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Bacon J, Kitchel H, Stutz J, Chen JH, Smith A, Van Horn RD, Moreland C, Abraham T, Baker T, Aihara E, Hillgren K. Porcine intestinal organoids cultured in an organ-on-a-chip microphysiological system. Biochem Biophys Rep 2025; 42:102036. [PMID: 40421277 PMCID: PMC12104630 DOI: 10.1016/j.bbrep.2025.102036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 04/16/2025] [Accepted: 04/25/2025] [Indexed: 05/28/2025] Open
Abstract
Preclinical studies are a vital component of pharmaceutical development and improvements in the predictive value of in vitro studies are essential. Organ-on-a-chip in vitro models are a recent advancement in the pursuit of improved reproduction of in vivo tissue complexity. Here, we report the development and characterization of porcine intestinal cells from organoids on chips with microfluid dynamics and peristaltic-like strain in a microphysiological system. Intestinal epithelial cells were grown on a porous membrane as a co-culture with human intestinal microvascular endothelial cells for up to 12 days. These cultures formed villi-like structures and established a tight barrier replete with F-actin and tight junctions. A demarcated region of the epithelial cells was in an actively proliferative stage, reminiscent of intestinal crypts. The intestinal epithelial cell growth was characterized for the presence of enterocytes, goblet cells and enteroendocrine cells. Notable drug transporters and CYP450 metabolic activity were present in these cultures. The organoid chip maintained barrier function as the paracellular permeability was low. In contrast, the permeability enhancer, sodium caprate (C10), increased the apparent permeability of molecular weight marker compounds by 2- to 3-fold, and upon removal of C10, the barrier was shown to be recovered. The porcine intestinal chip represents a new in vitro model with potential application in multiple aspects of pharmaceutical testing including drug metabolism, drug transporters and safety.
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Affiliation(s)
- James Bacon
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Halie Kitchel
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - John Stutz
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Jack Hua Chen
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Aaron Smith
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Robert D. Van Horn
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | | | - Trent Abraham
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | | | - Eitaro Aihara
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Kathleen Hillgren
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
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2
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Pike CM, Levi JA, Boone LA, Peddibhotla S, Johnson J, Zwarycz B, Bunger MK, Thelin W, Boazak EM. High-throughput assay for predicting diarrhea risk using a 2D human intestinal stem cell-derived model. Toxicol In Vitro 2025; 106:106040. [PMID: 40086646 DOI: 10.1016/j.tiv.2025.106040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 01/29/2025] [Accepted: 03/05/2025] [Indexed: 03/16/2025]
Abstract
Gastrointestinal toxicities (GITs) in clinical trials often lead to dose-limitations that reduce drug efficacy and delay treatment optimization. Preclinical animal models do not accurately replicate human physiology, leaving few options for early detection of GITs, such as diarrhea, before human studies. Chemotherapeutic agents, known to cause clinical diarrhea, frequently target mitotic cells. Therefore, we hypothesized a model utilizing proliferative cell populations derived from human intestinal crypts would predict clinical diarrhea occurrence with high accuracy. Here, we describe the development of a diarrhea prediction assay utilizing RepliGut® Planar, a primary intestinal stem cell-derived platform. To evaluate the ability of this model to predict clinical diarrhea risk, we assessed toxicity of 30 marketed drugs by measuring cell proliferation (EdU incorporation), cell abundance (nuclei quantification), and barrier formation (TEER) in cells derived from three human donors. Dose response curves were generated for each drug, and the IC15 to Cmax ratio was used to identify a threshold for assay positivity. This model accurately predicted diarrhea potential, achieving an accuracy of 91 % for proliferation, 90 % for abundance, and 88 % for barrier formation. In vitro toxicity screening using primary proliferative cells may reduce clinical diarrhea and ultimately lead to safer and more effective treatments for patients.
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3
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Wang CM, Oberoi HS, Law D, Li Y, Kassis T, Griffith LG, Breault DT, Carrier RL. Human mesofluidic intestinal model for studying transport of drug carriers and bacteria through a live mucosal barrier. LAB ON A CHIP 2025. [PMID: 40392585 DOI: 10.1039/d4lc00774c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2025]
Abstract
The intestinal mucosal barrier forms a critical interface between lumen contents such as bacteria, drugs, and drug carriers and the underlying tissue. Current in vitro intestinal models, while recapitulating certain aspects of this barrier, generally present challenges with respect to imaging transport across mucus and uptake into enterocytes. A human mesofluidic small intestinal chip was designed to enable facile visualization of a mucosal interface created by growing primary human intestinal cells on a vertical hydrogel wall separating channels representing the intestinal lumen and circulatory flow. Type I collagen, fortified via cross-linking to prevent deformation and leaking during culture, was identified as a suitable gel wall material for supporting primary organoid-derived human duodenal epithelial cell attachment and monolayer formation. Addition of DAPT and PGE2 to culture medium paired with air-liquid interface culture increased the thickness of the mucus layer on epithelium grown within the device for 5 days from approximately 5 μm to 50 μm, making the model suitable for revealing intriguing features of interactions between luminal contents and the mucus barrier using live cell imaging. Time-lapse imaging of nanoparticle diffusion within mucus revealed a zone adjacent to the epithelium largely devoid of nanoparticles up to 4.5 h after introduction to the lumen channel, as well as pockets of dimly lectin-stained mucus within which particles freely diffused, and apparent clumping of particles by mucus components. Multiple particle tracking conducted on the intact mucus layer in the chip revealed significant size-dependent differences in measured diffusion coefficients. E. coli introduced to the lumen channel were freely mobile within the mucus layer and appeared to intermittently contact the epithelial surface over 30 minute periods of culture. Mucus shedding into the lumen and turnover of mucus components within cells were visualized. Taken together, this system represents a powerful tool for visualization of interactions between luminal contents and an intact live mucosal barrier.
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Affiliation(s)
- Chia-Ming Wang
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA.
| | - Hardeep S Oberoi
- NCE-Formulation Sciences, Abbvie Inc., North Chicago, IL, 60064, USA
| | - Devalina Law
- NCE-Formulation Sciences, Abbvie Inc., North Chicago, IL, 60064, USA
| | - Yuan Li
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA
| | - Timothy Kassis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Rebecca L Carrier
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA.
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
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4
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Hsieh HC, Han Q, Brenes D, Bishop KW, Wang R, Wang Y, Poudel C, Glaser AK, Freedman BS, Vaughan JC, Allbritton NL, Liu JTC. Imaging 3D cell cultures with optical microscopy. Nat Methods 2025:10.1038/s41592-025-02647-w. [PMID: 40247123 DOI: 10.1038/s41592-025-02647-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 01/16/2025] [Indexed: 04/19/2025]
Abstract
Three-dimensional (3D) cell cultures have gained popularity in recent years due to their ability to represent complex tissues or organs more faithfully than conventional two-dimensional (2D) cell culture. This article reviews the application of both 2D and 3D microscopy approaches for monitoring and studying 3D cell cultures. We first summarize the most popular optical microscopy methods that have been used with 3D cell cultures. We then discuss the general advantages and disadvantages of various microscopy techniques for several broad categories of investigation involving 3D cell cultures. Finally, we provide perspectives on key areas of technical need in which there are clear opportunities for innovation. Our goal is to guide microscope engineers and biomedical end users toward optimal imaging methods for specific investigational scenarios and to identify use cases in which additional innovations in high-resolution imaging could be helpful.
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Affiliation(s)
- Huai-Ching Hsieh
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Qinghua Han
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - David Brenes
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Kevin W Bishop
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Rui Wang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Yuli Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Adam K Glaser
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Benjamin S Freedman
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Medicine, Division of Nephrology, Kidney Research Institute and Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
- Plurexa LLC, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jonathan T C Liu
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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5
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Roegiers I, Gheysens T, Minsart M, De Clercq P, Vanbeversluys K, Rać N, Stroka G, de Croock J, Van de Wiele T, Dubruel P, Arroyo MC. GelMA as scaffold material for epithelial cells to emulate the small intestinal microenvironment. Sci Rep 2025; 15:8214. [PMID: 40064943 PMCID: PMC11893807 DOI: 10.1038/s41598-024-81533-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 11/27/2024] [Indexed: 03/14/2025] Open
Abstract
Host-microbe interactions in the intestine play a significant role in health and disease. Novel scaffolds for host cells, capable of potentially supporting these intricate interactions, are necessary to improve our current systems for mimicking host-microbiota interplay in vitro/ex vivo. In this research paper, we study the application of gelatin methacrylamide (GelMA) as scaffold material for intestinal epithelial cells in terms of permeability, mechanical strength, and biocompatibility. We investigated whether the degree of substitution (DS) of GelMA influences the permeability and found that both high and low DS GelMA show sufficient permeability of biorelevant transport markers. Additionally, we researched epithelial cell adherence and viability, as well as mechanical characteristics of different concentrations of GelMA. All concentrations of hydrogel show long-term biocompatibility for the mono- and co-cultures, despite the goblet-like cells (LS174T) showing lower performance than enterocyte-like cells (Caco-2). The mechanical strength of all hydrogel concentrations was in a physiologically relevant range to be used as scaffold material for intestinal cells. Lastly, we examined the effect of the two sterilization methods, ethylene oxide (EO) and 70% ethanol followed by UVC (EtOH/UVC). We found that the impact of the two methods on the mechanical characteristics was minimal, and we did not find a significant effect between the two methods on cell viability and confluency of Caco-2 cells seeded on the GelMA hydrogels. Based on these results, we conclude that GelMA is a suitable material as a scaffold for intestinal cell types in terms of permeability, mechanical strength and biocompatibility. These findings contribute to the growing field of in vitro modeling of the gut and moves the field further to ensuring more translatable research on host-microbe interactions.
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Affiliation(s)
- Inez Roegiers
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
- Polymer Chemistry and Biomaterials Group (PBM), Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium.
| | - Tom Gheysens
- Polymer Chemistry and Biomaterials Group (PBM), Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Manon Minsart
- Polymer Chemistry and Biomaterials Group (PBM), Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Pieter De Clercq
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kim Vanbeversluys
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Nikoletta Rać
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Grzegorz Stroka
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jana de Croock
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Peter Dubruel
- Polymer Chemistry and Biomaterials Group (PBM), Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Marta Calatayud Arroyo
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Valencia, Spain
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Rose EC, Simon JM, Gomez-Martinez I, Magness ST, Odle J, Blikslager AT, Ziegler AL. Single-cell transcriptomics predict novel potential regulators of acute epithelial restitution in the ischemia-injured intestine. Am J Physiol Gastrointest Liver Physiol 2025; 328:G182-G196. [PMID: 39853303 DOI: 10.1152/ajpgi.00194.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/05/2024] [Accepted: 01/07/2025] [Indexed: 01/26/2025]
Abstract
Intestinal ischemic injury damages the epithelial barrier and predisposes patients to life-threatening sepsis unless that barrier is rapidly restored. There is an age dependency in intestinal recovery in that neonates are the most susceptible to succumb to disease of the intestinal barrier compared with older patients. We have developed a pig model that demonstrates age-dependent failure of intestinal barrier restitution in neonatal pigs, which can be rescued by the direct application of juvenile pig mucosal tissue, but the mechanisms of rescue remain undefined. We hypothesized that by identifying a subpopulation of restituting enterocytes by their expression of cell migration transcriptional pathways, we can then predict novel upstream regulators of age-dependent restitution response programs. Superficial mucosal epithelial cells from recovering ischemic jejunum of juvenile pigs underwent single-cell transcriptomics and the predicted upstream regulator, colony stimulating factor-1 (CSF-1), was interrogated in our model. A subcluster of absorptive enterocytes expressed several cell migration pathways key to restitution. Differentially expressed genes in this subcluster predicted their upstream regulation by colony stimulating factor-1 (CSF-1). We validated age-dependent induction of CSF-1 by ischemia and documented that CSF-1 and colony-stimulating factor-1 receptor (CSF1R) co-localized in ischemic juvenile, but not neonatal, wound-adjacent epithelial cells and in the restituted epithelium of juveniles and rescued neonates. Furthermore, the CSF-1 blockade reduced restitution in vitro, and CSF-1 improved barrier function in injured neonatal pigs in preliminary ex vivo experiments. These studies validate an approach to inform potential novel therapeutic targets, such as CSF-1, to improve outcomes in neonates with intestinal injury in a unique pig model.NEW & NOTEWORTHY These studies validate an approach to identify and predict upstream regulation of restituting epithelium in a unique pig intestinal ischemic injury model. Identification of potential molecular mediators of restitution, such as CSF-1, will inform the development of targeted therapeutic interventions for the medical management of patients with ischemia-mediated intestinal injury.
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Affiliation(s)
- Elizabeth C Rose
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States
| | - Jeremy M Simon
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Ismael Gomez-Martinez
- Bioinformatics and Analytics Research Collaborative, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Scott T Magness
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Jack Odle
- Department of Animal Science, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, North Carolina, United States
| | - Anthony T Blikslager
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States
| | - Amanda L Ziegler
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States
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7
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Klein JA, Heidmann JD, Kiyota T, Fullerton A, Homan KA, Co JY. The differentiation state of small intestinal organoid models influences prediction of drug-induced toxicity. Front Cell Dev Biol 2025; 13:1508820. [PMID: 39917568 PMCID: PMC11799252 DOI: 10.3389/fcell.2025.1508820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Accepted: 01/03/2025] [Indexed: 02/09/2025] Open
Abstract
Drug-induced intestinal toxicity (GIT) is a frequent dose-limiting adverse event that can impact patient compliance and treatment outcomes. In vivo, there are proliferative and differentiated cell types critical to maintaining intestinal homeostasis. Traditional in vitro models using transformed cell lines do not capture this cellular complexity, and often fail to predict intestinal toxicity. Primary tissue-derived intestinal organoids, on the other hand, are a scalable Complex in vitro Model (CIVM) that recapitulates major intestinal cell lineages and function. Intestinal organoid toxicity assays have been shown to correlate with clinical incidence of drug-induced diarrhea, however existing studies do not consider how differentiation state of the organoids impacts assay readouts and predictivity. We employed distinct proliferative and differentiated organoid models of the small intestine to assess whether differentiation state alone can alter toxicity responses to small molecule compounds in cell viability assays. In doing so, we identified several examples of small molecules which elicit differential toxicity in proliferative and differentiated organoid models. This proof of concept highlights the need to consider which cell types are present in CIVMs, their differentiation state, and how this alters interpretation of toxicity assays.
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Affiliation(s)
- Jessica A. Klein
- Complex In Vitro Systems, Translational Safety, Genentech Inc., South San Francisco, CA, United States
| | - Julia D. Heidmann
- Investigative Toxicology, Translational Safety, Genentech Inc., South San Francisco, CA, United States
| | - Tomomi Kiyota
- Investigative Toxicology, Translational Safety, Genentech Inc., South San Francisco, CA, United States
| | - Aaron Fullerton
- Investigative Toxicology, Translational Safety, Genentech Inc., South San Francisco, CA, United States
| | - Kimberly A. Homan
- Complex In Vitro Systems, Translational Safety, Genentech Inc., South San Francisco, CA, United States
| | - Julia Y. Co
- Complex In Vitro Systems, Translational Safety, Genentech Inc., South San Francisco, CA, United States
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8
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Gonzalez La Corte S, Stevens CA, Cárcamo-Oyarce G, Ribbeck K, Wingreen NS, Datta SS. Morphogenesis of bacterial cables in polymeric environments. SCIENCE ADVANCES 2025; 11:eadq7797. [PMID: 39823332 PMCID: PMC11740958 DOI: 10.1126/sciadv.adq7797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 12/17/2024] [Indexed: 01/19/2025]
Abstract
Many bacteria live in polymeric fluids, such as mucus, environmental polysaccharides, and extracellular polymers in biofilms. However, laboratory studies typically focus on cells in polymer-free fluids. Here, we show that interactions with polymers shape a fundamental feature of bacterial life-how they proliferate in space in multicellular colonies. Using experiments, we find that when polymer is sufficiently concentrated, cells generically and reversibly form large serpentine "cables" as they proliferate. By combining experiments with biophysical theory and simulations, we demonstrate that this distinctive form of colony morphogenesis arises from an interplay between polymer-induced entropic attraction between neighboring cells and their hindered ability to diffusely separate from each other in a viscous polymer solution. Our work thus reveals a pivotal role of polymers in sculpting proliferating bacterial colonies, with implications for how they interact with hosts and with the natural environment, and uncovers quantitative principles governing colony morphogenesis in such complex environments.
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Affiliation(s)
| | - Corey A. Stevens
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gerardo Cárcamo-Oyarce
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sujit S. Datta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
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9
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Masete KV, Günzel D, Schulzke JD, Epple HJ, Hering NA. Matrix-free human 2D organoids recapitulate duodenal barrier and transport properties. BMC Biol 2025; 23:2. [PMID: 39757172 DOI: 10.1186/s12915-024-02105-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 12/23/2024] [Indexed: 01/07/2025] Open
Abstract
BACKGROUND Traditionally, transformed cell line monolayers have been the standard model for studying epithelial barrier and transport function. Recently, intestinal organoids were proposed as superior in recapitulating the intestine. Typically, 3D organoids are digested and seeded as monolayers on gelatinous matrix pre-coated surfaces for anchorage. As this coat could potentially act as a diffusion barrier, we aimed to generate robust human duodenum-derived organoid monolayers that do not need a gelatinous matrix for anchorage to improve upon existing models to study epithelial transport and barrier function. RESULTS We characterized these monolayers phenotypically regarding polarization, tight junction formation and cellular composition, and functionally regarding uptake of nutrients, ion transport and cytokine-induced barrier dysfunction. The organoid monolayers recapitulated the duodenum phenotypically as well as functionally regarding glucose and short-chain fatty acid uptake. Tumour necrosis factor-alpha induced paracellular transport of 4-kDa Dextran and transcytosis of 44-kDa horseradish peroxidase. Notably, forskolin-stimulated chloride secretion was consistently lower when organoid monolayers were seeded on a layer of basement membrane extract (BME). CONCLUSIONS BME-free organoid monolayers represent an improved model for studying transcytotic, paracellular but especially transcellular transport. As BME is extracted from mice, our model furthers efforts to make organoid culture more animal-free.
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Affiliation(s)
- Kopano Valerie Masete
- Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Dorothee Günzel
- Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Jörg-Dieter Schulzke
- Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Hans-Jörg Epple
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
- Antibiotic Stewardship Team, Medical Directorate, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Nina A Hering
- Department of General and Visceral Surgery, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, 12203, Germany.
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10
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Massaro A, Villegas Novoa C, Wang Y, Allbritton NL. Fibroblasts modulate epithelial cell behavior within the proliferative niche and differentiated cell zone within a human colonic crypt model. Front Bioeng Biotechnol 2024; 12:1506976. [PMID: 39737053 PMCID: PMC11683563 DOI: 10.3389/fbioe.2024.1506976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Accepted: 11/22/2024] [Indexed: 01/01/2025] Open
Abstract
Colonic epithelium is situated above a layer of fibroblasts that provide supportive factors for stem cells at the crypt base and promote differentiation of cells in the upper crypt and luminal surface. To study the fibroblast-epithelial cell interactions, an in vitro crypt model was formed on a shaped collagen scaffold with primary epithelial cells growing above a layer of primary colonic fibroblasts. The crypts possessed a basal stem cell niche populated with proliferative cells and a differentiated, nondividing cell zone at the luminal crypt end. The presence of fibroblasts enhanced cell differentiation and accelerated the rate at which a high resistance epithelial cell layer formed relative to cultures without fibroblasts. The fibroblasts modulated cell proliferation within crypts increasing the number of crypts populated with proliferative cells but decreasing the total number of proliferative cells in each crypt. Bulk-RNA sequencing revealed 41 genes that were significantly upregulated and 190 genes that were significantly downregulated in cocultured epithelium relative to epithelium cultured without fibroblasts. This epithelium-fibroblast crypt model suggests bidirectional communication between the two cell types and has the potential to serve as a model to investigate fibroblast-epithelial cell interactions in health and disease.
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Affiliation(s)
| | | | | | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA, United States
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11
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Burclaff J, Magness ST. Preparing Chamber Slides With Pressed Collagen for Live Imaging Monolayers of Primary Human Intestinal Stem Cells. Bio Protoc 2024; 14:e5116. [PMID: 39600970 PMCID: PMC11588582 DOI: 10.21769/bioprotoc.5116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 09/27/2024] [Accepted: 09/27/2024] [Indexed: 11/29/2024] Open
Abstract
Primary human intestinal stem cells (ISCs) can be cultured and passaged indefinitely as two-dimensional monolayers grown on soft collagen. Culturing ISCs as monolayers enables easy access to the luminal side for chemical treatments and provides a simpler topology for high-resolution imaging compared to cells cultured as three-dimensional organoids. However, the soft collagen required to support primary ISC growth can pose a challenge for live imaging with an inverted microscope, as the collagen creates a steep meniscus when poured into wells. This may lead to uneven growth toward the center of the well, with cells at the edges often extending beyond the working distance of confocal microscopes. We have engineered a 3D-printed collagen mold that enables the preparation of chamber slides with flat, smooth, and reproducible thin collagen layers. These layers are adequate to support ISC growth while being thin enough to optimize live imaging with an inverted microscope. We present methods for constructing the collagen press, preparing chamber slides with pressed collagen, and plating primary human ISCs for growth and analysis. Key features • This protocol describes how to construct and use collagen presses for chamber slides, as demonstrated in Cotton et al. [1]. • The soft collagen and culture media presented are optimized for primary human intestinal stem cells. • The full protocol, including 3D printing, preparing collagen-coated chamber slides, and plating cells can be completed in under one week. • This protocol requires access to a 3D printer.
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Affiliation(s)
- Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott T. Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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12
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Walraven T, Busch M, Wang J, Donkers JM, Duijvestein M, van de Steeg E, Kramer NI, Bouwmeester H. Elevated risk of adverse effects from foodborne contaminants and drugs in inflammatory bowel disease: a review. Arch Toxicol 2024; 98:3519-3541. [PMID: 39249550 PMCID: PMC11489187 DOI: 10.1007/s00204-024-03844-w] [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: 06/04/2024] [Accepted: 08/19/2024] [Indexed: 09/10/2024]
Abstract
The global burden of Inflammatory bowel disease (IBD) has been rising over the last decades. IBD is an intestinal disorder with a complex and largely unknown etiology. The disease is characterized by a chronically inflamed gastrointestinal tract, with intermittent phases of exacerbation and remission. This compromised intestinal barrier can contribute to, enhance, or even enable the toxicity of drugs, food-borne chemicals and particulate matter. This review discusses whether the rising prevalence of IBD in our society warrants the consideration of IBD patients as a specific population group in toxicological safety assessment. Various in vivo, ex vivo and in vitro models are discussed that can simulate hallmarks of IBD and may be used to study the effects of prevalent intestinal inflammation on the hazards of these various toxicants. In conclusion, risk assessments based on healthy individuals may not sufficiently cover IBD patient safety and it is suggested to consider this susceptible subgroup of the population in future toxicological assessments.
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Affiliation(s)
- Tom Walraven
- Division of Toxicology, Wageningen University and Research, Wageningen, The Netherlands.
| | - Mathias Busch
- Division of Toxicology, Wageningen University and Research, Wageningen, The Netherlands
| | - Jingxuan Wang
- Division of Toxicology, Wageningen University and Research, Wageningen, The Netherlands
| | - Joanne M Donkers
- Department of Metabolic Health Research, Netherlands Organization for Applied Scientific Research (TNO), Leiden, The Netherlands
| | - Marjolijn Duijvestein
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evita van de Steeg
- Department of Metabolic Health Research, Netherlands Organization for Applied Scientific Research (TNO), Leiden, The Netherlands
| | - Nynke I Kramer
- Division of Toxicology, Wageningen University and Research, Wageningen, The Netherlands
| | - Hans Bouwmeester
- Division of Toxicology, Wageningen University and Research, Wageningen, The Netherlands
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13
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Streekstra EJ, Keuper-Navis M, van den Heuvel JJMW, van den Broek P, Stommel MWJ, de Boode W, Botden S, Bervoets S, O’Gorman L, Greupink R, Russel FGM, van de Steeg E, de Wildt SN. Enteroids to Study Pediatric Intestinal Drug Transport. Mol Pharm 2024; 21:4983-4994. [PMID: 39279643 PMCID: PMC11462498 DOI: 10.1021/acs.molpharmaceut.4c00339] [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: 03/29/2024] [Revised: 08/30/2024] [Accepted: 08/30/2024] [Indexed: 09/18/2024]
Abstract
Intestinal maturational changes after birth affect the pharmacokinetics (PK) of drugs, having major implications for drug safety and efficacy. However, little is known about ontogeny-related PK patterns in the intestine. To explore the accuracy of human enteroid monolayers for studying drug transport in the pediatric intestine, we compared the drug transporter functionality and expression in enteroid monolayers and tissue from pediatrics and adults. Enteroid monolayers were cultured of 14 pediatric [median (range) age: 44 weeks (2 days-13 years)] and 5 adult donors, in which bidirectional drug transport experiments were performed. In parallel, we performed similar experiments with tissue explants in Ussing chamber using 11 pediatric [median (range) age: 54 weeks (15 weeks-10 years)] and 6 adult tissues. Enalaprilat, propranolol, talinolol, and rosuvastatin were used to test paracellular, transcellular, and transporter-mediated efflux by P-gp and breast cancer resistance protein (BCRP), respectively. In addition, we compared the expression patterns of ADME-related genes in pediatric and adult enteroid monolayers with tissues using RNA sequencing. Efflux transport by P-gp and BCRP was comparable between the enteroids and tissue. Efflux ratios (ERs) of talinolol and rosuvastatin by P-gp and BCRP, respectively, were higher in enteroid monolayers compared to Ussing chamber, likely caused by experimental differences in model setup and cellular layers present. Explorative statistics on the correlation with age showed trends of increasing ER with age for P-gp in enteroid monolayers; however, it was not significant. In the Ussing chamber setup, lower enalaprilat and propranolol transport was observed with age. Importantly, the RNA sequencing pathway analysis revealed that age-related variation in drug metabolism between neonates and adults was present in both enteroids and intestinal tissue. Age-related differences between 0 and 6 months old and adults were observed in tissue as well as in enteroid monolayers, although to a lesser extent. This study provides the first data for the further development of pediatric enteroids as an in vitro model to study age-related variation in drug transport. Overall, drug transport in enteroids was in line with data obtained from ex vivo tissue (using chamber) experiments. Additionally, pathway analysis showed similar PK-related differences between neonates and adults in both tissue and enteroid monolayers. Given the challenge to elucidate the effect of developmental changes in the pediatric age range in human tissue, intestinal enteroids derived from pediatric patients could provide a versatile experimental platform to study pediatric phenotypes.
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Affiliation(s)
- Eva J. Streekstra
- Division
of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6525GA, The Netherlands
- Department
of Metabolic Health Research, Netherlands
Organization for Applied Scientific Research (TNO), Leiden 2333BE, The Netherlands
| | - Marit Keuper-Navis
- Department
of Metabolic Health Research, Netherlands
Organization for Applied Scientific Research (TNO), Leiden 2333BE, The Netherlands
- Division
of Pharmacology, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht 3584 CS, The Netherlands
| | - Jeroen J. M. W. van den Heuvel
- Division
of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6525GA, The Netherlands
| | - Petra van den Broek
- Division
of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6525GA, The Netherlands
| | - Martijn W. J. Stommel
- Department
of Surgery, Radboud University Medical Center, Nijmegen 6525GA, The Netherlands
| | - Willem de Boode
- Department
of Pediatrics, Division of Neonatology, Radboud University Medical Center, Amalia Children’s Hospital, Nijmegen 6525GA, The Netherlands
| | - Sanne Botden
- Department
of Surgery, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen 6525GA, The Netherlands
| | - Sander Bervoets
- Radboudumc
Technology Center for Bioinformatics, Department of Medical BioSciences, Radboud University Medical Center, Nijmegen 6525GA, The Netherlands
| | - Luke O’Gorman
- Radboudumc
Technology Center for Bioinformatics, Department of Medical BioSciences, Radboud University Medical Center, Nijmegen 6525GA, The Netherlands
| | - Rick Greupink
- Division
of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6525GA, The Netherlands
| | - Frans G. M. Russel
- Division
of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6525GA, The Netherlands
| | - Evita van de Steeg
- Department
of Metabolic Health Research, Netherlands
Organization for Applied Scientific Research (TNO), Leiden 2333BE, The Netherlands
| | - Saskia N. de Wildt
- Division
of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, Nijmegen 6525GA, The Netherlands
- Department
of Intensive Care, Radboud University Medical
Center, Nijmegen 6525GA, The Netherlands
- Department
of Neonatal and Pediatric Intensive Care, Erasmus MC Sophia Children’s Hospital, Rotterdam 3015 GD, The Netherlands
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14
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Streekstra EJ, Keuper-Navis M, van den Heuvel JJMW, van den Broek P, Stommel MWJ, Bervoets S, O'Gorman L, Greupink R, Russel FGM, van de Steeg E, de Wildt SN. Human enteroid monolayers as a potential alternative for Ussing chamber and Caco-2 monolayers to study passive permeability and drug efflux. Eur J Pharm Sci 2024; 201:106877. [PMID: 39154715 DOI: 10.1016/j.ejps.2024.106877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 08/09/2024] [Accepted: 08/10/2024] [Indexed: 08/20/2024]
Abstract
After oral administration, the intestine is the first site of drug absorption, making it a key determinant of the bioavailability of a drug, and hence drug efficacy and safety. Existing non-clinical models of the intestinal barrier in vitro often fail to mimic the barrier and absorption of the human intestine. We explore if human enteroid monolayers are a suitable tool for intestinal absorption studies compared to primary tissue (Ussing chamber) and Caco-2 cells. Bidirectional drug transport was determined in enteroid monolayers, fresh tissue (Ussing chamber methodology) and Caco-2 cells. Apparent permeability (Papp) and efflux ratios for enalaprilat (paracellular), propranolol (transcellular), talinolol (P-glycoprotein (P-gp)) and rosuvastatin (Breast cancer resistance protein (BCRP)) were determined and compared between all three methodologies and across intestinal regions. Bulk RNA sequencing was performed to compare gene expression between enteroid monolayers and primary tissue. All three models showed functional efflux transport by P-gp and BCRP with higher basolateral to apical (B-to-A) transport compared to apical-to-basolateral (A-to-B). B-to-A Papp values were similar for talinolol and rosuvastatin in tissue and enteroids. Paracellular transport of enalaprilat was lower and transcellular transport of propranolol was higher in enteroids compared to tissue. Enteroids appeared show more region- specific gene expression compared to tissue. Fresh tissue and enteroid monolayers both show active efflux by P-gp and BCRP in jejunum and ileum. Hence, the use of enteroid monolayers represents a promising and versatile experimental platform to complement current in vitro models.
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Affiliation(s)
- Eva J Streekstra
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen (Route 137), Nijmegen, the Netherlands; Department of Metabolic Health Research, Netherlands Organization for Applied Scientific Research (TNO), Leiden, the Netherlands
| | - Marit Keuper-Navis
- Department of Metabolic Health Research, Netherlands Organization for Applied Scientific Research (TNO), Leiden, the Netherlands; Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, the Netherlands
| | - Jeroen J M W van den Heuvel
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen (Route 137), Nijmegen, the Netherlands
| | - Petra van den Broek
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen (Route 137), Nijmegen, the Netherlands
| | - Martijn W J Stommel
- Department of Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sander Bervoets
- Radboudumc Technology Center for Bioinformatics, Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Luke O'Gorman
- Radboudumc Technology Center for Bioinformatics, Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rick Greupink
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen (Route 137), Nijmegen, the Netherlands
| | - Frans G M Russel
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen (Route 137), Nijmegen, the Netherlands
| | - Evita van de Steeg
- Department of Metabolic Health Research, Netherlands Organization for Applied Scientific Research (TNO), Leiden, the Netherlands
| | - Saskia N de Wildt
- Division of Pharmacology and Toxicology, Department of Pharmacy, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen (Route 137), Nijmegen, the Netherlands; Department of Intensive Care, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Neonatal and Pediatric Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands.
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15
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Wang CM, Oberoi HS, Law D, Li Y, Kassis T, Griffith LG, Breault DT, Carrier RL. Human Mesofluidic Intestinal Model for Studying Transport of Drug Carriers and Bacteria Through a Live Mucosal Barrier. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.613692. [PMID: 39345622 PMCID: PMC11429741 DOI: 10.1101/2024.09.18.613692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
The intestinal mucosal barrier forms a critical interface between lumen contents such as bacteria, drugs, and drug carriers and the underlying tissue. Current in vitro intestinal models, while recapitulating certain aspects of this barrier, generally present challenges with respect to imaging transport across mucus and uptake into enterocytes. A human mesofluidic small intestinal chip was designed to enable facile visualization of a mucosal interface created by growing primary human intestinal cells on a vertical hydrogel wall separating channels representing the intestinal lumen and circulatory flow. Type I collagen, fortified via cross-linking to prevent deformation and leaking during culture, was identified as a suitable gel wall material for supporting primary organoid-derived human duodenal epithelial cell attachment and monolayer formation. Addition of DAPT and PGE2 to culture medium paired with air-liquid interface culture increased the thickness of the mucus layer on epithelium grown within the device for 5 days from approximately 5 mm to 50 μm, making the model suitable for revealing intriguing features of interactions between luminal contents and the mucus barrier using live cell imaging. Time-lapse imaging of nanoparticle diffusion within mucus revealed a zone adjacent to the epithelium largely devoid of nanoparticles up to 4.5 hr after introduction to the lumen channel, as well as pockets of dimly lectin-stained mucus within which particles freely diffused, and apparent clumping of particles by mucus components. Multiple particle tracking conducted on the intact mucus layer in the chip revealed significant size-dependent differences in measured diffusion coefficients. E. coli introduced to the lumen channel were freely mobile within the mucus layer and appeared to intermittently contact the epithelial surface over 30 minute periods of culture. Mucus shedding into the lumen and turnover of mucus components within cells were visualized. Taken together, this system represents a powerful tool for visualization of interactions between luminal contents and an intact live mucosal barrier.
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Affiliation(s)
- Chia-Ming Wang
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Hardeep S Oberoi
- NCE-Formulation Sciences, Abbvie Inc., North Chicago, IL, 60064, USA
| | - Devalina Law
- NCE-Formulation Sciences, Abbvie Inc., North Chicago, IL, 60064, USA
| | - Yuan Li
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA
| | - Timothy Kassis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Rebecca L Carrier
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
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16
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Magnusson MK, Bas Forsberg A, Verveda A, Sapnara M, Lorent J, Savolainen O, Wettergren Y, Strid H, Simrén M, Öhman L. Exposure of Colon-Derived Epithelial Monolayers to Fecal Luminal Factors from Patients with Colon Cancer and Ulcerative Colitis Results in Distinct Gene Expression Patterns. Int J Mol Sci 2024; 25:9886. [PMID: 39337373 PMCID: PMC11431989 DOI: 10.3390/ijms25189886] [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: 08/22/2024] [Revised: 09/05/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Microbiota and luminal components may affect epithelial integrity and thus participate in the pathophysiology of colon cancer (CC) and inflammatory bowel disease (IBD). Therefore, we aimed to determine the effects of fecal luminal factors derived from patients with CC and ulcerative colitis (UC) on the colonic epithelium using a standardized colon-derived two-dimensional epithelial monolayer. The complex primary human stem cell-derived intestinal epithelium model, termed RepliGut® Planar, was expanded and passaged in a two-dimensional culture which underwent stimulation for 48 h with fecal supernatants (FS) from CC patients (n = 6), UC patients with active disease (n = 6), and healthy subjects (HS) (n = 6). mRNA sequencing of monolayers was performed and cytokine secretion in the basolateral cell culture compartment was measured. The addition of fecal supernatants did not impair the integrity of the colon-derived epithelial monolayer. However, monolayers stimulated with fecal supernatants from CC patients and UC patients presented distinct gene expression patterns. Comparing UC vs. CC, 29 genes were downregulated and 33 genes were upregulated, for CC vs. HS, 17 genes were downregulated and five genes were upregulated, and for UC vs. HS, three genes were downregulated and one gene was upregulated. The addition of FS increased secretion of IL8 with no difference between the study groups. Fecal luminal factors from CC patients and UC patients induce distinct colonic epithelial gene expression patterns, potentially reflecting the disease pathophysiology. The culture of colonic epithelial monolayers with fecal supernatants derived from patients may facilitate the exploration of IBD- and CC-related intestinal microenvironmental and barrier interactions.
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Affiliation(s)
- Maria K Magnusson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Anna Bas Forsberg
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Alexandra Verveda
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Maria Sapnara
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Julie Lorent
- National Bioinformatics Infrastructure Stockholm (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70210 Kuopio, Finland
| | - Yvonne Wettergren
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden
- Department of Surgery, Sahlgrenska University Hospital, Region Västra Götaland, 416 85 Gothenburg, Sweden
| | - Hans Strid
- Department of Internal Medicine, Södra Älvsborg Hospital, 501 82 Borås, Sweden
| | - Magnus Simrén
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden
- Center for Functional GI and Motility Disorders, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lena Öhman
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
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17
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Chen D, Ji F, Zhou Q, Cheung H, Pan Y, Lau HCH, Liang C, Yang Z, Huang P, Wei Q, Cheung AHK, Kang W, Chen H, Yu J, Wong CC. RUVBL1/2 Blockade Targets YTHDF1 Activity to Suppress m6A-Dependent Oncogenic Translation and Colorectal Tumorigenesis. Cancer Res 2024; 84:2856-2872. [PMID: 38900944 PMCID: PMC11372367 DOI: 10.1158/0008-5472.can-23-2081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/28/2023] [Accepted: 06/14/2024] [Indexed: 06/22/2024]
Abstract
The N6-methyladenosine (m6A) RNA-binding protein YTHDF1 is frequently overexpressed in colorectal cancer and drives chemotherapeutic resistance. To systematically identify druggable targets in colorectal cancer with high expression of YTHDF1, this study used a CRISPR/Cas9 screening strategy that revealed RUVBL1 and RUVBL2 as putative targets. RUVBL1/2 were overexpressed in primary colorectal cancer samples and represented independent predictors of poor patient prognosis. Functionally, loss of RUVBL1/2 preferentially impaired the growth of YTHDF1-high colorectal cancer cells, patient-derived primary colorectal cancer organoids, and subcutaneous xenografts. Mechanistically, YTHFD1 and RUVBL1/2 formed a positive feedforward circuit to accelerate oncogenic translation. YTHDF1 bound to m6A-modified RUVBL1/2 mRNA to promote translation initiation and protein expression. Coimmunoprecipitation and mass spectrometry identified that RUVBL1/2 reciprocally interacted with YTHDF1 at 40S translation initiation complexes. Consequently, RUVBL1/2 depletion stalled YTHDF1-driven oncogenic translation and nascent protein biosynthesis, leading to proliferative arrest and apoptosis. Ribosome sequencing revealed that RUVBL1/2 loss impaired the activation of MAPK, RAS, and PI3K-AKT signaling induced by YTHDF1. Finally, the blockade of RUVBL1/2 by the pharmacological inhibitor CB6644 or vesicle-like nanoparticle-encapsulated siRNAs preferentially arrested the growth of YTHDF1-expressing colorectal cancer in vitro and in vivo. Our findings show that RUVBL1/2 are potential prognostic markers and druggable targets that regulate protein translation in YTHDF1-high colorectal cancer. Significance: RUVBL1/2 inhibition is a therapeutic strategy to abrogate YTHDF1-driven oncogenic translation and overcome m6A dysregulation in colorectal cancer.
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Affiliation(s)
- Danyu Chen
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Fenfen Ji
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Qiming Zhou
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Henley Cheung
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Yasi Pan
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Harry C.-H. Lau
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Cong Liang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Zhenjie Yang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Pingmei Huang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Qinyao Wei
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Alvin H.-K. Cheung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Huarong Chen
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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18
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Kim R, Allbritton NL. A Microphysiological System with an Anaerobic Air-Liquid Interface and Functional Mucus Layer for Coculture of Intestinal Bacteria and Primary Human Colonic Epithelium. ADVANCED MATERIALS INTERFACES 2024; 11:2400093. [PMID: 39386255 PMCID: PMC11460523 DOI: 10.1002/admi.202400093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Indexed: 10/12/2024]
Abstract
Coculture of intestinal bacteria with primary human intestinal epithelium provides a valuable tool for investigating host-colon bacterial interactions and for testing and screening therapeutics. However, most current intestinal model systems lack key physiological features of the in vivo colon, such as both a proper oxygen microenvironment and a mucus layer. In this work, a new in vitro colonic microphysiological system is demonstrated with a cell-derived, functional mucus that closely resembles the in vivo colonic mucosa and apical microenvironment by employing an anaerobic air-liquid interface culture. The human primary colon epithelial cells in this new in vitro system exhibit high cell viability (>98%) with ≈100 μm thick functional mucus layer on average. Successful coculture of model anaerobic gut bacterial strains Lactobacillus rhamnosus GG and Anaerobutyricum hallii without loss in human cell viability demonstrates that this new model can be an invaluable tool for future studies of the impact of commensal and pathogenic bacteria on the colon.
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Affiliation(s)
- Raehyun Kim
- Department of Biological and Chemical Engineering, Hongik University, Sejong-si 30016, Republic of Korea
| | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
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19
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Pike CM, Levi JA, Boone LA, Peddibhotla S, Johnson J, Zwarycz B, Bunger MK, Thelin W, Boazak EM. High-Throughput Assay for Predicting Diarrhea Risk Using a 2D Human Intestinal Stem Cell-Derived Model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.610072. [PMID: 39257790 PMCID: PMC11383669 DOI: 10.1101/2024.08.28.610072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Gastrointestinal toxicities (GITs) are the most prevalent adverse events (AE) reported in clinical trials, often resulting in dose-limitations that reduce drug efficacy and delay development and treatment optimization. Preclinical animal models do not accurately replicate human GI physiology, leaving few options for early detection of GI side effects prior to human studies. Development of an accurate model that predicts GIT earlier in drug discovery programs would better support successful clinical trial outcomes. Chemotherapeutics, which exhibit high rates of clinical GIT, frequently target mitotic cells. Therefore, we hypothesized that a model utilizing proliferative cell populations derived from human intestinal crypts would predict the occurrence of clinical GITs with high accuracy. Here, we describe the development of a multiparametric assay utilizing the RepliGut® Planar system, an intestinal stem cell-derived platform cultured in an accessible high throughput Transwell™ format. This assay addresses key physiological elements of GIT by assessing cell proliferation (EdU incorporation), cell abundance (DAPI quantification), and barrier function (TEER). Using this approach, we demonstrate that primary proliferative cell populations reproducibly respond to marketed chemotherapeutics at physiologic concentrations. To determine the ability of this model to predict clinical diarrhea risk, we evaluated a set of 30 drugs with known clinical diarrhea incidence in three human donors, comparing results to known plasma drug concentrations. This resulted in highly accurate predictions of diarrhea potential for each endpoint (balanced accuracy of 91% for DAPI, 90% for EdU, 88% for TEER) with minimal variation across human donors. In vitro toxicity screening using primary proliferative cells may enable improved safety evaluations, reducing the risk of AEs in clinical trials and ultimately lead to safer and more effective treatments for patients.
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20
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Baas FS, Brusselaers N, Nagtegaal ID, Engstrand L, Boleij A. Navigating beyond associations: Opportunities to establish causal relationships between the gut microbiome and colorectal carcinogenesis. Cell Host Microbe 2024; 32:1235-1247. [PMID: 39146796 DOI: 10.1016/j.chom.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/17/2024]
Abstract
The gut microbiota has been recognized as an important determinant in the initiation and progression of colorectal cancer (CRC), with recent studies shining light on the molecular mechanisms that may contribute to the interactions between microbes and the CRC microenvironment. Despite the increasing wealth of associations being established in the field, proving causality remains challenging. Obstacles include the high variability of the microbiome and its context, both across individuals and across time. Additionally, there is a lack of large and representative cohort studies with long-term follow-up and/or appropriate sampling methods for studying the mucosal microbiome. Finally, most studies focus on CRC, whereas interactions between host and bacteria in early events in carcinogenesis remain elusive, reinforced by the heterogeneity of CRC development. Here, we discuss these current most prominent obstacles, the recent developments, and research needs.
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Affiliation(s)
- Floor S Baas
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nele Brusselaers
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Karolinska Hospital, Stockholm, Sweden; Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Karolinska Hospital, Stockholm, Sweden
| | - Annemarie Boleij
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.
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21
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Villegas-Novoa C, Wang Y, Sims CE, Allbritton NL. Creation of a spatially complex mucus bilayer on an in vitro colon model. Sci Rep 2024; 14:16849. [PMID: 39039235 PMCID: PMC11263341 DOI: 10.1038/s41598-024-67591-9] [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: 02/28/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024] Open
Abstract
The colonic epithelium is comprised of three-dimensional crypts (3D) lined with mucus secreted by a heterogeneous population of goblet cells. In this study, we report the formation of a long-lived, and self-renewing replica of human 3D crypts with a mucus layer patterned in the X-Y-Z dimensions. Primary colon cells were cultured on a shaped scaffold under an air-liquid interface to yield architecturally accurate crypts with a mucus bilayer (605 ± 180 μm thick) possessing an inner (149 ± 50 μm) and outer (435 ± 111 μm) region. Lectins with distinct carbohydrate-binding preferences demonstrated that the mucus in the intercrypt regions was chemically distinct from that above and within the crypts replicating in vivo chemical patterning. Constitutive mucus secretion ejected beads from crypt lumens in 8-10 days, while agonist-stimulated secretion increased mucus thickness by 17-fold in 8 h. The tissue was long-lived, > 50 days, the longest time assessed. In conclusion, the in vitro mucus replicated key physiology of the human mucus, including the bilayer (Z) structure and intercrypt-crypt (X-Y) zones, constitutive mucus flow, spatially complex chemical attributes, and mucus secretion response to stimulation, with the potential to reveal local and global determinants of mucus function and its breakdown in disease.
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Affiliation(s)
| | - Yuli Wang
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Christopher E Sims
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
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22
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Cotton MJ, Ariel P, Chen K, Walcott VA, Dixit M, Breau KA, Hinesley CM, Kedziora KM, Tang CY, Zheng A, Magness ST, Burclaff J. An in vitro platform for quantifying cell cycle phase lengths in primary human intestinal epithelial cells. Sci Rep 2024; 14:15195. [PMID: 38956443 PMCID: PMC11219882 DOI: 10.1038/s41598-024-66042-9] [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: 03/20/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
The intestinal epithelium dynamically controls cell cycle, yet no experimental platform exists for directly analyzing cell cycle phases in non-immortalized human intestinal epithelial cells (IECs). Here, we present two reporters and a complete platform for analyzing cell cycle phases in live primary human IECs. We interrogate the transcriptional identity of IECs grown on soft collagen, develop two fluorescent cell cycle reporter IEC lines, design and 3D print a collagen press to make chamber slides for optimal imaging while supporting primary human IEC growth, live image cell cycle dynamics, then assemble a computational pipeline building upon free-to-use programs for semi-automated analysis of cell cycle phases. The PIP-FUCCI construct allows for assigning cell cycle phase from a single image of living cells, and our PIP-H2A construct allows for semi-automated direct quantification of cell cycle phase lengths using our publicly available computational pipeline. Treating PIP-FUCCI IECs with oligomycin demonstrates that inhibiting mitochondrial respiration lengthens G1 phase, and PIP-H2A cells allow us to measure that oligomycin differentially lengthens S and G2/M phases across heterogeneous IECs. These platforms provide opportunities for future studies on pharmaceutical effects on the intestinal epithelium, cell cycle regulation, and more.
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Affiliation(s)
- Michael J Cotton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Pablo Ariel
- Microscopy Services Laboratory, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kaiwen Chen
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Vanessa A Walcott
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michelle Dixit
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Caroline M Hinesley
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Katarzyna M Kedziora
- Department of Cell Biology, Center for Biologic Imaging (CBI), University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Cynthia Y Tang
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anna Zheng
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA.
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA.
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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23
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Rose EC, Simon JM, Gomez-Martinez I, Magness ST, Odle J, Blikslager AT, Ziegler AL. Single-cell transcriptomics predict novel potential regulators of acute epithelial restitution in the ischemia-injured intestine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601271. [PMID: 38979337 PMCID: PMC11230382 DOI: 10.1101/2024.06.28.601271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Intestinal ischemic injury damages the epithelial barrier predisposes patients to life-threatening sepsis unless that barrier is rapidly restored. There is an age-dependency of intestinal recovery in that neonates are the most susceptible to succumb to disease of the intestinal barrier versus older patients. We have developed a pig model that demonstrates age-dependent failure of intestinal barrier restitution in neonatal pigs which can be rescued by the direct application of juvenile pig mucosal tissue, but the mechanisms of rescue remain undefined. We hypothesized that by identifying a subpopulation of restituting enterocytes by their expression of cell migration transcriptional pathways, we can then predict novel upstream regulators of age-dependent restitution response programs. Superficial mucosal epithelial cells from recovering ischemic jejunum of juvenile pigs were processed for single cell RNA sequencing analysis, and predicted upstream regulators were assessed in a porcine intestinal epithelial cell line (IPEC-J2) and banked tissues. A subcluster of absorptive enterocytes expressed several cell migration pathways key to restitution. Differentially expressed genes in this subcluster predicted their upstream regulation included colony stimulating factor-1 (CSF-1). We validated age-dependent induction of CSF-1 by ischemia and documented that CSF-1 and CSF1R co-localized in ischemic juvenile, but not neonatal, wound-adjacent epithelial cells and in the restituted epithelium of juveniles and rescued (but not control) neonates. Further, the CSF1R inhibitor BLZ945 reduced restitution in scratch wounded IPEC-J2 cells. These studies validate an approach to inform potential novel therapeutic targets, such as CSF-1, to improve outcomes in neonates with intestinal injury in a unique pig model. NEW & NOTEWORTHY These studies validate an approach to identify and predict upstream regulation of restituting epithelium in a unique pig intestinal ischemic injury model. Identification of potential molecular mediators of restitution, such as CSF-1, will inform the development of targeted therapeutic interventions for medical management of patients with ischemia-mediated intestinal injury.
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24
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Furtado KL, Plott L, Markovetz M, Powers D, Wang H, Hill DB, Papin J, Allbritton NL, Tamayo R. Clostridioides difficile-mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. mSphere 2024; 9:e0008124. [PMID: 38837404 PMCID: PMC11332178 DOI: 10.1128/msphere.00081-24] [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: 02/01/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024] Open
Abstract
In a healthy colon, the stratified mucus layer serves as a crucial innate immune barrier to protect the epithelium from microbes. Mucins are complex glycoproteins that serve as a nutrient source for resident microflora and can be exploited by pathogens. We aimed to understand how the intestinal pathogen, Clostridioides difficile, independently uses or manipulates mucus to its benefit, without contributions from members of the microbiota. Using a 2-D primary human intestinal epithelial cell model to generate physiologic mucus, we assessed C. difficile-mucus interactions through growth assays, RNA-Seq, biophysical characterization of mucus, and contextualized metabolic modeling. We found that host-derived mucus promotes C. difficile growth both in vitro and in an infection model. RNA-Seq revealed significant upregulation of genes related to central metabolism in response to mucus, including genes involved in sugar uptake, the Wood-Ljungdahl pathway, and the glycine cleavage system. In addition, we identified differential expression of genes related to sensing and transcriptional control. Analysis of mutants with deletions in highly upregulated genes reflected the complexity of C. difficile-mucus interactions, with potential interplay between sensing and growth. Mucus also stimulated biofilm formation in vitro, which may in turn alter the viscoelastic properties of mucus. Context-specific metabolic modeling confirmed differential metabolism and the predicted importance of enzymes related to serine and glycine catabolism with mucus. Subsequent growth experiments supported these findings, indicating mucus is an important source of serine. Our results better define responses of C. difficile to human gastrointestinal mucus and highlight flexibility in metabolism that may influence pathogenesis. IMPORTANCE Clostridioides difficile results in upward of 250,000 infections and 12,000 deaths annually in the United States. Community-acquired infections continue to rise, and recurrent disease is common, emphasizing a vital need to understand C. difficile pathogenesis. C. difficile undoubtedly interacts with colonic mucus, but the extent to which the pathogen can independently respond to and take advantage of this niche has not been explored extensively. Moreover, the metabolic complexity of C. difficile remains poorly understood but likely impacts its capacity to grow and persist in the host. Here, we demonstrate that C. difficile uses native colonic mucus for growth, indicating C. difficile possesses mechanisms to exploit the mucosal niche. Furthermore, mucus induces metabolic shifts and biofilm formation in C. difficile, which has potential ramifications for intestinal colonization. Overall, our work is crucial to better understand the dynamics of C. difficile-mucus interactions in the context of the human gut.
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Affiliation(s)
- Kathleen L. Furtado
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Lucas Plott
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Matthew Markovetz
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Deborah Powers
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Hao Wang
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - David B. Hill
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Physics and Astronomy, College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jason Papin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
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25
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Singh A, Beaupre M, Villegas-Novoa C, Shiomitsu K, Gaudino SJ, Tawch S, Damle R, Kempen C, Choudhury B, McAleer JP, Sheridan BS, Denoya P, Blumberg RS, Hearing P, Allbritton NL, Kumar P. IL-22 promotes mucin-type O-glycosylation and MATH1 + cell-mediated amelioration of intestinal inflammation. Cell Rep 2024; 43:114206. [PMID: 38733584 PMCID: PMC11328608 DOI: 10.1016/j.celrep.2024.114206] [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: 08/30/2023] [Revised: 03/26/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
The interleukin (IL)-22 cytokine can be protective or inflammatory in the intestine. It is unclear if IL-22 receptor (IL-22Ra1)-mediated protection involves a specific type of intestinal epithelial cell (IEC). By using a range of IEC type-specific Il22Ra1 conditional knockout mice and a dextran sulfate sodium (DSS) colitis model, we demonstrate that IL-22Ra1 signaling in MATH1+ cells (goblet and progenitor cells) is essential for maintaining the mucosal barrier and intestinal tissue regeneration. The IL-22Ra1 signaling in IECs promotes mucin core-2 O-glycan extension and induces beta-1,3-galactosyltransferase 5 (B3GALT5) expression in the colon. Adenovirus-mediated expression of B3galt5 is sufficient to rescue Il22Ra1IEC mice from DSS colitis. Additionally, we observe a reduction in the expression of B3GALT5 and the Tn antigen, which indicates defective mucin O-glycan, in the colon tissue of patients with ulcerative colitis. Lastly, IL-22Ra1 signaling in MATH1+ progenitor cells promotes organoid regeneration after DSS injury. Our findings suggest that IL-22-dependent protective responses involve O-glycan modification, proliferation, and differentiation in MATH1+ progenitor cells.
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Affiliation(s)
- Ankita Singh
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael Beaupre
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Kiyoshi Shiomitsu
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Stephen J Gaudino
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Suzanne Tawch
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ruhee Damle
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Cody Kempen
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Biswa Choudhury
- GlycoAnalytics Core, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeremy P McAleer
- Department of Pharmaceutical Sciences, Marshall University School of Pharmacy, Huntington, WV 25701, USA
| | - Brian S Sheridan
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Paula Denoya
- Division of Colon and Rectal Surgery, Department of Surgery, Stony Brook University Hospital, Stony Brook, NY 11794, USA
| | - Richard S Blumberg
- Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick Hearing
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Pawan Kumar
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
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26
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Han W, Lu G, Zhao S, Wang R, Zhang H, Liu K, Nie Y, Dong J. Rapid, Efficient, and Universally Applicable Genetic Engineering of Intestinal Organoid with a Sequential Monolayer to Three-Dimensional Strategy. Stem Cells Int 2024; 2024:2005845. [PMID: 38882597 PMCID: PMC11178405 DOI: 10.1155/2024/2005845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 04/14/2024] [Accepted: 05/06/2024] [Indexed: 06/18/2024] Open
Abstract
Genetically modified intestinal organoids are being explored as potential surrogates of immortalized cell lines and gene-engineered animals. However, genetic manipulation of intestinal organoids is time-consuming, and the efficiency is far beyond satisfactory. To ensure the yield of the genetically modified organoids, large quantity of starting materials is required, and the procedure usually takes more than 10 days. Two major obstacles that restrict the genetic delivery efficiency are the three-dimensional culture condition and that the genetic delivery is carried out in cell suspensions. In the present study, we introduce a novel highly efficient strategy for building genetically modified intestinal organoids in which genetic delivery was performed in freshly established monolayer primary intestinal epithelial cells under two-dimensional conditions and subsequentially transformed into three-dimensional organoids. The total procedure can be finished within 10 hr while displaying much higher efficiency than the traditional methods. Furthermore, this strategy allowed for the selection of transgenic cells in monolayer conditions before establishing high-purity genetically modified intestinal organoids.
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Affiliation(s)
- Weili Han
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases Xijing Hospital of Digestive Diseases Fourth Military Medical University, Xi'an 710032, China
| | - Guofang Lu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases Xijing Hospital of Digestive Diseases Fourth Military Medical University, Xi'an 710032, China
| | - Sheng Zhao
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases Xijing Hospital of Digestive Diseases Fourth Military Medical University, Xi'an 710032, China
| | - Rui Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases Xijing Hospital of Digestive Diseases Fourth Military Medical University, Xi'an 710032, China
- Department of Psychiatry The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China
| | - Haohao Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases Xijing Hospital of Digestive Diseases Fourth Military Medical University, Xi'an 710032, China
| | - Kun Liu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases Xijing Hospital of Digestive Diseases Fourth Military Medical University, Xi'an 710032, China
| | - Yongzhan Nie
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases Xijing Hospital of Digestive Diseases Fourth Military Medical University, Xi'an 710032, China
| | - Jiaqiang Dong
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases Xijing Hospital of Digestive Diseases Fourth Military Medical University, Xi'an 710032, China
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27
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Ingelman-Sundberg M, Lauschke VM. Individualized Pharmacotherapy Utilizing Genetic Biomarkers and Novel In Vitro Systems As Predictive Tools for Optimal Drug Development and Treatment. Drug Metab Dispos 2024; 52:467-475. [PMID: 38575185 DOI: 10.1124/dmd.123.001302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/15/2024] [Accepted: 03/12/2024] [Indexed: 04/06/2024] Open
Abstract
In the area of drug development and clinical pharmacotherapy, a profound understanding of the pharmacokinetics and potential adverse reactions associated with the drug under investigation is paramount. Essential to this endeavor is a comprehensive understanding about interindividual variations in absorption, distribution, metabolism, and excretion (ADME) genetics and the predictive capabilities of in vitro systems, shedding light on metabolite formation and the risk of adverse drug reactions (ADRs). Both the domains of pharmacogenomics and the advancement of in vitro systems are experiencing rapid expansion. Here we present an update on these burgeoning fields, providing an overview of their current status and illuminating potential future directions. SIGNIFICANCE STATEMENT: There is very rapid development in the area of pharmacogenomics and in vitro systems for predicting drug pharmacokinetics and risk for adverse drug reactions. We provide an update of the current status of pharmacogenomics and developed in vitro systems on these aspects aimed to achieve a better personalized pharmacotherapy.
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Affiliation(s)
- Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (M.I.-S., V.M.L.); Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.); and University of Tübingen, Tübingen, Germany (V.M.L.)
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (M.I.-S., V.M.L.); Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.); and University of Tübingen, Tübingen, Germany (V.M.L.)
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28
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La Corte SG, Stevens CA, Cárcamo-Oyarce G, Ribbeck K, Wingreen NS, Datta SS. Morphogenesis of bacterial colonies in polymeric environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590088. [PMID: 38712130 PMCID: PMC11071276 DOI: 10.1101/2024.04.18.590088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Many bacteria live in polymeric fluids, such as mucus, environmental polysaccharides, and extracellular polymers in biofilms. However, lab studies typically focus on cells in polymer-free fluids. Here, we show that interactions with polymers shape a fundamental feature of bacterial life-how they proliferate in space in multicellular colonies. Using experiments, we find that when polymer is sufficiently concentrated, cells generically and reversibly form large serpentine "cables" as they proliferate. By combining experiments with biophysical theory and simulations, we demonstrate that this distinctive form of colony morphogenesis arises from an interplay between polymer-induced entropic attraction between neighboring cells and their hindered ability to diffusely separate from each other in a viscous polymer solution. Our work thus reveals a pivotal role of polymers in sculpting proliferating bacterial colonies, with implications for how they interact with hosts and with the natural environment, and uncovers quantitative principles governing colony morphogenesis in such complex environments.
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29
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Wang H, Kim R, Wang Y, Furtado KL, Sims CE, Tamayo R, Allbritton NL. In vitro co-culture of Clostridium scindens with primary human colonic epithelium protects the epithelium against Staphylococcus aureus. Front Bioeng Biotechnol 2024; 12:1382389. [PMID: 38681959 PMCID: PMC11045926 DOI: 10.3389/fbioe.2024.1382389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
A complex and dynamic network of interactions exists between human gastrointestinal epithelium and intestinal microbiota. Therefore, comprehending intestinal microbe-epithelial cell interactions is critical for the understanding and treatment of intestinal diseases. Primary human colonic epithelial cells derived from a healthy human donor were co-cultured with Clostridium scindens (C. scindens), a probiotic obligate anaerobe; Staphylococcus aureus (S. aureus), a facultative anaerobe and intestinal pathogen; or both bacterial species in tandem. The co-culture hanging basket platform used for these experiments possessed walls of controlled oxygen (O2) permeability to support the formation of an O2 gradient across the intestinal epithelium using cellular O2 consumption, resulting in an anaerobic luminal and aerobic basal compartment. Both the colonic epithelial cells and C. scindens remained viable over 48 h during co-culture. In contrast, co-culture with S. aureus elicited significant damage to colonic epithelial cells within 24 h. To explore the influence of the intestinal pathogen on the epithelium in the presence of the probiotic bacteria, colonic epithelial cells were inoculated sequentially with the two bacterial species. Under these conditions, C. scindens was capable of repressing the production of S. aureus enterotoxin. Surprisingly, although C. scindens converted cholic acid to secondary bile acids in the luminal medium, the growth of S. aureus was not significantly inhibited. Nevertheless, this combination of probiotic and pathogenic bacteria was found to benefit the survival of the colonic epithelial cells compared with co-culture of the epithelial cells with S. aureus alone. This platform thus provides an easy-to-use and low-cost tool to study the interaction between intestinal bacteria and colonic cells in vitro to better understand the interplay of intestinal microbiota with human colonic epithelium.
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Affiliation(s)
- Hao Wang
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Raehyun Kim
- Department of Bioengineering, University of Washington, Seattle, WA, United States
- Department of Biological and Chemical Engineering, Hongik University, Sejong, Republic of Korea
| | - Yuli Wang
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Kathleen L. Furtado
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Christopher E. Sims
- Department of Bioengineering, University of Washington, Seattle, WA, United States
- Department of Medicine/Division of Rheumatology, University of Washington, Seattle, WA, United States
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA, United States
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30
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Zhang J, Huang YJ, Trapecar M, Wright C, Schneider K, Kemmitt J, Hernandez-Gordillo V, Yoon JY, Poyet M, Alm EJ, Breault DT, Trumper DL, Griffith LG. An immune-competent human gut microphysiological system enables inflammation-modulation by Faecalibacterium prausnitzii. NPJ Biofilms Microbiomes 2024; 10:31. [PMID: 38553449 PMCID: PMC10980819 DOI: 10.1038/s41522-024-00501-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/11/2024] [Indexed: 04/02/2024] Open
Abstract
Crosstalk of microbes with human gut epithelia and immune cells is crucial for gut health. However, there is no existing system for a long-term co-culture of human innate immune cells with epithelium and oxygen-intolerant commensal microbes, hindering the understanding of microbe-immune interactions in a controlled manner. Here, we established a gut epithelium-microbe-immune (GuMI) microphysiological system to maintain the long-term continuous co-culture of Faecalibacterium prausnitzii/Faecalibacterium duncaniae with colonic epithelium, antigen-presenting cells (APCs, herein dendritic cells and macrophages), and CD4+ naive T cells circulating underneath the colonic epithelium. In GuMI-APC condition, multiplex cytokine assays suggested that APCs contribute to the elevated level of cytokines and chemokines secreted into both apical and basolateral compartments compared to GuMI condition that lacks APC. In GuMI-APC with F. prausnitzii (GuMI-APC-FP), F. prausnitzii increased the transcription of pro-inflammatory genes such as toll-like receptor 1 (TLR1) and interferon alpha 1 (IFNA1) in the colonic epithelium, without a significant effect on cytokine secretion, compared to the GuMI-APC without bacteria (GuMI-APC-NB). In contrast, in the presence of CD4+ naive T cells (GuMI-APCT-FP), TLR1, IFNA1, and IDO1 transcription levels decreased with a simultaneous increase in F. prausnitzii-induced secretion of pro-inflammatory cytokines (e.g., IL8) compared to GuMI-APC-FP that lacks T cells. These results highlight the contribution of individual innate immune cells in regulating the immune response triggered by the gut commensal F. prausnitzii. The integration of defined populations of immune cells in the gut microphysiological system demonstrated the usefulness of GuMI physiomimetic platform to study microbe-epithelial-immune interactions in healthy and disease conditions.
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Affiliation(s)
- Jianbo Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Amsterdam, the Netherlands.
| | - Yu-Ja Huang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin Trapecar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Charles Wright
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kirsten Schneider
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John Kemmitt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jun Young Yoon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, Yonsei University, Seoul, South Korea
| | - Mathilde Poyet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute of Experimental Medicine, University of Kiel, Kiel, Germany
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David T Breault
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - David L Trumper
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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31
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Inciuraite R, Steponaitiene R, Raudze O, Kulokiene U, Kiudelis V, Lukosevicius R, Ugenskiene R, Adamonis K, Kiudelis G, Jonaitis LV, Kupcinskas J, Skieceviciene J. Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level. Sci Rep 2024; 14:4456. [PMID: 38396014 PMCID: PMC10891043 DOI: 10.1038/s41598-024-55076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/19/2024] [Indexed: 02/25/2024] Open
Abstract
Patient-derived human intestinal organoids are becoming an indispensable tool for the research of digestive system in health and disease. However, very little is still known about the long-term culturing effect on global genomic methylation level in colonic epithelial organoids derived from healthy individuals as well as active and quiescent ulcerative colitis (UC) patients. In this study, we aimed to evaluate the epigenetic stability of these organoids by assessing the methylation level of LINE-1 during prolonged culturing. We found that LINE-1 region of both healthy control and UC patient colon tissues as well as corresponding epithelial organoids is highly methylated (exceeding 60%). We also showed that long-term culturing of colonic epithelial organoids generated from stem cells of healthy and diseased (both active and quiescent UC) individuals results in decrease of LINE-1 (up to 8%) methylation level, when compared to tissue of origin and short-term cultures. Moreover, we revealed that LINE-1 methylation level in sub-cultured organoids decreases at different pace depending on the patient diagnosis (healthy control, active or quiescent UC). Therefore, we propose LINE-1 as a potential and convenient biomarker for reliable assessment of global methylation status of patient-derived intestinal epithelial organoids in routine testing of ex vivo cultures.
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Affiliation(s)
- Ruta Inciuraite
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Ruta Steponaitiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Odeta Raudze
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Ugne Kulokiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Vytautas Kiudelis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Rasa Ugenskiene
- Department of Genetics and Molecular Medicine, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Kestutis Adamonis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Gediminas Kiudelis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Laimas Virginijus Jonaitis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania.
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32
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Li X, Yao Z, Qian J, Li H, Li H. Lactate Protects Intestinal Epithelial Barrier Function from Dextran Sulfate Sodium-Induced Damage by GPR81 Signaling. Nutrients 2024; 16:582. [PMID: 38474712 DOI: 10.3390/nu16050582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
The dysregulation of the intestinal epithelial barrier significantly contributes to the inflammatory progression of ulcerative colitis. Recent studies have indicated that lactate, produced by gut bacteria or derived from fermented foods, plays a key role in modulating inflammation via G-protein-coupled receptor 81 (GPR81). In this study, we aimed to investigate the potential role of GPR81 in the progression of colitis and to assess the impact of lactate/GPR81 signaling on intestinal epithelial barrier function. Our findings demonstrated a downregulation of GPR81 protein expression in patients with colitis. Functional verification experiments showed that Gpr81-deficient mice exhibited more severe damage to the intestinal epithelial barrier and increased susceptibility to DSS-induced colitis, characterized by exacerbated oxidative stress, elevated inflammatory cytokine secretion, and impaired expression of tight-junction proteins. Mechanistically, we found that lactate could suppress TNF-α-induced MMP-9 expression and prevent the disruption of tight-junction proteins by inhibiting NF-κB activation through GPR81 in vitro. Furthermore, our study showed that dietary lactate could preserve intestinal epithelial barrier function against DSS-induced damage in a GPR81-dependent manner in vivo. Collectively, these results underscore the crucial involvement of the lactate/GPR81 signaling pathway in maintaining intestinal epithelial barrier function, providing a potential therapeutic strategy for ulcerative colitis.
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Affiliation(s)
- Xiaojing Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhijie Yao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jin Qian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hongling Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Haitao Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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33
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Madsen O, Rikkers RSC, Wells JM, Bergsma R, Kar SK, Taverne N, Taverne-Thiele AJ, Ellen ED, Woelders H. Transcriptomic analysis of intestinal organoids, derived from pigs divergent in feed efficiency, and their response to Escherichia coli. BMC Genomics 2024; 25:173. [PMID: 38350904 PMCID: PMC10863143 DOI: 10.1186/s12864-024-10064-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND There is increasing interest in using intestinal organoids to study complex traits like feed efficiency (FE) and host-microbe interactions. The aim of this study was to investigate differences in the molecular phenotype of organoids derived from pigs divergent for FE as well as their responses to challenge with adherent and invasive Escherichia coli (E. coli). RESULTS Colon and ileum tissue from low and high FE pigs was used to generate 3D organoids and two dimensional (2D) monolayers of organoid cells for E. coli challenge. Genome-wide gene expression was used to investigate molecular differences between pigs that were phenotypically divergent for FE and to study the difference in gene expression after challenge with E. coli. We showed, (1) minor differences in gene expression of colon organoids from pigs with low and high FE phenotypes, (2) that an E. coli challenge results in a strong innate immune gene response in both colon and ileum organoids, (3) that the immune response seems to be less pronounced in the colon organoids of high FE pigs and (4) a slightly stronger immune response was observed in ileum than in colon organoids. CONCLUSIONS These findings demonstrate the potential for using organoids to gain insights into complex biological mechanisms such as FE.
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Affiliation(s)
- Ole Madsen
- Animal Breeding & Genomics, Wageningen University & Research, PO Box 338, Wageningen, 6700 AH, the Netherlands.
| | - Roxann S C Rikkers
- Animal Breeding & Genomics, Wageningen University & Research, PO Box 338, Wageningen, 6700 AH, the Netherlands
| | - Jerry M Wells
- Host-Microbe Interactomics, Wageningen University & Research, PO Box 338, Wageningen, 6700 AH, the Netherlands
| | - Rob Bergsma
- Topigs Norsvin, Schoenaker 6, 6641 SZ, Beuningen, the Netherlands
| | - Soumya K Kar
- Animal Nutrition, Wageningen University & Research, PO Box 338, Wageningen, 6700 AH, the Netherlands
| | - Nico Taverne
- Host-Microbe Interactomics, Wageningen University & Research, PO Box 338, Wageningen, 6700 AH, the Netherlands
| | - Anja J Taverne-Thiele
- Host-Microbe Interactomics, Wageningen University & Research, PO Box 338, Wageningen, 6700 AH, the Netherlands
| | - Esther D Ellen
- Animal Breeding & Genomics, Wageningen University & Research, PO Box 338, Wageningen, 6700 AH, the Netherlands
| | - Henri Woelders
- Animal Breeding & Genomics, Wageningen University & Research, PO Box 338, Wageningen, 6700 AH, the Netherlands
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34
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Chu JTS, Lamers MM. Organoids in virology. NPJ VIRUSES 2024; 2:5. [PMID: 40295690 PMCID: PMC11721363 DOI: 10.1038/s44298-024-00017-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 04/30/2025]
Abstract
To adequately prepare against imminent disease outbreaks from diverse and ever-changing viral pathogens, improved experimental models that can accurately recapitulate host-virus responses and disease pathogenesis in human are essential. Organoid platforms have emerged in recent years as amenable in vitro tools that can bridge the limitations of traditional 2D cell lines and animal models for viral disease research. We highlight in this review the key insights that have contributed by organoid models to virus research, the limitations that exist in current platforms, and outline novel approaches that are being applied to address these shortcomings.
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Affiliation(s)
- Julie T S Chu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Mart M Lamers
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
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35
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Furtado KL, Plott L, Markovetz M, Powers D, Wang H, Hill DB, Papin J, Allbritton NL, Tamayo R. Clostridioides difficile-mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578425. [PMID: 38352512 PMCID: PMC10862863 DOI: 10.1101/2024.02.01.578425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
In a healthy colon, the stratified mucus layer serves as a crucial innate immune barrier to protect the epithelium from microbes. Mucins are complex glycoproteins that serve as a nutrient source for resident microflora and can be exploited by pathogens. We aimed to understand how the intestinal pathogen, Clostridioides diffiicile, independently uses or manipulates mucus to its benefit, without contributions from members of the microbiota. Using a 2-D primary human intestinal epithelial cell model to generate physiologic mucus, we assessed C. difficile-mucus interactions through growth assays, RNA-Seq, biophysical characterization of mucus, and contextualized metabolic modeling. We found that host-derived mucus promotes C. difficile growth both in vitro and in an infection model. RNA-Seq revealed significant upregulation of genes related to central metabolism in response to mucus, including genes involved in sugar uptake, the Wood-Ljungdahl pathway, and the glycine cleavage system. In addition, we identified differential expression of genes related to sensing and transcriptional control. Analysis of mutants with deletions in highly upregulated genes reflected the complexity of C. difficile-mucus interactions, with potential interplay between sensing and growth. Mucus also stimulated biofilm formation in vitro, which may in turn alter viscoelastic properties of mucus. Context-specific metabolic modeling confirmed differential metabolism and predicted importance of enzymes related to serine and glycine catabolism with mucus. Subsequent growth experiments supported these findings, indicating mucus is an important source of serine. Our results better define responses of C. difficile to human gastrointestinal mucus and highlight a flexibility in metabolism that may influence pathogenesis.
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Affiliation(s)
- Kathleen L. Furtado
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Lucas Plott
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Matthew Markovetz
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Deborah Powers
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Hao Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - David B. Hill
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Physics and Astronomy, College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason Papin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
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36
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McCoy R, Oldroyd S, Yang W, Wang K, Hoven D, Bulmer D, Zilbauer M, Owens RM. In Vitro Models for Investigating Intestinal Host-Pathogen Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306727. [PMID: 38155358 PMCID: PMC10885678 DOI: 10.1002/advs.202306727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/01/2023] [Indexed: 12/30/2023]
Abstract
Infectious diseases are increasingly recognized as a major threat worldwide due to the rise of antimicrobial resistance and the emergence of novel pathogens. In vitro models that can adequately mimic in vivo gastrointestinal physiology are in high demand to elucidate mechanisms behind pathogen infectivity, and to aid the design of effective preventive and therapeutic interventions. There exists a trade-off between simple and high throughput models and those that are more complex and physiologically relevant. The complexity of the model used shall be guided by the biological question to be addressed. This review provides an overview of the structure and function of the intestine and the models that are developed to emulate this. Conventional models are discussed in addition to emerging models which employ engineering principles to equip them with necessary advanced monitoring capabilities for intestinal host-pathogen interrogation. Limitations of current models and future perspectives on the field are presented.
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Affiliation(s)
- Reece McCoy
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Sophie Oldroyd
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Woojin Yang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Kaixin Wang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Darius Hoven
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - David Bulmer
- Department of PharmacologyUniversity of CambridgeCambridgeCB2 1PDUK
| | - Matthias Zilbauer
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Róisín M. Owens
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
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37
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Pinto S, Hosseini M, Buckley ST, Yin W, Garousi J, Gräslund T, van Ijzendoorn S, Santos HA, Sarmento B. Nanoparticles targeting the intestinal Fc receptor enhance intestinal cellular trafficking of semaglutide. J Control Release 2024; 366:621-636. [PMID: 38215986 DOI: 10.1016/j.jconrel.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Semaglutide is the first oral glucagon-like peptide-1 (GLP-1) analog commercially available for the treatment of type 2 diabetes. In this work, semaglutide was incorporated into poly(lactic-co-glycolic acid)-poly(ethylene glycol) (PLGA-PEG) nanoparticles (NPs) to improve its delivery across the intestinal barrier. The nanocarriers were surface-decorated with either a peptide or an affibody that target the human neonatal Fc receptor (hFcRn), located on the luminal cell surface of the enterocytes. Both ligands were successfully conjugated with the PLGA-PEG via maleimide-thiol chemistry and thereafter, the functionalized polymers were used to produce semaglutide-loaded NPs. Monodisperse NPs with an average size of 170 nm, neutral surface charge and 3% of semaglutide loading were obtained. Both FcRn-targeted NPs exhibited improved interaction and association with Caco-2 cells (cells that endogenously express the hFcRn), compared to non-targeted NPs. Additionally, the uptake of FcRn-targeted NPs was also observed to occur in human intestinal organoids (HIOs) expressing hFcRn through microinjection into the lumen of HIOs, resulting in potential increase of semaglutide permeability for both ligand-functionalized nanocarriers. Herein, our study demonstrates valuable data and insights that the FcRn-targeted NPs has the capacity to promote intestinal absorption of therapeutic peptides.
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Affiliation(s)
- Soraia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Mahya Hosseini
- Department of Biomedical Sciences of Cell and Systems, Section Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9713, AV, Groningen, the Netherlands
| | - Stephen T Buckley
- Global Research Technologies, Novo Nordisk, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | - Wen Yin
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Roslagstullsbacken 21, 114 17 Stockholm, Sweden
| | - Javad Garousi
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Roslagstullsbacken 21, 114 17 Stockholm, Sweden; Department of Immunology, Genetics and Pathology, Uppsala University, 75185 Uppsala, Sweden
| | - Torbjörn Gräslund
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Roslagstullsbacken 21, 114 17 Stockholm, Sweden
| | - Sven van Ijzendoorn
- Department of Biomedical Sciences of Cell and Systems, Section Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9713, AV, Groningen, the Netherlands
| | - Hélder A Santos
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, Helsinki FI-00014, Finland; W.J. Kolff Institute for Biomedical Engineering and Materials Science, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands; Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands.
| | - Bruno Sarmento
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Instituto Universitário de Ciências da Saúde (IUCS-CESPU), Rua Central de Gandra 1317, 4585-116 Gandra, Portugal.
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38
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Wu H, Mu C, Xu L, Yu K, Shen L, Zhu W. Host-microbiota interaction in intestinal stem cell homeostasis. Gut Microbes 2024; 16:2353399. [PMID: 38757687 PMCID: PMC11110705 DOI: 10.1080/19490976.2024.2353399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024] Open
Abstract
Intestinal stem cells (ISCs) play a pivotal role in gut physiology by governing intestinal epithelium renewal through the precise regulation of proliferation and differentiation. The gut microbiota interacts closely with the epithelium through myriad of actions, including immune and metabolic interactions, which translate into tight connections between microbial activity and ISC function. Given the diverse functions of the gut microbiota in affecting the metabolism of macronutrients and micronutrients, dietary nutrients exert pronounced effects on host-microbiota interactions and, consequently, the ISC fate. Therefore, understanding the intricate host-microbiota interaction in regulating ISC homeostasis is imperative for improving gut health. Here, we review recent advances in understanding host-microbiota immune and metabolic interactions that shape ISC function, such as the role of pattern-recognition receptors and microbial metabolites, including lactate and indole metabolites. Additionally, the diverse regulatory effects of the microbiota on dietary nutrients, including proteins, carbohydrates, vitamins, and minerals (e.g. iron and zinc), are thoroughly explored in relation to their impact on ISCs. Thus, we highlight the multifaceted mechanisms governing host-microbiota interactions in ISC homeostasis. Insights gained from this review provide strategies for the development of dietary or microbiota-based interventions to foster gut health.
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Affiliation(s)
- Haiqin Wu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Chunlong Mu
- Food Informatics, AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Laipeng Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Kaifan Yu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Le Shen
- Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
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39
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Bornholdt J, Müller CV, Nielsen MJ, Strickertsson J, Rago D, Chen Y, Maciag G, Skov J, Wellejus A, Schweiger PJ, Hansen SL, Broholm C, Gögenur I, Maimets M, Sloth S, Hendel J, Baker A, Sandelin A, Jensen KB. Detecting host responses to microbial stimulation using primary epithelial organoids. Gut Microbes 2023; 15:2281012. [PMID: 37992398 PMCID: PMC10730191 DOI: 10.1080/19490976.2023.2281012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/05/2023] [Indexed: 11/24/2023] Open
Abstract
The intestinal epithelium is constantly exposed to microbes residing in the lumen. Traditionally, the response to microbial interactions has been studied in cell lines derived from cancerous tissues, e.g. Caco-2. It is, however, unclear how the responses in these cancer cell lines reflect the responses of a normal epithelium and whether there might be microbial strain-specific effects. To address these questions, we derived organoids from the small intestine from a cohort of healthy individuals. Culturing intestinal epithelium on a flat laminin matrix induced their differentiation, facilitating analysis of microbial responses via the apical membrane normally exposed to the luminal content. Here, it was evident that the healthy epithelium across multiple individuals (n = 9) demonstrates robust acute both common and strain-specific responses to a range of probiotic bacterial strains (BB-12Ⓡ, LGGⓇ, DSM33361, and Bif195). Importantly, parallel experiments using the Caco-2 cell line provide no acute response. Collectively, we demonstrate that primary epithelial cells maintained as organoids represent a valuable resource for assessing interactions between the epithelium and luminal microbes across individuals, and that these models are likely to contribute to a better understanding of host microbe interactions.
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Affiliation(s)
- Jette Bornholdt
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Human Health Research, Chr. Hansen AS, Hørsholm, Denmark
| | - Christina V. Müller
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Maria Juul Nielsen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Daria Rago
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yun Chen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Human Health Research, Chr. Hansen AS, Hørsholm, Denmark
| | - Grzegorz Maciag
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Skov
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Anja Wellejus
- Human Health Research, Chr. Hansen AS, Hørsholm, Denmark
| | - Pawel J. Schweiger
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Stine L. Hansen
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | | | - Ismail Gögenur
- Center for Surgical Science, Department of Surgery, Zealand University Hospital, Koge, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Martti Maimets
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Stine Sloth
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Hendel
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Adam Baker
- Human Health Research, Chr. Hansen AS, Hørsholm, Denmark
| | - Albin Sandelin
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kim B. Jensen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
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Macedo MH, Dias Neto M, Pastrana L, Gonçalves C, Xavier M. Recent Advances in Cell-Based In Vitro Models to Recreate Human Intestinal Inflammation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301391. [PMID: 37736674 PMCID: PMC10625086 DOI: 10.1002/advs.202301391] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/03/2023] [Indexed: 09/23/2023]
Abstract
Inflammatory bowel disease causes a major burden to patients and healthcare systems, raising the need to develop effective therapies. Technological advances in cell culture, allied with ethical issues, have propelled in vitro models as essential tools to study disease aetiology, its progression, and possible therapies. Several cell-based in vitro models of intestinal inflammation have been used, varying in their complexity and methodology to induce inflammation. Immortalized cell lines are extensively used due to their long-term survival, in contrast to primary cultures that are short-lived but patient-specific. Recently, organoids and organ-chips have demonstrated great potential by being physiologically more relevant. This review aims to shed light on the intricate nature of intestinal inflammation and cover recent works that report cell-based in vitro models of human intestinal inflammation, encompassing diverse approaches and outcomes.
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Affiliation(s)
- Maria Helena Macedo
- INL – International Iberian Nanotechnology LaboratoryAvenida Mestre José VeigaBraga4715‐330Portugal
| | - Mafalda Dias Neto
- INL – International Iberian Nanotechnology LaboratoryAvenida Mestre José VeigaBraga4715‐330Portugal
| | - Lorenzo Pastrana
- INL – International Iberian Nanotechnology LaboratoryAvenida Mestre José VeigaBraga4715‐330Portugal
| | - Catarina Gonçalves
- INL – International Iberian Nanotechnology LaboratoryAvenida Mestre José VeigaBraga4715‐330Portugal
| | - Miguel Xavier
- INL – International Iberian Nanotechnology LaboratoryAvenida Mestre José VeigaBraga4715‐330Portugal
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Zhang J, Huang YJ, Trapecar M, Wright C, Schneider K, Kemmit J, Hernandez-Gordillo V, Yoon JY, Alm EJ, Breault DT, Trumper D, Griffith LG. An immune-competent human gut microphysiological system enables inflammation-modulation of Faecalibacterium prausnitzii. RESEARCH SQUARE 2023:rs.3.rs-3373576. [PMID: 37886530 PMCID: PMC10602192 DOI: 10.21203/rs.3.rs-3373576/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Crosstalk of microbes with human gut epithelia and immune cells is crucial for gut health. However, there is no existing system for a long-term co-culture of human innate immune cells with epithelium and oxygen-intolerant commensal microbes, hindering the understanding of microbe-immune interactions in a controlled manner. Here, we establish a gut epithelium-microbe-immune microphysiological system to maintain the long-term continuous co-culture of Faecalibacterium prausnitzii/Faecalibacterium duncaniae with colonic epithelium, antigen-presenting cells (APCs, herein dendritic cells and macrophages), with CD4+ naïve T cells circulating underneath the colonic epithelium. Multiplex cytokine assays suggested that APCs contribute to the elevated level of cytokines and chemokines being secreted into both apical and basolateral compartments. In contrast, the absence of APCs does not allow reliable detection of these cytokines. In the presence of APCs, F. prausnitzii increased the transcription of pro-inflammatory genes such as toll-like receptor 1 (TLR1) and interferon alpha 1 (IFNA1) in the colonic epithelium, but no significant change on the secreted cytokines. In contrast, integration of CD4+ naïve T cells reverses this effect by decreasing the transcription of TLR1, IFNA1, and indoleamine 2,3-dioxygenase, and increasing the F. prausnitzii-induced secretion of pro-inflammatory cytokines such as IL-8, MCP-1/CCL2, and IL1A. These results highlight the contribution of individual innate immune cells in the regulation of the immune response triggered by the gut commensal F. prausnitzii. The successful integration of defined populations of immune cells in this gut microphysiological system demonstrated the usefulness of the GuMI physiomimetic platform to study microbe-epithelial-immune interactions in health and disease.
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Affiliation(s)
- Jianbo Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Yu-Ja Huang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin Trapecar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Charles Wright
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kirsten Schneider
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John Kemmit
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jun Young Yoon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, Yonsei University, Seoul, South Korea
| | - Eric J. Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David T. Breault
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - David Trumper
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Linda G. Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, MA, USA
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42
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Cotton MJ, Ariel P, Chen K, Walcott VA, Dixit M, Breau KA, Hinesley CM, Kedziora K, Tang CY, Zheng A, Magness ST, Burclaff J. An in vitro platform for quantifying cell cycle phase lengths in primary human intestinal stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561410. [PMID: 37873351 PMCID: PMC10592697 DOI: 10.1101/2023.10.09.561410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background and Aims The intestinal epithelium exhibits dynamic control of cell cycle phase lengths, yet no experimental platform exists for directly analyzing cell cycle phases in living human intestinal stem cells (ISCs). Here, we develop primary human ISC lines with two different reporter constructs to provide fluorescent readouts to analyze cell cycle phases in cycling ISCs. Methods 3D printing was used to construct a collagen press for making chamber slides that support primary human ISC growth and maintenance within the working distance of a confocal microscope objective. The PIP-FUCCI fluorescent cell cycle reporter and a variant with H2A-mScarlet that allows for automated tracking of cell cycle phases (PIP-H2A) were used in human ISCs along with live imaging and EdU pulsing. An analysis pipeline combining free-to-use programs and publicly available code was compiled to analyze live imaging results. Results Chamber slides with soft collagen pressed to a thickness of 0.3 mm concurrently support ISC cycling and confocal imaging. PIP-FUCCI ISCs were found to be optimal for snapshot analysis wherein all nuclei are assigned to a cell cycle phase from a single image. PIP-H2A ISCs were better suited for live imaging since constant nuclear signal allowed for more automated analysis. CellPose2 and TrackMate were used together to track cycling cells. Conclusions We present two complete platforms for analyzing cell cycle phases in living primary human ISCs. The PIP-FUCCI construct allows for cell cycle phase assignment from one image of living cells, the PIP-H2A construct allows for semi-automated direct quantification of cell cycle phase lengths in human ISCs using our computational pipeline. These platforms hold great promise for future studies on how pharmaceutical agents affect the intestinal epithelium, how cell cycle is regulated in human ISCs, and more.
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Affiliation(s)
- Michael J Cotton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina
| | - Pablo Ariel
- Microscopy Services Laboratory, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kaiwen Chen
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina
| | - Vanessa A Walcott
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michelle Dixit
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Caroline M Hinesley
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kasia Kedziora
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Cynthia Y Tang
- Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri
| | - Anna Zheng
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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Pike CM, Zwarycz B, McQueen BE, Castillo M, Barron C, Morowitz JM, Levi JA, Phadke D, Balik-Meisner M, Mav D, Shah R, Glasspoole DLC, Laetham R, Thelin W, Bunger MK, Boazak EM. Characterization and optimization of variability in a human colonic epithelium culture model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559007. [PMID: 37790345 PMCID: PMC10542543 DOI: 10.1101/2023.09.22.559007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Animal models have historically been poor preclinical predictors of gastrointestinal (GI) directed therapeutic efficacy and drug-induced GI toxicity. Human stem and primary cell-derived culture systems are a major focus of efforts to create biologically relevant models that enhance preclinical predictive value of intestinal efficacy and toxicity. The inherent variability in stem-cell-based complex cultures makes development of useful models a challenge; the stochastic nature of stem-cell differentiation interferes with the ability to build and validate robust, reproducible assays that query drug responses and pharmacokinetics. In this study, we aimed to characterize and reduce potential sources of variability in a complex stem cell-derived intestinal epithelium model, termed RepliGut® Planar, across cells from multiple human donors, cell lots, and passage numbers. Assessment criteria included barrier formation and integrity, gene expression, and cytokine responses. Gene expression and culture metric analyses revealed that controlling for stem/progenitor-cell passage number reduces variability and maximizes physiological relevance of the model. After optimizing passage number, donor-specific differences in cytokine responses were observed in a case study, suggesting biologic variability is observable in cell cultures derived from multiple human sources. Our findings highlight key considerations for designing assays that can be applied to additional primary-cell derived systems, as well as establish utility of the RepliGut® Planar platform for robust development of human-predictive drug-response assays.
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Sarma S, Catella CM, San Pedro ET, Xiao X, Durmusoglu D, Menegatti S, Crook N, Magness ST, Hall CK. Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells. Commun Biol 2023; 6:878. [PMID: 37634026 PMCID: PMC10460389 DOI: 10.1038/s42003-023-05242-x] [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: 03/17/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023] Open
Abstract
Infections by Clostridioides difficile, a bacterium that targets the large intestine (colon), impact a large number of people worldwide. Bacterial colonization is mediated by two exotoxins: toxins A and B. Short peptides that can be delivered to the gut and inhibit the biocatalytic activity of these toxins represent a promising therapeutic strategy to prevent and treat C. diff. infection. We describe an approach that combines a Peptide Binding Design (PepBD) algorithm, molecular-level simulations, a rapid screening assay to evaluate peptide:toxin binding, a primary human cell-based assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in colon epithelial cells. One peptide, SA1, is found to block TcdA toxicity in primary-derived human colon (large intestinal) epithelial cells. SA1 binds TcdA with a KD of 56.1 ± 29.8 nM as measured by surface plasmon resonance (SPR).
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Affiliation(s)
- Sudeep Sarma
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Carly M Catella
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Ellyce T San Pedro
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Xingqing Xiao
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Deniz Durmusoglu
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Stefano Menegatti
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, 27695, USA
| | - Nathan Crook
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Scott T Magness
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Carol K Hall
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA.
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Rivera KR, Bliton RJ, Burclaff J, Czerwinski MJ, Liu J, Trueblood JM, Hinesley CM, Breau KA, Deal HE, Joshi S, Pozdin VA, Yao M, Ziegler AL, Blikslager AT, Daniele MA, Magness ST. Hypoxia Primes Human ISCs for Interleukin-Dependent Rescue of Stem Cell Activity. Cell Mol Gastroenterol Hepatol 2023; 16:823-846. [PMID: 37562653 PMCID: PMC10520368 DOI: 10.1016/j.jcmgh.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND AND AIMS Hypoxia in the intestinal epithelium can be caused by acute ischemic events or chronic inflammation in which immune cell infiltration produces inflammatory hypoxia starving the mucosa of oxygen. The epithelium has the capacity to regenerate after some ischemic and inflammatory conditions suggesting that intestinal stem cells (ISCs) are highly tolerant to acute and chronic hypoxia; however, the impact of hypoxia on human ISC (hISC) function has not been reported. Here we present a new microphysiological system (MPS) to investigate how hypoxia affects hISCs from healthy donors and test the hypothesis that prolonged hypoxia modulates how hISCs respond to inflammation-associated interleukins (ILs). METHODS hISCs were exposed to <1.0% oxygen in the MPS for 6, 24, 48, and 72 hours. Viability, hypoxia-inducible factor 1a (HIF1a) response, transcriptomics, cell cycle dynamics, and response to cytokines were evaluated in hISCs under hypoxia. HIF stabilizers and inhibitors were screened to evaluate HIF-dependent responses. RESULTS The MPS enables precise, real-time control and monitoring of oxygen levels at the cell surface. Under hypoxia, hISCs maintain viability until 72 hours and exhibit peak HIF1a at 24 hours. hISC activity was reduced at 24 hours but recovered at 48 hours. Hypoxia induced increases in the proportion of hISCs in G1 and expression changes in 16 IL receptors. Prolyl hydroxylase inhibition failed to reproduce hypoxia-dependent IL-receptor expression patterns. hISC activity increased when treated IL1β, IL2, IL4, IL6, IL10, IL13, and IL25 and rescued hISC activity caused by 24 hours of hypoxia. CONCLUSIONS Hypoxia pushes hISCs into a dormant but reversible proliferative state and primes hISCs to respond to a subset of ILs that preserves hISC activity. These findings have important implications for understanding intestinal epithelial regeneration mechanisms caused by inflammatory hypoxia.
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Affiliation(s)
- Kristina R Rivera
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina
| | - R Jarrett Bliton
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina
| | - Michael J Czerwinski
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jintong Liu
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jessica M Trueblood
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Caroline M Hinesley
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Halston E Deal
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina
| | - Shlok Joshi
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Vladimir A Pozdin
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, North Carolina
| | - Ming Yao
- Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, North Carolina
| | - Amanda L Ziegler
- Comparative Medicine Institute, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Anthony T Blikslager
- Comparative Medicine Institute, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Michael A Daniele
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina; Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, North Carolina
| | - Scott T Magness
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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Sotra A, Jozani KA, Zhang B. A vascularized crypt-patterned colon model for high-throughput drug screening and disease modelling. LAB ON A CHIP 2023. [PMID: 37335565 DOI: 10.1039/d3lc00211j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
The colon serves as a primary target for pharmaceutical compound screening and disease modelling. To better study colon diseases and develop treatments, engineered in vitro models with colon-specific physiological features are required. Existing colon models lack integration of colonic crypt structures with underlying perfusable vasculature, where vascular-epithelial crosstalk is affected by disease progression. We present a colon epithelium barrier model with vascularized crypts that recapitulates relevant cytokine gradients in both healthy and inflammatory conditions. Using our previously published IFlowPlate384 platform, we initially imprinted crypt topography and populated the patterned scaffold with colon cells. Proliferative colon cells spontaneously localized to the crypt niche and differentiated into epithelial barriers with a tight brush border. Toxicity of the colon cancer drug, capecitabine, was tested and showed a dose-dependent response and recovery from crypt-patterned colon epithelium exclusively. Perfusable microvasculature was then incorporated around the colon crypts followed by treatment with pro-inflammatory TNFα and IFNγ cytokines to simulate inflammatory bowel disease (IBD)-like conditions. We observed in vivo-like stromal basal-to-apical cytokine gradients in tissues with vascularized crypts and gradient reversals upon inflammation. Taken together, we demonstrated crypt topography integrated with underlying perfusable microvasculature has significant value for emulating colon physiology and in advanced disease modelling.
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Affiliation(s)
- Alexander Sotra
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada.
| | - Kimia Asadi Jozani
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada.
| | - Boyang Zhang
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada.
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
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Marr EE, Mulhern TJ, Welch M, Keegan P, Caballero-Franco C, Johnson BG, Kasaian M, Azizgolshani H, Petrie T, Charest J, Wiellette E. A platform to reproducibly evaluate human colon permeability and damage. Sci Rep 2023; 13:8922. [PMID: 37264117 DOI: 10.1038/s41598-023-36020-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/27/2023] [Indexed: 06/03/2023] Open
Abstract
The intestinal epithelium comprises diverse cell types and executes many specialized functions as the primary interface between luminal contents and internal organs. A key function provided by the epithelium is maintenance of a barrier that protects the individual from pathogens, irritating luminal contents, and the microbiota. Disruption of this barrier can lead to inflammatory disease within the intestinal mucosa, and, in more severe cases, to sepsis. Animal models to study intestinal permeability are costly and not entirely predictive of human biology. Here we present a model of human colon barrier function that integrates primary human colon stem cells into Draper's PREDICT96 microfluidic organ-on-chip platform to yield a high-throughput system appropriate to predict damage and healing of the human colon epithelial barrier. We have demonstrated pharmacologically induced barrier damage measured by both a high throughput molecular permeability assay and transepithelial resistance. Using these assays, we developed an Inflammatory Bowel Disease-relevant model through cytokine induced damage that can support studies of disease mechanisms and putative therapeutics.
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Affiliation(s)
| | | | | | - Philip Keegan
- Draper, 555 Technology Sq., Cambridge, MA, 02139, USA
| | | | - Bryce G Johnson
- Pfizer Inflammation and Immunology, 1 Portland St., Cambridge, MA, 02139, USA
| | - Marion Kasaian
- Pfizer Inflammation and Immunology, 1 Portland St., Cambridge, MA, 02139, USA
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Furone F, Bellomo C, Carpinelli M, Nicoletti M, Hewa-Munasinghege FN, Mordaa M, Mandile R, Barone MV, Nanayakkara M. The protective role of Lactobacillus rhamnosus GG postbiotic on the alteration of autophagy and inflammation pathways induced by gliadin in intestinal models. Front Med (Lausanne) 2023; 10:1085578. [PMID: 37215707 PMCID: PMC10192745 DOI: 10.3389/fmed.2023.1085578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/21/2023] [Indexed: 05/24/2023] Open
Abstract
Celiac disease (CD) is an autoimmune enteropathy caused by an abnormal immune response to gliadin peptides in genetically predisposed individuals. For people with CD, the only available therapy thus far is the lifelong necessity for a gluten-free diet (GFD). Innovative therapies include probiotics and postbiotics as dietary supplements, both of which may benefit the host. Therefore, the present study aimed to investigate the possible beneficial effects of the postbiotic Lactobacillus rhamnosus GG (LGG) in preventing the effects induced by indigested gliadin peptides on the intestinal epithelium. In this study, these effects on the mTOR pathway, autophagic function, and inflammation have been evaluated. Furthermore, in this study, we stimulated the Caco-2 cells with the undigested gliadin peptide (P31-43) and with the crude gliadin peptic-tryptic peptides (PTG) and pretreated the samples with LGG postbiotics (ATCC 53103) (1 × 108). In this study, the effects induced by gliadin before and after pretreatment have also been investigated. The phosphorylation levels of mTOR, p70S6K, and p4EBP-1 were increased after treatment with PTG and P31-43, indicating that the intestinal epithelial cells responded to the gliadin peptides by activating the mTOR pathway. Moreover, in this study, an increase in the phosphorylation of NF-κβ was observed. Pretreatment with LGG postbiotic prevented both the activation of the mTOR pathway and the NF-κβ phosphorylation. In addition, P31-43 reduced LC3II staining, and the postbiotic treatment was able to prevent this reduction. Subsequently, to evaluate the inflammation in a more complex intestinal model, the intestinal organoids derived from celiac disease patient biopsies (GCD-CD) and controls (CTR) were cultured. Stimulation with peptide 31-43 in the CD intestinal organoids induced NF-κβ activation, and pretreatment with LGG postbiotic could prevent it. These data showed that the LGG postbiotic can prevent the P31-43-mediated increase in inflammation in both Caco-2 cells and in intestinal organoids derived from CD patients.
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Affiliation(s)
- Francesca Furone
- Department of Translational Medical Science (Section of Paediatrics), University of Naples Federico II, Naples, Italy
| | - Claudia Bellomo
- Department of Translational Medical Science (Section of Paediatrics), University of Naples Federico II, Naples, Italy
| | - Martina Carpinelli
- Department of Translational Medical Science (Section of Paediatrics), University of Naples Federico II, Naples, Italy
| | - Martina Nicoletti
- Department of Translational Medical Science (Section of Paediatrics), University of Naples Federico II, Naples, Italy
| | | | - Majed Mordaa
- Department of Translational Medical Science (Section of Paediatrics), University of Naples Federico II, Naples, Italy
| | - Roberta Mandile
- Department of Translational Medical Sciences, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Maria Vittoria Barone
- Department of Translational Medical Science (Section of Paediatrics), University of Naples Federico II, Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Naples, Italy
| | - Merlin Nanayakkara
- Department of Translational Medical Science (Section of Paediatrics), University of Naples Federico II, Naples, Italy
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Ok MT, Liu J, Bliton RJ, Hinesley CM, San Pedro EET, Breau KA, Gomez-Martinez I, Burclaff J, Magness ST. A leaky human colon model reveals uncoupled apical/basal cytotoxicity in early Clostridioides difficile toxin exposure. Am J Physiol Gastrointest Liver Physiol 2023; 324:G262-G280. [PMID: 36749911 PMCID: PMC10010926 DOI: 10.1152/ajpgi.00251.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 02/09/2023]
Abstract
Clostridioides difficile (C. difficile) toxins A (TcdA) and B (TcdB) cause antibiotic-associated colitis in part by disrupting epithelial barrier function. Accurate in vitro models are necessary to detect early toxicity kinetics, investigate disease etiology, and develop preclinical models for new therapies. Properties of cancer cell lines and organoids inherently limit these efforts. We developed adult stem cell-derived monolayers of differentiated human colonic epithelium (hCE) with barrier function, investigated the impact of toxins on apical/basal aspects of monolayers, and evaluated whether a leaky epithelial barrier enhances toxicity. Single-cell RNA-sequencing (scRNAseq) mapped C. difficile-relevant genes to human lineages. Transcriptomics compared hCE to Caco-2, informed timing of in vitro stem cell differentiation, and revealed transcriptional responses to TcdA. Transepithelial electrical resistance (TEER) and fluorescent permeability assays measured cytotoxicity. Contribution of TcdB toxicity was evaluated in a diclofenac-induced leaky gut model. scRNAseq demonstrated broad and variable toxin receptor expression. Absorptive colonocytes in vivo displayed increased toxin receptor, Rho GTPase, and cell junction gene expression. Advanced TcdA toxicity generally decreased cytokine/chemokine and increased tight junction and death receptor genes. Differentiated Caco-2 cells remained immature whereas hCE monolayers were similar to mature colonocytes in vivo. Basal exposure of TcdA/B caused greater toxicity and apoptosis than apical exposure. Apical exposure to toxins was enhanced by diclofenac. Apical/basal toxicities are uncoupled with more rapid onset and increased magnitude postbasal toxin exposure. Leaky junctions enhance toxicity of apical TcdB exposure. hCE monolayers represent a physiologically relevant and sensitive system to evaluate the impact of microbial toxins on gut epithelium.NEW & NOTEWORTHY Novel human colonocyte monolayer cultures, benchmarked by transcriptomics for physiological relevance, detect early cytopathic impacts of Clostridioides difficile toxins TcdA and TcdB. A fluorescent ZO-1 reporter in primary human colonocytes is used to track epithelial barrier disruption in response to TcdA. Basal TcdA/B exposure generally caused more rapid onset and cytotoxicity than apical exposure. Transcriptomics demonstrate changes in tight junction, chemokine, and cytokine receptor gene expression post-TcdA exposure. Diclofenac-induced leaky epithelium enhanced apical exposure toxicity.
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Affiliation(s)
- Meryem T Ok
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - Jintong Liu
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - R Jarrett Bliton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - Caroline M Hinesley
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - Ekaterina Ellyce T San Pedro
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Ismael Gomez-Martinez
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
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50
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Chen Z, Leung TCN, Lui YL, Ngai SM, Chung HY. Combination of untargeted and targeted proteomics for secretome analysis of L-WRN cells. Anal Bioanal Chem 2023; 415:1465-1476. [PMID: 36656349 DOI: 10.1007/s00216-023-04534-9] [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: 12/05/2022] [Revised: 12/25/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023]
Abstract
Organoid culture is a promising biomedical technology that requires specialized growth factors. Recently, a recombinant L-WRN cell line has been extensively used to generate conditioned medium (L-CM) for organoid culture. Nevertheless, methods for evaluating the stability of the L-WRN cells have been limited. In this study, a novel proteomics-based approach was developed to analyze the secretome of the cells. Serum-free L-CM was lyophilized, precipitated by trichloroacetic acid, and desalted prior to analysis by liquid chromatography-tandem mass spectrometry. Data-dependent acquisition (DDA) was conducted for the untargeted secretome profiling of the cells, and parallel reaction monitoring (PRM) was applied for the targeted quantification of the Wnt3A, R-spondin3, and noggin proteins (WRNs). This study also compared the performance of two types of PRM methods, namely MS1-independent PRM and MS1-dependent PRM, that can be executed on an Orbitrap instrument. The results showed that the growth of mouse intestinal organoids was closely related to the use of L-CM. The composition of L-CM could be markedly affected by the medium collection scheme. A total of 1725, 2302, and 2681 proteins were identified from the L-CM collected on day 5, day 9, and day 13, respectively. The MS1-independent PRM outperformed the MS1-dependent PRM and effectively quantified the WRNs with high repeatability and specificity. In conclusion, by integrating untargeted and targeted proteomics, this study develops a mass spectrometry-based method for the secretome analysis and quality control of the L-WRN cells. The methodology and findings of the present work will benefit future studies on organoids and secretomes.
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Affiliation(s)
- Zixing Chen
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Thomas Chun Ning Leung
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Ying Lam Lui
- Cell and Molecular Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Sai Ming Ngai
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hau Yin Chung
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
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