151
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Yin Y, Zhou D. Organoid and Enteroid Modeling of Salmonella Infection. Front Cell Infect Microbiol 2018; 8:102. [PMID: 29670862 PMCID: PMC5894114 DOI: 10.3389/fcimb.2018.00102] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 03/16/2018] [Indexed: 12/12/2022] Open
Abstract
Salmonella are Gram-negative rod-shaped facultative anaerobic bacteria that are comprised of over 2,000 serovars. They cause gastroenteritis (salmonellosis) with headache, abdominal pain and diarrhea clinical symptoms. Salmonellosis brings a heavy burden for the public health in both developing and developed countries. Antibiotics are usually effective in treating the infected patients with severe gastroenteritis, although antibiotic resistance is on the rise. Understanding the molecular mechanisms of Salmonella infection is vital to combat the disease. In vitro immortalized 2-D cell lines, ex vivo tissues/organs and several animal models have been successfully utilized to study Salmonella infections. Although these infection models have contributed to uncovering the molecular virulence mechanisms, some intrinsic shortcomings have limited their wider applications. Notably, cell lines only contain a single cell type, which cannot reproduce some of the hallmarks of natural infections. While ex vivo tissues/organs alleviate some of these concerns, they are more difficult to maintain, in particular for long term experiments. In addition, non-human animal models are known to reflect only part of the human disease process. Enteroids and induced intestinal organoids are emerging as effective infection models due to their closeness in mimicking the infected tissues/organs. Induced intestinal organoids are derived from iPSCs and contain mesenchymal cells whereas enteroids are derive from intestinal stem cells and are comprised of epithelial cells only. Both enteroids and induced intestinal organoids mimic the villus and crypt domains comparable to the architectures of the in vivo intestine. We review here that enteroids and induced intestinal organoids are emerging as desired infection models to study bacterial-host interactions of Salmonella.
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Affiliation(s)
- Yuebang Yin
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Daoguo Zhou
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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152
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Okkelman IA, Foley T, Papkovsky DB, Dmitriev RI. Multi-Parametric Imaging of Hypoxia and Cell Cycle in Intestinal Organoid Culture. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1035:85-103. [PMID: 29080132 DOI: 10.1007/978-3-319-67358-5_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dynamics of oxygenation of tissue and stem cell niches are important for understanding physiological function of the intestine in normal and diseased states. Only a few techniques allow live visualization of tissue hypoxia at cellular level and in three dimensions. We describe an optimized protocol, which uses cell-penetrating O2-sensitive probe, Pt-Glc and phosphorescence lifetime imaging microscopy (PLIM), to analyze O2 distribution in mouse intestinal organoids. Unlike the other indirect and end-point hypoxia stains, or point measurements with microelectrodes, this method provides high-resolution real-time visualization of O2 in organoids. Multiplexing with conventional fluorescent live cell imaging probes such as the Hoechst 33342-based FLIM assay of cell proliferation, and immunofluorescence staining of endogenous proteins, allows analysis of key physiologic parameters under O2 control in organoids. The protocol is useful for gastroenterology and physiology of intestinal tissue, hypoxia research, regenerative medicine, studying host-microbiota interactions and bioenergetics.
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Affiliation(s)
- Irina A Okkelman
- Laboratory of Biophysics and Bioanalysis, School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Tara Foley
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Dmitri B Papkovsky
- Laboratory of Biophysics and Bioanalysis, School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ruslan I Dmitriev
- Metabolic Imaging Group, School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
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153
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Liu C, Oikonomopoulos A, Sayed N, Wu JC. Modeling human diseases with induced pluripotent stem cells: from 2D to 3D and beyond. Development 2018. [PMID: 29519889 DOI: 10.1242/dev.156166] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The advent of human induced pluripotent stem cells (iPSCs) presents unprecedented opportunities to model human diseases. Differentiated cells derived from iPSCs in two-dimensional (2D) monolayers have proven to be a relatively simple tool for exploring disease pathogenesis and underlying mechanisms. In this Spotlight article, we discuss the progress and limitations of the current 2D iPSC disease-modeling platform, as well as recent advancements in the development of human iPSC models that mimic in vivo tissues and organs at the three-dimensional (3D) level. Recent bioengineering approaches have begun to combine different 3D organoid types into a single '4D multi-organ system'. We summarize the advantages of this approach and speculate on the future role of 4D multi-organ systems in human disease modeling.
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Affiliation(s)
- Chun Liu
- Stanford Cardiovascular Institute, Stanford, CA 94035, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA 94305, USA.,Department of Medicine (Division of Cardiology), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Angelos Oikonomopoulos
- Stanford Cardiovascular Institute, Stanford, CA 94035, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA 94305, USA.,Department of Medicine (Division of Cardiology), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nazish Sayed
- Stanford Cardiovascular Institute, Stanford, CA 94035, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA 94305, USA.,Department of Medicine (Division of Cardiology), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford, CA 94035, USA .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA 94305, USA.,Department of Medicine (Division of Cardiology), Stanford University School of Medicine, Stanford, CA 94305, USA
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154
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Abstract
More than a century ago, infections by Salmonella were already associated with foodborne enteric diseases with high morbidity in humans and cattle. Intestinal inflammation and diarrhea are hallmarks of infections caused by nontyphoidal Salmonella serovars, and these pathologies facilitate pathogen transmission to the environment. In those early times, physicians and microbiologists also realized that typhoid and paratyphoid fever caused by some Salmonella serovars could be transmitted by "carriers," individuals outwardly healthy or at most suffering from some minor chronic complaint. In his pioneering study of the nontyphoidal serovar Typhimurium in 1967, Takeuchi published the first images of intracellular bacteria enclosed by membrane-bound vacuoles in the initial stages of the intestinal epithelium penetration. These compartments, called Salmonella-containing vacuoles, are highly dynamic phagosomes with differing biogenesis depending on the host cell type. Single-cell studies involving real-time imaging and gene expression profiling, together with new approaches based on genetic reporters sensitive to growth rate, have uncovered unprecedented heterogeneous responses in intracellular bacteria. Subpopulations of intracellular bacteria displaying fast, reduced, or no growth, as well as cytosolic and intravacuolar bacteria, have been reported in both in vitro and in vivo infection models. Recent investigations, most of them focused on the serovar Typhimurium, point to the selection of persisting bacteria inside macrophages or following an autophagy attack in fibroblasts. Here, we discuss these heterogeneous intracellular lifestyles and speculate on how these disparate behaviors may impact host-to-host transmissibility of Salmonella serovars.
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155
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Novel Segment- and Host-Specific Patterns of Enteroaggregative Escherichia coli Adherence to Human Intestinal Enteroids. mBio 2018; 9:mBio.02419-17. [PMID: 29463660 PMCID: PMC5821088 DOI: 10.1128/mbio.02419-17] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) is an important diarrheal pathogen and a cause of both acute and chronic diarrhea. It is a common cause of pediatric bacterial diarrhea in developing countries. Despite its discovery in 1987, the intestinal tropism of the pathogen remains unknown. Cell lines used to study EAEC adherence include the HEp-2, T-84, and Caco-2 lines, but they exhibit abnormal metabolism and large variations in gene expression. Animal models either do not faithfully manifest human clinical symptoms or are cumbersome and expensive. Using human intestinal enteroids derived from all four segments of the human intestine, we find that EAEC demonstrates aggregative adherence to duodenal and ileal enteroids, with donor-driven differences driving a sheet-like and layered pattern. This contrasts with the colon, where segment-specific tropisms yielded a mesh-like adherence pattern dominated by interconnecting filaments. Very little to no aggregative adherence to jejunal enteroids was observed, regardless of the strain or donor, in contrast to a strong duodenal association across all donors and strains. These unique patterns of intestinal segment- or donor-specific adherence, but not the overall numbers of associated bacteria, were dependent on the major subunit protein of aggregative adherence fimbriae II (AafA), implying that the morphology of adherent clusters and the overall intestinal cell association of EAEC occur by different mechanisms. Our results suggest that we must give serious consideration to inter- and intrapatient variations in what is arguably the first step in pathogenesis, that of adherence, when considering the clinical manifestation of these infections. EAEC is a leading cause of pediatric bacterial diarrhea and a common cause of diarrhea among travelers and immunocompromised individuals. Heterogeneity in EAEC strains and lack of a good model system are major roadblocks to the understanding of its pathogenesis. Utilizing human intestinal enteroids to study the adherence of EAEC, we demonstrate that unique patterns of adherence are largely driven by unidentified factors present in different intestinal segments and from different donors. These patterns are also dependent on aggregative adherence fimbriae II encoded by EAEC. These results imply that we must also consider the contribution of the host to understand the pathogenesis of EAEC-induced inflammation and diarrhea.
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156
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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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157
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Blutt SE, Crawford SE, Ramani S, Zou WY, Estes MK. Engineered Human Gastrointestinal Cultures to Study the Microbiome and Infectious Diseases. Cell Mol Gastroenterol Hepatol 2017; 5:241-251. [PMID: 29675450 PMCID: PMC5904028 DOI: 10.1016/j.jcmgh.2017.12.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/04/2017] [Indexed: 02/07/2023]
Abstract
New models to study the intestine are key to understanding intestinal diseases and developing novel treatments. Intestinal organ-like culture systems (organoids and enteroids) have substantially advanced the study of the human gastrointestinal tract. Stem cell-derived cultures produce self-organizing structures that contain the multiple differentiated intestinal epithelial cell types including enterocytes, goblet, Paneth, and enteroendocrine cells. Understanding host-microbial interactions is one area in which these cultures are expediting major advancements. This review discusses how organoid and enteroid cultures are biologically and physiologically relevant systems to investigate the effects of commensal organisms and study the pathogenesis of human infectious diseases. These cultures can be established from many donors and they retain the genetic and biologic properties of the donors, which can lead to the discovery of host-specific factors that affect susceptibility to infection and result in personalized approaches to treat individuals. The continued development of these cultures to incorporate more facets of the gastrointestinal tract, including neurons, immune cells, and the microbiome, will unravel new mechanisms regulating host-microbial interactions with the long-term goal of translating findings into novel preventive or therapeutic treatments for gastrointestinal infections.
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Affiliation(s)
| | | | | | | | - Mary K. Estes
- Correspondence Address correspondence to: Mary K. Estes, PhD, Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030. fax: (713) 798-3586.
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158
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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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159
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Barquist L, Westermann AJ, Vogel J. Molecular phenotyping of infection-associated small non-coding RNAs. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0081. [PMID: 27672158 DOI: 10.1098/rstb.2016.0081] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2016] [Indexed: 02/07/2023] Open
Abstract
Infection is a complicated balance, with both pathogen and host struggling to tilt the result in their favour. Bacterial infection biology has relied on forward genetics for many of its advances, defining phenotype in terms of replication in model systems. However, many known virulence factors fail to produce robust phenotypes, particularly in the systems most amenable to genetic manipulation, such as cell-culture models. This has particularly been limiting for the study of the bacterial regulatory small RNAs (sRNAs) in infection. We argue that new sequencing-based technologies can work around this problem by providing a 'molecular phenotype', defined in terms of the specific transcriptional dysregulation in the infection system induced by gene deletion. We illustrate this using the example of our recent study of the PinT sRNA using dual RNA-seq, that is, simultaneous RNA sequencing of host and pathogen during infection. We additionally discuss how other high-throughput technologies, in particular genetic interaction mapping using transposon insertion sequencing, may be used to further dissect molecular phenotypes. We propose a strategy for how high-throughput technologies can be integrated in the study of non-coding regulators as well as bacterial virulence factors, enhancing our ability to rapidly generate hypotheses with regards to their function.This article is part of the themed issue 'The new bacteriology'.
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Affiliation(s)
- Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
| | - Alexander J Westermann
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97070 Würzburg, Germany
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160
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Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
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161
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Hill DR, Huang S, Nagy MS, Yadagiri VK, Fields C, Mukherjee D, Bons B, Dedhia PH, Chin AM, Tsai YH, Thodla S, Schmidt TM, Walk S, Young VB, Spence JR. Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. eLife 2017; 6:29132. [PMID: 29110754 PMCID: PMC5711377 DOI: 10.7554/elife.29132] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/29/2017] [Indexed: 12/19/2022] Open
Abstract
The human gastrointestinal tract is immature at birth, yet must adapt to dramatic changes such as oral nutrition and microbial colonization. The confluence of these factors can lead to severe inflammatory disease in premature infants; however, investigating complex environment-host interactions is difficult due to limited access to immature human tissue. Here, we demonstrate that the epithelium of human pluripotent stem-cell-derived human intestinal organoids is globally similar to the immature human epithelium and we utilize HIOs to investigate complex host-microbe interactions in this naive epithelium. Our findings demonstrate that the immature epithelium is intrinsically capable of establishing a stable host-microbe symbiosis. Microbial colonization leads to complex contact and hypoxia driven responses resulting in increased antimicrobial peptide production, maturation of the mucus layer, and improved barrier function. These studies lay the groundwork for an improved mechanistic understanding of how colonization influences development of the immature human intestine.
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Affiliation(s)
- David R Hill
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Sha Huang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Melinda S Nagy
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Veda K Yadagiri
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Courtney Fields
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Dishari Mukherjee
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Brooke Bons
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Priya H Dedhia
- Department of Surgery, University of Michigan, Ann Arbor, United States
| | - Alana M Chin
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Yu-Hwai Tsai
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Shrikar Thodla
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Seth Walk
- Department of Microbiology and Immunology, Montana State University, Bozeman, United States
| | - Vincent B Young
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States.,Department of Cell andDevelopmental Biology, University of Michigan, Ann Arbor, United States
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162
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Kuadkitkan A, Wikan N, Smith DR. Induced pluripotent stem cells: A new addition to the virologists armamentarium. J Virol Methods 2017; 235:191-195. [PMID: 27544025 DOI: 10.1016/j.jviromet.2016.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/23/2016] [Accepted: 03/23/2016] [Indexed: 12/01/2022]
Abstract
A significant amount of our understanding of the molecular events occurring during viral replication has originated from studies utilizing cell lines. These cell lines are normally obtained by the culture of samples from spontaneously occurring tumors or are derived by genetic manipulation of primary cells. The genetic events inducing immortalization and/or transformation to allow continual passage in culture can have profound effects resulting in a marked loss of cell type fidelity. The development of induced pluripotent stem cells (iPSCs) has revolutionized the field of developmental biology and is ushering in an era of personalized medicine for a wide range of inherited genetic diseases. Previously, development of iPSCs required dedicated facilities as well as highly detailed technical knowledge. The pace of development in this field however has been so rapid, that iPSCs are moving into an era of "off the shelf" use, whereby the use and manipulation of these cells is well within the ability of the majority of laboratories with standard tissue culture facilities. The introduction of iPSCs to studies in the field of virology is still in its infancy, and so far has been largely confined to viruses that are difficult to propagate in other experimental systems, but it is likely that this technology will become a standard methodology in the virologists armamentarium.
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Affiliation(s)
- Atichat Kuadkitkan
- Institute of Molecular Biosciences, Mahidol University, Bangkok, Thailand
| | - Nitwara Wikan
- Institute of Molecular Biosciences, Mahidol University, Bangkok, Thailand
| | - Duncan R Smith
- Institute of Molecular Biosciences, Mahidol University, Bangkok, Thailand; Center for Emerging and Neglected Infectious Diseases, Mahidol University, Bangkok, Thailand.
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163
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Zhang K, Griffiths G, Repnik U, Hornef M. Seeing is understanding: Salmonella's way to penetrate the intestinal epithelium. Int J Med Microbiol 2017; 308:97-106. [PMID: 28939439 DOI: 10.1016/j.ijmm.2017.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023] Open
Abstract
The molecular processes that govern host-microbial interaction illustrate not only the sophisticated and multifaceted mechanisms that protect the host from infection, but also the elaborated features of microbial pathogens that have evolved to overcome or evade the host's immune system. Here we focus on Salmonella that like other enteric pathogens must overcome the intestinal mucosal immune system, a surface constantly on alert and evolved to restrict the enteric microbiota. We discuss the initial step of Salmonella infection, the penetration of the intestinal epithelial barrier and the models used to study this fascinating aspect of microbial pathogenesis.
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Affiliation(s)
- Kaiyi Zhang
- Institute of Medical Microbiology, RWTH University Hospital Aachen, Aachen, Germany
| | | | - Urska Repnik
- Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Mathias Hornef
- Institute of Medical Microbiology, RWTH University Hospital Aachen, Aachen, Germany.
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164
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Functional Enterospheres Derived In Vitro from Human Pluripotent Stem Cells. Stem Cell Reports 2017; 9:897-912. [PMID: 28867347 PMCID: PMC5599260 DOI: 10.1016/j.stemcr.2017.07.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 02/07/2023] Open
Abstract
Intestinal organoids derived from human pluripotent stem cells (hPSCs) are valuable in vitro research models that enable simplified access to human gastrointestinal tissues. Here, we report the in vitro generation of enterospheres (hEnS) from hPSC-derived gastrointestinal epithelial precursors. hEnS are cystic spheroids with a simple uniform structure composed entirely of intestinal epithelium. hEnS express markers of mature brush border cells and share a transcriptome profile similar to that of more mature intestinal organoids. Modulation of signaling cues enables control of hEnS growth and differentiation, including long-term propagation. We show that hEnS can be exploited for functional studies: hEnS display an innate immune response when treated with enteric pathogens, and transgenic modification of hEnS with a fluorescence cell-cycle reporter enables hEnS-forming stem cell enrichment. Our work establishes hEnS as an accessible and tractable in vitro modeling system for studying human gastrointestinal biology.
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165
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Dutta D, Clevers H. Organoid culture systems to study host-pathogen interactions. Curr Opin Immunol 2017; 48:15-22. [PMID: 28756233 PMCID: PMC7126332 DOI: 10.1016/j.coi.2017.07.012] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/09/2017] [Accepted: 07/12/2017] [Indexed: 01/04/2023]
Abstract
Recent advances in host-microbe interaction studies in organoid cultures have shown great promise and have laid the foundation for much more refined future studies using these systems. Modeling of Zika virus (ZIKV) infection in cerebral organoids have helped us understand its association with microcephaly. Similarly, the pathogenesis of bacterial (Helicobacter pylori, Clostridium difficile) and viral (Norovirus, Rotaviruses) infections have been precisely dissected in organoid cultures. Additionally, direct associations between microbial colonization of tissues and diseases like cancer have also been deciphered. Here we discuss the most recent and striking studies on host-microbe interactions in organoid cultures, highlighting various methods which can be used for developing microbe-organoid co-culture systems.
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Affiliation(s)
- Devanjali Dutta
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University, Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University, Netherlands; Utrecht Medical Center, 3584 CT, Utrecht, Netherlands.
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166
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Abstract
Recent advances allow access to human cell-based intestinal organoids that recreate human physiology to levels not possible with conventional 2D cell cultures. Despite their huge potential, there are many challenges that remain. This review will cover recent bioengineering approaches to improve organoid maturation, scale up, reproducibility and analysis. The first section covers the advances in engineering the culture environment, followed by the section on tools for micro-manipulation and analysis of organoids. The last section reviews the computational models developed to guide the use of engineered materials and tools, and to interpret observed results as well. The ability to use organoids for discovery research, and the need to both exert exquisite experimental control and obtain quantitative measurements from organoid models means that the field is ripe for collaborative efforts between biologists, engineers, clinicians and industry.
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Affiliation(s)
- Ge-Ah Kim
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jason R Spence
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Shuichi Takayama
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Macromolecular Science and Engineering Program, University of Michigan, Ann Arbor, MI 48109, USA.
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167
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Akhtar AA, Sances S, Barrett R, Breunig JJ. Organoid and Organ-On-A-Chip Systems: New Paradigms for Modeling Neurological and Gastrointestinal Disease. CURRENT STEM CELL REPORTS 2017; 3:98-111. [PMID: 28983454 PMCID: PMC5624725 DOI: 10.1007/s40778-017-0080-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW The modeling of biological processes in vitro provides an important tool to better understand mechanisms of development and disease, allowing for the rapid testing of therapeutics. However, a critical constraint in traditional monolayer culture systems is the absence of the multicellularity, spatial organization, and overall microenvironment present in vivo. This limitation has resulted in numerous therapeutics showing efficacy in vitro, but failing in patient trials. In this review, we discuss several organoid and "organ-on-a-chip" systems with particular regard to the modeling of neurological diseases and gastrointestinal disorders. RECENT FINDINGS Recently, the in vitro generation of multicellular organ-like structures, coined organoids, has allowed the modeling of human development, tissue architecture, and disease with human-specific pathophysiology. Additionally, microfluidic "organ-on-a-chip" technologies add another level of physiological mimicry by allowing biological mediums to be shuttled through 3D cultures. SUMMARY Organoids and organ-chips are rapidly evolving in vitro platforms which hold great promise for the modeling of development and disease.
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Affiliation(s)
- Aslam Abbasi Akhtar
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Samuel Sances
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Robert Barrett
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Joshua J. Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
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168
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Hou Q, Ye L, Huang L, Yu Q. The Research Progress on Intestinal Stem Cells and Its Relationship with Intestinal Microbiota. Front Immunol 2017; 8:599. [PMID: 28588586 PMCID: PMC5440531 DOI: 10.3389/fimmu.2017.00599] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/08/2017] [Indexed: 12/12/2022] Open
Abstract
The intestine is home to trillions of microorganisms, and the vast diversity within this gut microbiota exists in a balanced state to protect the intestinal mucosal barrier. Research into the association of the intestinal microbiota with health and disease (including diet, nutrition, obesity, inflammatory bowel disease, and cancer) continues to expand, with the field advancing at a rapid rate. Intestinal stem cells (ISCs) are the fundamental component of the mucosal barrier; they undergo continuous proliferation to replace the epithelium, which is also intimately involved in intestinal diseases. The intestinal microbiota, such as Lactobacillus, communicates with ISCs both directly and indirectly to regulate the proliferation and differentiation of ISCs. Moreover, Salmonella infection significantly decreased the expression of intestinal stem cell markers Lgr5 and Bmi1. However, the detailed interaction of intestinal microbiota and ISCs are still unclear. This review considers the progress of research on the model and niches of ISCs, as well as the complex interplay between the gut microbiota and ISCs, which will be crucial for explaining the mechanisms of intestinal diseases related to imbalances in the intestinal microbiota and ISCs.
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Affiliation(s)
- Qihang Hou
- College of veterinary medicine, Nanjing Agricultural University, Nanjing, China
| | - Lulu Ye
- College of veterinary medicine, Nanjing Agricultural University, Nanjing, China
| | - Lulu Huang
- College of veterinary medicine, Nanjing Agricultural University, Nanjing, China
| | - Qinghua Yu
- College of veterinary medicine, Nanjing Agricultural University, Nanjing, China
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169
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Abstract
The intestinal microbiota consists of a dynamic organization of bacteria, viruses, archaea, and fungal species essential for maintaining gut homeostasis and protecting the host against pathogenic invasion. When dysregulated, the intestinal microbiota can contribute to colorectal cancer development. Though the microbiota is multifaceted in its ability to induce colorectal cancer, this review will focus on the capability of the microbiota to induce colorectal cancer through the modulation of immune function and the production of microbial-derived metabolites. We will also explore an experimental technique that is revolutionizing intestinal research. By elucidating the interactions of microbial species with epithelial tissue, and allowing for drug screening of patients with colorectal cancers, organoid development is a novel culturing technique that is innovating intestinal research. As a cancer that remains one of the leading causes of cancer-related deaths worldwide, it is imperative that scientific findings are translated into the creation of effective therapeutics to treat colorectal cancer.
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Affiliation(s)
- Sofia Oke
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Alberto Martin
- Department of Immunology, University of Toronto, 1 King’s College Cir, MSB 7302, Toronto, Ontario M5S 1A1, Canada
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170
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Using 3D Organoid Cultures to Model Intestinal Physiology and Colorectal Cancer. CURRENT COLORECTAL CANCER REPORTS 2017; 13:183-191. [PMID: 29276469 DOI: 10.1007/s11888-017-0363-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The three-dimensional (3D) structure of the intestine is a key determinant of differentiation and function; thus, preserving this architecture is an important consideration for studies of intestinal homeostasis and disease. Over the past decade, a number of systems for 3D intestinal organoid cultures have been developed and adapted to model a wide variety of biological phenomenon. Purpose of this review We discuss the current state of intestinal and colorectal cancer (CRC) 3D modeling, the most common methods for generating organoid cultures, and how these have yielded insights into intestinal physiology and tumor biology. Recent findings Organoids have been used to model numerous aspects of intestinal physiology and disease. Recent adaptations have further improved disease modeling and high-throughput therapeutic screening. Summary These studies show intestinal organoid models are a robust, highly tractable system which maintains many vital features of intestinal tissue, making them a pivotal step forward in the field of gastroenterology.
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171
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Shah SB, Singh A. Cellular self-assembly and biomaterials-based organoid models of development and diseases. Acta Biomater 2017; 53:29-45. [PMID: 28159716 DOI: 10.1016/j.actbio.2017.01.075] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/29/2016] [Accepted: 01/27/2017] [Indexed: 12/11/2022]
Abstract
Organogenesis and morphogenesis have informed our understanding of physiology, pathophysiology, and avenues to create new curative and regenerative therapies. Thus far, this understanding has been hindered by the lack of a physiologically relevant yet accessible model that affords biological control. Recently, three-dimensional ex vivo cellular cultures created through cellular self-assembly under natural extracellular matrix cues or through biomaterial-based directed assembly have been shown to physically resemble and recapture some functionality of target organs. These "organoids" have garnered momentum for their applications in modeling human development and disease, drug screening, and future therapy design or even organ replacement. This review first discusses the self-organizing organoids as materials with emergent properties and their advantages and limitations. We subsequently describe biomaterials-based strategies used to afford more control of the organoid's microenvironment and ensuing cellular composition and organization. In this review, we also offer our perspective on how multifunctional biomaterials with precise spatial and temporal control could ultimately bridge the gap between in vitro organoid platforms and their in vivo counterparts. STATEMENT OF SIGNIFICANCE Several notable reviews have highlighted PSC-derived organoids and 3D aggregates, including embryoid bodies, from a development and cellular assembly perspective. The focus of this review is to highlight the materials-based approaches that cells, including PSCs and others, adopt for self-assembly and the controlled development of complex tissues, such as that of the brain, gut, and immune system.
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172
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Willemse J, Lieshout R, van der Laan LJW, Verstegen MMA. From organoids to organs: Bioengineering liver grafts from hepatic stem cells and matrix. Best Pract Res Clin Gastroenterol 2017. [PMID: 28624103 DOI: 10.1016/j.bpg.2017.03.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Due to the complex function and structure of the liver, resourceful solutions for treating end-stage liver disease are required. Currently, liver transplantation is the only curative therapeutic option. However, due to a worldwide donor shortage, researchers have been looking in other fields for alternative sources of transplantable liver tissue. Recent advances in our understanding of liver physiology, stem cell and matrix biology, have accelerated tissue engineering research. Most notable is the discovery of a culture system to grow liver-like organoids from human hepatic stem cells. The extensive expansion capacity of these stem cells has contributed greatly to the availability of hepatocyte-like cells for tissue engineering. In addition, new techniques are explored to obtain biological liver scaffolds from full size donor organs. This review summarizes these state-of-art techniques which may lay the groundwork towards re-creating transplantable tissue from autologous or allogenic stem cells in the coming decade.
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Affiliation(s)
- Jorke Willemse
- Dept. Surgery, Erasmus MC - Rotterdam Medical Center, Rotterdam, The Netherlands
| | - Ruby Lieshout
- Dept. Surgery, Erasmus MC - Rotterdam Medical Center, Rotterdam, The Netherlands
| | - Luc J W van der Laan
- Dept. Surgery, Erasmus MC - Rotterdam Medical Center, Rotterdam, The Netherlands
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173
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Disease Modeling in Stem Cell-Derived 3D Organoid Systems. Trends Mol Med 2017; 23:393-410. [PMID: 28341301 DOI: 10.1016/j.molmed.2017.02.007] [Citation(s) in RCA: 498] [Impact Index Per Article: 71.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/31/2017] [Accepted: 02/21/2017] [Indexed: 02/06/2023]
Abstract
Organoids are 3D in vitro culture systems derived from self-organizing stem cells. They can recapitulate the in vivo architecture, functionality, and genetic signature of original tissues. Thus, organoid technology has been rapidly applied to understanding stem cell biology, organogenesis, and various human pathologies. The recent development of human patient-derived organoids has enabled disease modeling with precision, highlighting their great potential in biomedical applications, translational medicine, and personalized therapy. In light of recent breakthroughs using organoids, it is only apt that we appreciate the advantages and shortcomings of this technology to exploit its full potential. We discuss recent advances in the application of organoids in studying cancer and hereditary diseases, as well as in the examination of host cell-microorganism interactions.
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174
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Abstract
Background Organoid is an in vitro three-dimensional organ-bud that shows realistic microanatomy and physiologic relevance. The progress in generating organoids that faithfully recapitulate human in vivo tissue composition has extended organoid applications from being just a basic research tool to a translational platform with a wide range of uses. Study of host-microbial interactions relies on model systems to mimic the in vivo infection. Researchers have developed various experimental models in vitro and in vivo to examine the dynamic host-microbial interactions. For some infectious pathogens, model systems are lacking whereas some of the used systems are far from optimal. Objective In the present work, we will review the brief history and recent findings using organoids for studying host-microbial interactions. Methods A systematic literature search was performed using the PubMed search engine. We also shared our data and research contribution to the field. Results we summarize the brief history of 3D organoids. We discuss the feasibility of using organoids in studying host-microbial interactions, focusing on the development of intestinal organoids and gastric organoids. We highlight the advantage and challenges of the new experimental models. Further, we discuss the future direction in using organoids in studying host-microbial interactions and its potential application in biomedical studies. Conclusion In combination with genetic, transcriptome and proteomic profiling, both murine- and human-derived organoids have revealed crucial aspects of development, homeostasis and diseases. Specifically, human organoids from susceptible host will be used to test their responses to pathogens, probiotics, and drugs. Organoid system is an exciting tool for studying infectious disease, microbiome, and therapy.
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175
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Hill DR, Spence JR. Gastrointestinal Organoids: Understanding the Molecular Basis of the Host-Microbe Interface. Cell Mol Gastroenterol Hepatol 2017; 3:138-149. [PMID: 28275681 PMCID: PMC5331777 DOI: 10.1016/j.jcmgh.2016.11.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/09/2016] [Indexed: 02/07/2023]
Abstract
In recent years, increasing attention has been devoted to the concept that microorganisms play an integral role in human physiology and pathophysiology. Despite this, the molecular basis of host-pathogen and host-symbiont interactions in the human intestine remains poorly understood owing to the limited availability of human tissue, and the biological complexity of host-microbe interactions. Over the past decade, technological advances have enabled long-term culture of organotypic intestinal tissue derived from human subjects and from human pluripotent stem cells, and these in vitro culture systems already have shown the potential to inform our understanding significantly of host-microbe interactions. Gastrointestinal organoids represent a substantial advance in structural and functional complexity over traditional in vitro cell culture models of the human gastrointestinal epithelium while retaining much of the genetic and molecular tractability that makes in vitro experimentation so appealing. The opportunity to model epithelial barrier dynamics, cellular differentiation, and proliferation more accurately in specific intestinal segments and in tissue containing a proportional representation of the diverse epithelial subtypes found in the native gut greatly enhances the translational potential of organotypic gastrointestinal culture systems. By using these tools, researchers have uncovered novel aspects of host-pathogen and host-symbiont interactions with the intestinal epithelium. Application of these tools promises to reveal new insights into the pathogenesis of infectious disease, inflammation, cancer, and the role of microorganisms in intestinal development. This review summarizes research on the use of gastrointestinal organoids as a model of the host-microbe interface.
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Key Words
- 3D, 3-dimensional
- CDI, Clostridium difficile infection
- ECM, extracellular matrix
- Enteroids
- Epithelium
- GI, gastrointestinal
- HIO, human intestinal organoids
- IFN, interferon
- IL, interleukin
- Intestine
- Model Systems
- NEC, necrotizing enterocolitis
- Pathogenesis
- SCFA, short-chain fatty acid
- Symbiosis
- TcdB, C difficile toxin B
- hPSC, human pluripotent stem cell
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Affiliation(s)
- David R. Hill
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jason R. Spence
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
- Center for Organogenesis, University of Michigan Medical School, Ann Arbor, Michigan
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176
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Barrila J, Yang J, Crabbé A, Sarker SF, Liu Y, Ott CM, Nelman-Gonzalez MA, Clemett SJ, Nydam SD, Forsyth RJ, Davis RR, Crucian BE, Quiriarte H, Roland KL, Brenneman K, Sams C, Loscher C, Nickerson CA. Three-dimensional organotypic co-culture model of intestinal epithelial cells and macrophages to study Salmonella enterica colonization patterns. NPJ Microgravity 2017; 3:10. [PMID: 28649632 PMCID: PMC5460263 DOI: 10.1038/s41526-017-0011-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/23/2016] [Accepted: 12/12/2016] [Indexed: 12/21/2022] Open
Abstract
Three-dimensional models of human intestinal epithelium mimic the differentiated form and function of parental tissues often not exhibited by two-dimensional monolayers and respond to Salmonella in key ways that reflect in vivo infections. To further enhance the physiological relevance of three-dimensional models to more closely approximate in vivo intestinal microenvironments encountered by Salmonella, we developed and validated a novel three-dimensional co-culture infection model of colonic epithelial cells and macrophages using the NASA Rotating Wall Vessel bioreactor. First, U937 cells were activated upon collagen-coated scaffolds. HT-29 epithelial cells were then added and the three-dimensional model was cultured in the bioreactor until optimal differentiation was reached, as assessed by immunohistochemical profiling and bead uptake assays. The new co-culture model exhibited in vivo-like structural and phenotypic characteristics, including three-dimensional architecture, apical-basolateral polarity, well-formed tight/adherens junctions, mucin, multiple epithelial cell types, and functional macrophages. Phagocytic activity of macrophages was confirmed by uptake of inert, bacteria-sized beads. Contribution of macrophages to infection was assessed by colonization studies of Salmonella pathovars with different host adaptations and disease phenotypes (Typhimurium ST19 strain SL1344 and ST313 strain D23580; Typhi Ty2). In addition, Salmonella were cultured aerobically or microaerobically, recapitulating environments encountered prior to and during intestinal infection, respectively. All Salmonella strains exhibited decreased colonization in co-culture (HT-29-U937) relative to epithelial (HT-29) models, indicating antimicrobial function of macrophages. Interestingly, D23580 exhibited enhanced replication/survival in both models following invasion. Pathovar-specific differences in colonization and intracellular co-localization patterns were observed. These findings emphasize the power of incorporating a series of related three-dimensional models within a study to identify microenvironmental factors important for regulating infection.
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Affiliation(s)
- Jennifer Barrila
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Jiseon Yang
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Aurélie Crabbé
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Shameema F. Sarker
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Yulong Liu
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - C. Mark Ott
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX USA
| | | | | | - Seth D. Nydam
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Rebecca J. Forsyth
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Richard R. Davis
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Brian E. Crucian
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX USA
| | | | - Kenneth L. Roland
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Karen Brenneman
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Clarence Sams
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX USA
| | - Christine Loscher
- Immunomodulation Research Group, School of Biotechnology, Dublin City University, Glasnevin, Ireland
| | - Cheryl A. Nickerson
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
- School of Life Sciences, Arizona State University, Tempe, AZ USA
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177
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Yu H, Hasan NM, In JG, Estes MK, Kovbasnjuk O, Zachos NC, Donowitz M. The Contributions of Human Mini-Intestines to the Study of Intestinal Physiology and Pathophysiology. Annu Rev Physiol 2017; 79:291-312. [PMID: 28192061 PMCID: PMC5549102 DOI: 10.1146/annurev-physiol-021115-105211] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lack of accessibility to normal and diseased human intestine and the inability to separate the different functional compartments of the intestine even when tissue could be obtained have held back the understanding of human intestinal physiology. Clevers and his associates identified intestinal stem cells and established conditions to grow "mini-intestines" ex vivo in differentiated and undifferentiated conditions. This pioneering work has made a new model of the human intestine available and has begun making contributions to the understanding of human intestinal transport in normal physiologic conditions and the pathophysiology of intestinal diseases. However, this model is reductionist and lacks many of the complexities of normal intestine. Consequently, it is not yet possible to predict how great the advances using this model will be for understanding human physiology and pathophysiology, nor how the model will be modified to include multiple other intestinal cell types and physical forces necessary to more closely approximate normal intestine. This review describes recent studies using mini-intestines, which have readdressed previously established models of normal intestinal transport physiology and newly examined intestinal pathophysiology. The emphasis is on studies with human enteroids grown either as three-dimensional spheroids or two-dimensional monolayers. In addition, comments are provided on mouse studies in cases when human studies have not yet been described.
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Affiliation(s)
- Huimin Yu
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Nesrin M Hasan
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Julie G In
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Olga Kovbasnjuk
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Nicholas C Zachos
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
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Wang B, Yao M, Lv L, Ling Z, Li L. The Human Microbiota in Health and Disease. ENGINEERING 2017; 3:71-82. [DOI: 10.1016/j.eng.2017.01.008] [Citation(s) in RCA: 430] [Impact Index Per Article: 61.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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179
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Saxena K, Simon LM, Zeng XL, Blutt SE, Crawford SE, Sastri NP, Karandikar UC, Ajami NJ, Zachos NC, Kovbasnjuk O, Donowitz M, Conner ME, Shaw CA, Estes MK. A paradox of transcriptional and functional innate interferon responses of human intestinal enteroids to enteric virus infection. Proc Natl Acad Sci U S A 2017; 114:E570-E579. [PMID: 28069942 PMCID: PMC5278484 DOI: 10.1073/pnas.1615422114] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The intestinal epithelium can limit enteric pathogens by producing antiviral cytokines, such as IFNs. Type I IFN (IFN-α/β) and type III IFN (IFN-λ) function at the epithelial level, and their respective efficacies depend on the specific pathogen and site of infection. However, the roles of type I and type III IFN in restricting human enteric viruses are poorly characterized as a result of the difficulties in cultivating these viruses in vitro and directly obtaining control and infected small intestinal human tissue. We infected nontransformed human intestinal enteroid cultures from multiple individuals with human rotavirus (HRV) and assessed the host epithelial response by using RNA-sequencing and functional assays. The dominant transcriptional pathway induced by HRV infection is a type III IFN-regulated response. Early after HRV infection, low levels of type III IFN protein activate IFN-stimulated genes. However, this endogenous response does not restrict HRV replication because replication-competent HRV antagonizes the type III IFN response at pre- and posttranscriptional levels. In contrast, exogenous IFN treatment restricts HRV replication, with type I IFN being more potent than type III IFN, suggesting that extraepithelial sources of type I IFN may be the critical IFN for limiting enteric virus replication in the human intestine.
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Affiliation(s)
- Kapil Saxena
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Lukas M Simon
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Narayan P Sastri
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Umesh C Karandikar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Nadim J Ajami
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Nicholas C Zachos
- Department of Medicine, Gastroenterology Division, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Olga Kovbasnjuk
- Department of Medicine, Gastroenterology Division, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Mark Donowitz
- Department of Medicine, Gastroenterology Division, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Margaret E Conner
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Chad A Shaw
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030;
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180
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Genome engineering of stem cell organoids for disease modeling. Protein Cell 2017; 8:315-327. [PMID: 28102490 PMCID: PMC5413597 DOI: 10.1007/s13238-016-0368-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/28/2016] [Indexed: 12/17/2022] Open
Abstract
Precision medicine emerges as a new approach that takes into account individual variability. Successful realization of precision medicine requires disease models that are able to incorporate personalized disease information and recapitulate disease development processes at the molecular, cellular and organ levels. With recent development in stem cell field, a variety of tissue organoids can be derived from patient specific pluripotent stem cells and adult stem cells. In combination with the state-of-the-art genome editing tools, organoids can be further engineered to mimic disease-relevant genetic and epigenetic status of a patient. This has therefore enabled a rapid expansion of sophisticated in vitro disease models, offering a unique system for fundamental and biomedical research as well as the development of personalized medicine. Here we summarize some of the latest advances and future perspectives in engineering stem cell organoids for human disease modeling.
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In JG, Foulke-Abel J, Estes MK, Zachos NC, Kovbasnjuk O, Donowitz M. Human mini-guts: new insights into intestinal physiology and host-pathogen interactions. Nat Rev Gastroenterol Hepatol 2016; 13:633-642. [PMID: 27677718 PMCID: PMC5079760 DOI: 10.1038/nrgastro.2016.142] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The development of indefinitely propagating human 'mini-guts' has led to a rapid advance in gastrointestinal research related to transport physiology, developmental biology, pharmacology, and pathophysiology. These mini-guts, also called enteroids or colonoids, are derived from LGR5+ intestinal stem cells isolated from the small intestine or colon. Addition of WNT3A and other growth factors promotes stemness and results in viable, physiologically functional human intestinal or colonic cultures that develop a crypt-villus axis and can be differentiated into all intestinal epithelial cell types. The success of research using human enteroids has highlighted the limitations of using animals or in vitro, cancer-derived cell lines to model transport physiology and pathophysiology. For example, curative or preventive therapies for acute enteric infections have been limited, mostly due to the lack of a physiological human intestinal model. However, the human enteroid model enables specific functional studies of secretion and absorption in each intestinal segment as well as observations of the earliest molecular events that occur during enteric infections. This Review describes studies characterizing these human mini-guts as a physiological model to investigate intestinal transport and host-pathogen interactions.
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Affiliation(s)
- Julie G In
- Department of Medicine, Division of Gastroenterology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, Maryland 21205, USA
| | - Jennifer Foulke-Abel
- Department of Medicine, Division of Gastroenterology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, Maryland 21205, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Nicholas C Zachos
- Department of Medicine, Division of Gastroenterology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, Maryland 21205, USA
| | - Olga Kovbasnjuk
- Department of Medicine, Division of Gastroenterology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, Maryland 21205, USA
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, Maryland 21205, USA
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182
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Flood P, Alvarez L, Reynaud EG. Free-floating epithelial micro-tissue arrays: a low cost and versatile technique. Biofabrication 2016; 8:045006. [DOI: 10.1088/1758-5090/8/4/045006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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183
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Liu F, Huang J, Ning B, Liu Z, Chen S, Zhao W. Drug Discovery via Human-Derived Stem Cell Organoids. Front Pharmacol 2016; 7:334. [PMID: 27713700 PMCID: PMC5032635 DOI: 10.3389/fphar.2016.00334] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/09/2016] [Indexed: 12/18/2022] Open
Abstract
Patient-derived cell lines and animal models have proven invaluable for the understanding of human intestinal diseases and for drug development although both inherently comprise disadvantages and caveats. Many genetically determined intestinal diseases occur in specific tissue microenvironments that are not adequately modeled by monolayer cell culture. Likewise, animal models incompletely recapitulate the complex pathologies of intestinal diseases of humans and fall short in predicting the effects of candidate drugs. Patient-derived stem cell organoids are new and effective models for the development of novel targeted therapies. With the use of intestinal organoids from patients with inherited diseases, the potency and toxicity of drug candidates can be evaluated better. Moreover, owing to the novel clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 genome-editing technologies, researchers can use organoids to precisely modulate human genetic status and identify pathogenesis-related genes of intestinal diseases. Therefore, here we discuss how patient-derived organoids should be grown and how advanced genome-editing tools may be applied to research on modeling of cancer and infectious diseases. We also highlight practical applications of organoids ranging from basic studies to drug screening and precision medicine.
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Affiliation(s)
- Fangkun Liu
- Department of Neurosurgery, Xiangya Hospital, Central South UniversityChangsha, China; Center for Inflammation and Epigenetics, Houston Methodist Research Institute, HoustonTX, USA
| | - Jing Huang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, HoustonTX, USA; Department of Psychiatry, The Second Xiangya Hospital, Central South University, ChangshaHunan, China; Mental Health Institute of the Second Xiangya Hospital, Central South University, ChangshaHunan, China; Chinese National Clinical Research Center on Mental Disorders, ChangshaHunan, China; Chinese National Technology Institute on Mental Disorders, ChangshaHunan, China; Hunan Key Laboratory of Psychiatry and Mental Health, ChangshaHunan, China
| | - Bo Ning
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston TX, USA
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University Changsha, China
| | - Shen Chen
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen UniversityGuangzhou, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen UniversityGuangzhou, China
| | - Wei Zhao
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen UniversityGuangzhou, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen UniversityGuangzhou, China
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184
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Modeling infectious diseases and host-microbe interactions in gastrointestinal organoids. Dev Biol 2016; 420:262-270. [PMID: 27640087 DOI: 10.1016/j.ydbio.2016.09.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 12/18/2022]
Abstract
Advances in stem cell research have allowed the development of 3-dimensional (3D) primary cell cultures termed organoid cultures, as they closely mimic the in vivo organization of different cell lineages. Bridging the gap between 2-dimensional (2D) monotypic cancer cell lines and whole organisms, organoids are now widely applied to model development and disease. Organoids hold immense promise for addressing novel questions in host-microbe interactions, infectious diseases and the resulting inflammatory conditions. Researchers have started to use organoids for modeling infection with pathogens, such as Helicobacter pylori or Salmonella enteritica, gut-microbiota interactions and inflammatory bowel disease. Future studies will broaden the spectrum of microbes used and continue to establish organoids as a standard model for human host-microbial interactions. Moreover, they will increasingly exploit the unique advantages of organoids, for example to address patient-specific responses to microbes.
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185
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Fatehullah A, Tan SH, Barker N. Organoids as an in vitro model of human development and disease. Nat Cell Biol 2016; 18:246-54. [PMID: 26911908 DOI: 10.1038/ncb3312] [Citation(s) in RCA: 898] [Impact Index Per Article: 112.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The in vitro organoid model is a major technological breakthrough that has already been established as an essential tool in many basic biology and clinical applications. This near-physiological 3D model facilitates an accurate study of a range of in vivo biological processes including tissue renewal, stem cell/niche functions and tissue responses to drugs, mutation or damage. In this Review, we discuss the current achievements, challenges and potential applications of this technique.
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Affiliation(s)
- Aliya Fatehullah
- A*STAR Institute of Medical Biology, 8A Biomedical Grove, 06-06 Immunos, 138648, Singapore
| | - Si Hui Tan
- A*STAR Institute of Medical Biology, 8A Biomedical Grove, 06-06 Immunos, 138648, Singapore
| | - Nick Barker
- A*STAR Institute of Medical Biology, 8A Biomedical Grove, 06-06 Immunos, 138648, Singapore.,Centre for Regenerative Medicine, 47 Little France Crescent, University of Edinburgh, Edinburgh, EH16 4TJ, UK.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore
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186
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Schweiger PJ, Jensen KB. Modeling human disease using organotypic cultures. Curr Opin Cell Biol 2016; 43:22-29. [PMID: 27474805 DOI: 10.1016/j.ceb.2016.07.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 06/21/2016] [Accepted: 07/05/2016] [Indexed: 12/18/2022]
Abstract
Reliable disease models are needed in order to improve quality of healthcare. This includes gaining better understanding of disease mechanisms, developing new therapeutic interventions and personalizing treatment. Up-to-date, the majority of our knowledge about disease states comes from in vivo animal models and in vitro cell culture systems. However, it has been exceedingly difficult to model disease at the tissue level. Since recently, the gap between cell line studies and in vivo modeling has been narrowing thanks to progress in biomaterials and stem cell research. Development of reliable 3D culture systems has enabled a rapid expansion of sophisticated in vitro models. Here we focus on some of the latest advances and future perspectives in 3D organoids for human disease modeling.
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Affiliation(s)
- Pawel J Schweiger
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Kim B Jensen
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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187
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Nutrient Deprivation Affects Salmonella Invasion and Its Interaction with the Gastrointestinal Microbiota. PLoS One 2016; 11:e0159676. [PMID: 27437699 PMCID: PMC4954642 DOI: 10.1371/journal.pone.0159676] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/06/2016] [Indexed: 01/30/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a foodborne enteric pathogen and a major cause of gastroenteritis in humans. It is known that molecules derived from the human fecal microbiota downregulate S. Typhimurium virulence gene expression and induce a starvation-like response. In this study, S. Typhimurium was cultured in minimal media to mimic starvation conditions such as that experienced by S. Typhimurium in the human intestinal tract, and the pathogen’s virulence in vitro and in vivo was measured. S. Typhimurium cultured in minimal media displayed a reduced ability to invade human epithelial cells in a manner that was at least partially independent of the Salmonella Pathogenicity Island 1 (SPI-1) type III secretion system. Nutrient deprivation did not, however, alter the ability of S. Typhimurium to replicate and survive inside epithelial cells. In a murine model of S. Typhimurium-induced gastroenteritis, prior cultivation in minimal media did not alter the pathogen’s ability to colonize mice, nor did it affect levels of gastrointestinal inflammation. Upon examining the post-infection fecal gastrointestinal microbiota, we found that specifically in the 129Sv/ImJ murine strain S. Typhimurium cultured in minimal media induced differential microbiota compositional shifts compared to that of S. Typhimurium cultured in rich media. Together these findings demonstrate that S. Typhimurium remains a potent pathogen even in the face of nutritional deprivation, but nevertheless that nutrient deprivation encountered in this environment elicits significant changes in the bacterium genetic programme, as well as its capacity to alter host microbiota composition.
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188
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Emerging Technologies for Gut Microbiome Research. Trends Microbiol 2016; 24:887-901. [PMID: 27426971 DOI: 10.1016/j.tim.2016.06.008] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/06/2016] [Accepted: 06/23/2016] [Indexed: 02/06/2023]
Abstract
Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies, including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches, will improve the efficiency and quality of microbiome research. Here, we discuss emerging technologies and their potential impact on gut microbiome studies.
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189
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Mills M, Estes MK. Physiologically relevant human tissue models for infectious diseases. Drug Discov Today 2016; 21:1540-1552. [PMID: 27352632 DOI: 10.1016/j.drudis.2016.06.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 06/15/2016] [Accepted: 06/21/2016] [Indexed: 12/16/2022]
Abstract
Limitations of animal infection models have engendered longstanding obstacles in basic science and translational research. Lack of suitable animal models, the need for better predictors of human immune responses and pathogens that grow poorly or not at all outside the human host impact our ability to study infectious agents that cause human disease, generation of essential tools for genetic manipulation of microbial pathogens and development of vaccines, therapeutics and host-targeted immunotherapies. The advent of conceptual and methodological advances in tissue engineering along with collaborative efforts between the bioengineering and infectious diseases scientific communities hold great promise to overcome these significant barriers.
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Affiliation(s)
- Melody Mills
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Mary K Estes
- Molecular Virology and Microbiology and Medicine-GI, Baylor College of Medicine, Houston, TX, USA
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190
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Aurora M, Spence JR. hPSC-derived lung and intestinal organoids as models of human fetal tissue. Dev Biol 2016; 420:230-238. [PMID: 27287882 DOI: 10.1016/j.ydbio.2016.06.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/23/2016] [Accepted: 06/04/2016] [Indexed: 02/07/2023]
Abstract
In vitro human pluripotent stem cell (hPSC) derived tissues are excellent models to study certain aspects of normal human development. Current research in the field of hPSC derived tissues reveals these models to be inherently fetal-like on both a morphological and gene expression level. In this review we briefly discuss current methods for differentiating lung and intestinal tissue from hPSCs into individual 3-dimensional units called organoids. We discuss how these methods mirror what is known about in vivo signaling pathways of the developing embryo. Additionally, we will review how the inherent immaturity of these models lends them to be particularly valuable in the study of immature human tissues in the clinical setting of premature birth. Human lung organoids (HLOs) and human intestinal organoids (HIOs) not only model normal development, but can also be utilized to study several important diseases of prematurity such as respiratory distress syndrome (RDS), bronchopulmonary dysplasia (BPD), and necrotizing enterocolitis (NEC).
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Affiliation(s)
- Megan Aurora
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States; Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI, United States
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191
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Dedhia PH, Bertaux-Skeirik N, Zavros Y, Spence JR. Organoid Models of Human Gastrointestinal Development and Disease. Gastroenterology 2016; 150:1098-1112. [PMID: 26774180 PMCID: PMC4842135 DOI: 10.1053/j.gastro.2015.12.042] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 12/21/2022]
Abstract
We have greatly advanced our ability to grow a diverse range of tissue-derived and pluripotent stem cell-derived gastrointestinal (GI) tissues in vitro. These systems, broadly referred to as organoids, have allowed the field to move away from the often nonphysiological, transformed cell lines that have been used for decades in GI research. Organoids are derived from primary tissues and have the capacity for long-term growth. They contain varying levels of cellular complexity and physiological similarity to native organ systems. We review the latest discoveries from studies of tissue-derived and pluripotent stem cell-derived intestinal, gastric, esophageal, liver, and pancreatic organoids. These studies have provided important insights into GI development, tissue homeostasis, and disease and might be used to develop personalized medicines.
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Affiliation(s)
- Priya H. Dedhia
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA,Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nina Bertaux-Skeirik
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Yana Zavros
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, Ohio.
| | - Jason R. Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA,Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA,Authors for Correspondence: Jason R. Spence – , Twitter: @TheSpenceLab, Yana Zavros –
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192
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iPSCs: A Minireview from Bench to Bed, including Organoids and the CRISPR System. Stem Cells Int 2016; 2016:5934782. [PMID: 26880972 PMCID: PMC4736429 DOI: 10.1155/2016/5934782] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 10/19/2015] [Accepted: 10/25/2015] [Indexed: 12/22/2022] Open
Abstract
When Dolly the sheep was born, the first probe into an adult mammalian genome traveling back in time and generating a whole new animal appeared. Ten years later, the reprogramming process became a defined method of producing induced pluripotent stem cells (iPSCs) through the overexpression of four transcription factors. iPSCs are capable of originating virtually all types of cells and tissues, including a whole new animal. The reprogramming strategies based on patient-derived cells should make the development of clinical applications of cell based therapy much more straightforward. Here, we analyze the current state, opportunities, and challenges of iPSCs from bench to bed, including organoids and the CRISPR system.
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193
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Johnson JZ, Hockemeyer D. Human stem cell-based disease modeling: prospects and challenges. Curr Opin Cell Biol 2015; 37:84-90. [PMID: 26546888 DOI: 10.1016/j.ceb.2015.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/10/2015] [Accepted: 10/14/2015] [Indexed: 01/10/2023]
Abstract
Human stem cell-based disease models have great promise to advance our understanding of human disease. These models can be derived from patients with genetic disorders and manipulated with genome editing and myriad differentiation protocols to model pathologies in vitro. However, several challenges have impeded the full potential of stem cell-based in vitro disease modeling. Many genetically predisposed diseases take time to manifest and occur in specific tissue microenvironments, and these parameters are often not adequately modeled using conventional shorter-term monolayer cultures. These challenges must be overcome especially for cases where animal models also incompletely recapitulate the complex pathologies found in humans. As prominent ways to tackle these challenges we discuss here how advanced genome editing tools in human stem cells and human organoid cultures, specifically the example of intestinal organoids, contribute genetically defined models that recapitulate phenotypes of disease.
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Affiliation(s)
- Joshua Z Johnson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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194
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Leslie JL, Young VB. A whole new ball game: Stem cell-derived epithelia in the study of host-microbe interactions. Anaerobe 2015; 37:25-8. [PMID: 26549696 DOI: 10.1016/j.anaerobe.2015.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 10/30/2015] [Accepted: 10/31/2015] [Indexed: 01/02/2023]
Abstract
Recent advances in developmental and stem cell biology have resulted in techniques that enable the generation and maintenance of complex epithelium in vitro. While these models have been utilized to study host development and disease, a renewed appreciation of host-microbe interactions has sparked interest in employing these new techniques to study microbes at the epithelial interface. Here we review the current advances in host-microbe interactions that have resulted from experiments using these complex epithelia. Furthermore we highlight aspects of these techniques that warrant further development to facilitate the study of host-microbe interactions.
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Affiliation(s)
- Jhansi L Leslie
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 W Medical Center Dr., Ann Arbor, MI 48109, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 W Medical Center Dr., Ann Arbor, MI 48109, USA; Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, 1150 W Medical Center Dr., Ann Arbor, MI 48109, USA.
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