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Montes-Olivas S, Legge D, Lund A, Fletcher AG, Williams AC, Marucci L, Homer M. In-silico and in-vitro morphometric analysis of intestinal organoids. PLoS Comput Biol 2023; 19:e1011386. [PMID: 37578984 PMCID: PMC10473498 DOI: 10.1371/journal.pcbi.1011386] [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: 02/06/2023] [Revised: 09/01/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023] Open
Abstract
Organoids offer a powerful model to study cellular self-organisation, the growth of specific tissue morphologies in-vitro, and to assess potential medical therapies. However, the intrinsic mechanisms of these systems are not entirely understood yet, which can result in variability of organoids due to differences in culture conditions and basement membrane extracts used. Improving the standardisation of organoid cultures is essential for their implementation in clinical protocols. Developing tools to assess and predict the behaviour of these systems may produce a more robust and standardised biological model to perform accurate clinical studies. Here, we developed an algorithm to automate crypt-like structure counting on intestinal organoids in both in-vitro and in-silico images. In addition, we modified an existing two-dimensional agent-based mathematical model of intestinal organoids to better describe the system physiology, and evaluated its ability to replicate budding structures compared to new experimental data we generated. The crypt-counting algorithm proved useful in approximating the average number of budding structures found in our in-vitro intestinal organoid culture images on days 3 and 7 after seeding. Our changes to the in-silico model maintain the potential to produce simulations that replicate the number of budding structures found on days 5 and 7 of in-vitro data. The present study aims to aid in quantifying key morphological structures and provide a method to compare both in-vitro and in-silico experiments. Our results could be extended later to 3D in-silico models.
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Affiliation(s)
- Sandra Montes-Olivas
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Danny Legge
- Colorectal Tumour Biology Group, School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Abbie Lund
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Alexander G. Fletcher
- School of Mathematics and Statistics, University of Sheffield, Sheffield, United Kingdom
- Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Ann C. Williams
- Colorectal Tumour Biology Group, School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- BrisSynBio, Bristol, United Kingdom
| | - Martin Homer
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
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2
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Kayisoglu O, Weiss F, Niklas C, Pierotti I, Pompaiah M, Wallaschek N, Germer CT, Wiegering A, Bartfeld S. Location-specific cell identity rather than exposure to GI microbiota defines many innate immune signalling cascades in the gut epithelium. Gut 2021; 70:687-697. [PMID: 32571970 PMCID: PMC7948175 DOI: 10.1136/gutjnl-2019-319919] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 05/06/2020] [Accepted: 05/19/2020] [Indexed: 01/10/2023]
Abstract
OBJECTIVE The epithelial layer of the GI tract is equipped with innate immune receptors to sense invading pathogens. Dysregulation in innate immune signalling pathways is associated with severe inflammatory diseases, but the responsiveness of GI epithelial cells to bacterial stimulation remains unclear. DESIGN We generated 42 lines of human and murine organoids from gastric and intestinal segments of both adult and fetal tissues. Genome-wide RNA-seq of the organoids provides an expression atlas of the GI epithelium. The innate immune response in epithelial cells was assessed using several functional assays in organoids and two-dimensional monolayers of cells from organoids. RESULTS Results demonstrate extensive spatial organisation of innate immune signalling components along the cephalocaudal axis. A large part of this organisation is determined before birth and independent of exposure to commensal gut microbiota. Spatially restricted expression of Toll-like receptor 4 (Tlr4) in stomach and colon, but not in small intestine, is matched by nuclear factor kappa B (NF-κB) responses to lipopolysaccharide (LPS) exposure. Gastric epithelial organoids can sense LPS from the basal as well as from the apical side. CONCLUSION We conclude that the epithelial innate immune barrier follows a specific pattern per GI segment. The majority of the expression patterns and the function of TLR4 is encoded in the tissue-resident stem cells and determined primarily during development.
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Affiliation(s)
- Ozge Kayisoglu
- Research Center for Infectious Diseases (ZINF)/Institute for Molecular Infection Biology (IMIB), Julius Maximilian University of Wuerzburg, Wuerzburg, Germany
| | - Franziska Weiss
- Research Center for Infectious Diseases (ZINF)/Institute for Molecular Infection Biology (IMIB), Julius Maximilian University of Wuerzburg, Wuerzburg, Germany
| | - Carolin Niklas
- Research Center for Infectious Diseases (ZINF)/Institute for Molecular Infection Biology (IMIB), Julius Maximilian University of Wuerzburg, Wuerzburg, Germany
| | - Isabella Pierotti
- Research Center for Infectious Diseases (ZINF)/Institute for Molecular Infection Biology (IMIB), Julius Maximilian University of Wuerzburg, Wuerzburg, Germany
| | - Malvika Pompaiah
- Research Center for Infectious Diseases (ZINF)/Institute for Molecular Infection Biology (IMIB), Julius Maximilian University of Wuerzburg, Wuerzburg, Germany
| | - Nina Wallaschek
- Research Center for Infectious Diseases (ZINF)/Institute for Molecular Infection Biology (IMIB), Julius Maximilian University of Wuerzburg, Wuerzburg, Germany
| | - Christoph-Thomas Germer
- Department of General, Visceral, Vascular and Pediatric Surgery, University Hospital of Wuerzburg, Wuerzburg, Germany
| | - Armin Wiegering
- Department of General, Visceral, Vascular and Pediatric Surgery, University Hospital of Wuerzburg, Wuerzburg, Germany
| | - Sina Bartfeld
- Research Center for Infectious Diseases (ZINF)/Institute for Molecular Infection Biology (IMIB), Julius Maximilian University of Wuerzburg, Wuerzburg, Germany
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3
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Jose SS, De Zuani M, Tidu F, Hortová Kohoutková M, Pazzagli L, Forte G, Spaccapelo R, Zelante T, Frič J. Comparison of two human organoid models of lung and intestinal inflammation reveals Toll-like receptor signalling activation and monocyte recruitment. Clin Transl Immunology 2020; 9:e1131. [PMID: 32377340 PMCID: PMC7200218 DOI: 10.1002/cti2.1131] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/28/2022] Open
Abstract
Objectives The activation of immune responses in mucosal tissues is a key factor for the development and sustainment of several pathologies including infectious diseases and autoimmune diseases. However, translational research and personalised medicine struggle to advance because of the lack of suitable preclinical models that successfully mimic the complexity of human tissues without relying on in vivo mouse models. Here, we propose two in vitro human 3D tissue models, deprived of any resident leucocytes, to model mucosal tissue inflammatory processes. Methods We developed human 3D lung and intestinal organoids differentiated from induced pluripotent stem cells to model mucosal tissues. We then compared their response to a panel of microbial ligands and investigated their ability to attract and host human primary monocytes. Results Mature lung and intestinal organoids comprised epithelial (EpCAM+) and mesenchymal (CD73+) cells which responded to Toll‐like receptor stimulation by releasing pro‐inflammatory cytokines and expressing tissue inflammatory markers including MMP9, COX2 and CRP. When added to the organoid culture, primary human monocytes migrated towards the organoids and began to differentiate to an ‘intermediate‐like’ phenotype characterised by increased levels of CD14 and CD16. Conclusion We show that human mucosal organoids exhibit proper immune functions and successfully mimic an immunocompetent tissue microenvironment able to host patient‐derived immune cells. Our experimental set‐up provides a novel tool to tackle the complexity of immune responses in mucosal tissues which can be tailored to different human pathologies.
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Affiliation(s)
- Shyam Sushama Jose
- International Clinical Research Center St. Anne's University Hospital Brno Brno Czech Republic
| | - Marco De Zuani
- International Clinical Research Center St. Anne's University Hospital Brno Brno Czech Republic
| | - Federico Tidu
- International Clinical Research Center St. Anne's University Hospital Brno Brno Czech Republic.,Department of Biology Faculty of Medicine Masaryk University Brno Czech Republic
| | | | - Lucia Pazzagli
- Department of Experimental Medicine and University Research Center for Functional Genomic (C.U.R.Ge.F) University of Perugia Perugia Italy
| | - Giancarlo Forte
- International Clinical Research Center St. Anne's University Hospital Brno Brno Czech Republic
| | - Roberta Spaccapelo
- Department of Experimental Medicine and University Research Center for Functional Genomic (C.U.R.Ge.F) University of Perugia Perugia Italy
| | - Teresa Zelante
- Department of Experimental Medicine and University Research Center for Functional Genomic (C.U.R.Ge.F) University of Perugia Perugia Italy
| | - Jan Frič
- International Clinical Research Center St. Anne's University Hospital Brno Brno Czech Republic.,Institute of Hematology and Blood Transfusion Prague Czech Republic
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4
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Kolawole AO, Mirabelli C, Hill DR, Svoboda SA, Janowski AB, Passalacqua KD, Rodriguez BN, Dame MK, Freiden P, Berger RP, Vu DL, Hosmillo M, O'Riordan MXD, Schultz-Cherry S, Guix S, Spence JR, Wang D, Wobus CE. Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape. PLoS Pathog 2019; 15:e1008057. [PMID: 31671153 PMCID: PMC6957189 DOI: 10.1371/journal.ppat.1008057] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 01/13/2020] [Accepted: 08/30/2019] [Indexed: 12/26/2022] Open
Abstract
Human astroviruses (HAstV) are understudied positive-strand RNA viruses that cause gastroenteritis mostly in children and the elderly. Three clades of astroviruses, classic, MLB-type and VA-type have been reported in humans. One limitation towards a better understanding of these viruses has been the lack of a physiologically relevant cell culture model that supports growth of all clades of HAstV. Herein, we demonstrate infection of HAstV strains belonging to all three clades in epithelium-only human intestinal enteroids (HIE) isolated from biopsy-derived intestinal crypts. A detailed investigation of infection of VA1, a member of the non-canonical HAstV-VA/HMO clade, showed robust replication in HIE derived from different patients and from different intestinal regions independent of the cellular differentiation status. Flow cytometry and immunofluorescence analysis revealed that VA1 infects several cell types, including intestinal progenitor cells and mature enterocytes, in HIE cultures. RNA profiling of VA1-infected HIE uncovered that the host response to infection is dominated by interferon (IFN)-mediated innate immune responses. A comparison of the antiviral host response in non-transformed HIE and transformed human colon carcinoma Caco-2 cells highlighted significant differences between these cells, including an increased magnitude of the response in HIE. Additional studies confirmed the sensitivity of VA1 to exogenous IFNs, and indicated that the endogenous IFN response of HIE to curtail the growth of strains from all three clades. Genotypic variation in the permissiveness of different HIE lines to HAstV could be overcome by pharmacologic inhibition of JAK/STAT signaling. Collectively, our data identify HIE as a universal infection model for HAstV and an improved model of the intestinal epithelium to investigate enteric virus-host interactions. Human astroviruses (HAstV) are understudied positive-strand RNA viruses that typically cause gastroenteritis mostly in children and the elderly, but more recent studies also implicate them in neurological disease in immunocompromised patients. To better understand these viruses, a physiologically relevant cell culture model that supports growth of all clades of HAstV would be highly beneficial. Herein, we demonstrated robust infection of HAstV strains belonging to all three clades in epithelium-only human intestinal enteroids (HIE) isolated from biopsy-derived intestinal crypts from different patients and intestinal regions, making HIE a valuable model to study HAstV biology. Using this system, we identify for the first time that VA1 infects several cell types, including intestinal progenitor cells and mature enterocytes. Analysis of the antiviral host response to infection demonstrated that HIE respond to infection with a type I and III interferon response. This response reduced HAstV replication and when blocked resulted in increased infection. Establishment of the HIE system for HAstV research lays the foundation for future basic and translational discoveries.
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Affiliation(s)
- Abimbola O Kolawole
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David R Hill
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sophia A Svoboda
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrew B Janowski
- Department of Pediatrics, Washington University, St. Louis, Missouri, United States of America
| | - Karla D Passalacqua
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Benancio N Rodriguez
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michael K Dame
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Pamela Freiden
- St. Jude Children's Hospital, Memphis, Tennessee, United States of America
| | - Ryan P Berger
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Diem-Lan Vu
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Mary X D O'Riordan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America.,Department of Biomedical Engineering, University of Michigan, Ann arbor, Michigan, United States of America
| | - David Wang
- Departments of Molecular Microbiology, and Pathology and Immunology, Washington University, St. Louis, Missouri, United States of America
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
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5
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George MM, Rahman M, Connors J, Stadnyk AW. Opinion: Are Organoids the End of Model Evolution for Studying Host Intestinal Epithelium/Microbe Interactions? Microorganisms 2019; 7:microorganisms7100406. [PMID: 31569537 PMCID: PMC6843211 DOI: 10.3390/microorganisms7100406] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/21/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022] Open
Abstract
In the pursuit to understand intestinal epithelial cell biology in health and disease, researchers have established various model systems, from whole animals (typically rodents) with experimentally induced disease to transformed human carcinomas. The obvious limitation to the ex vivo or in vitro cell systems was enriching, maintaining, and expanding differentiated intestinal epithelial cell types. The popular concession was human and rodent transformed cells of mainly undifferentiated cells, with a few select lines differentiating along the path to becoming goblet cells. Paneth cells, in particular, remained unculturable. The breakthrough came in the last decade with the report of conditions to grow mouse intestinal organoids. Organoids are 3-dimensional ex vivo “mini-organs” of the organ from which the stem cells were derived. Intestinal organoids contain fully differentiated epithelial cells in the same spatial organization as in the native epithelium. The cells are suitably polarized and produce and secrete mucus onto the apical surface. This review introduces intestinal organoids and provide some thoughts on strengths and weaknesses in the application of organoids to further advance our understanding of the intestinal epithelial–microbe relationship.
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Affiliation(s)
- Michelle M George
- Department of Pediatrics, Division of Gastroenterology & Nutrition, Dalhousie University, 5850 University Avenue, Halifax, NS B3K 6R8, Canada.
| | - Mushfiqur Rahman
- Department of Pediatrics, Division of Gastroenterology & Nutrition, Dalhousie University, 5850 University Avenue, Halifax, NS B3K 6R8, Canada.
| | - Jessica Connors
- Department of Pediatrics, Division of Gastroenterology & Nutrition, Dalhousie University, 5850 University Avenue, Halifax, NS B3K 6R8, Canada.
| | - Andrew W Stadnyk
- Department of Pediatrics, Division of Gastroenterology & Nutrition, Dalhousie University, 5850 University Avenue, Halifax, NS B3K 6R8, Canada.
- Department of Microbiology & Immunology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
- Department of Pathology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
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6
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Yang Y, Zhang L, Jiang G, Lei A, Yu Q, Xie J, Chen Y. Evaluation of the protective effects of Ganoderma atrum polysaccharide on acrylamide-induced injury in small intestine tissue of rats. Food Funct 2019; 10:5863-5872. [DOI: 10.1039/c9fo01452g] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This research confirmed the protective effects of Ganoderma atrum polysaccharide (PSG-1) on acrylamide (AA) induced intestinal injury in rats.
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Affiliation(s)
- Ying Yang
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Lulu Zhang
- Hefei Taksong Biotech Co
- Ltd
- Hefei 230022
- China
| | - Guoyong Jiang
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Aitong Lei
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Qiang Yu
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Jianhua Xie
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Yi Chen
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
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7
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Modeling Host-Pathogen Interactions in the Context of the Microenvironment: Three-Dimensional Cell Culture Comes of Age. Infect Immun 2018; 86:IAI.00282-18. [PMID: 30181350 DOI: 10.1128/iai.00282-18] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Tissues and organs provide the structural and biochemical landscapes upon which microbial pathogens and commensals function to regulate health and disease. While flat two-dimensional (2-D) monolayers composed of a single cell type have provided important insight into understanding host-pathogen interactions and infectious disease mechanisms, these reductionist models lack many essential features present in the native host microenvironment that are known to regulate infection, including three-dimensional (3-D) architecture, multicellular complexity, commensal microbiota, gas exchange and nutrient gradients, and physiologically relevant biomechanical forces (e.g., fluid shear, stretch, compression). A major challenge in tissue engineering for infectious disease research is recreating this dynamic 3-D microenvironment (biological, chemical, and physical/mechanical) to more accurately model the initiation and progression of host-pathogen interactions in the laboratory. Here we review selected 3-D models of human intestinal mucosa, which represent a major portal of entry for infectious pathogens and an important niche for commensal microbiota. We highlight seminal studies that have used these models to interrogate host-pathogen interactions and infectious disease mechanisms, and we present this literature in the appropriate historical context. Models discussed include 3-D organotypic cultures engineered in the rotating wall vessel (RWV) bioreactor, extracellular matrix (ECM)-embedded/organoid models, and organ-on-a-chip (OAC) models. Collectively, these technologies provide a more physiologically relevant and predictive framework for investigating infectious disease mechanisms and antimicrobial therapies at the intersection of the host, microbe, and their local microenvironments.
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Schoenborn AA, von Furstenberg RJ, Valsaraj S, Hussain FS, Stein M, Shanahan MT, Henning SJ, Gulati AS. The enteric microbiota regulates jejunal Paneth cell number and function without impacting intestinal stem cells. Gut Microbes 2018; 10:45-58. [PMID: 29883265 PMCID: PMC6363071 DOI: 10.1080/19490976.2018.1474321] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 04/06/2018] [Accepted: 05/01/2018] [Indexed: 02/03/2023] Open
Abstract
Paneth cells (PCs) are epithelial cells found in the small intestine, next to intestinal stem cells (ISCs) at the base of the crypts. PCs secrete antimicrobial peptides (AMPs) that regulate the commensal gut microbiota. In contrast, little is known regarding how the enteric microbiota reciprocally influences PC function. In this study, we sought to characterize the impact of the enteric microbiota on PC biology in the mouse small intestine. This was done by first enumerating jejunal PCs in germ-free (GF) versus conventionally raised (CR) mice. We next evaluated the possible functional consequences of altered PC biology in these experimental groups by assessing epithelial proliferation, ISC numbers, and the production of AMPs. We found that PC numbers were significantly increased in CR versus GF mice; however, there were no differences in ISC numbers or cycling activity between groups. Of the AMPs assessed, only Reg3γ transcript expression was significantly increased in CR mice. Intriguingly, this increase was abrogated in cultured CR versus GF enteroids, and could not be re-induced with various bacterial ligands. Our findings demonstrate the enteric microbiota regulates PC function by increasing PC numbers and inducing Reg3γ expression, though the latter effect may not involve direct interactions between bacteria and the intestinal epithelium. In contrast, the enteric microbiota does not appear to regulate jejunal ISC census and proliferation. These are critical findings for investigators using GF mice and the enteroid system to study PC and ISC biology.
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Affiliation(s)
- Alexi A Schoenborn
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Richard J von Furstenberg
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Smrithi Valsaraj
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Farah S Hussain
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Molly Stein
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Michael T Shanahan
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Susan J Henning
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- d Department of Cellular and Molecular Physiology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Ajay S Gulati
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- e Department of Pathology and Laboratory Medicine , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
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9
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Parker A, Lawson MAE, Vaux L, Pin C. Host-microbe interaction in the gastrointestinal tract. Environ Microbiol 2018; 20:2337-2353. [PMID: 28892253 PMCID: PMC6175405 DOI: 10.1111/1462-2920.13926] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/25/2017] [Accepted: 08/31/2017] [Indexed: 12/13/2022]
Abstract
The gastrointestinal tract is a highly complex organ in which multiple dynamic physiological processes are tightly coordinated while interacting with a dense and extremely diverse microbial population. From establishment in early life, through to host-microbe symbiosis in adulthood, the gut microbiota plays a vital role in our development and health. The effect of the microbiota on gut development and physiology is highlighted by anatomical and functional changes in germ-free mice, affecting the gut epithelium, immune system and enteric nervous system. Microbial colonisation promotes competent innate and acquired mucosal immune systems, epithelial renewal, barrier integrity, and mucosal vascularisation and innervation. Interacting or shared signalling pathways across different physiological systems of the gut could explain how all these changes are coordinated during postnatal colonisation, or after the introduction of microbiota into germ-free models. The application of cell-based in-vitro experimental systems and mathematical modelling can shed light on the molecular and signalling pathways which regulate the development and maintenance of homeostasis in the gut and beyond.
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Affiliation(s)
- Aimée Parker
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
| | | | - Laura Vaux
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
| | - Carmen Pin
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
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10
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Lipopolysaccharide from Crypt-Specific Core Microbiota Modulates the Colonic Epithelial Proliferation-to-Differentiation Balance. mBio 2017; 8:mBio.01680-17. [PMID: 29042502 PMCID: PMC5646255 DOI: 10.1128/mbio.01680-17] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We identified a crypt-specific core microbiota (CSCM) dominated by strictly aerobic, nonfermentative bacteria in murine cecal and proximal colonic (PC) crypts and hypothesized that, among its possible functions, it may affect epithelial regeneration. In the present work, we isolated representative CSCM strains using selective media based upon our initial 16S rRNA-based molecular identification (i.e., Acinetobacter, Delftia, and Stenotrophomonas). Their tropism for the crypt was confirmed, and their influence on epithelial regeneration was demonstrated in vivo by monocolonization of germfree mice. We also showed that lipopolysaccharide (LPS), through its endotoxin activity, was the dominant bacterial agonist controlling proliferation. The relevant molecular mechanisms were analyzed using colonic crypt-derived organoids exposed to bacterial sonicates or highly purified LPS as agonists. We identified a Toll-like receptor 4 (TLR4)-dependent program affecting crypts at different stages of epithelial differentiation. LPS played a dual role: it repressed cell proliferation through RIPK3-mediated necroptosis of stem cells and cells of the transit-amplifying compartment and concurrently enhanced cell differentiation, particularly the goblet cell lineage. The LPS from crypt-specific core microbiota controls intestinal epithelium proliferation through necroptosis of stem cells and enhances cell differentiation, mainly the goblet cell lineage.
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11
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Pierzchalska M, Panek M, Czyrnek M, Gielicz A, Mickowska B, Grabacka M. Probiotic Lactobacillus acidophilus bacteria or synthetic TLR2 agonist boost the growth of chicken embryo intestinal organoids in cultures comprising epithelial cells and myofibroblasts. Comp Immunol Microbiol Infect Dis 2017; 53:7-18. [PMID: 28750869 DOI: 10.1016/j.cimid.2017.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 05/31/2017] [Accepted: 06/08/2017] [Indexed: 02/06/2023]
Abstract
The intestinal epithelial cells reside in close proximity to myofibroblasts and microbiota, which are supposed to have an impact on intestinal stem cells fate and to influence processes of tissue maturation and regeneration. Mechanism underlying these phenomena and their diversity among vertebrates can be studied in 3D organoid cultures. We investigated the growth of chicken embryo intestinal epithelial organoids in Matrigel with and without Toll-like receptors (TLRs) stimulation. The organoid cultures contained also some myofibroblasts with potential to promote intestinal stem cell survival. Organoid cells, expressing TLR4, TLR2 type 1 and TLR2 type 2 were incubated with their agonists (lipopolysaccharide - LPS and Pam3CSK4) or co-cultured with Lactobacillus acidophilus bacteria (LA-5). Pam3CSK4 and LA-5 promoted organoid growth, which was demonstrated by comparing the morphological parameters (mean number and area of organoids). The profile of prostaglandins (PG), known to promote intestinal regeneration, in supernatants from organoid and fibroblast cultures were evaluated. Both PGE2 and PGD2 were detected. As compared to unstimulated controls, supernatants from the Pam3CSK4-stimulated organoids contained twice as much of PGE2 and PGD2. The changes in production of prostaglandins and the support of epithelial cell growth by myofibroblasts are factors potentially responsible for stimulatory effect of TLR2 activation.
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Affiliation(s)
- Malgorzata Pierzchalska
- Department of Food Biotechnology, Faculty of Food Technology, The University of Agriculture in Kraków, Balicka 122, 30-149, Kraków, Poland.
| | - Malgorzata Panek
- Department of Food Biotechnology, Faculty of Food Technology, The University of Agriculture in Kraków, Balicka 122, 30-149, Kraków, Poland
| | - Malgorzata Czyrnek
- Department of Food Biotechnology, Faculty of Food Technology, The University of Agriculture in Kraków, Balicka 122, 30-149, Kraków, Poland
| | - Anna Gielicz
- Department of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland
| | - Barbara Mickowska
- Malopolska Center of Food Monitoring, Faculty of Food Technology, The University of Agriculture in Kraków, Balicka 122, 30-149, Kraków, Poland
| | - Maja Grabacka
- Department of Food Biotechnology, Faculty of Food Technology, The University of Agriculture in Kraków, Balicka 122, 30-149, Kraków, Poland
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Modeling infectious diseases and host-microbe interactions in gastrointestinal organoids. Dev Biol 2016; 420:262-270. [PMID: 27640087 DOI: 10.1016/j.ydbio.2016.09.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 12/18/2022]
Abstract
Advances in stem cell research have allowed the development of 3-dimensional (3D) primary cell cultures termed organoid cultures, as they closely mimic the in vivo organization of different cell lineages. Bridging the gap between 2-dimensional (2D) monotypic cancer cell lines and whole organisms, organoids are now widely applied to model development and disease. Organoids hold immense promise for addressing novel questions in host-microbe interactions, infectious diseases and the resulting inflammatory conditions. Researchers have started to use organoids for modeling infection with pathogens, such as Helicobacter pylori or Salmonella enteritica, gut-microbiota interactions and inflammatory bowel disease. Future studies will broaden the spectrum of microbes used and continue to establish organoids as a standard model for human host-microbial interactions. Moreover, they will increasingly exploit the unique advantages of organoids, for example to address patient-specific responses to microbes.
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Matsumoto T, Mochizuki W, Nibe Y, Akiyama S, Matsumoto Y, Nozaki K, Fukuda M, Hayashi A, Mizutani T, Oshima S, Watanabe M, Nakamura T. Retinol Promotes In Vitro Growth of Proximal Colon Organoids through a Retinoic Acid-Independent Mechanism. PLoS One 2016; 11:e0162049. [PMID: 27564706 PMCID: PMC5001647 DOI: 10.1371/journal.pone.0162049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 08/16/2016] [Indexed: 01/21/2023] Open
Abstract
Retinol (ROL), the alcohol form of vitamin A, is known to control cell fate decision of various types of stem cells in the form of its active metabolite, retinoic acid (RA). However, little is known about whether ROL has regulatory effects on colonic stem cells. We examined in this study the effect of ROL on the growth of murine normal colonic cells cultured as organoids. As genes involved in RA synthesis from ROL were differentially expressed along the length of the colon, we tested the effect of ROL on proximal and distal colon organoids separately. We found that organoid forming efficiency and the expression level of Lgr5, a marker gene for colonic stem cells were significantly enhanced by ROL in the proximal colon organoids, but not in the distal ones. Interestingly, neither retinaldehyde (RAL), an intermediate product of the ROL-RA pathway, nor RA exhibited growth promoting effects on the proximal colon organoids, suggesting that ROL-dependent growth enhancement in organoids involves an RA-independent mechanism. This was confirmed by the observation that an inhibitor for RA-mediated gene transcription did not abrogate the effect of ROL on organoids. This novel role of ROL in stem cell maintenance in the proximal colon provides insights into the mechanism of region-specific regulation for colonic stem cell maintenance.
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Affiliation(s)
- Taichi Matsumoto
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
| | - Wakana Mochizuki
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
| | - Yoichi Nibe
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
| | - Shintaro Akiyama
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
| | - Yuka Matsumoto
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
| | - Kengo Nozaki
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
| | - Masayoshi Fukuda
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
| | - Ayumi Hayashi
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
| | - Tomohiro Mizutani
- Department of Advanced Therapeutics for GI Diseases, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
| | - Shigeru Oshima
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
| | - Mamoru Watanabe
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
| | - Tetsuya Nakamura
- Department of Advanced Therapeutics for GI Diseases, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113–8519, Japan
- * E-mail:
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Henning SJ, von Furstenberg RJ. GI stem cells - new insights into roles in physiology and pathophysiology. J Physiol 2016; 594:4769-79. [PMID: 27107928 DOI: 10.1113/jp271663] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/19/2016] [Indexed: 12/21/2022] Open
Abstract
This overview gives a brief historical summary of key discoveries regarding stem cells of the small intestine. The current concept is that there are two pools of intestinal stem cells (ISCs): an actively cycling pool that is marked by Lgr5, is relatively homogeneous and is responsible for daily turnover of the epithelium; and a slowly cycling or quiescent pool that functions as reserve ISCs. The latter pool appears to be quite heterogeneous and may include partially differentiated epithelial lineages that can reacquire stem cell characteristics following injury to the intestine. Markers and methods of isolation for active and quiescent ISC populations are described as well as the numerous important advances that have been made in approaches to the in vitro culture of ISCs and crypts. Factors regulating ISC biology are briefly summarized and both known and unknown aspects of the ISC niche are discussed. Although most of our current knowledge regarding ISC physiology and pathophysiology has come from studies with mice, recent work with human tissue highlights the potential translational applications arising from this field of research. Many of these topics are further elaborated in the following articles.
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Affiliation(s)
- Susan J Henning
- Department of Medicine - Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7555, USA
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Use of Cancer Stem Cells to Investigate the Pathogenesis of Colitis-associated Cancer. Inflamm Bowel Dis 2016; 22:976-83. [PMID: 26963566 PMCID: PMC4794128 DOI: 10.1097/mib.0000000000000756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Colitis-associated cancer (CAC) can develop in patients with inflammatory bowel disease with long-term uncontrolled inflammation. The mutational history and tumor microenvironment observed in CAC patients is distinct from that observed in sporadic colon cancer and suggests a different etiology. Recently, much attention has been focused on understanding the cellular origin of cancer and the cancer stem cells, which is key to growth and progression. Cancer stem cells are often chemo-resistant making them attractive targets for improving patient outcomes. New techniques have rapidly been evolving allowing for a better understanding of the normal intestinal stem cell function and behavior in the niche. Use of these new technologies will be crucial to understanding cancer stem cells in both sporadic and CAC. In this review, we will explore emerging methods related to the study of normal and cancer stem cells in the intestine, and examine potential avenues of investigation and application to understanding the pathogenesis of CAC.
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