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Hollingsworth LR, Veeraraghavan P, Paulo JA, Harper JW, Rauch I. Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590338. [PMID: 38659763 PMCID: PMC11042255 DOI: 10.1101/2024.04.19.590338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 3 (NLRP3) is an innate immune sensor that forms an inflammasome in response to various cellular stressors. Gain-of-function mutations in NLRP3 cause autoinflammatory diseases and NLRP3 signalling itself exacerbates the pathogenesis of many other human diseases. Despite considerable therapeutic interest, the primary drivers of NLRP3 activation remain controversial due to the diverse array of signals that are integrated through NLRP3. Here, we mapped subcellular proteome changes to lysosomes, mitochondrion, EEA1-positive endosomes, and Golgi caused by the NLRP3 inflammasome agonists nigericin and CL097. We identified several common disruptions to retrograde trafficking pathways, including COPI and Shiga toxin-related transport, in line with recent studies. We further characterized mouse NLRP3 trafficking throughout its activation using temporal proximity proteomics, which supports a recent model of NLRP3 recruitment to endosomes during inflammasome activation. Collectively, these findings provide additional granularity to our understanding of the molecular events driving NLRP3 activation and serve as a valuable resource for cell biological research. We have made our proteomics data accessible through an open-access Shiny browser to facilitate future research within the community, available at: https://harperlab.connect.hms.harvard.edu/inflame/. We will display anonymous peer review for this manuscript on pubpub.org (https://harperlab.pubpub.org/pub/nlrp3/) rather than a traditional journal. Moreover, we invite community feedback on the pubpub version of this manuscript, and we will address criticisms accordingly.
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Affiliation(s)
- L. Robert Hollingsworth
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University
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2
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Levic DS, Niedzwiecki D, Kandakatla A, Karlovich NS, Juneja A, Park J, Stolarchuk C, Adams S, Willer JR, Schaner MR, Lian G, Beasley C, Marjoram L, Flynn AD, Valentine JF, Onken JE, Sheikh SZ, Davis EE, Evason KJ, Garman KS, Bagnat M. TNF promoter hypomethylation is associated with mucosal inflammation in IBD and anti-TNF response. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.05.24302343. [PMID: 38370739 PMCID: PMC10871362 DOI: 10.1101/2024.02.05.24302343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Background and aims Inflammatory Bowel Diseases (IBD) are chronic inflammatory conditions influenced heavily by environmental factors. DNA methylation is a form of epigenetic regulation linking environmental stimuli to gene expression changes and inflammation. Here, we investigated how DNA methylation of the TNF promoter differs between inflamed and uninflamed mucosa of IBD patients, including anti-TNF responders and non-responders. Methods We obtained mucosal biopsies from 200 participants (133 IBD and 67 controls) and analyzed TNF promoter methylation using bisulfite sequencing, comparing inflamed with uninflamed segments, in addition to paired inflamed/uninflamed samples from individual patients. We conducted similar analyses on purified intestinal epithelial cells from bowel resections. We also compared TNF methylation levels of inflamed and uninflamed mucosa from a separate cohort of 15 anti-TNF responders and 17 non-responders. Finally, we sequenced DNA methyltransferase genes to identify rare variants in IBD patients and functionally tested them using rescue experiments in a zebrafish genetic model of DNA methylation deficiency. Results TNF promoter methylation levels were decreased in inflamed mucosa of IBD patients and correlated with disease severity. Isolated IECs from inflamed tissue showed proportional decreases in TNF methylation. Anti-TNF non-responders showed lower levels of TNF methylation than responders in uninflamed mucosa. Our sequencing analysis revealed two missense variants in DNMT1, one of which had reduced function in vivo. Conclusions Our study reveals an association of TNF promoter hypomethylation with mucosal inflammation, suggesting that IBD patients may be particularly sensitive to inflammatory environmental insults affecting DNA methylation. Together, our analyses indicate that TNF promoter methylation analysis may aid in the characterization of IBD status and evaluation of anti-TNF therapy response.
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Affiliation(s)
- Daniel S. Levic
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Donna Niedzwiecki
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Apoorva Kandakatla
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
| | - Norah S. Karlovich
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
| | - Arjun Juneja
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Jieun Park
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Christina Stolarchuk
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
| | - Shanté Adams
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Jason R. Willer
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Matthew R. Schaner
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Grace Lian
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caroline Beasley
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Ann D. Flynn
- Division of Gastroenterology, Hepatology and Nutrition, University of Utah Health, Salt Lake City, Utah
| | - John F. Valentine
- Division of Gastroenterology, Hepatology and Nutrition, University of Utah Health, Salt Lake City, Utah
| | - Jane E. Onken
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
| | - Shehzad Z. Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica E. Davis
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Kimberley J. Evason
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Katherine S. Garman
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
| | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC, USA
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Maji S, Pirozzi M, Ruturaj, Pandey R, Ghosh T, Das S, Gupta A. Copper-independent lysosomal localisation of the Wilson disease protein ATP7B. Traffic 2023; 24:587-609. [PMID: 37846526 DOI: 10.1111/tra.12919] [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: 10/20/2022] [Revised: 09/10/2023] [Accepted: 09/23/2023] [Indexed: 10/18/2023]
Abstract
In hepatocytes, the Wilson disease protein ATP7B resides on the trans-Golgi network (TGN) and traffics to peripheral lysosomes to export excess intracellular copper through lysosomal exocytosis. We found that in basal copper or even upon copper chelation, a significant amount of ATP7B persists in the endolysosomal compartment of hepatocytes but not in non-hepatic cells. These ATP7B-harbouring lysosomes lie in close proximity of ~10 nm to the TGN. ATP7B constitutively distributes itself between the sub-domain of the TGN with a lower pH and the TGN-proximal lysosomal compartments. The presence of ATP7B on TGN-lysosome colocalising sites upon Golgi disruption suggested a possible exchange of ATP7B directly between the TGN and its proximal lysosomes. Manipulating lysosomal positioning significantly alters the localisation of ATP7B in the cell. Contrary to previous understanding, we found that upon copper chelation in a copper-replete hepatocyte, ATP7B is not retrieved back to TGN from peripheral lysosomes; rather, ATP7B recycles to these TGN-proximal lysosomes to initiate the next cycle of copper transport. We report a hitherto unknown copper-independent lysosomal localisation of ATP7B and the importance of TGN-proximal lysosomes but not TGN as the terminal acceptor organelle of ATP7B in its retrograde pathway.
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Affiliation(s)
- Saptarshi Maji
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | | | - Ruturaj
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Raviranjan Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Tamal Ghosh
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Santanu Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Arnab Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
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4
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Thottacherry JJ, Chen J, Johnston DS. Apical-basal polarity in the gut. Semin Cell Dev Biol 2023; 150-151:15-22. [PMID: 36670034 DOI: 10.1016/j.semcdb.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/24/2022] [Accepted: 12/22/2022] [Indexed: 01/20/2023]
Abstract
Apical-Basal polarity is a fundamental property of all epithelial cells that underlies both their form and function. The gut is made up of a single layer of intestinal epithelial cells, with distinct apical, lateral and basal domains. Occluding junctions at the apical side of the lateral domains create a barrier between the gut lumen and the body, which is crucial for tissue homeostasis, protection against gastrointestinal pathogens and for the maintenance of the immune response. Apical-basal polarity in most epithelia is established by conserved polarity factors, but recent evidence suggests that the gut epithelium in at least some organisms polarises by novel mechanisms. In this review, we discuss the recent advances in understanding polarity factors by focussing on work in C. elegans, Drosophila, Zebrafish and Mouse.
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Affiliation(s)
- Joseph Jose Thottacherry
- The Gurdon Institute and the Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Jia Chen
- The Gurdon Institute and the Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Daniel St Johnston
- The Gurdon Institute and the Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom.
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5
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de Caestecker C, Macara IG. A Size Filter Regulates Apical Protein Sorting. RESEARCH SQUARE 2023:rs.3.rs-3210598. [PMID: 37577471 PMCID: PMC10418535 DOI: 10.21203/rs.3.rs-3210598/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Despite decades of research, apical sorting of epithelial membrane proteins remains incompletely understood. We noted that apical cytoplasmic domains are smaller than those of basolateral proteins; however, the reason for this discrepancy is unknown. We investigated whether a size barrier at the trans-Golgi network (TGN) might hinder apical sorting of proteins with large cytoplasmic tails. We focused on Crb3 and Ace2 as representative apical proteins with short cytoplasmic tails. By incorporating a streptavidin-binding peptide, these proteins can be trapped in the endoplasmic reticulum (ER) until addition of biotin, which triggers synchronous release to the Golgi and subsequent transport to the apical cortex. Strikingly, departure from the Golgi could be significantly delayed simply by increasing cytoplasmic bulk. Moreover, large and small Crb3 segregated into spatially distinct Golgi regions as detected by super resolution imaging. Biologically, Crb3 forms a complex through its cytoplasmic tail with the Pals1 protein, which could also delay departure, but although associated at the ER and Golgi, we found that Pals1 disassociates prior to Crb3 departure. Notably, a non-dissociable mutant Pals1 hampers the exit of Crb3. We conclude that an unexpected mechanism involving a size filter at the TGN facilitates apical sorting of proteins with small cytoplasmic domains and that timely release of Pals1, to reduce cytoplasmic domain size, is essential for the normal kinetics of Crb3 sorting.
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Affiliation(s)
- Christian de Caestecker
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine; Nashville TN 37205, U.S
| | - Ian G. Macara
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine; Nashville TN 37205, U.S
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Shih SW, Yan JJ, Lu SW, Chuang YT, Lin HW, Chou MY, Hwang PP. Molecular Physiological Evidence for the Role of Na+-Cl− Co-Transporter in Branchial Na+ Uptake in Freshwater Teleosts. Int J Mol Sci 2023; 24:ijms24076597. [PMID: 37047570 PMCID: PMC10094795 DOI: 10.3390/ijms24076597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/23/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
The gills are the major organ for Na+ uptake in teleosts. It was proposed that freshwater (FW) teleosts adopt Na+/H+ exchanger 3 (Nhe3) as the primary transporter for Na+ uptake and Na+-Cl− co-transporter (Ncc) as the backup transporter. However, convincing molecular physiological evidence to support the role of Ncc in branchial Na+ uptake is still lacking due to the limitations of functional assays in the gills. Thus, this study aimed to reveal the role of branchial Ncc in Na+ uptake with an in vivo detection platform (scanning ion-selective electrode technique, SIET) that has been recently established in fish gills. First, we identified that Ncc2-expressing cells in zebrafish gills are a specific subtype of ionocyte (NCC ionocytes) by using single-cell transcriptome analysis and immunofluorescence. After a long-term low-Na+ FW exposure, zebrafish increased branchial Ncc2 expression and the number of NCC ionocytes and enhanced gill Na+ uptake capacity. Pharmacological treatments further suggested that Na+ is indeed taken up by Ncc, in addition to Nhe, in the gills. These findings reveal the uptake roles of both branchial Ncc and Nhe under FW and shed light on osmoregulatory physiology in adult fish.
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Affiliation(s)
- Shang-Wu Shih
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115201, Taiwan
- Department of Life Science, National Taiwan University, Taipei 106319, Taiwan
| | - Jia-Jiun Yan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115201, Taiwan
| | - Shao-Wei Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115201, Taiwan
| | - Ya-Ting Chuang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115201, Taiwan
| | - How-Wei Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115201, Taiwan
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Ming-Yi Chou
- Department of Life Science, National Taiwan University, Taipei 106319, Taiwan
| | - Pung-Pung Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115201, Taiwan
- Department of Life Science, National Taiwan University, Taipei 106319, Taiwan
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7
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Karaica D, Mihaljević I, Vujica L, Bošnjak A, Dragojević J, Otten C, Babić N, Lončar J, Smital T. Stage-dependent localization of F-actin and Na + /K + -ATPase in zebrafish embryos detected using optimized cryosectioning immunostaining protocol. Microsc Res Tech 2023; 86:294-310. [PMID: 36453864 DOI: 10.1002/jemt.24270] [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: 07/01/2022] [Revised: 11/10/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022]
Abstract
The increasing use of the zebrafish model in biomedical and (eco)toxicological studies aimed at understanding the function of various proteins highlight the importance of optimizing existing methods to study gene and protein expression and localization in this model. In this context, zebrafish cryosections are still underutilized compared with whole-mount preparations. In this study, we used zebrafish embryos (24-120 hpf) to determine key factors for the preparation of high-quality zebrafish cryosections and to determine the optimal protocol for (immuno)fluorescence analyses of Na+ /K+ -ATPase and F-actin, across developmental stages from 1 to 5 dpf. The results showed that the highest quality zebrafish cryosections were obtained after the samples were fixed in 4% paraformaldehyde (PFA) for 1 h, incubated in 2.5% bovine gelatin/25% sucrose mixture, embedded in OCT, and then sectioned to 8 μm thickness at -20°C. Fluorescence microscopy analysis of phalloidin-labeled zebrafish skeletal muscle revealed that 1-h-4% PFA-fixed samples allowed optimal binding of phalloidin to F-actin. Further immunofluorescence analyses revealed detailed localization of F-actin and Na+ /K+ -ATPase in various tissues of the zebrafish and a stage-dependent increase in their respective expression in the somitic muscles and pronephros. Finally, staining of zebrafish cryosections and whole-mount samples revealed organ-specific and zone-dependent localizations of the Na+ /K+ -ATPase α1-subunit. RESEARCH HIGHLIGHTS: This study brings optimization of existing protocols for preparation and use of zebrafish embryos cryosections in (immuno)histological analyses. It reveals stage-dependent localization/expression of F-actin and Na+ /K+ -ATPase in zebrafish embryos.
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Affiliation(s)
- Dean Karaica
- Molecular Toxicology Unit, Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | - Ivan Mihaljević
- Laboratory for Molecular Ecotoxicology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Lana Vujica
- Laboratory for Molecular Ecotoxicology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Arvena Bošnjak
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Jelena Dragojević
- Laboratory for Molecular Ecotoxicology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Cecile Otten
- Laboratory for Molecular Ecotoxicology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Nency Babić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Jovica Lončar
- Laboratory for Molecular Ecotoxicology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tvrtko Smital
- Laboratory for Molecular Ecotoxicology, Ruđer Bošković Institute, Zagreb, Croatia
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8
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Klee KMC, Hess MW, Lohmüller M, Herzog S, Pfaller K, Müller T, Vogel GF, Huber LA. A CRISPR screen in intestinal epithelial cells identifies novel factors for polarity and apical transport. eLife 2023; 12:e80135. [PMID: 36661306 PMCID: PMC9889089 DOI: 10.7554/elife.80135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 01/19/2023] [Indexed: 01/21/2023] Open
Abstract
Epithelial polarization and polarized cargo transport are highly coordinated and interdependent processes. In our search for novel regulators of epithelial polarization and protein secretion, we used a genome-wide CRISPR/Cas9 screen and combined it with an assay based on fluorescence-activated cell sorting (FACS) to measure the secretion of the apical brush-border hydrolase dipeptidyl peptidase 4 (DPP4). In this way, we performed the first CRISPR screen to date in human polarized epithelial cells. Using high-resolution microscopy, we detected polarization defects and mislocalization of DPP4 to late endosomes/lysosomes after knockout of TM9SF4, anoctamin 8, and ARHGAP33, confirming the identification of novel factors for epithelial polarization and apical cargo secretion. Thus, we provide a powerful tool suitable for studying polarization and cargo secretion in epithelial cells. In addition, we provide a dataset that serves as a resource for the study of novel mechanisms for epithelial polarization and polarized transport and facilitates the investigation of novel congenital diseases associated with these processes.
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Affiliation(s)
- Katharina MC Klee
- Institute of Cell Biology, Medical University of InnsbruckInnsbruckAustria
- Institute of Histology and Embryology, Medical University of InnsbruckInnsbruckAustria
| | - Michael W Hess
- Institute of Histology and Embryology, Medical University of InnsbruckInnsbruckAustria
| | - Michael Lohmüller
- Institute of Developmental Immunology, Medical University of InnsbruckInnsbruckAustria
| | - Sebastian Herzog
- Institute of Developmental Immunology, Medical University of InnsbruckInnsbruckAustria
| | - Kristian Pfaller
- Institute of Histology and Embryology, Medical University of InnsbruckInnsbruckAustria
| | - Thomas Müller
- Department of Paediatrics I, Medical University of InnsbruckInnsbruckAustria
| | - Georg F Vogel
- Institute of Cell Biology, Medical University of InnsbruckInnsbruckAustria
- Department of Paediatrics I, Medical University of InnsbruckInnsbruckAustria
| | - Lukas A Huber
- Institute of Cell Biology, Medical University of InnsbruckInnsbruckAustria
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9
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Levic DS, Bagnat M. Polarized transport of membrane and secreted proteins during lumen morphogenesis. Semin Cell Dev Biol 2023; 133:65-73. [PMID: 35307284 PMCID: PMC9481742 DOI: 10.1016/j.semcdb.2022.03.016] [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: 12/03/2021] [Revised: 03/09/2022] [Accepted: 03/12/2022] [Indexed: 10/18/2022]
Abstract
A ubiquitous feature of animal development is the formation of fluid-filled cavities or lumina, which transport gases and fluids across tissues and organs. Among different species, lumina vary drastically in size, scale, and complexity. However, all lumen formation processes share key morphogenetic principles that underly their development. Fundamentally, a lumen simply consists of epithelial cells that encapsulate a continuous internal space, and a common way of building a lumen is via opening and enlarging by filling it with fluid and/or macromolecules. Here, we discuss how polarized targeting of membrane and secreted proteins regulates lumen formation, mainly focusing on ion transporters in vertebrate model systems. We also discuss mechanistic differences observed among invertebrates and vertebrates and describe how the unique properties of the Na+/K+-ATPase and junctional proteins can promote polarization of immature epithelia to build lumina de novo in developing organs.
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Affiliation(s)
- Daniel S Levic
- Department of Cell Biology, Duke University, Durham, NC 27710, USA.
| | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC 27710, USA.
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10
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De Renzis S, Sokac AM. Editorial: Membrane dynamics during tissue morphogenesis and differentiation. Semin Cell Dev Biol 2023; 133:1-2. [PMID: 35753907 DOI: 10.1016/j.semcdb.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Stefano De Renzis
- Developmental Biology Unit, European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany.
| | - Anna Marie Sokac
- Department of Cell and Developmental Biology, University of Illinois at Urbana, Champaign, Urbana, IL 61801, USA.
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11
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Alfonso-Pérez T, Baonza G, Herranz G, Martín-Belmonte F. Deciphering the interplay between autophagy and polarity in epithelial tubulogenesis. Semin Cell Dev Biol 2022; 131:160-172. [PMID: 35641407 DOI: 10.1016/j.semcdb.2022.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/14/2022]
Abstract
The Metazoan complexity arises from a primary building block, the epithelium, which comprises a layer of polarized cells that divide the organism into compartments. Most of these body compartments are organs formed by epithelial tubes that enclose an internal hollow space or lumen. Over the last decades, multiple studies have unmasked the paramount events required to form this lumen de novo. In epithelial cells, these events mainly involve recognizing external clues, establishing and maintaining apicobasal polarity, endo-lysosomal trafficking, and expanding the created lumen. Although canonical autophagy has been classically considered a catabolic process needed for cell survival, multiple studies have also emphasized its crucial role in epithelial polarity, morphogenesis and cellular homeostasis. Furthermore, non-canonical autophagy pathways have been recently discovered as atypical secretory routes. Both canonical and non-canonical pathways play essential roles in epithelial polarity and lumen formation. This review addresses how the molecular machinery for epithelial polarity and autophagy interplay in different processes and how autophagy functions influence lumenogenesis, emphasizing its role in the lumen formation key events.
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Affiliation(s)
- Tatiana Alfonso-Pérez
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo, Ochoa", CSIC-UAM, Madrid 28049, Spain; Ramon & Cajal Health Research Institute (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid 28034, Spain
| | - Gabriel Baonza
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo, Ochoa", CSIC-UAM, Madrid 28049, Spain
| | - Gonzalo Herranz
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo, Ochoa", CSIC-UAM, Madrid 28049, Spain; Ramon & Cajal Health Research Institute (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid 28034, Spain
| | - Fernando Martín-Belmonte
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo, Ochoa", CSIC-UAM, Madrid 28049, Spain; Ramon & Cajal Health Research Institute (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid 28034, Spain.
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12
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Sun-Wada GH, Wada Y. Exploring the Link between Vacuolar-Type Proton ATPase and Epithelial Cell Polarity. Biol Pharm Bull 2022; 45:1419-1425. [PMID: 36184498 DOI: 10.1248/bpb.b22-00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vacuolar-type H+-ATPase (V-ATPase) was first identified as an electrogenic proton pump that acidifies the lumen of intracellular organelles. Subsequently, it was observed that the proton pump also participates in the acidification of extracellular compartments. V-ATPase plays important roles in a wide range of cell biological processes and physiological functions by generating an acidic pH; therefore, it has attracted much attention not only in basic research but also in pathological and clinical aspects. Emerging evidence indicates that the luminal acidic endocytic organelles and their trafficking may function as important hubs that connect and coordinate various signaling pathways. Various pharmacological analyses have suggested that acidic endocytic organelles are important for the maintenance of cell polarity. Recently, several studies using genetic approaches have revealed the involvement of V-ATPase in the establishment and maintenance of apico-basal polarity. This review provides a brief overview of the relationship between the polarity of epithelial cells and V-ATPase as well as V-ATPase driven luminal acidification.
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Affiliation(s)
- Ge-Hong Sun-Wada
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts
| | - Yoh Wada
- Division of Biological Science, Institute of Scientific and Industrial Research, Osaka University
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13
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Francis CR, Kushner EJ. Trafficking in blood vessel development. Angiogenesis 2022; 25:291-305. [PMID: 35449244 PMCID: PMC9249721 DOI: 10.1007/s10456-022-09838-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/03/2022] [Indexed: 02/17/2023]
Abstract
Blood vessels demonstrate a multitude of complex signaling programs that work in concert to produce functional vasculature networks during development. A known, but less widely studied, area of endothelial cell regulation is vesicular trafficking, also termed sorting. After moving through the Golgi apparatus, proteins are shuttled to organelles, plugged into membranes, recycled, or degraded depending on the internal and extrinsic cues. A snapshot of these protein-sorting systems can be viewed as a trafficking signature that is not only unique to endothelial tissue, but critically important for blood vessel form and function. In this review, we will cover how vesicular trafficking impacts various aspects of angiogenesis, such as sprouting, lumen formation, vessel stabilization, and secretion, emphasizing the role of Rab GTPase family members and their various effectors.
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Affiliation(s)
- Caitlin R Francis
- Department of Biological Sciences, University of Denver, Denver, CO, 80210, USA
| | - Erich J Kushner
- Department of Biological Sciences, University of Denver, Denver, CO, 80210, USA.
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Levic DS, Bagnat M. Self-organization of apical membrane protein sorting in epithelial cells. FEBS J 2022; 289:659-670. [PMID: 33864720 PMCID: PMC8522177 DOI: 10.1111/febs.15882] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/25/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023]
Abstract
Polarized epithelial cells are characterized by the asymmetric distribution of proteins between apical and basolateral domains of the plasma membrane. This asymmetry is highly conserved and is fundamental to epithelial cell physiology, development, and homeostasis. How proteins are segregated for apical or basolateral delivery, a process known as sorting, has been the subject of considerable investigation for decades. Despite these efforts, the rules guiding apical sorting are poorly understood and remain controversial. Here, we consider mechanisms of apical membrane protein sorting and argue that they are largely driven by self-organization and biophysical principles. The preponderance of data to date is consistent with the idea that apical sorting is not ruled by a dedicated protein-based sorting machinery and relies instead on the concerted effects of oligomerization, phase separation of lipids and proteins in membranes, and pH-dependent glycan interactions.
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Affiliation(s)
- Daniel S. Levic
- Department of Cell Biology, Duke University, Durham, NC 27710, USA,Correspondence to Michel Bagnat: or Dan Levic:
| | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC 27710, USA,Correspondence to Michel Bagnat: or Dan Levic:
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15
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Levic DS, Yamaguchi N, Wang S, Knaut H, Bagnat M. Knock-in tagging in zebrafish facilitated by insertion into non-coding regions. Development 2021; 148:dev199994. [PMID: 34495314 PMCID: PMC8513609 DOI: 10.1242/dev.199994] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/27/2021] [Indexed: 11/20/2022]
Abstract
Zebrafish provide an excellent model for in vivo cell biology studies because of their amenability to live imaging. Protein visualization in zebrafish has traditionally relied on overexpression of fluorescently tagged proteins from heterologous promoters, making it difficult to recapitulate endogenous expression patterns and protein function. One way to circumvent this problem is to tag the proteins by modifying their endogenous genomic loci. Such an approach is not widely available to zebrafish researchers because of inefficient homologous recombination and the error-prone nature of targeted integration in zebrafish. Here, we report a simple approach for tagging proteins in zebrafish on their N or C termini with fluorescent proteins by inserting PCR-generated donor amplicons into non-coding regions of the corresponding genes. Using this approach, we generated endogenously tagged alleles for several genes that are crucial for epithelial biology and organ development, including the tight junction components ZO-1 and Cldn15la, the trafficking effector Rab11a, the apical polarity protein aPKC and the ECM receptor Integrin β1b. Our approach facilitates the generation of knock-in lines in zebrafish, opening the way for accurate quantitative imaging studies.
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Affiliation(s)
- Daniel S. Levic
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Naoya Yamaguchi
- Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, Department of Cell Biology, New York, NY 10016, USA
| | - Siyao Wang
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Holger Knaut
- Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, Department of Cell Biology, New York, NY 10016, USA
| | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
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16
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Santra P, Amack JD. Loss of vacuolar-type H+-ATPase induces caspase-independent necrosis-like death of hair cells in zebrafish neuromasts. Dis Model Mech 2021; 14:dmm048997. [PMID: 34296747 PMCID: PMC8319552 DOI: 10.1242/dmm.048997] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/15/2021] [Indexed: 01/24/2023] Open
Abstract
The vacuolar-type H+-ATPase (V-ATPase) is a multi-subunit proton pump that regulates cellular pH. V-ATPase activity modulates several cellular processes, but cell-type-specific functions remain poorly understood. Patients with mutations in specific V-ATPase subunits can develop sensorineural deafness, but the underlying mechanisms are unclear. Here, we show that V-ATPase mutations disrupt the formation of zebrafish neuromasts, which serve as a model to investigate hearing loss. V-ATPase mutant neuromasts are small and contain pyknotic nuclei that denote dying cells. Molecular markers and live imaging show that loss of V-ATPase induces mechanosensory hair cells in neuromasts, but not neighboring support cells, to undergo caspase-independent necrosis-like cell death. This is the first demonstration that loss of V-ATPase can lead to necrosis-like cell death in a specific cell type in vivo. Mechanistically, loss of V-ATPase reduces mitochondrial membrane potential in hair cells. Modulating the mitochondrial permeability transition pore, which regulates mitochondrial membrane potential, improves hair cell survival. These results have implications for understanding the causes of sensorineural deafness, and more broadly, reveal functions for V-ATPase in promoting survival of a specific cell type in vivo.
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Affiliation(s)
- Peu Santra
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
| | - Jeffrey D. Amack
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
- BioInspired Syracuse: Institute for Material and Living Systems, Syracuse, NY 13244, USA
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17
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Serra ND, Sundaram MV. Transcytosis in the development and morphogenesis of epithelial tissues. EMBO J 2021; 40:e106163. [PMID: 33792936 DOI: 10.15252/embj.2020106163] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/21/2020] [Accepted: 01/14/2021] [Indexed: 12/15/2022] Open
Abstract
Transcytosis is a form of specialized transport through which an extracellular cargo is endocytosed, shuttled across the cytoplasm in membrane-bound vesicles, and secreted at a different plasma membrane surface. This important process allows membrane-impermeable macromolecules to pass through a cell and become accessible to adjacent cells and tissue compartments. Transcytosis also promotes redistribution of plasma membrane proteins and lipids to different regions of the cell surface. Here we review transcytosis and highlight in vivo studies showing how developing epithelial cells use it to change shape, to migrate, and to relocalize signaling molecules.
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Affiliation(s)
- Nicholas D Serra
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Meera V Sundaram
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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