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Zheng L, Zhan Y, Wang C, Fan Q, Sun D, Li Y, Xiong Y. Technological advances and challenges in constructing complex gut organoid systems. Front Cell Dev Biol 2024; 12:1432744. [PMID: 39206092 PMCID: PMC11349554 DOI: 10.3389/fcell.2024.1432744] [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: 05/14/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Recent advancements in organoid technology have heralded a transformative era in biomedical research, characterized by the emergence of gut organoids that replicate the structural and functional complexity of the human intestines. These stem cell-derived structures provide a dynamic platform for investigating intestinal physiology, disease pathogenesis, and therapeutic interventions. This model outperforms traditional two-dimensional cell cultures in replicating cell interactions and tissue dynamics. Gut organoids represent a significant leap towards personalized medicine. They provide a predictive model for human drug responses, thereby minimizing reliance on animal models and paving the path for more ethical and relevant research approaches. However, the transition from basic organoid models to more sophisticated, biomimetic systems that encapsulate the gut's multifaceted environment-including its interactions with microbial communities, immune cells, and neural networks-presents significant scientific challenges. This review concentrates on recent technological strides in overcoming these barriers, emphasizing innovative engineering approaches for integrating diverse cell types to replicate the gut's immune and neural components. It also explores the application of advanced fabrication techniques, such as 3D bioprinting and microfluidics, to construct organoids that more accurately replicate human tissue architecture. They provide insights into the intricate workings of the human gut, fostering the development of targeted, effective treatments. These advancements hold promise in revolutionizing disease modeling and drug discovery. Future research directions aim at refining these models further, making them more accessible and scalable for wider applications in scientific inquiry and clinical practice, thus heralding a new era of personalized and predictive medicine.
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Affiliation(s)
- Longjin Zheng
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
| | - Yang Zhan
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
| | - Chenxuan Wang
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
| | - Qigui Fan
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
| | - Denglong Sun
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
| | - Yingmeng Li
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
| | - Yanxia Xiong
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
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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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Andres SF, Zhang Y, Kuhn M, Scottoline B. Building better barriers: how nutrition and undernutrition impact pediatric intestinal health. Front Immunol 2023; 14:1192936. [PMID: 37545496 PMCID: PMC10401430 DOI: 10.3389/fimmu.2023.1192936] [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: 03/24/2023] [Accepted: 06/26/2023] [Indexed: 08/08/2023] Open
Abstract
Chronic undernutrition is a major cause of death for children under five, leaving survivors at risk for adverse long-term consequences. This review focuses on the role of nutrients in normal intestinal development and function, from the intestinal epithelium, to the closely-associated mucosal immune system and intestinal microbiota. We examine what is known about the impacts of undernutrition on intestinal physiology, with focus again on the same systems. We provide a discussion of existing animal models of undernutrition, and review the evidence demonstrating that correcting undernutrition alone does not fully ameliorate effects on intestinal function, the microbiome, or growth. We review efforts to treat undernutrition that incorporate data indicating that improved recovery is possible with interventions focused not only on delivery of sufficient energy, macronutrients, and micronutrients, but also on efforts to correct the abnormal intestinal microbiome that is a consequence of undernutrition. Understanding of the role of the intestinal microbiome in the undernourished state and correction of the phenotype is both complex and a subject that holds great potential to improve recovery. We conclude with critical unanswered questions in the field, including the need for greater mechanistic research, improved models for the impacts of undernourishment, and new interventions that incorporate recent research gains. This review highlights the importance of understanding the mechanistic effects of undernutrition on the intestinal ecosystem to better treat and improve long-term outcomes for survivors.
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Affiliation(s)
- Sarah F. Andres
- Division of Pediatric Gastroenterology, Department of Pediatrics, Oregon Health and Science University, Portland, OR, United States
| | - Yang Zhang
- Division of Pediatric Gastroenterology, Department of Pediatrics, Oregon Health and Science University, Portland, OR, United States
| | - Madeline Kuhn
- Division of Pediatric Gastroenterology, Department of Pediatrics, Oregon Health and Science University, Portland, OR, United States
| | - Brian Scottoline
- Division of Neonatology, Department of Pediatrics, Oregon Health and Science University, Portland, OR, United States
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Mesfin FM, Manohar K, Shelley WC, Brokaw JP, Liu J, Ma M, Markel TA. Stem cells as a therapeutic avenue for active and long-term complications of Necrotizing Enterocolitis. Semin Pediatr Surg 2023; 32:151311. [PMID: 37276782 PMCID: PMC10330659 DOI: 10.1016/j.sempedsurg.2023.151311] [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] [Indexed: 06/07/2023]
Abstract
Necrotizing enterocolitis (NEC) is a devastating neonatal intestinal disease associated with significant morbidity and mortality. Although decades of research have been dedicated to understanding the pathogenesis of NEC and developing therapies, it remains the leading cause of death among neonatal gastrointestinal diseases. Mesenchymal stem cells (MSCs) have garnered significant interest recently as potential therapeutic agents for the treatment of NEC. They have been shown to rescue intestinal injury and reduce the incidence and severity of NEC in various preclinical animal studies. MSCs and MSC-derived organoids and tissue engineered small intestine (TESI) have shown potential for the treatment of long-term sequela of NEC such as short bowel syndrome, neurodevelopmental delay, and chronic lung disease. Although the advances made in the use of MSCs are promising, further research is needed prior to the widespread use of these cells for the treatment of NEC.
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Affiliation(s)
- Fikir M Mesfin
- Department of Surgery, Section of Pediatric Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Krishna Manohar
- Department of Surgery, Section of Pediatric Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - W Christopher Shelley
- Department of Surgery, Section of Pediatric Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - John P Brokaw
- Department of Surgery, Section of Pediatric Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jianyun Liu
- Department of Surgery, Section of Pediatric Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Minglin Ma
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Troy A Markel
- Department of Surgery, Section of Pediatric Surgery, Indiana University School of Medicine, Indianapolis, IN, USA; Riley Hospital for Children at Indiana University Health, Indianapolis, IN, USA.
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Londoño-Berrio M, Castro C, Cañas A, Ortiz I, Osorio M. Advances in Tumor Organoids for the Evaluation of Drugs: A Bibliographic Review. Pharmaceutics 2022; 14:pharmaceutics14122709. [PMID: 36559203 PMCID: PMC9784359 DOI: 10.3390/pharmaceutics14122709] [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: 11/01/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/11/2022] Open
Abstract
Tumor organoids are defined as self-organized three-dimensional assemblies of heterogeneous cell types derived from patient samples that mimic the key histopathological, genetic, and phenotypic characteristics of the original tumor. This technology is proposed as an ideal candidate for the evaluation of possible therapies against cancer, presenting advantages over other models which are currently used. However, there are no reports in the literature that relate the techniques and material development of tumor organoids or that emphasize in the physicochemical and biological properties of materials that intent to biomimicry the tumor extracellular matrix. There is also little information regarding the tools to identify the correspondence of native tumors and tumoral organoids (tumoroids). Moreover, this paper relates the advantages of organoids compared to other models for drug evaluation. A growing interest in tumoral organoids has arisen from 2009 to the present, aimed at standardizing the process of obtaining organoids, which more accurately resemble patient-derived tumor tissue. Likewise, it was found that the characteristics to consider for the development of organoids, and therapeutic responses of them, are cell morphology, physiology, the interaction between cells, the composition of the cellular matrix, and the genetic, phenotypic, and epigenetic characteristics. Currently, organoids have been used for the evaluation of drugs for brain, lung, and colon tumors, among others. In the future, tumor organoids will become closer to being considered a better model for studying cancer in clinical practice, as they can accurately mimic the characteristics of tumors, in turn ensuring that the therapeutic response aligns with the clinical response of patients.
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Affiliation(s)
- Maritza Londoño-Berrio
- Systems Biology Research Group, Pontifical Bolivarian University (Universidad Pontificia Bolivariana), Carrera 78B No. 72a-109, Medellin 050034, Colombia
| | - Cristina Castro
- New Materials Research Group, School of Engineering, Pontifical Bolivarian University, Circular 1 No. 70-01, Medellin 050031, Colombia
| | - Ana Cañas
- Corporation for Biological Research, Medical, and Experimental Research Group, Carrera 72A # 78b-141, Medellin 050034, Colombia
| | - Isabel Ortiz
- Systems Biology Research Group, Pontifical Bolivarian University (Universidad Pontificia Bolivariana), Carrera 78B No. 72a-109, Medellin 050034, Colombia
| | - Marlon Osorio
- Systems Biology Research Group, Pontifical Bolivarian University (Universidad Pontificia Bolivariana), Carrera 78B No. 72a-109, Medellin 050034, Colombia
- New Materials Research Group, School of Engineering, Pontifical Bolivarian University, Circular 1 No. 70-01, Medellin 050031, Colombia
- Correspondence:
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Günther C, Winner B, Neurath MF, Stappenbeck TS. Organoids in gastrointestinal diseases: from experimental models to clinical translation. Gut 2022; 71:1892-1908. [PMID: 35636923 PMCID: PMC9380493 DOI: 10.1136/gutjnl-2021-326560] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/13/2022] [Indexed: 12/12/2022]
Abstract
We are entering an era of medicine where increasingly sophisticated data will be obtained from patients to determine proper diagnosis, predict outcomes and direct therapies. We predict that the most valuable data will be produced by systems that are highly dynamic in both time and space. Three-dimensional (3D) organoids are poised to be such a highly valuable system for a variety of gastrointestinal (GI) diseases. In the lab, organoids have emerged as powerful systems to model molecular and cellular processes orchestrating natural and pathophysiological human tissue formation in remarkable detail. Preclinical studies have impressively demonstrated that these organs-in-a-dish can be used to model immunological, neoplastic, metabolic or infectious GI disorders by taking advantage of patient-derived material. Technological breakthroughs now allow to study cellular communication and molecular mechanisms of interorgan cross-talk in health and disease including communication along for example, the gut-brain axis or gut-liver axis. Despite considerable success in culturing classical 3D organoids from various parts of the GI tract, some challenges remain to develop these systems to best help patients. Novel platforms such as organ-on-a-chip, engineered biomimetic systems including engineered organoids, micromanufacturing, bioprinting and enhanced rigour and reproducibility will open improved avenues for tissue engineering, as well as regenerative and personalised medicine. This review will highlight some of the established methods and also some exciting novel perspectives on organoids in the fields of gastroenterology. At present, this field is poised to move forward and impact many currently intractable GI diseases in the form of novel diagnostics and therapeutics.
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Affiliation(s)
- Claudia Günther
- Department of Medicine 1, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Beate Winner
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Stem Cell Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Center of Rare Diseases Erlangen (ZSEER), University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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7
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Differential gene expression in iPSC-derived human intestinal epithelial cell layers following exposure to two concentrations of butyrate, propionate and acetate. Sci Rep 2022; 12:13988. [PMID: 35977967 PMCID: PMC9385623 DOI: 10.1038/s41598-022-17296-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/22/2022] [Indexed: 11/08/2022] Open
Abstract
Intestinal epithelial cells and the intestinal microbiota are in a mutualistic relationship that is dependent on communication. This communication is multifaceted, but one aspect is communication through compounds produced by the microbiota such as the short-chain fatty acids (SCFAs) butyrate, propionate and acetate. Studying the effects of SCFAs and especially butyrate in intestinal epithelial cell lines like Caco-2 cells has been proven problematic. In contrast to the in vivo intestinal epithelium, Caco-2 cells do not use butyrate as an energy source, leading to a build-up of butyrate. Therefore, we used human induced pluripotent stem cell derived intestinal epithelial cells, grown as a cell layer, to study the effects of butyrate, propionate and acetate on whole genome gene expression in the cells. For this, cells were exposed to concentrations of 1 and 10 mM of the individual short-chain fatty acids for 24 h. Unique gene expression profiles were observed for each of the SCFAs in a concentration-dependent manner. Evaluation on both an individual gene level and pathway level showed that butyrate induced the biggest effects followed by propionate and then acetate. Several known effects of SCFAs on intestinal cells were confirmed, such as effects on metabolism and immune responses. The changes in metabolic pathways in the intestinal epithelial cell layers in this study demonstrate that there is a switch in energy homeostasis, this is likely associated with the use of SCFAs as an energy source by the induced pluripotent stem cell derived intestinal epithelial cells similar to in vivo intestinal tissues where butyrate is an important energy source.
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8
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Nolan LS, Baldridge MT. Advances in understanding interferon-mediated immune responses to enteric viruses in intestinal organoids. Front Immunol 2022; 13:943334. [PMID: 35935957 PMCID: PMC9354881 DOI: 10.3389/fimmu.2022.943334] [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: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Interferons (IFN) are antiviral cytokines with critical roles in regulating pathogens at epithelial barriers, but their capacity to restrict human enteric viruses has been incompletely characterized in part due to challenges in cultivating some viruses in vitro, particularly human norovirus. Accordingly, advancements in the development of antiviral therapies and vaccine strategies for enteric viral infections have been similarly constrained. Currently emerging is the use of human intestinal enteroids (HIEs) to investigate mechanisms of human enteric viral pathogenesis. HIEs provide a unique opportunity to investigate host-virus interactions using an in vitro system that recapitulates the cellular complexity of the in vivo gastrointestinal epithelium. This approach permits the exploration of intestinal epithelial cell interactions with enteric viruses as well as the innate immune responses mediated by IFNs and IFN-stimulated genes. Here, we describe recent findings related to the production, signaling, and function of IFNs in the response to enteric viral infections, which will ultimately help to reveal important aspects of pathogenesis and facilitate the future development of therapeutics and vaccines.
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Affiliation(s)
- Lila S. Nolan
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis Children’s Hospital, St. Louis, MO, United States
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Megan T. Baldridge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, United States
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
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9
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Kim MB, Hwangbo S, Jang S, Jo YK. Bioengineered Co-culture of organoids to recapitulate host-microbe interactions. Mater Today Bio 2022; 16:100345. [PMID: 35847376 PMCID: PMC9283667 DOI: 10.1016/j.mtbio.2022.100345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 11/05/2022] Open
Abstract
The recent spike in the instances of complex physiological host-microbe interactions has raised the demand for developing in vitro models that recapitulate the microbial microenvironment in the human body. Organoids are steadily emerging as an in vitro culture system that closely mimics the structural, functional, and genetic features of complex human organs, particularly for better understanding host-microbe interactions. Recent advances in organoid culture technology have become new avenues for assessing the pathogenesis of symbiotic interactions, pathogen-induced infectious diseases, and various other diseases. The co-cultures of organoids with microbes have shown great promise in simulating host-microbe interactions with a high level of complexity for further advancement in related fields. In this review, we provide an overview of bioengineering approaches for microbe-co-cultured organoids. Latest developments in the applications of microbe-co-cultured organoids to study human physiology and pathophysiology are also highlighted. Further, an outlook on future research on bioengineered organoid co-cultures for various applications is presented.
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Pearce SC, Weber GJ, Doherty LA, Soares JW. Human iPSC colon organoid function is improved by exposure to fecal fermentates. FASEB Bioadv 2022; 4:468-484. [PMID: 35812075 PMCID: PMC9254220 DOI: 10.1096/fba.2021-00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/01/2022] [Accepted: 03/18/2022] [Indexed: 11/11/2022] Open
Abstract
The host-microbe interaction is critical for intestinal homeostasis. By-products from microbial metabolism of unabsorbed dietary components have been studied increasingly as potential contributors to health and disease. In vitro fermentation systems provide a way to simulate microbial activity and by-product production of the colon using human fecal samples. Objectives of the study were to determine how clarified supernatants from two different fermentation conditions affect markers of cell proliferation, differentiation, barrier function, and immune function in a human-induced pluripotent (iPSC) colon organoid model. SCFA and BCFA's of the supernatants were analyzed and were similar to known in vivo concentrations. Molecular results showed 25% of the clarified supernatant from batch fermentation led to a more physiological intestinal phenotype including increased markers of differentiation, including alkaline phosphatase, chromogranin A, SCFA transport monocarboxylate transporter-1, (6.2-fold, 2.1-fold, and 1.8-fold, respectively; p < 0.05). Mucin production (mucin-2, mucin-4) was increased in cells treated with 25% supernatant, as observed by confocal microscopy. In addition, increased tight junction expression (claudin-3) was noted by immunofluorescence in 25% supernatant- treated cells. A dose-response increase in barrier function was observed over the 72-h time course, with a twofold increase in transepithelial electrical resistance (TER) in the 25% group compared to the control group (p < 0.05). To further investigate host effects, clarified supernatants from a continuous multistage fermentation representing the ascending (AC), transverse (TC), and descending (DC) colonic domains were utilized and some regional differences were observed including increased markers of inflammation (IL-1β, 6.15 pg/ml; IL-6, 27.58 pg/ml; TNFα, 4.49 pg/ml; p < 0.05) in DC-treated samples only. Overall, clarified supernatants represent a valuable model to examine effects of microbial by-products on host intestinal development and function and future efforts will be designed to further understand microbial communities and metabolites, along with additional host response measures.
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Affiliation(s)
- Sarah C. Pearce
- Soldier Sustainment Directorate, Combat Capabilities Development Command Soldier CenterNatickMassachusettsUSA
- USDA‐ARS National Laboratory for Agriculture and the EnvironmentAmesIowaUSA
| | - Gregory J. Weber
- Soldier Sustainment Directorate, Combat Capabilities Development Command Soldier CenterNatickMassachusettsUSA
| | - Laurel A. Doherty
- Soldier Effectiveness Directorate, Combat Capabilities Development Command Soldier CenterNatickMassachusettsUSA
| | - Jason W. Soares
- Soldier Effectiveness Directorate, Combat Capabilities Development Command Soldier CenterNatickMassachusettsUSA
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Grzymajlo K. The Game for Three: Salmonella–Host–Microbiota Interaction Models. Front Microbiol 2022; 13:854112. [PMID: 35516427 PMCID: PMC9062650 DOI: 10.3389/fmicb.2022.854112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
Colonization of the gastrointestinal (GI) tract by enteric pathogens occurs in a context strongly determined by host-specific gut microbiota, which can significantly affect the outcome of infection. The complex gameplay between the trillions of microbes that inhabit the GI tract, the host, and the infecting pathogen defines a specific triangle of interaction; therefore, a complete model of infection should consider all of these elements. Many different infection models have been developed to explain the complexity of these interactions. This review sheds light on current knowledge, along with the strengths and limitations of in vitro and in vivo models utilized in the study of Salmonella–host–microbiome interactions. These models range from the simplest experiment simulating environmental conditions using dedicated growth media through in vitro interaction with cell lines and 3-D organoid structure, and sophisticated “gut on a chip” systems, ending in various animal models. Finally, the challenges facing this field of research and the important future directions are outlined.
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Zhou C, Zhang Y, Bassey A, Huang J, Zou Y, Ye K. Expansion of Intestinal Secretory Cell Population Induced by Listeria monocytogenes Infection: Accompanied With the Inhibition of NOTCH Pathway. Front Cell Infect Microbiol 2022; 12:793335. [PMID: 35402308 PMCID: PMC8990097 DOI: 10.3389/fcimb.2022.793335] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/04/2022] [Indexed: 01/17/2023] Open
Abstract
Listeria monocytogenes, as a model organism, is a causative agent of enteric pathogen that causes systemic infection. However, the interaction of L. monocytogenes and small intestinal epithelium has not been fully elucidated yet. In this study, mice and intestinal organoids were chosen as the models to investigate the influence of L. monocytogenes infection on the intestinal secretory cells and its differentiation-related pathways. Results confirmed the phenomenon of intestinal damage that L. monocytogenes infection could lead to villi damage in mice, which was accompanied by the increase of TNF-α production in jejunum as well as lipopolysaccharide (LPS) secretion in serum. Moreover, it was demonstrated that L. monocytogenes infection increased the number of goblet and Paneth cells in mice and intestinal organoids and upregulated the expression of Muc2 and Lyz. Furthermore, L. monocytogenes decreased the relative expression of Notch pathway-related genes (Jag1, Dll4, Notch1, and Hes1) while upregulating the relative expression of Math1 gene in mice and intestinal organoids. This indicated that L. monocytogenes infection caused the inhibition of Notch pathway, which may be the reason for the increased number of goblet and Paneth cells in the intestine. Collectively, these results are expected to provide more information on the mechanism of L. monocytogenes infection in the intestine.
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Hegab R, Van Volkenburg T, Ohiri K, Sebeck N, Bessling S, Theodore M, Rossick K, Pellicore M, Benkoski J, Patrone J. Design of experiments approach to developing a robust ink for bioprinting. Biomed Phys Eng Express 2022; 8. [PMID: 35290975 DOI: 10.1088/2057-1976/ac5de1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/15/2022] [Indexed: 11/11/2022]
Abstract
Despite advancements in tissue engineering, the methods used to generate three-dimensional (3D)in vitromodels for rapid screening and characterization studies remain time and labor intensive. Bioprinting offers an opportunity to offset these limitations by providing a scalable, high-throughput method with precise control over biomaterial scaffold and cellular deposition. However, the process of formulating bioinks can be complex in terms of balancing the mechanical integrity of a bioscaffold and viability of cells. One key factor, especially in alginate-based bioinks, is the rate of bioscaffold dissolution. It must allow cells to replace the bioscaffold with extracellular matrix (ECM), yet remain durable during extended tissue culture. This study uses a Design of Experiments (DoE) approach to understand the dependencies of multiple variables involved in the formulation and processing of an alginate-based bioink. The focus of the DoE was to understand the effects of hydrogel composition on bioink durability while maintaining cell viability. Three ingredients were varied in all: alginate, nanocellulose, and fibrinogen. Their effects on the bioink were then measured with respect to extrudability, strength, and stiffness as determined by dynamic mechanical analysis (DMA). The DoE demonstrated that mechanical integrity increased with increasing alginate concentration. In contrast, fibrinogen and nanofibril concentration had no statistically significant effect. The optimized ink containing fibroblasts was printable using multiple nozzle sizes while also supporting fibroblast cell viability. DMA characterization further showed that the composition of the cell culture medium did not modulate the degradation rate of the hydrogel. Ultimately, the study outlines a methodology for formulating a bioink that will result in robust bioscaffolds forin vitromodel development.
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Affiliation(s)
- Rachel Hegab
- The Johns Hopkins Applied Physics Laboratory, Laurel, MD, United States of America
| | - Tessa Van Volkenburg
- The Johns Hopkins Applied Physics Laboratory, Laurel, MD, United States of America
| | - Korine Ohiri
- The Johns Hopkins Applied Physics Laboratory, Laurel, MD, United States of America
| | - Natalie Sebeck
- The Johns Hopkins Applied Physics Laboratory, Laurel, MD, United States of America
| | - Seneca Bessling
- The Johns Hopkins Applied Physics Laboratory, Laurel, MD, United States of America
| | - Mellisa Theodore
- The Johns Hopkins Applied Physics Laboratory, Laurel, MD, United States of America
| | - Katelyn Rossick
- The Johns Hopkins Applied Physics Laboratory, Laurel, MD, United States of America
| | - Matthew Pellicore
- The Johns Hopkins Applied Physics Laboratory, Laurel, MD, United States of America
| | - Jason Benkoski
- The Johns Hopkins Applied Physics Laboratory, Laurel, MD, United States of America
| | - Julia Patrone
- The Johns Hopkins Applied Physics Laboratory, Laurel, MD, United States of America
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14
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Warschkau D, Delgado-Betancourt E, Holthaus D, Müller A, Kliem G, Krug SM, Schulzke JD, Aebischer T, Klotz C, Seeber F. From 3D to 2D: Harmonization of Protocols for Two-dimensional Cultures on Cell Culture Inserts of Intestinal Organoids from Various Species. Bio Protoc 2022; 12:e4295. [PMID: 35127985 PMCID: PMC8799680 DOI: 10.21769/bioprotoc.4295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 09/25/2023] Open
Abstract
In the expanding field of intestinal organoid research, various protocols for three- and two-dimensional organoid-derived cell cultures exist. Two-dimensional organoid-derived monolayers are used to overcome some limitations of three-dimensional organoid cultures. They are increasingly used also in infection research, to study physiological processes and tissue barrier functions, where easy experimental access of pathogens to the luminal and/or basolateral cell surface is required. This has resulted in an increasing number of publications reporting different protocols and media compositions for organoid manipulation, precluding direct comparisons of research outcomes in some cases. With this in mind, here we describe a protocol aimed at the harmonization of seeding conditions for three-dimensional intestinal organoids of four commonly used research species onto cell culture inserts, to create organoid-derived monolayers that form electrophysiologically tight epithelial barriers. We give an in-depth description of media compositions and culture conditions for creating these monolayers, enabling also the less experienced researchers to obtain reproducible results within a short period of time, and which should simplify the comparison of future studies between labs, but also encourage others to consider these systems as alternative cell culture models in their research. Graphic abstract: Schematic workflow of organoid-derived monolayer generation from intestinal spheroid cultures. ECM, extracellular matrix; ODM, organoid-derived monolayer.
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Affiliation(s)
- David Warschkau
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | | | - David Holthaus
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Antonia Müller
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Gudrun Kliem
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Susanne M. Krug
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Joerg-Dieter Schulzke
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Toni Aebischer
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Christian Klotz
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Frank Seeber
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
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15
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Glowacki RWP, Engelhart MJ, Ahern PP. Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology. Front Microbiol 2021; 12:735562. [PMID: 34646255 PMCID: PMC8503645 DOI: 10.3389/fmicb.2021.735562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/24/2021] [Indexed: 12/26/2022] Open
Abstract
The profound impact of the gut microbiome on host health has led to a revolution in biomedical research, motivating researchers from disparate fields to define the specific molecular mechanisms that mediate host-beneficial effects. The advent of genomic technologies allied to the use of model microbiomes in gnotobiotic mouse models has transformed our understanding of intestinal microbial ecology and the impact of the microbiome on the host. However, despite incredible advances, our understanding of the host-microbiome dialogue that shapes host physiology is still in its infancy. Progress has been limited by challenges associated with developing model systems that are both tractable enough to provide key mechanistic insights while also reflecting the enormous complexity of the gut ecosystem. Simplified model microbiomes have facilitated detailed interrogation of transcriptional and metabolic functions of the microbiome but do not recapitulate the interactions seen in complex communities. Conversely, intact complex communities from mice or humans provide a more physiologically relevant community type, but can limit our ability to uncover high-resolution insights into microbiome function. Moreover, complex microbiomes from lab-derived mice or humans often do not readily imprint human-like phenotypes. Therefore, improved model microbiomes that are highly defined and tractable, but that more accurately recapitulate human microbiome-induced phenotypic variation are required to improve understanding of fundamental processes governing host-microbiome mutualism. This improved understanding will enhance the translational relevance of studies that address how the microbiome promotes host health and influences disease states. Microbial exposures in wild mice, both symbiotic and infectious in nature, have recently been established to more readily recapitulate human-like phenotypes. The development of synthetic model communities from such "wild mice" therefore represents an attractive strategy to overcome the limitations of current approaches. Advances in microbial culturing approaches that allow for the generation of large and diverse libraries of isolates, coupled to ever more affordable large-scale genomic sequencing, mean that we are now ideally positioned to develop such systems. Furthermore, the development of sophisticated in vitro systems is allowing for detailed insights into host-microbiome interactions to be obtained. Here we discuss the need to leverage such approaches and highlight key challenges that remain to be addressed.
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Affiliation(s)
- Robert W. P. Glowacki
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Morgan J. Engelhart
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Philip P. Ahern
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, United States
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16
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Goodman C, Lyon KN, Scotto A, Smith C, Sebrell TA, Gentry AB, Bala G, Stoner GD, Bimczok D. A High-Throughput Metabolic Microarray Assay Reveals Antibacterial Effects of Black and Red Raspberries and Blackberries against Helicobacter pylori Infection. Antibiotics (Basel) 2021; 10:845. [PMID: 34356766 PMCID: PMC8300682 DOI: 10.3390/antibiotics10070845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/17/2022] Open
Abstract
Helicobacter pylori infection is commonly treated with a combination of antibiotics and proton pump inhibitors. However, since H. pylori is becoming increasingly resistant to standard antibiotic regimens, novel treatment strategies are needed. Previous studies have demonstrated that black and red berries may have antibacterial properties. Therefore, we analyzed the antibacterial effects of black and red raspberries and blackberries on H. pylori. Freeze-dried powders and organic extracts from black and red raspberries and blackberries were prepared, and high-performance liquid chromatography was used to measure the concentrations of anthocyanins, which are considered the major active ingredients. To monitor antibiotic effects of the berry preparations on H. pylori, a high-throughput metabolic growth assay based on the Biolog system was developed and validated with the antibiotic metronidazole. Biocompatibility was analyzed using human gastric organoids. All berry preparations tested had significant bactericidal effects in vitro, with MIC90 values ranging from 0.49 to 4.17%. Antimicrobial activity was higher for extracts than powders and appeared to be independent of the anthocyanin concentration. Importantly, human gastric epithelial cell viability was not negatively impacted by black raspberry extract applied at the concentration required for complete bacterial growth inhibition. Our data suggest that black and red raspberry and blackberry extracts may have potential applications in the treatment and prevention of H. pylori infection but differ widely in their MICs. Moreover, we demonstrate that the Biolog metabolic assay is suitable for high-throughput antimicrobial susceptibility screening of H. pylori.
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Affiliation(s)
- Candace Goodman
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA; (C.G.); (G.B.)
| | - Katrina N. Lyon
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA; (K.N.L.); (A.S.); (C.S.); (T.A.S.); (G.D.S.)
| | - Aitana Scotto
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA; (K.N.L.); (A.S.); (C.S.); (T.A.S.); (G.D.S.)
| | - Cyra Smith
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA; (K.N.L.); (A.S.); (C.S.); (T.A.S.); (G.D.S.)
| | - Thomas A. Sebrell
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA; (K.N.L.); (A.S.); (C.S.); (T.A.S.); (G.D.S.)
| | - Andrew B. Gentry
- Bozeman Health GI Clinic, Bozeman Health Deaconess Hospital, Bozeman, MT 59715, USA;
| | - Ganesh Bala
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA; (C.G.); (G.B.)
| | - Gary D. Stoner
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA; (K.N.L.); (A.S.); (C.S.); (T.A.S.); (G.D.S.)
| | - Diane Bimczok
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA; (K.N.L.); (A.S.); (C.S.); (T.A.S.); (G.D.S.)
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17
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Zubareva EV, Nadezhdin SV, Nadezhdina NA, Belyaeva VS, Burda YE, Avtina TV, Gudyrev OS, Kolesnik IM, Kulikova SY, Mishenin MO. 3D organotypic cell structures for drug development and Microorganism-Host interaction research. RESEARCH RESULTS IN PHARMACOLOGY 2021. [DOI: 10.3897/rrpharmacology.7.62118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Introduction: The article describes a new method of tissue engineering, which is based on the use of three-dimensional multicellular constructs consisting of stem cells that mimic the native tissue in vivo – organoids.
3D cell cultures: The currently existing model systems of three-dimensional cultures are described.
Characteristics of organoids and strategies for their culturing: The main approaches to the fabrication of 3D cell constructs using pluripotent (embryonic and induced) stem cells or adult stem cells are described.
Brain organoids (Cerebral organoids): Organoids of the brain, which are used to study the development of the human brain, are characterized, with the description of biology of generating region-specific cerebral organoids.
Lung organoids: Approaches to the generation of lung organoids are described, by means of pluripotent stem cells and lung tissue cell lines.
Liver organoids: The features of differentiation of stem cells into hepatocyte-like cells and the creation of 3D hepatic organoids are characterized.
Intestinal organoids: The formation of small intestine organoids from stem cells is described.
Osteochondral organoids: Fabrication of osteochondral organoids is characterised.
Use of organoids as test systems for drugs screening: The information on drug screening using organoids is provided.
Using organoids to model infectious diseases and study adaptive responses of microorganisms when interacting with the host: The use of organoids for modeling infectious diseases and studying the adaptive responses of microorganisms when interacting with the host organism is described.
Conclusion: The creation of three-dimensional cell structures that reproduce the structural and functional characteristics of tissue in vivo, makes it possible to study the biology of the body’s development, the features of intercellular interactions, screening drugs and co-cultivating with viruses, bacteria and parasites.
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18
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Younes M, Aggett P, Aguilar F, Crebelli R, Dusemund B, Filipič M, Frutos MJ, Galtier P, Gundert‐Remy U, Kuhnle GG, Lambré C, Leblanc J, Lillegaard IT, Moldeus P, Mortensen A, Oskarsson A, Stankovic I, Waalkens‐Berendsen I, Woutersen RA, Wright M, Di Domenico A, Fairweather‐Tait S, McArdle HJ, Smeraldi C, Gott D. Guidance on safety evaluation of sources of nutrients and bioavailability of nutrient from the sources (Revision 1). EFSA J 2021; 19:e06552. [PMID: 33815621 PMCID: PMC8002907 DOI: 10.2903/j.efsa.2021.6552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
[Table: see text] This guidance describes the scientific data required to allow an evaluation of the safety of new substances that are proposed for use as sources of nutrients in food supplements, foods for the general population or foods for specific groups and an assessment of the bioavailability of the nutrient from the proposed source. This guidance describes the scientific data required to allow an evaluation of the safety of the source within the established framework for risk assessment of food additives and novel food ingredients and the bioavailability of the nutrient from this source. This document is arranged in five main sections: one on technical data aimed at characterising the proposed source and at identifying potential hazards resulting from its manufacture and stability in food; one on existing authorisations and evaluation, providing an overview of previous assessments on the proposed source and their conclusions; one on proposed uses and exposure assessment section, allowing an estimate of the dietary exposure to the source and the nutrient based on the proposed uses and use levels; one on toxicological data, describing approaches which can be used to identify (in conjunction with data on manufacture and composition) and to characterise hazards of the source and any relevant breakdown products; the final section on bioavailability focuses on determining the extent to which the nutrient from the proposed source is available for use by the body in comparison with one or more forms of the same nutrient that are already permitted for use on the positive lists. This guidance was adopted by the Panel on Food Additives and Nutrient Sources added to Food (ANS Panel) on 16 May 2018. Upon request from EFSA, the present guidance has been revised to inform applicants of new provisions set out in Regulation (EC) No 178/2002, as amended by Regulation (EU) 2019/1381 on the transparency and sustainability of the EU risk assessment in the food chain.
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19
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Holthaus D, Delgado-Betancourt E, Aebischer T, Seeber F, Klotz C. Harmonization of Protocols for Multi-Species Organoid Platforms to Study the Intestinal Biology of Toxoplasma gondii and Other Protozoan Infections. Front Cell Infect Microbiol 2021; 10:610368. [PMID: 33692963 PMCID: PMC7937733 DOI: 10.3389/fcimb.2020.610368] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/30/2020] [Indexed: 12/20/2022] Open
Abstract
The small intestinal epithelium is the primary route of infection for many protozoan parasites. Understanding the mechanisms of infection, however, has been hindered due to the lack of appropriate models that recapitulate the complexity of the intestinal epithelium. Here, we describe an in vitro platform using stem cell-derived intestinal organoids established for four species that are important hosts of Apicomplexa and other protozoa in a zoonotic context: human, mouse, pig and chicken. The focus was set to create organoid-derived monolayers (ODMs) using the transwell system amenable for infection studies, and we provide straightforward guidelines for their generation and differentiation from organ-derived intestinal crypts. To this end, we reduced medium variations to an absolute minimum, allowing generation and differentiation of three-dimensional organoids for all four species and the subsequent generation of ODMs. Quantitative RT-PCR, immunolabeling with antibodies against marker proteins as well as transepithelial-electrical resistance (TEER) measurements were used to characterize ODM's integrity and functional state. These experiments show an overall uniform generation of monolayers suitable for Toxoplasma gondii infection, although robustness in terms of generation of stable TEER levels and cell differentiation status varies from species to species. Murine duodenal ODMs were then infected with T. gondii and/or Giardia duodenalis, two parasites that temporarily co-inhabit the intestinal niche but have not been studied previously in cellular co-infection models. T. gondii alone did not alter TEER values, integrity and transcriptional abundance of tight junction components. In contrast, in G. duodenalis-infected ODMs all these parameters were altered and T. gondii had no apparent influence on the G. duodenalis-triggered phenotype. In conclusion, we provide robust protocols for the generation, differentiation and characterization of intestinal organoids and ODMs from four species. We show their applications for comparative studies on parasite-host interactions during the early phase of a T. gondii infection but also its use for co-infections with other relevant intestinal protozoans.
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Affiliation(s)
| | | | | | | | - Christian Klotz
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
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20
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Advances in modelling the human microbiome-gut-brain axis in vitro. Biochem Soc Trans 2021; 49:187-201. [PMID: 33544117 PMCID: PMC7924999 DOI: 10.1042/bst20200338] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/23/2020] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
The human gut microbiome has emerged as a key player in the bidirectional communication of the gut–brain axis, affecting various aspects of homeostasis and pathophysiology. Until recently, the majority of studies that seek to explore the mechanisms underlying the microbiome–gut–brain axis cross-talk, relied almost exclusively on animal models, and particularly gnotobiotic mice. Despite the great progress made with these models, various limitations, including ethical considerations and interspecies differences that limit the translatability of data to human systems, pushed researchers to seek for alternatives. Over the past decades, the field of in vitro modelling of tissues has experienced tremendous growth, thanks to advances in 3D cell biology, materials, science and bioengineering, pushing further the borders of our ability to more faithfully emulate the in vivo situation. The discovery of stem cells has offered a new source of cells, while their use in generating gastrointestinal and brain organoids, among other tissues, has enabled the development of novel 3D tissues that better mimic the native tissue structure and function, compared with traditional assays. In parallel, organs-on-chips technology and bioengineered tissues have emerged as highly promising alternatives to animal models for a wide range of applications. Here, we discuss how recent advances and trends in this area can be applied in host–microbe and host–pathogen interaction studies. In addition, we highlight paradigm shifts in engineering more robust human microbiome-gut-brain axis models and their potential to expand our understanding of this complex system and hence explore novel, microbiome-based therapeutic approaches.
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21
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Donowitz M, Turner JR, Verkman AS, Zachos NC. Current and potential future applications of human stem cell models in drug development. J Clin Invest 2021; 130:3342-3344. [PMID: 32452833 PMCID: PMC7324189 DOI: 10.1172/jci138645] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Mark Donowitz
- Division of Gastroenterology, Department of Medicine, and.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jerrold R Turner
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Alan S Verkman
- Departments of Medicine and Physiology, UCSF, San Francisco, California, USA
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22
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Creff J, Malaquin L, Besson A. In vitro models of intestinal epithelium: Toward bioengineered systems. J Tissue Eng 2021; 12:2041731420985202. [PMID: 34104387 PMCID: PMC8164551 DOI: 10.1177/2041731420985202] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/12/2020] [Indexed: 12/17/2022] Open
Abstract
The intestinal epithelium, the fastest renewing tissue in human, is a complex
tissue hosting multiple cell types with a dynamic and multiparametric
microenvironment, making it particularly challenging to recreate in
vitro. Convergence of recent advances in cellular biology and
microfabrication technologies have led to the development of various
bioengineered systems to model and study the intestinal epithelium. Theses
microfabricated in vitro models may constitute an alternative
to current approaches for studying the fundamental mechanisms governing
intestinal homeostasis and pathologies, as well as for in vitro
drug screening and testing. Herein, we review the recent advances in
bioengineered in vitro intestinal models.
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Affiliation(s)
- Justine Creff
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse Cedex, France.,LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | | | - Arnaud Besson
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse Cedex, France
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23
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Workman MJ, Troisi E, Targan SR, Svendsen CN, Barrett RJ. Modeling Intestinal Epithelial Response to Interferon-γ in Induced Pluripotent Stem Cell-Derived Human Intestinal Organoids. Int J Mol Sci 2020; 22:E288. [PMID: 33396621 PMCID: PMC7794932 DOI: 10.3390/ijms22010288] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 12/16/2022] Open
Abstract
Human intestinal organoids (HIOs) are increasingly being used to model intestinal responses to various stimuli, yet few studies have confirmed the fidelity of this modeling system. Given that the interferon-gamma (IFN-γ) response has been well characterized in various other cell types, our goal was to characterize the response to IFN-γ in HIOs derived from induced pluripotent stem cells (iPSCs). To achieve this, iPSCs were directed to form HIOs and subsequently treated with IFN-γ. Our results demonstrate that IFN-γ phosphorylates STAT1 but has little effect on the expression or localization of tight and adherens junction proteins in HIOs. However, transcriptomic profiling by microarray revealed numerous upregulated genes such as IDO1, GBP1, CXCL9, CXCL10 and CXCL11, which have previously been shown to be upregulated in other cell types in response to IFN-γ. Notably, "Response to Interferon Gamma" was determined to be one of the most significantly upregulated gene sets in IFN-γ-treated HIOs using gene set enrichment analysis. Interestingly, similar genes and pathways were upregulated in publicly available datasets contrasting the gene expression of in vivo biopsy tissue from patients with IBD against healthy controls. These data confirm that the iPSC-derived HIO modeling system represents an appropriate platform to evaluate the effects of various stimuli and specific environmental factors responsible for the alterations in the intestinal epithelium seen in various gastrointestinal conditions such as inflammatory bowel disease.
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Affiliation(s)
- Michael J. Workman
- Cedars-Sinai Medical Center, Board of Governors Regenerative Medicine Institute, Los Angeles, CA 90048, USA; (M.J.W.); (E.T.); (C.N.S.)
| | - Elissa Troisi
- Cedars-Sinai Medical Center, Board of Governors Regenerative Medicine Institute, Los Angeles, CA 90048, USA; (M.J.W.); (E.T.); (C.N.S.)
| | - Stephan R. Targan
- Cedars-Sinai Medical Center, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA 90048, USA;
| | - Clive N. Svendsen
- Cedars-Sinai Medical Center, Board of Governors Regenerative Medicine Institute, Los Angeles, CA 90048, USA; (M.J.W.); (E.T.); (C.N.S.)
- Cedars-Sinai Medical Center, Department of Biomedical Sciences, Los Angeles, CA 90048, USA
| | - Robert J. Barrett
- Cedars-Sinai Medical Center, Board of Governors Regenerative Medicine Institute, Los Angeles, CA 90048, USA; (M.J.W.); (E.T.); (C.N.S.)
- Cedars-Sinai Medical Center, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA 90048, USA;
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24
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Barron MR, Cieza RJ, Hill DR, Huang S, Yadagiri VK, Spence JR, Young VB. The Lumen of Human Intestinal Organoids Poses Greater Stress to Bacteria Compared to the Germ-Free Mouse Intestine: Escherichia coli Deficient in RpoS as a Colonization Probe. mSphere 2020; 5:e00777-20. [PMID: 33177212 PMCID: PMC7657587 DOI: 10.1128/msphere.00777-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/23/2020] [Indexed: 02/07/2023] Open
Abstract
Pluripotent stem-cell-derived human intestinal organoids (HIOs) are three-dimensional, multicellular structures that model a naive intestinal epithelium in an in vitro system. Several published reports have investigated the use of HIOs to study host-microbe interactions. We recently demonstrated that microinjection of the nonpathogenic Escherichia coli strain ECOR2 into HIOs induced morphological and functional maturation of the HIO epithelium, including increased secretion of mucins and cationic antimicrobial peptides. In the current work, we use ECOR2 as a biological probe to further characterize the environment present in the HIO lumen. We generated an isogenic mutant in the general stress response sigma factor RpoS and employed this mutant to compare challenges faced by a bacterium during colonization of the HIO lumen relative to the germ-free mouse intestine. We demonstrate that the loss of RpoS significantly decreases the ability of ECOR2 to colonize HIOs, although it does not prevent colonization of germ-free mice. These results indicate that the HIO lumen is a more restrictive environment to E. coli than the germ-free mouse intestine, thus increasing our understanding of the HIO model system as it pertains to studying the establishment of intestinal host-microbe symbioses.IMPORTANCE Technological advancements have driven and will continue to drive the adoption of organotypic systems for investigating host-microbe interactions within the human intestinal ecosystem. Using E. coli deficient in the RpoS-mediated general stress response, we demonstrate that the type or severity of microbial stressors within the HIO lumen is more restrictive than those of the in vivo environment of the germ-free mouse gut. This study provides important insight into the nature of the HIO microenvironment from a microbiological standpoint.
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Affiliation(s)
- Madeline R Barron
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Roberto J Cieza
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - David R Hill
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Sha Huang
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Veda K Yadagiri
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
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25
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van IJzendoorn SCD, Derkinderen P. The Intestinal Barrier in Parkinson's Disease: Current State of Knowledge. JOURNAL OF PARKINSONS DISEASE 2020; 9:S323-S329. [PMID: 31561386 PMCID: PMC6839484 DOI: 10.3233/jpd-191707] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The intestinal barrier, which primarily consists of epithelial cells stitched together with connecting proteins called tight junctions, plays a critical role in health and disease. It is in close contact with the gut microbiota on its luminal side and with the enteric neurons on the tissue side. Both microbiota and the enteric nervous system are regulatory housekeepers of the intestinal barrier. Therefore, the recently observed enteric neuropathology along with gut dysbiosis in Parkinson's disease have prompted research on intestinal permeability in this neurodegenerative disorder. In this mini-review we attempt to concisely summarize the current knowledge on intestinal barrier in Parkinson's disease. We envision future direction research that should be pursued in order to demonstrate its possible role in disease development and progression.
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Affiliation(s)
- Sven C D van IJzendoorn
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pascal Derkinderen
- Inserm, U1235, Nantes, France.,University Nantes, Nantes, France.,Department of Neurology, CHU Nantes, Nantes, France
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Zhang M, Liu Y, Chen YG. Generation of 3D human gastrointestinal organoids: principle and applications. ACTA ACUST UNITED AC 2020; 9:6. [PMID: 32588198 PMCID: PMC7306834 DOI: 10.1186/s13619-020-00040-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The stomach and intestine are important organs for food digestion, nutrient absorption, immune protection and hormone production. Gastrointestinal diseases such as cancer and ulcer are big threats to human health. Appropriate disease models are in sore need for mechanistic understanding and drug discovery. Organoids are three-dimensional in vitro cultured structures derived from tissues and pluripotent stem cells with multiple types of cells and mimicking in vivo tissues in major aspects. They have a great potential in regenerative medicine and personalized medicine. Here, we review the major signaling pathways regulating gastrointestinal epithelial homeostasis, summarize different methods to generate human gastrointestinal organoids and highlight their applications in biological research and medical practice.
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Affiliation(s)
- Mengxian Zhang
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuan Liu
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ye-Guang Chen
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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27
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Lau HCH, Kranenburg O, Xiao H, Yu J. Organoid models of gastrointestinal cancers in basic and translational research. Nat Rev Gastroenterol Hepatol 2020; 17:203-222. [PMID: 32099092 DOI: 10.1038/s41575-019-0255-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/11/2019] [Indexed: 12/24/2022]
Abstract
Cancer is a major public health problem worldwide. Gastrointestinal cancers account for approximately one-third of the total global cancer incidence and mortality. Historically, the mechanisms of tumour initiation and progression in the gastrointestinal tract have been studied using cancer cell lines in vitro and animal models. Traditional cell culture methods are associated with a strong selection of aberrant genomic variants that no longer reflect the original tumours in terms of their (metastatic) behaviour or response to therapy. Organoid technology has emerged as a powerful alternative method for culturing gastrointestinal tumours and the corresponding normal tissues in a manner that preserves their genetic, phenotypic and behavioural traits. Importantly, accumulating evidence suggests that organoid cultures have great value in predicting the outcome of therapy in individual patients. Herein, we review the current literature on organoid models of the most common gastrointestinal cancers, including colorectal cancer, gastric cancer, oesophageal cancer, liver cancer and pancreatic cancer, and their value in modelling tumour initiation, metastatic progression and therapy response. We also explore the limitations of current organoid models and discuss how they could be improved to maximally benefit basic and translational research in the future, especially in the fields of drug discovery and personalized medicine.
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Affiliation(s)
- Harry Cheuk Hay Lau
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Onno Kranenburg
- UMC Utrecht Cancer Center, Utrecht Platform for Organoid Technology, Utrecht University, Utrecht, Netherlands
| | - Haipeng Xiao
- Department of Endocrinology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jun Yu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong.
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Tsuruta S, Uchida H, Akutsu H. Intestinal Organoids Generated from Human Pluripotent Stem Cells. JMA J 2020; 3:9-19. [PMID: 33324771 PMCID: PMC7733741 DOI: 10.31662/jmaj.2019-0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/23/2019] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal system is one of the most complex organ systems in the human body, and consists of numerous cell types originating from three germ layers. To understand intestinal development and homeostasis and elucidate the pathogenesis of intestinal disorders, including unidentified diseases, several in vitro models have been developed. Human pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), have remarkable developmental plasticity and possess the potential for a wide variety of applications. Three-dimensional organs, termed organoids and produced in vitro by PSCs, contain not only epithelium but also mesenchymal tissue and partially recapitulate intestinal functions. Such intestinal organoids have begun to be applied in disease models and drug development and have contributed to a detailed analysis of molecular interactions and findings in the synergistic development of biomedicine for human digestive organs. In this review, we describe gastrointestinal organoid technology derived from PSCs and consider its potential applications.
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Affiliation(s)
- Satoru Tsuruta
- Department of Gastroenterological Surgery, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
- Centre for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hajime Uchida
- Transplantation Centre, National Centre for Child Health and Development, Tokyo, Japan
| | - Hidenori Akutsu
- Centre for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
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Abstract
Recent advances in culturing of intestinal stem cells and pluripotent stem cells have led to the development of intestinal organoids. These are self-organizing 3D structures, which recapitulate the characteristics and physiological features of in vivo intestinal epithelium. Intestinal organoids have allowed the development of novel in vitro models to study various gastrointestinal diseases expanding our understanding of the pathophysiology of diseases and leading to the development of innovative therapies. This article aims to summarize the current usage of intestinal organoids as a model of gastrointestinal diseases and the potential applications of intestinal organoids in infants and children. Intestinal organoids allow the study of intestinal epithelium responses to stress factors. Mimicking intestinal injury such as necrotizing enterocolitis, intestinal organoids increases the expression of pro-inflammatory cytokine genes and shows disruption of tight junctions after they are injured by lipopolysaccharide and hypoxia. In cystic fibrosis, intestinal organoids derived from rectal biopsies have provided benefits in genetic studies and development of novel therapeutic gene modulation. Transplantation of intestinal organoids via enema has been shown to rescue damaged colonic epithelium in mice. In addition, tissue-engineered small intestine derived from intestinal organoids have been successfully established providing a potential novel treatment and a new hope for children with short bowel syndrome.
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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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Flatres C, Loffet É, Neunlist M, Mahé MM. Façonner l’intestin à partir des cellules souches pluripotentes humaines. Med Sci (Paris) 2019; 35:549-555. [DOI: 10.1051/medsci/2019096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
L’étude des maladies digestives est parfois limitée par l’accès aux tissus de patients et les modèles précliniques ne sont pas toujours fidèles aux pathologies observées chez l’homme. Dans ce contexte, le développement d’organoïdes intestinaux à partir de cellules souches pluripotentes humaines représente une avancée importante dans l’étude des processus physiologiques et des pathologies digestives. Dans cette revue, nous rappelons les étapes majeures du développement du tractus digestif chez l’homme et décrivons le rationnel de la différenciation dirigée des cellules souches pluripotentes humaines. Nous faisons également un état des lieux sur les différents types d’organoïdes intestinaux existants et leurs applications en recherche fondamentale et préclinique. Enfin, nous discutons des opportunités offertes par les organoïdes intestinaux humains dans un contexte de médecine de précision et de médecine réparatrice.
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32
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Ji YJ, Li H, Xie PF, Li ZH, Li HW, Yin YL, Blachier F, Kong XF. Stages of pregnancy and weaning influence the gut microbiota diversity and function in sows. J Appl Microbiol 2019; 127:867-879. [PMID: 31237071 PMCID: PMC6852164 DOI: 10.1111/jam.14344] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/07/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022]
Abstract
Aims The gut microbiota is believed to play important roles in the health of pregnant mammals, including their nutrient metabolism, immune programming and metabolic regulation. However, until recently, the shifts in gut microbiota composition and faecal and blood metabolic activity during different stages of pregnancy had not been investigated. Methods and Results We investigated the shifts in backfat thickness, plasma and faecal metabolites and gut microbiota on days 30, 60, 90 and 110 of pregnancy and on day 21 after parturition (weaning) in sows. The backfat thickness of sows did not significantly differ among the different stages of pregnancy. The plasma concentrations of lipid metabolites, including triacylglycerol (TG), total cholesterol, high‐density lipoprotein‐cholesterol, low‐density lipoprotein‐cholesterol and calcium were reduced (P < 0·05) during pregnancy. In addition, the concentration of these metabolites, except TG, reached their maximum at the time of weaning. We also found that Tenericutes, Fibrobacteres and Cyanobacteria varied significantly according to the stages of pregnancy in sows (P < 0·05). Most of the genera, such as Clostridiales, Desulfovibrio, Mogibacteriaceae and Prevotella, increased (P < 0·05) with the progression of pregnancy and decreased (P < 0·05) at weaning. The alpha diversity values (i.e., Shannon diversity and observed species) of sow gut microbiota increased (P < 0·05) from pregnancy to weaning. Pregnancy stages also significantly influenced (P < 0·05) the community structure (beta diversity) of gut microbiota. The progression of pregnancy was associated with changes in lipid metabolism and several carbohydrate‐degradation bacteria (i.e., Prevotella, Succinivibrio, Bacteroides and Parabacteroides). Conclusions Although causal links between the measured parameters remain hypothetical, these findings suggest that the increased diversity and concentration of beneficial gut microbes are associated with the metabolism of pregnant sows. Significance and Impact of the Study Manipulation of the sow gut microbiota composition may potentially influence metabolism and health during pregnancy.
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Affiliation(s)
- Y J Ji
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - H Li
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - P F Xie
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Z H Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - H W Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Y L Yin
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - F Blachier
- UMR PNCA, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
| | - X F Kong
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
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Clarke G, Sandhu KV, Griffin BT, Dinan TG, Cryan JF, Hyland NP. Gut Reactions: Breaking Down Xenobiotic–Microbiome Interactions. Pharmacol Rev 2019; 71:198-224. [DOI: 10.1124/pr.118.015768] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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34
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Intestinal organoids: A new paradigm for engineering intestinal epithelium in vitro. Biomaterials 2019; 194:195-214. [DOI: 10.1016/j.biomaterials.2018.12.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/22/2018] [Accepted: 12/08/2018] [Indexed: 12/11/2022]
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35
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Hung L, Obernolte H, Sewald K, Eiwegger T. Human ex vivo and in vitro disease models to study food allergy. Asia Pac Allergy 2019; 9:e4. [PMID: 30740352 PMCID: PMC6365658 DOI: 10.5415/apallergy.2019.9.e4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/11/2019] [Indexed: 12/25/2022] Open
Abstract
Food allergy is a growing global public health concern. As treatment strategies are currently limited to allergen avoidance and emergency interventions, there is an increasing demand for appropriate models of food allergy for the development of new therapeutics. Many models of food allergy rely heavily on the use of animals, and while useful, many are unable to accurately reflect the human system. In order to bridge the gap between in vivo animal models and clinical trials with human patients, human models of food allergy are of great importance. This review will summarize the commonly used human ex vivo and in vitro models of food allergy and highlight their advantages and limitations regarding how accurately they represent the human in vivo system. We will cover biopsy-based systems, precision cut organ slices, and coculture systems as well as organoids and organ-on-a-chip. The availability of appropriate experimental models will allow us to move forward in the field of food allergy research, to search for effective treatment options and to further explore the cause and progression of this disorder.
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Affiliation(s)
- Lisa Hung
- Department of Immunology, University of Toronto, Toronto, ON, Canada.,Translational Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Helena Obernolte
- Department of Preclinical Pharmacology and In-Vitro Toxicology, Fraunhofer ITEM, Hannover, Germany
| | - Katherina Sewald
- Department of Preclinical Pharmacology and In-Vitro Toxicology, Fraunhofer ITEM, Hannover, Germany
| | - Thomas Eiwegger
- Department of Immunology, University of Toronto, Toronto, ON, Canada.,Translational Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Clinical Immunology and Allergy, Food Allergy and Anaphylaxis Program, The Hospital for Sick Children, Toronto, ON, Canada
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36
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Mittal R, Woo FW, Castro CS, Cohen MA, Karanxha J, Mittal J, Chhibber T, Jhaveri VM. Organ‐on‐chip models: Implications in drug discovery and clinical applications. J Cell Physiol 2018; 234:8352-8380. [DOI: 10.1002/jcp.27729] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology University of Miami Miller School of Medicine Miami Florida
| | - Frank W. Woo
- Department of Otolaryngology University of Miami Miller School of Medicine Miami Florida
| | - Carlo S. Castro
- Department of Otolaryngology University of Miami Miller School of Medicine Miami Florida
| | - Madeline A. Cohen
- Department of Otolaryngology University of Miami Miller School of Medicine Miami Florida
| | - Joana Karanxha
- Department of Otolaryngology University of Miami Miller School of Medicine Miami Florida
| | - Jeenu Mittal
- Department of Otolaryngology University of Miami Miller School of Medicine Miami Florida
| | - Tanya Chhibber
- University Institute of Pharmaceutical Sciences, UGC Centre of Advanced Studies, Panjab University Chandigarh India
| | - Vasanti M. Jhaveri
- Department of Otolaryngology University of Miami Miller School of Medicine Miami Florida
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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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Nakamura T. Recent progress in organoid culture to model intestinal epithelial barrier functions. Int Immunol 2018; 31:13-21. [DOI: 10.1093/intimm/dxy065] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022] Open
Affiliation(s)
- Tetsuya Nakamura
- Department of Advanced Therapeutics for GI Diseases, Tokyo Medical and Dental University Yushima, Bunkyo-ku, Tokyo, Japan
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Saberi S, Pournasr B, Farzaneh Z, Esmaeili M, Hosseini ME, Baharvand H, Mohammadi M. A simple and cost-efficient adherent culture platform for human gastric primary cells, as an in vitro model for Helicobacter pylori infection. Helicobacter 2018; 23:e12489. [PMID: 29774633 DOI: 10.1111/hel.12489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Most two- dimensional in vitro models for studying host- H. pylori interactions rely on tumor-derived cell lines, which harbor malignant alterations. The recent development of human gastric organoids has overcome this limitation and provides a highly sophisticated, yet costly, short-term model for H. pylori infection, with restricted use in low-budget centers. METHOD Tissue specimens from upper, middle, and lower stomachs of H. pylori-negative volunteers were collectively dispersed and cultured on mouse embryonic fibroblast (MEF) or collagen-coated plates. Gastric primary cells (GPCs) were evaluated by light microscopy, immunostaining, qRT-PCR and ELISA analysis of cellular secretions, before and after H. pylori infection. RESULTS The formation and long-term (up to 1 year) maintenance of GPCs was highly dependent on adherent inactivated MEF cells, cultured in enriched media. These cells were multipassageable and able to undergo stable freezer storage and subsequent revival. The cellular composition of GPCs included the combination of cytokeratin 18 (CK18) and E-cadherin (E-cad)-positive epithelial cells, MUC5AC-positive gastric cells, and leucine-rich repeat containing G protein-coupled receptor 5 (LGR5)-positive progenitor cells. These cells produced significant amounts of gastric pepsinogens I and II. GPCs also allowed for extended (up to 96 hours) H. pylori infection, during which they underwent morphological alterations (cellular vacuolation and elongation) and hyperproduction of gastric pepsinogens and inflammatory cytokines (IL-8 and TNF-α). CONCLUSION We, hereby, present a simple, consistent, and cost-efficient gastric cell culture system, which provides a suitable model for extended in vitro infection of H. pylori. This platform can be employed for a variety of gastric-related research.
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Affiliation(s)
- Samaneh Saberi
- HPGC Research Group, Department of Medical Biotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Behshad Pournasr
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Zahra Farzaneh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Maryam Esmaeili
- HPGC Research Group, Department of Medical Biotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Mahmoud Eshagh Hosseini
- Gastroenterology Department, Amiralam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Marjan Mohammadi
- HPGC Research Group, Department of Medical Biotechnology, Pasteur Institute of Iran, Tehran, Iran
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40
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Younes M, Aggett P, Aguilar F, Crebelli R, Dusemund B, Filipicč M, Frutos MJ, Galtier P, Gundert-Remy U, Kuhnle GG, Lambré C, Leblanc JC, Lillegaard IT, Moldeus P, Mortensen A, Oskarsson A, Stankovic I, Waalkens-Berendsen I, Woutersen RA, Wright M, Di Domenico A, Fairweather-Tait S, McArdle H, Smeraldi C, Gott D. Guidance on safety evaluation of sources of nutrients and bioavailability of nutrient from the sources. EFSA J 2018; 16:e05294. [PMID: 32625933 PMCID: PMC7009562 DOI: 10.2903/j.efsa.2018.5294] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Whenever new substances are proposed for use as sources of nutrients in food supplements, foods for the general population or foods for specific groups, EFSA is requested by the European Commission to perform an assessment of their safety and of the bioavailability of the nutrient from the proposed source. This guidance describes the scientific data required to allow an evaluation of the safety of the source within the established framework for risk assessment of food additives and novel food ingredients and the bioavailability of the nutrient from this source. This document is arranged in five main sections: one on technical data aimed at characterising the proposed source and at identifying potential hazards resulting from its manufacture and stability in food; one on existing authorisations and evaluation, providing an overview of previous assessments on the proposed source and their conclusions; one on proposed uses and exposure assessment section, allowing an estimate of the dietary exposure to the source and the nutrient based on the proposed uses and use levels; one on toxicological data, describing approaches which can be used to identify (in conjunction with data on manufacture and composition) and to characterise hazards of the source and any relevant breakdown products; the final section on bioavailability focuses on determining the extent to which the nutrient from the proposed source is available for use by the body in comparison with one or more forms of the same nutrient that are already permitted for use on the positive lists. This guidance document should replace the previous guidance issued by the Scientific Committee for Food and published in 2001. This publication is linked to the following EFSA Supporting Publications article: http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2018.EN-1439/full
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41
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Alessandrini L, Manchi M, De Re V, Dolcetti R, Canzonieri V. Proposed Molecular and miRNA Classification of Gastric Cancer. Int J Mol Sci 2018; 19:E1683. [PMID: 29882766 PMCID: PMC6032377 DOI: 10.3390/ijms19061683] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/13/2022] Open
Abstract
Gastric cancer (GC) is a common malignant neoplasm worldwide and one of the main cause of cancer-related deaths. Despite some advances in therapies, long-term survival of patients with advanced disease remains poor. Different types of classification have been used to stratify patients with GC for shaping prognosis and treatment planning. Based on new knowledge of molecular pathways associated with different aspect of GC, new pathogenetic classifications for GC have been and continue to be proposed. These novel classifications create a new paradigm in the definition of cancer biology and allow the identification of relevant GC genomic subsets by using different techniques such as genomic screenings, functional studies and molecular or epigenetic characterization. An improved prognostic classification for GC is essential for the development of a proper therapy for a proper patient population. The aim of this review is to discuss the state-of-the-art on combining histological and molecular classifications of GC to give an overview of the emerging therapeutic possibilities connected to the latest discoveries regarding GC.
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Affiliation(s)
- Lara Alessandrini
- Pathology, IRCCS CRO National Cancer Institute, 33081 Aviano, Italy.
| | - Melissa Manchi
- Pathology, IRCCS CRO National Cancer Institute, 33081 Aviano, Italy.
| | - Valli De Re
- Immunopathology and Cancer Biomarkers, IRCCS CRO National Cancer Institute, 33081 Aviano, Italy.
| | - Riccardo Dolcetti
- The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD 4102, Australia.
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Williamson IA, Arnold JW, Samsa LA, Gaynor L, DiSalvo M, Cocchiaro JL, Carroll I, Azcarate-Peril MA, Rawls JF, Allbritton NL, Magness ST. A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology. Cell Mol Gastroenterol Hepatol 2018; 6:301-319. [PMID: 30123820 PMCID: PMC6092482 DOI: 10.1016/j.jcmgh.2018.05.004] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022]
Abstract
Background & Aims The human gut microbiota is becoming increasingly recognized as a key factor in homeostasis and disease. The lack of physiologically relevant in vitro models to investigate host-microbe interactions is considered a substantial bottleneck for microbiota research. Organoids represent an attractive model system because they are derived from primary tissues and embody key properties of the native gut lumen; however, access to the organoid lumen for experimental perturbation is challenging. Here, we report the development and validation of a high-throughput organoid microinjection system for cargo delivery to the organoid lumen and high-content sampling. Methods A microinjection platform was engineered using off-the-shelf and 3-dimensional printed components. Microinjection needles were modified for vertical trajectories and reproducible injection volumes. Computer vision (CVis) and microfabricated CellRaft Arrays (Cell Microsystems, Research Triangle Park, NC) were used to increase throughput and enable high-content sampling of mock bacterial communities. Modeling preformed using the COMSOL Multiphysics platform predicted a hypoxic luminal environment that was functionally validated by transplantation of fecal-derived microbial communities and monocultures of a nonsporulating anaerobe. Results CVis identified and logged locations of organoids suitable for injection. Reproducible loads of 0.2 nL could be microinjected into the organoid lumen at approximately 90 organoids/h. CVis analyzed and confirmed retention of injected cargos in approximately 500 organoids over 18 hours and showed the requirement to normalize for organoid growth for accurate assessment of barrier function. CVis analyzed growth dynamics of a mock community of green fluorescent protein- or Discosoma sp. red fluorescent protein-expressing bacteria, which grew within the organoid lumen even in the presence of antibiotics to control media contamination. Complex microbiota communities from fecal samples survived and grew in the colonoid lumen without appreciable changes in complexity. Conclusions High-throughput microinjection into organoids represents a next-generation in vitro approach to investigate gastrointestinal luminal physiology and the gastrointestinal microbiota.
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Key Words
- 2D, 2-dimensional
- 3D, 3-dimensional
- Anaerobic
- Barrier Function
- CAG, chicken beta-actin promoter with CMV enhancer
- CFU, colony-forming unit
- CRA, CellRaft Array
- CVis, computer vision
- EGFP, enhanced green fluorescent protein
- FITC, fluorescein isothiocyanate
- Fecal Microbiota
- GFP, green fluorescent protein
- GI, gastrointestinal
- HF, hydrogen fluoride
- High-Content Sampling
- High-Throughput
- Microinjection
- OUT, operational taxonomic unit
- Organoid
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- QIIME, Quantitative Insights Into Microbial Ecology
- WT, wild-type
- hiPS, Human Induced Pluripotent Stem Cell
- rRNA, ribosomal RNA
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Affiliation(s)
- Ian A. Williamson
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Jason W. Arnold
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Leigh Ann Samsa
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Liam Gaynor
- Graduate Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Matthew DiSalvo
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Jordan L. Cocchiaro
- Department of Molecular Genetics and Microbiology Medicine, Duke University, Durham, North Carolina
| | - Ian Carroll
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - M. Andrea Azcarate-Peril
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology Medicine, Duke University, Durham, North Carolina
| | - Nancy L. Allbritton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
- Department of Chemistry, 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/North Carolina State University, Chapel Hill, North Carolina
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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Ramani S, Crawford SE, Blutt SE, Estes MK. Human organoid cultures: transformative new tools for human virus studies. Curr Opin Virol 2018; 29:79-86. [PMID: 29656244 PMCID: PMC5944856 DOI: 10.1016/j.coviro.2018.04.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/02/2018] [Accepted: 04/02/2018] [Indexed: 12/23/2022]
Abstract
Studies of human infectious diseases have been limited by the paucity of functional models that mimic normal human physiology and pathophysiology. Recent advances in the development of multicellular, physiologically active organotypic cultures produced from embryonic and pluripotent stem cells, as well as from stem cells isolated from biopsies and surgical specimens are allowing unprecedented new studies and discoveries about host-microbe interactions. Here, we summarize recent developments in the use of organoids for studying human viral pathogens, including intestinal infections with human rotavirus, norovirus, enteroviruses and adenoviruses (intestinal organoids and enteroids), neuronal infections with Zika virus (cerebral organoids) and respiratory infections with respiratory syncytial virus in (lung bud organoids). Biologic discovery of host-specific genetic and epigenetic factors affecting infection, and responses to infection that lead to disease are possible with the use of organoid cultures. Continued development to increase the complexity of these cultures by including components of the normal host tissue microenvironment such as immune cells, blood vessels and microbiome, will facilitate studies on human viral pathogenesis, and advance the development of platforms for pre-clinical evaluation of vaccines, antivirals and therapeutics.
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Affiliation(s)
- Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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Abstract
Microbiome science is revealing that the phenotype and health of animals, including humans, depend on the sustained function of their resident microorganisms. In this essay, I argue for thoughtful choice of model systems for human microbiome science. A greater variety of experimental systems, including wider use of invertebrate models, would benefit biomedical research, while systems ill-suited to experimental and genetic manipulation can be used to address very limited sets of scientific questions. Microbiome science benefits from the coordinated use of multiple systems, which is facilitated by networks of researchers with expertise in different experimental systems.
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Affiliation(s)
- Angela E. Douglas
- Department of Entomology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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45
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Abstract
Studies on the intestinal epithelial response to viral infection have previously been limited by the absence of in vitro human intestinal models that recapitulate the multicellular complexity of the gastrointestinal tract. Recent technological advances have led to the development of “mini-intestine” models, which mimic the diverse cellular nature and physiological activity of the small intestine. Utilizing adult or embryonic intestinal tissue, enteroid and organoid systems, respectively, represent an opportunity to effectively model cellular differentiation, proliferation, and interactions that are specific to the specialized environment of the intestine. Enteroid and organoid systems represent a significant advantage over traditional in vitro methods because they model the structure and function of the small intestine while also maintaining the genetic identity of the host. These more physiologic models also allow for novel approaches to investigate the interaction of enteric viruses with the gastrointestinal tract, making them ideal to study the complexities of host-pathogen interactions in this unique cellular environment. This review aims to provide a summary on the use of human enteroid and organoid systems as models to study virus pathogenesis.
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Affiliation(s)
- Wyatt E Lanik
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Madison A Mara
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Belgacem Mihi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Carolyn B Coyne
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
- Center for Microbial Pathogenesis, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA.
| | - Misty Good
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Jardé T, Kerr G, Akhtar R, Abud HE. Modelling Intestinal Carcinogenesis Using In Vitro Organoid Cultures. Methods Mol Biol 2018; 1725:41-52. [PMID: 29322407 DOI: 10.1007/978-1-4939-7568-6_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mouse models of intestinal carcinogenesis are very powerful for studying the impact of specific mutations on tumour initiation and progression. Mutations can be studied both singularly and in combination using conditional alleles that can be induced in a temporal manner. The steps in intestinal carcinogenesis are complex and can be challenging to image in live animals at a cellular level. The ability to culture intestinal epithelial tissue in three-dimensional organoids in vitro provides an accessible system that can be genetically manipulated and easily visualised to assess specific biological impacts in living tissue. Here, we describe methodology for conditional mutation of genes in organoids from genetically modified mice via induction of Cre recombinase induced by tamoxifen or by transient exposure to TAT-Cre protein. This methodology provides a rapid platform for assessing the cellular changes induced by specific mutations in intestinal tissue.
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Affiliation(s)
- Thierry Jardé
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- The Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Genevieve Kerr
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- The Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Reyhan Akhtar
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- The Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Helen E Abud
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- The Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.
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La Fata G, Rastall RA, Lacroix C, Harmsen HJM, Mohajeri MH, Weber P, Steinert RE. Recent Development of Prebiotic Research-Statement from an Expert Workshop. Nutrients 2017; 9:E1376. [PMID: 29261110 PMCID: PMC5748826 DOI: 10.3390/nu9121376] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 12/22/2022] Open
Abstract
A dietary prebiotic is defined as 'a substrate that is selectively utilized by host microorganisms conferring a health benefit'. Although this definition evolved concomitantly with the knowledge and technological developments that accrued in the last twenty years, what qualifies as prebiotic continues to be a matter of debate. In this statement, we report the outcome of a workshop where academic experts working in the field of prebiotic research met with scientists from industry. The workshop covered three main topics: (i) evolution of the prebiotic concept/definition; (ii) the gut modeling in vitro technology PolyFermS to study prebiotic effects; and (iii) the potential novel microbiome-modulating effects associated with vitamins. The future of prebiotic research is very promising. Indeed, the technological developments observed in recent years provide scientists with powerful tools to investigate the complex ecosystem of gut microbiota. Combining multiple in vitro approaches with in vivo studies is key to understanding the mechanisms of action of prebiotics consumption and their potential beneficial effects on the host.
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Affiliation(s)
- Giorgio La Fata
- DSM Nutritional Products Ltd., R & D Human Nutrition and Health, P.O. Box 2676, CH-4002 Basel, Switzerland.
| | - Robert A Rastall
- Department of Food and Nutritional Science, The University of Reading, Whiteknights Campus, Reading RG6 6AP, UK.
| | - Christophe Lacroix
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, CH-8092 Zürich, Switzerland.
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands.
| | - M Hasan Mohajeri
- DSM Nutritional Products Ltd., R & D Human Nutrition and Health, P.O. Box 2676, CH-4002 Basel, Switzerland.
| | - Peter Weber
- DSM Nutritional Products Ltd., R & D Human Nutrition and Health, P.O. Box 2676, CH-4002 Basel, Switzerland.
| | - Robert E Steinert
- DSM Nutritional Products Ltd., R & D Human Nutrition and Health, P.O. Box 2676, CH-4002 Basel, Switzerland.
- Department of Surgery, Division of Visceral and Transplantation Surgery, University Hospital Zürich, 8091 Zürich, Switzerland.
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48
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Hill DR, Huang S, Tsai YH, Spence JR, Young VB. Real-time Measurement of Epithelial Barrier Permeability in Human Intestinal Organoids. J Vis Exp 2017:56960. [PMID: 29286482 PMCID: PMC5755602 DOI: 10.3791/56960] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Advances in 3D culture of intestinal tissues obtained through biopsy or generated from pluripotent stem cells via directed differentiation, have resulted in sophisticated in vitro models of the intestinal mucosa. Leveraging these emerging model systems will require adaptation of tools and techniques developed for 2D culture systems and animals. Here, we describe a technique for measuring epithelial barrier permeability in human intestinal organoids in real-time. This is accomplished by microinjection of fluorescently-labeled dextran and imaging on an inverted microscope fitted with epifluorescent filters. Real-time measurement of the barrier permeability in intestinal organoids facilitates the generation of high-resolution temporal data in human intestinal epithelial tissue, although this technique can also be applied to fixed timepoint imaging approaches. This protocol is readily adaptable for the measurement of epithelial barrier permeability following exposure to pharmacologic agents, bacterial products or toxins, or live microorganisms. With minor modifications, this protocol can also serve as a general primer on microinjection of intestinal organoids and users may choose to supplement this protocol with additional or alternative downstream applications following microinjection.
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Affiliation(s)
- David R Hill
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan;
| | - Sha Huang
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan; Department of Cell and Developmental Biology, University of Michigan
| | - Vincent B Young
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan; Department of Internal Medicine, Division of Infectious Disease, University of Michigan
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49
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Cacciò SM, Lalle M, Svärd SG. Host specificity in the Giardia duodenalis species complex. INFECTION GENETICS AND EVOLUTION 2017; 66:335-345. [PMID: 29225147 DOI: 10.1016/j.meegid.2017.12.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 12/15/2022]
Abstract
Giardia duodenalis is a unicellular flagellated parasite that infects the gastrointestinal tract of a wide range of mammalian species, including humans. Investigations of protein and DNA polymorphisms revealed that G. duodenalis should be considered as a species complex, whose members, despite being morphologically indistinguishable, can be classified into eight groups, or Assemblages, separated by large genetic distances. Assemblages display various degree of host specificity, with Assemblages A and B occurring in humans and many other hosts, Assemblage C and D in canids, Assemblage E in hoofed animals, Assemblage F in cats, Assemblage G in rodents, and Assemblage H in pinnipeds. The factors determining host specificity are only partially understood, and clearly involve both the host and the parasite. Here, we review the results of in vitro and in vivo experiments, and clinical observations to highlight relevant biological and genetic differences between Assemblages, with a focus on human infection.
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Affiliation(s)
- Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Marco Lalle
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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50
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Organoids, organs-on-chips and other systems, and microbiota. Emerg Top Life Sci 2017; 1:385-400. [PMID: 33525777 PMCID: PMC7289039 DOI: 10.1042/etls20170047] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 12/15/2022]
Abstract
The human gut microbiome is considered an organ in its entirety and has been the subject of extensive research due to its role in physiology, metabolism, digestion, and immune regulation. Disequilibria of the normal microbiome have been associated with the development of several gastrointestinal diseases, but the exact underlying interactions are not well understood. Conventional in vivo and in vitro modelling systems fail to faithfully recapitulate the complexity of the human host–gut microbiome, emphasising the requirement for novel systems that provide a platform to study human host–gut microbiome interactions with a more holistic representation of the human in vivo microenvironment. In this review, we outline the progression and applications of new and old modelling systems with particular focus on their ability to model and to study host–microbiome cross-talk.
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