spectrometry and identified galectin-9 was required for rerouting Vamp-3-containing endosomes upon DC activation as the underlying mechanism. Overall, this study identifies galectin-9 as a necessary mechanistic component for intracellular trafficking. This may impact our general understanding of vesicle transport and sheds new light into the multiple roles galectins play in governing cell function.
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Affiliation(s)
- Rui Santalla Méndez
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Andrea Rodgers Furones
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands
| | - René Classens
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands
| | - Kristina Fedorova
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands
| | - Manon Haverdil
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands
| | - Marta Canela Capdevila
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands
| | - Anne van Duffelen
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands
| | - Cornelia G Spruijt
- Department of Molecular Biology, Faculty of Science, Oncode Institute, Radboud University Nijmegen, 6525 GA, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Oncode Institute, Radboud University Nijmegen, 6525 GA, Nijmegen, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martin Ter Beest
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands
| | - Annemiek B van Spriel
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands
| | - Laia Querol Cano
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands.
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3
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Xie LY, Huang HY, Hao YL, Yu M, Zhang W, Wei E, Gao C, Wang C, Zeng L. Development and validation of a tumor immune cell infiltration-related gene signature for recurrence prediction by weighted gene co-expression network analysis in prostate cancer. Front Genet 2023; 14:1067172. [PMID: 37007952 PMCID: PMC10061146 DOI: 10.3389/fgene.2023.1067172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
Introduction: Prostate cancer (PCa) is the second most common malignancy in men. Despite multidisciplinary treatments, patients with PCa continue to experience poor prognoses and high rates of tumor recurrence. Recent studies have shown that tumor-infiltrating immune cells (TIICs) are associated with PCa tumorigenesis.Methods: The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets were used to derive multi-omics data for prostate adenocarcinoma (PRAD) samples. The CIBERSORT algorithm was used to calculate the landscape of TIICs. Weighted gene co-expression network analysis (WGCNA) was performed to determine the candidate module most significantly associated with TIICs. LASSO Cox regression was applied to screen a minimal set of genes and construct a TIIC-related prognostic gene signature for PCa. Then, 78 PCa samples with CIBERSORT output p-values of less than 0.05 were selected for analysis. WGCNA identified 13 modules, and the MEblue module with the most significant enrichment result was selected. A total of 1143 candidate genes were cross-examined between the MEblue module and active dendritic cell-related genes.Results: According to LASSO Cox regression analysis, a risk model was constructed with six genes (STX4, UBE2S, EMC6, EMD, NUCB1 and GCAT), which exhibited strong correlations with clinicopathological variables, tumor microenvironment context, antitumor therapies, and tumor mutation burden (TMB) in TCGA-PRAD. Further validation showed that the UBE2S had the highest expression level among the six genes in five different PCa cell lines.Discussion: In conclusion, our risk-score model contributes to better predicting PCa patient prognosis and understanding the underlying mechanisms of immune responses and antitumor therapies in PCa.
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Affiliation(s)
- Lin-Ying Xie
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
- International Center of Future Science, Jillin University, Changchun, Jilin, China
| | - Han-Ying Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yu-Lei Hao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Miaomiao Yu
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
- International Center of Future Science, Jillin University, Changchun, Jilin, China
| | - Wenju Zhang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
- International Center of Future Science, Jillin University, Changchun, Jilin, China
| | - Enwei Wei
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
- International Center of Future Science, Jillin University, Changchun, Jilin, China
| | - Chunfeng Gao
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
- International Center of Future Science, Jillin University, Changchun, Jilin, China
| | - Chang Wang
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Chang Wang, ; Lei Zeng,
| | - Lei Zeng
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
- International Center of Future Science, Jillin University, Changchun, Jilin, China
- *Correspondence: Chang Wang, ; Lei Zeng,
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4
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Auer JMT, Murphy LC, Xiao D, Li DU, Wheeler AP. Non-fitting FLIM-FRET facilitates analysis of protein interactions in live zebrafish embryos. J Microsc 2022. [PMID: 36448983 DOI: 10.1111/jmi.13162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022]
Abstract
Molecular interactions are key to all cellular processes, and particularly interesting to investigate in the context of gene regulation. Protein-protein interactions are challenging to examine in vivo as they are dynamic, and require spatially and temporally resolved studies to interrogate them. Foerster Resonance Energy Transfer (FRET) is a highly sensitive imaging method, which can interrogate molecular interactions. FRET can be detected by Fluorescence Lifetime Imaging Microscopy (FLIM-FRET), which is more robust to concentration variations and photobleaching than intensity-based FRET but typically needs long acquisition times to achieve high photon counts. New variants of non-fitting lifetime-based FRET perform well in samples with lower signal and require less intensive instrument calibration and analysis, making these methods ideal for probing protein-protein interactions in more complex live 3D samples. Here we show that a non-fitting FLIM-FRET variant, based on the Average Arrival Time of photons per pixel (AAT- FRET), is a sensitive and simple way to detect and measure protein-protein interactions in live early stage zebrafish embryos.
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Affiliation(s)
- Julia M T Auer
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Dong Xiao
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, UK
| | - David U Li
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, UK
| | - Ann P Wheeler
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
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5
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Linders PTA, Ioannidis M, ter Beest M, van den Bogaart G. Fluorescence Lifetime Imaging of pH along the Secretory Pathway. ACS Chem Biol 2022; 17:240-251. [PMID: 35000377 PMCID: PMC8787756 DOI: 10.1021/acschembio.1c00907] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Many cellular processes
are dependent on correct pH levels, and
this is especially important for the secretory pathway. Defects in
pH homeostasis in distinct organelles cause a wide range of diseases,
including disorders of glycosylation and lysosomal storage diseases.
Ratiometric imaging of the pH-sensitive mutant of green fluorescent
protein, pHLuorin, has allowed for targeted pH measurements in various
organelles, but the required sequential image acquisition is intrinsically
slow and therefore the temporal resolution is unsuitable to follow
the rapid transit of cargo between organelles. Therefore, we applied
fluorescence lifetime imaging microscopy (FLIM) to measure intraorganellar
pH with just a single excitation wavelength. We first validated this
method by confirming the pH in multiple compartments along the secretory
pathway and compared the pH values obtained by the FLIM-based measurements
with those obtained by conventional ratiometric imaging. Then, we
analyzed the dynamic pH changes within cells treated with Bafilomycin
A1, to block the vesicular ATPase, and Brefeldin A, to block endoplasmic
reticulum (ER)–Golgi trafficking. Finally, we followed the
pH changes of newly synthesized molecules of the inflammatory cytokine
tumor necrosis factor-α while they were in transit from the
ER via the Golgi to the plasma membrane. The toolbox we present here
can be applied to measure intracellular pH with high spatial and temporal
resolution and can be used to assess organellar pH in disease models.
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Affiliation(s)
- Peter T. A. Linders
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Melina Ioannidis
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Martin ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
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6
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Bošnjak B, Do KTH, Förster R, Hammerschmidt SI. Imaging dendritic cell functions. Immunol Rev 2021; 306:137-163. [PMID: 34859450 DOI: 10.1111/imr.13050] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/14/2022]
Abstract
Dendritic cells (DCs) are crucial for the appropriate initiation of adaptive immune responses. During inflammation, DCs capture antigens, mature, and migrate to lymphoid tissues to present foreign material to naïve T cells. These cells get activated and differentiate either into pathogen-specific cytotoxic CD8+ T cells that destroy infected cells or into CD4+ T helper cells that, among other effector functions, orchestrate antibody production by B cells. DC-mediated antigen presentation is equally important in non-inflammatory conditions. Here, DCs mediate induction of tolerance by presenting self-antigens or harmless environmental antigens and induce differentiation of regulatory T cells or inactivation of self-reactive immune cells. Detailed insights into the biology of DCs are, therefore, crucial for the development of novel vaccines as well as the prevention of autoimmune diseases. As in many other life science areas, our understanding of DC biology would be extremely restricted without bioimaging, a compilation of methods that visualize biological processes. Spatiotemporal tracking of DCs relies on various imaging tools, which not only enable insights into their positioning and migration within tissues or entire organs but also allow visualization of subcellular and molecular processes. This review aims to provide an overview of the imaging toolbox and to provide examples of diverse imaging techniques used to obtain fundamental insights into DC biology.
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Affiliation(s)
- Berislav Bošnjak
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Kim Thi Hoang Do
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155) Hannover Medical School, Hannover, Germany.,German Centre for Infection Research (DZIF), Hannover, Germany
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7
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Congenital disorder of glycosylation caused by starting site-specific variant in syntaxin-5. Nat Commun 2021; 12:6227. [PMID: 34711829 PMCID: PMC8553859 DOI: 10.1038/s41467-021-26534-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/05/2021] [Indexed: 12/26/2022] Open
Abstract
The SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein syntaxin-5 (Stx5) is essential for Golgi transport. In humans, the STX5 mRNA encodes two protein isoforms, Stx5 Long (Stx5L) from the first starting methionine and Stx5 Short (Stx5S) from an alternative starting methionine at position 55. In this study, we identify a human disorder caused by a single missense substitution in the second starting methionine (p.M55V), resulting in complete loss of the short isoform. Patients suffer from an early fatal multisystem disease, including severe liver disease, skeletal abnormalities and abnormal glycosylation. Primary human dermal fibroblasts isolated from these patients show defective glycosylation, altered Golgi morphology as measured by electron microscopy, mislocalization of glycosyltransferases, and compromised ER-Golgi trafficking. Measurements of cognate binding SNAREs, based on biotin-synchronizable forms of Stx5 (the RUSH system) and Förster resonance energy transfer (FRET), revealed that the short isoform of Stx5 is essential for intra-Golgi transport. Alternative starting codons of Stx5 are thus linked to human disease, demonstrating that the site of translation initiation is an important new layer of regulating protein trafficking.
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8
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Clague MJ, Urbé S. Data mining for traffic information. Traffic 2021; 21:162-168. [PMID: 31596015 DOI: 10.1111/tra.12702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/23/2022]
Abstract
Modern cell biology is now rich with data acquired at the whole genome and proteome level. We can add value to this data through integration and application of specialist knowledge. To illustrate, we will focus on the SNARE and RAB proteins; key regulators of intracellular fusion specificity and organelle identity. We examine published mass spectrometry data to gain an estimate of protein copy number and organelle distribution in HeLa cells for each family member. We also survey recent global CRISPR/Cas9 screens for essential genes from these families. We highlight instances of co-essentiality with other genes across a large panel of cell lines that allows for the identification of functionally coherent clusters. Examples of such correlations include RAB10 with the SNARE protein Syntaxin4 (STX4) and RAB7/RAB21 with the WASH and the CCC (COMMD/CCDC22/CCDC93) complexes, both of which are linked to endosomal recycling pathways.
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Affiliation(s)
- Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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9
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Baranov MV, Kumar M, Sacanna S, Thutupalli S, van den Bogaart G. Modulation of Immune Responses by Particle Size and Shape. Front Immunol 2021; 11:607945. [PMID: 33679696 PMCID: PMC7927956 DOI: 10.3389/fimmu.2020.607945] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/23/2020] [Indexed: 12/12/2022] Open
Abstract
The immune system has to cope with a wide range of irregularly shaped pathogens that can actively move (e.g., by flagella) and also dynamically remodel their shape (e.g., transition from yeast-shaped to hyphal fungi). The goal of this review is to draw general conclusions of how the size and geometry of a pathogen affect its uptake and processing by phagocytes of the immune system. We compared both theoretical and experimental studies with different cells, model particles, and pathogenic microbes (particularly fungi) showing that particle size, shape, rigidity, and surface roughness are important parameters for cellular uptake and subsequent immune responses, particularly inflammasome activation and T cell activation. Understanding how the physical properties of particles affect immune responses can aid the design of better vaccines.
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Affiliation(s)
- Maksim V. Baranov
- Department of Molecular Immunology and Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Manoj Kumar
- Simons Center for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
| | - Stefano Sacanna
- Molecular Design Institute, Department of Chemistry, New York University, New York, NY, United States
| | - Shashi Thutupalli
- Simons Center for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
- International Centre for Theoretical Sciences, Tata Institute for Fundamental Research, Bangalore, India
| | - Geert van den Bogaart
- Department of Molecular Immunology and Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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10
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Du Y, Qi Y, Jin Z, Tian J. Noninvasive imaging in cancer immunotherapy: The way to precision medicine. Cancer Lett 2019; 466:13-22. [DOI: 10.1016/j.canlet.2019.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/13/2019] [Accepted: 08/20/2019] [Indexed: 12/16/2022]
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11
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Revelo NH, ter Beest M, van den Bogaart G. Membrane trafficking as an active regulator of constitutively secreted cytokines. J Cell Sci 2019; 133:133/5/jcs234781. [DOI: 10.1242/jcs.234781] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/19/2019] [Indexed: 01/02/2023] Open
Abstract
ABSTRACT
Immune-cell activation by inflammatory stimuli triggers the transcription and translation of large amounts of cytokines. The transport of newly synthesized cytokines to the plasma membrane by vesicular trafficking can be rate-limiting for the production of these cytokines, and immune cells upregulate their exocytic machinery concomitantly with increased cytokine expression in order to cope with the increasing demand for trafficking. Whereas it is logical that trafficking is rate-limiting for regulated secretion where an intracellular pool of molecules is waiting to be released, the reason for this is not obvious for constitutively secreted cytokines, such as interleukin-6 (IL-6), interleukin-12 (IL-12) and tumor necrosis factor-α (TNF-α). These constitutively secreted cytokines are primarily regulated at the transcriptional and/or translational level but mounting evidence presented here shows that cells might also increase or decrease the rate of post-Golgi cytokine trafficking to modulate their production. Therefore, in this Hypothesis, we ask the question: why is there a need to limit the trafficking of constitutively secreted cytokines? We propose a model where cells monitor and adjust their production rate of cytokines by sensing the intracellular level of cytokines while they are in transit to the plasma membrane. This self-regulation of cytokine production could prevent an overshooting response of acute-phase cytokines, such as IL-6, IL-12 and TNF-α, upon acute infection.
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Affiliation(s)
- Natalia H. Revelo
- Tumor Immunology Lab, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, 6500HB Nijmegen, The Netherlands
| | - Martin ter Beest
- Tumor Immunology Lab, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, 6500HB Nijmegen, The Netherlands
| | - Geert van den Bogaart
- Tumor Immunology Lab, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, 6500HB Nijmegen, The Netherlands
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
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12
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Verboogen DRJ, Revelo NH, ter Beest M, van den Bogaart G. Interleukin-6 secretion is limited by self-signaling in endosomes. J Mol Cell Biol 2019; 11:144-157. [PMID: 30016456 PMCID: PMC6392102 DOI: 10.1093/jmcb/mjy038] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 05/04/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022] Open
Abstract
Cells producing cytokines often express the receptor for the same cytokine, which makes them prone to autocrine signaling. How cytokine release and signaling are regulated in the same cell is not understood. In this study, we demonstrate that signaling by exogenous and self-synthesized inflammatory cytokine interleukin-6 (IL-6) within endosomal compartments acts as a cellular brake that limits the synthesis of IL-6. Our data show that IL-6 is internalized by dendritic cells and signals from endosomal compartments containing the IL-6 receptor. Newly synthesized IL-6 also traffics via these endosomal compartments and signals in transit to the plasma membrane. This allows activation of STAT3 which in turn limits toll-like receptor 4 stimulant lipopolysaccharide (LPS) triggered transcription of IL-6. Long-term exposure to LPS removes this brake via inhibition of STAT3 by increased expression of suppressor of cytokine signaling 3 and results in fully fledged IL-6 production. This transient regulation could prevent excessive IL-6 production during early infections.
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Affiliation(s)
- Daniëlle R J Verboogen
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Natalia H Revelo
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martin ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, Groningen, The Netherlands
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13
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Dingjan I, Linders PTA, Verboogen DRJ, Revelo NH, Ter Beest M, van den Bogaart G. Endosomal and Phagosomal SNAREs. Physiol Rev 2018; 98:1465-1492. [PMID: 29790818 DOI: 10.1152/physrev.00037.2017] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein family is of vital importance for organelle communication. The complexing of cognate SNARE members present in both the donor and target organellar membranes drives the membrane fusion required for intracellular transport. In the endocytic route, SNARE proteins mediate trafficking between endosomes and phagosomes with other endosomes, lysosomes, the Golgi apparatus, the plasma membrane, and the endoplasmic reticulum. The goal of this review is to provide an overview of the SNAREs involved in endosomal and phagosomal trafficking. Of the 38 SNAREs present in humans, 30 have been identified at endosomes and/or phagosomes. Many of these SNAREs are targeted by viruses and intracellular pathogens, which thereby reroute intracellular transport for gaining access to nutrients, preventing their degradation, and avoiding their detection by the immune system. A fascinating picture is emerging of a complex transport network with multiple SNAREs being involved in consecutive trafficking routes.
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Affiliation(s)
- Ilse Dingjan
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Peter T A Linders
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Danielle R J Verboogen
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Natalia H Revelo
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Martin Ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
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14
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Verboogen DRJ, Ter Beest M, Honigmann A, van den Bogaart G. Secretory vesicles of immune cells contain only a limited number of interleukin 6 molecules. FEBS Lett 2018; 592:1535-1544. [PMID: 29570778 PMCID: PMC5969217 DOI: 10.1002/1873-3468.13036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/12/2018] [Accepted: 03/13/2018] [Indexed: 01/06/2023]
Abstract
Immune cells communicate by releasing large quantities of cytokines. Although the mechanisms of cytokine secretion are increasingly understood, quantitative knowledge of the number of cytokines per vesicle is still lacking. Here, we measured with quantitative microscopy the release rate of vesicles potentially carrying interleukin‐6 (IL‐6) in human dendritic cells. By comparing this to the total secreted IL‐6, we estimate that secretory vesicles contain about 0.5–3 IL‐6 molecules, but with a large spread among cells/donors. Moreover, IL‐6 did not accumulate within most cells, indicating that synthesis and not trafficking is the bottleneck for IL‐6 production. IL‐6 accumulated in the Golgi apparatus only in ~ 10% of the cells. Understanding how immune cells produce cytokines is important for designing new immunomodulatory drugs.
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Affiliation(s)
- Daniëlle R J Verboogen
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Martin Ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands
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15
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Verboogen DRJ, Baranov MV, Ter Beest M, van den Bogaart G. Visualizing Intracellular SNARE Trafficking by Fluorescence Lifetime Imaging Microscopy. J Vis Exp 2017. [PMID: 29364279 PMCID: PMC5908401 DOI: 10.3791/56745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Soluble N-ethylmaleimide sensitive fusion protein (NSF) attachment protein receptor (SNARE) proteins are key for membrane trafficking, as they catalyze membrane fusion within eukaryotic cells. The SNARE protein family consists of about 36 different members. Specific intracellular transport routes are catalyzed by specific sets of 3 or 4 SNARE proteins that thereby contribute to the specificity and fidelity of membrane trafficking. However, studying the precise function of SNARE proteins is technically challenging, because SNAREs are highly abundant and functionally redundant, with most SNAREs having multiple and overlapping functions. In this protocol, a new method for the visualization of SNARE complex formation in live cells is described. This method is based on expressing SNARE proteins C-terminally fused to fluorescent proteins and measuring their interaction by Förster resonance energy transfer (FRET) employing fluorescence lifetime imaging microscopy (FLIM). By fitting the fluorescence lifetime histograms with a multicomponent decay model, FRET-FLIM allows (semi-)quantitative estimation of the fraction of the SNARE complex formation at different vesicles. This protocol has been successfully applied to visualize SNARE complex formation at the plasma membrane and at endosomal compartments in mammalian cell lines and primary immune cells, and can be readily extended to study SNARE functions at other organelles in animal, plant, and fungal cells.
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Affiliation(s)
| | - Maksim V Baranov
- Department of Tumor Immunology, Radboud University Medical Center
| | - Martin Ter Beest
- Department of Tumor Immunology, Radboud University Medical Center
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16
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Dingjan I, Paardekooper LM, Verboogen DRJ, von Mollard GF, Ter Beest M, van den Bogaart G. VAMP8-mediated NOX2 recruitment to endosomes is necessary for antigen release. Eur J Cell Biol 2017; 96:705-714. [PMID: 28688576 PMCID: PMC5641923 DOI: 10.1016/j.ejcb.2017.06.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/21/2017] [Accepted: 06/21/2017] [Indexed: 11/24/2022] Open
Abstract
Climbing beans produced more than bush beans for 80% of the farmers. Both bean and maize responded positively to DAP fertilizer in 60% of the farms. Early planting increased fertilizer effects in bean-maize rotations. DAP is more profitable in climbing bean-rotation than in bush bean-maize rotation.
Cross-presentation of foreign antigen in major histocompatibility complex (MHC) class I by dendritic cells (DCs) requires activation of the NADPH-oxidase NOX2 complex. We recently showed that NOX2 is recruited to phagosomes by the SNARE protein VAMP8 where NOX2-produced reactive oxygen species (ROS) cause lipid oxidation and membrane disruption, promoting antigen translocation into the cytosol for cross-presentation. In this study, we extend these findings by showing that VAMP8 is also involved in NOX2 trafficking to endosomes. Moreover, we demonstrate in both human and mouse DCs that absence of VAMP8 leads to decreased ROS production, lipid peroxidation and antigen translocation, and that this impairs cross-presentation. In contrast, knockdown of VAMP8 did not affect recruitment of MHC class I and the transporter associated with antigen processing 1 (TAP1) to phagosomes, although surface levels of MHC class I were reduced. Thus, in addition to a secretory role, VAMP8-mediates trafficking of NOX2 to endosomes and phagosomes and this promotes induction of cytolytic T cell immune responses.
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Affiliation(s)
- Ilse Dingjan
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Laurent M Paardekooper
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Daniëlle R J Verboogen
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | | | - Martin Ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
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