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Banerjee P, Senapati S. Translational Utility of Organoid Models for Biomedical Research on Gastrointestinal Diseases. Stem Cell Rev Rep 2024; 20:1441-1458. [PMID: 38758462 DOI: 10.1007/s12015-024-10733-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 05/18/2024]
Abstract
Organoid models have recently been utilized to study 3D human-derived tissue systems to uncover tissue architecture and adult stem cell biology. Patient-derived organoids unambiguously provide the most suitable in vitro system to study disease biology with the actual genetic background. With the advent of much improved and innovative approaches, patient-derived organoids can potentially be used in regenerative medicine. Various human tissues were explored to develop organoids due to their multifold advantage over the conventional in vitro cell line culture approach and in vivo models. Gastrointestinal (GI) tissues have been widely studied to establish organoids and organ-on-chip for screening drugs, nutraceuticals, and other small molecules having therapeutic potential. The function of channel proteins, transporters, and transmembrane proteins was also explained. The successful application of genome editing in organoids using the CRISPR-Cas approach has been reported recently. GI diseases such as Celiac disease (CeD), Inflammatory bowel disease (IBD), and common GI cancers have been investigated using several patient-derived organoid models. Recent advancements on organoid bio-banking and 3D bio-printing contributed significantly in personalized disease management and therapeutics. This article reviews the available literature on investigations and translational applications of patient-derived GI organoid models, notably on elucidating gut-microbial interaction and epigenetic modifications.
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Affiliation(s)
- Pratibha Banerjee
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Sabyasachi Senapati
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India.
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2
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Kochanowsky R, Carothers K, Roxas BAP, Anwar F, Viswanathan VK, Vedantam G. Clostridioides difficile superoxide reductase mitigates oxygen sensitivity. J Bacteriol 2024; 206:e0017524. [PMID: 38953644 PMCID: PMC11270899 DOI: 10.1128/jb.00175-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Clostridioides difficile causes a serious diarrheal disease and is a common healthcare-associated bacterial pathogen. Although it has a major impact on human health, the mechanistic details of C. difficile intestinal colonization remain undefined. C. difficile is highly sensitive to oxygen and requires anaerobic conditions for in vitro growth. However, the mammalian gut is not devoid of oxygen, and C. difficile tolerates moderate oxidative stress in vivo. The C. difficile genome encodes several antioxidant proteins, including a predicted superoxide reductase (SOR) that is upregulated upon exposure to antimicrobial peptides. The goal of this study was to establish SOR enzymatic activity and assess its role in protecting C. difficile against oxygen exposure. Insertional inactivation of sor rendered C. difficile more sensitive to superoxide, indicating that SOR contributes to antioxidant defense. Heterologous C. difficile sor expression in Escherichia coli conferred protection against superoxide-dependent growth inhibition, and the corresponding cell lysates showed superoxide scavenging activity. Finally, a C. difficile SOR mutant exhibited global proteome changes under oxygen stress when compared to the parent strain. Collectively, our data establish the enzymatic activity of C. difficile SOR, confirm its role in protection against oxidative stress, and demonstrate SOR's broader impacts on the C. difficile vegetative cell proteome.IMPORTANCEClostridioides difficile is an important pathogen strongly associated with healthcare settings and capable of causing severe diarrheal disease. While considered a strict anaerobe in vitro, C. difficile has been shown to tolerate low levels of oxygen in the mammalian host. Among other well-characterized antioxidant proteins, the C. difficile genome encodes a predicted superoxide reductase (SOR), an understudied component of antioxidant defense in pathogens. The significance of the research reported herein is the characterization of SOR's enzymatic activity, including confirmation of its role in protecting C. difficile against oxidative stress. This furthers our understanding of C. difficile pathogenesis and presents a potential new avenue for targeted therapies.
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Affiliation(s)
- Rebecca Kochanowsky
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Katelyn Carothers
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Bryan Angelo P. Roxas
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Farhan Anwar
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - V. K. Viswanathan
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
- BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, USA
| | - Gayatri Vedantam
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
- BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, USA
- Southern Arizona VA Healthcare System, Tucson, Arizona, USA
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3
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Liu N, Liu S, Xu X, Nong X, Chen H. Organoids as an in vitro model to study human tumors and bacteria. J Surg Oncol 2024; 129:1390-1400. [PMID: 38534036 DOI: 10.1002/jso.27626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024]
Abstract
Organoids faithfully replicate the morphological structure, physiological functions, stable phenotype of the source tissue. Recent research indicates that bacteria can significantly influence the initiation, advancement, and treatment of tumors. This article provides a comprehensive review of the applications of organoid technology in tumor research, the relationship between bacteria and the genesis and development of tumors, and the exploration of the impact of bacteria on tumors and their applications in research.
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Affiliation(s)
- Naiyu Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shuxi Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaoyue Xu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - XianXian Nong
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hong Chen
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
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4
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Pourliotopoulou E, Karampatakis T, Kachrimanidou M. Exploring the Toxin-Mediated Mechanisms in Clostridioides difficile Infection. Microorganisms 2024; 12:1004. [PMID: 38792835 PMCID: PMC11124097 DOI: 10.3390/microorganisms12051004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Clostridioides difficile infection (CDI) is the leading cause of nosocomial antibiotic-associated diarrhea, and colitis, with increasing incidence and healthcare costs. Its pathogenesis is primarily driven by toxins produced by the bacterium C. difficile, Toxin A (TcdA) and Toxin B (TcdB). Certain strains produce an additional toxin, the C. difficile transferase (CDT), which further enhances the virulence and pathogenicity of C. difficile. These toxins disrupt colonic epithelial barrier integrity, and induce inflammation and cellular damage, leading to CDI symptoms. Significant progress has been made in the past decade in elucidating the molecular mechanisms of TcdA, TcdB, and CDT, which provide insights into the management of CDI and the future development of novel treatment strategies based on anti-toxin therapies. While antibiotics are common treatments, high recurrence rates necessitate alternative therapies. Bezlotoxumab, targeting TcdB, is the only available anti-toxin, yet limitations persist, prompting ongoing research. This review highlights the current knowledge of the structure and mechanism of action of C. difficile toxins and their role in disease. By comprehensively describing the toxin-mediated mechanisms, this review provides insights for the future development of novel treatment strategies and the management of CDI.
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Affiliation(s)
- Evdokia Pourliotopoulou
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
| | | | - Melania Kachrimanidou
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
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5
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Llorente C. The Imperative for Innovative Enteric Nervous System-Intestinal Organoid Co-Culture Models: Transforming GI Disease Modeling and Treatment. Cells 2024; 13:820. [PMID: 38786042 PMCID: PMC11119846 DOI: 10.3390/cells13100820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
This review addresses the need for innovative co-culture systems integrating the enteric nervous system (ENS) with intestinal organoids. The breakthroughs achieved through these techniques will pave the way for a transformative era in gastrointestinal (GI) disease modeling and treatment strategies. This review serves as an introduction to the companion protocol paper featured in this journal. The protocol outlines the isolation and co-culture of myenteric and submucosal neurons with small intestinal organoids. This review provides an overview of the intestinal organoid culture field to establish a solid foundation for effective protocol application. Remarkably, the ENS surpasses the number of neurons in the spinal cord. Referred to as the "second brain", the ENS orchestrates pivotal roles in GI functions, including motility, blood flow, and secretion. The ENS is organized into myenteric and submucosal plexuses. These plexuses house diverse subtypes of neurons. Due to its proximity to the gut musculature and its cell type complexity, there are methodological intricacies in studying the ENS. Diverse approaches such as primary cell cultures, three-dimensional (3D) neurospheres, and induced ENS cells offer diverse insights into the multifaceted functionality of the ENS. The ENS exhibits dynamic interactions with the intestinal epithelium, the muscle layer, and the immune system, influencing epithelial physiology, motility, immune responses, and the microbiome. Neurotransmitters, including acetylcholine (ACh), serotonin (5-HT), and vasoactive intestinal peptide (VIP), play pivotal roles in these intricate interactions. Understanding these dynamics is imperative, as the ENS is implicated in various diseases, ranging from neuropathies to GI disorders and neurodegenerative diseases. The emergence of organoid technology presents an unprecedented opportunity to study ENS interactions within the complex milieu of the small and large intestines. This manuscript underscores the urgent need for standardized protocols and advanced techniques to unravel the complexities of the ENS and its dynamic relationship with the gut ecosystem. The insights gleaned from such endeavors hold the potential to revolutionize GI disease modeling and treatment paradigms.
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Affiliation(s)
- Cristina Llorente
- Department of Medicine, University of California San Diego, MC0063, 9500 Gilman Drive, La Jolla, CA 92093, USA
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6
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Wu Z, Liu H, Wang X. Advancements in understanding bacterial enteritis pathogenesis through organoids. Mol Biol Rep 2024; 51:512. [PMID: 38622483 DOI: 10.1007/s11033-024-09495-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Bacterial enteritis has a substantial role in contributing to a large portion of the global disease burden and serves as a major cause of newborn mortality. Despite advancements gained from current animal and cell models in improving our understanding of pathogens, their widespread application is hindered by apparent drawbacks. Therefore, more precise models are imperatively required to develop more accurate studies on host-pathogen interactions and drug discovery. Since the emergence of intestinal organoids, massive studies utilizing organoids have been conducted to study the pathogenesis of bacterial enteritis, revealing new mechanisms and validating established ones. In this review, we focus on the advancements of several bacterial pathogenesis mechanisms observed in intestinal organoid/enteroid models, exploring the host response and bacterial effectors during the infection process. Finally, we address the features that warrant additional investigation or could be enhanced in existing organoid models in order to guide future research endeavors.
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Affiliation(s)
- Zhengyang Wu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hongyuan Liu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xianli Wang
- Shanghai Jiao Tong University School of Public Health, Shanghai, 200025, China.
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7
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Csukovich G, Wagner M, Walter I, Burger S, Tschulenk W, Steinborn R, Pratscher B, Burgener IA. Polarity reversal of canine intestinal organoids reduces proliferation and increases cell death. Cell Prolif 2024; 57:e13544. [PMID: 37697686 PMCID: PMC10849783 DOI: 10.1111/cpr.13544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/10/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023] Open
Abstract
Apical-out intestinal organoids are a relatively simple method of gaining access to the apical cell surface and have faced increasing scientific interest over the last few years. Apical-out organoids can thus be used for disease modelling to compare differing effects on the basolateral versus the apical cell surface. However, these 'inside-out' organoids die relatively quickly and cannot be propagated as long as their basal-out counterparts. Here, we show that apical-out organoids have drastically reduced proliferative potential, as evidenced by immunohistochemical staining and the incorporation of the thymidine analogue EdU. At the same time, cell death levels are increased. Nevertheless, these phenomena cannot be explained by an induction of differentiation, as the gene expression of key marker genes for various cell types does not change over time.
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Affiliation(s)
- Georg Csukovich
- Department for Companion Animals and Horses, Small Animal Internal MedicineVetmeduniViennaAustria
| | - Maximilian Wagner
- Department for Companion Animals and Horses, Small Animal Internal MedicineVetmeduniViennaAustria
| | - Ingrid Walter
- VetBioBank, VetCoreVetmeduniViennaAustria
- Institute of Morphology, Working Group HistologyVetmeduniViennaAustria
| | | | | | | | - Barbara Pratscher
- Department for Companion Animals and Horses, Small Animal Internal MedicineVetmeduniViennaAustria
| | - Iwan Anton Burgener
- Department for Companion Animals and Horses, Small Animal Internal MedicineVetmeduniViennaAustria
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Cameron O, Neves JF, Gentleman E. Listen to Your Gut: Key Concepts for Bioengineering Advanced Models of the Intestine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302165. [PMID: 38009508 PMCID: PMC10837392 DOI: 10.1002/advs.202302165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 10/12/2023] [Indexed: 11/29/2023]
Abstract
The intestine performs functions central to human health by breaking down food and absorbing nutrients while maintaining a selective barrier against the intestinal microbiome. Key to this barrier function are the combined efforts of lumen-lining specialized intestinal epithelial cells, and the supportive underlying immune cell-rich stromal tissue. The discovery that the intestinal epithelium can be reproduced in vitro as intestinal organoids introduced a new way to understand intestinal development, homeostasis, and disease. However, organoids reflect the intestinal epithelium in isolation whereas the underlying tissue also contains myriad cell types and impressive chemical and structural complexity. This review dissects the cellular and matrix components of the intestine and discusses strategies to replicate them in vitro using principles drawing from bottom-up biological self-organization and top-down bioengineering. It also covers the cellular, biochemical and biophysical features of the intestinal microenvironment and how these can be replicated in vitro by combining strategies from organoid biology with materials science. Particularly accessible chemistries that mimic the native extracellular matrix are discussed, and bioengineering approaches that aim to overcome limitations in modelling the intestine are critically evaluated. Finally, the review considers how further advances may extend the applications of intestinal models and their suitability for clinical therapies.
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Affiliation(s)
- Oliver Cameron
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
| | - Joana F. Neves
- Centre for Host‐Microbiome InteractionsKing's College LondonLondonSE1 9RTUK
| | - Eileen Gentleman
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
- Department of Biomedical SciencesUniversity of LausanneLausanne1005Switzerland
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9
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McCoy R, Oldroyd S, Yang W, Wang K, Hoven D, Bulmer D, Zilbauer M, Owens RM. In Vitro Models for Investigating Intestinal Host-Pathogen Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306727. [PMID: 38155358 PMCID: PMC10885678 DOI: 10.1002/advs.202306727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/01/2023] [Indexed: 12/30/2023]
Abstract
Infectious diseases are increasingly recognized as a major threat worldwide due to the rise of antimicrobial resistance and the emergence of novel pathogens. In vitro models that can adequately mimic in vivo gastrointestinal physiology are in high demand to elucidate mechanisms behind pathogen infectivity, and to aid the design of effective preventive and therapeutic interventions. There exists a trade-off between simple and high throughput models and those that are more complex and physiologically relevant. The complexity of the model used shall be guided by the biological question to be addressed. This review provides an overview of the structure and function of the intestine and the models that are developed to emulate this. Conventional models are discussed in addition to emerging models which employ engineering principles to equip them with necessary advanced monitoring capabilities for intestinal host-pathogen interrogation. Limitations of current models and future perspectives on the field are presented.
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Affiliation(s)
- Reece McCoy
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Sophie Oldroyd
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Woojin Yang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Kaixin Wang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Darius Hoven
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - David Bulmer
- Department of PharmacologyUniversity of CambridgeCambridgeCB2 1PDUK
| | - Matthias Zilbauer
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Róisín M. Owens
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
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10
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Vuotto C, Donelli G, Buckley A, Chilton C. Clostridioides difficile Biofilm. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:249-272. [PMID: 38175479 DOI: 10.1007/978-3-031-42108-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides difficile infection (CDI), previously Clostridium difficile infection, is a symptomatic infection of the large intestine caused by the spore-forming anaerobic, gram-positive bacterium Clostridioides difficile. CDI is an important healthcare-associated disease worldwide, characterized by high levels of recurrence, morbidity, and mortality. CDI is observed at a higher rate in immunocompromised patients after antimicrobial therapy, with antibiotics disrupting the commensal microbiota and promoting C. difficile colonization of the gastrointestinal tract.A rise in clinical isolates resistant to multiple antibiotics and the reduced susceptibility to the most commonly used antibiotic molecules have made the treatment of CDI more complicated, allowing the persistence of C. difficile in the intestinal environment.Gut colonization and biofilm formation have been suggested to contribute to the pathogenesis and persistence of C. difficile. In fact, biofilm growth is considered as a serious threat because of the related antimicrobial tolerance that makes antibiotic therapy often ineffective. This is the reason why the involvement of C. difficile biofilm in the pathogenesis and recurrence of CDI is attracting more and more interest, and the mechanisms underlying biofilm formation of C. difficile as well as the role of biofilm in CDI are increasingly being studied by researchers in the field.Findings on C. difficile biofilm, possible implications in CDI pathogenesis and treatment, efficacy of currently available antibiotics in treating biofilm-forming C. difficile strains, and some antimicrobial alternatives under investigation will be discussed here.
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Affiliation(s)
- Claudia Vuotto
- Microbial Biofilm Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy.
| | | | - Anthony Buckley
- Microbiome and Nutritional Sciences Group, School of Food Science & Nutrition, University of Leeds, Leeds, UK
| | - Caroline Chilton
- Healthcare Associated Infection Research Group, Section of Molecular Gastroenterology, Leeds Institute for Medical Research at St James, University of Leeds, Leeds, UK
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11
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Liu W, Wang Q, Bai Y, Xiao H, Li Z, Wang Y, Wang Q, Yang J, Sun H. Potential Application of Intestinal Organoids in Intestinal Diseases. Stem Cell Rev Rep 2024; 20:124-137. [PMID: 37938407 DOI: 10.1007/s12015-023-10651-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2023] [Indexed: 11/09/2023]
Abstract
To accurately reveal the scenario and mecahnism of gastrointestinal diseases, the establishment of in vitro models of intestinal diseases and drug screening platforms have become the focus of attention. Over the past few decades, animal models and immortalized cell lines have provided valuable but limited insights into gastrointestinal research. In recent years, the development of intestinal organoid culture system has revolutionized in vitro studies of intestinal diseases. Intestinal organoids are derived from self-renewal and self-organization intestinal stem cells (ISCs), which can replicate the genetic characteristics, functions, and structures of the original tissues. Consequently, they provide new stragety for studying various intestinal diseases in vitro. In the review, we will discuss the culture techniques of intestinal organoids and describe the use of intestinal organoids as research tools for intestinal diseases. The role of intestinal epithelial cells (IECs) played in the pathogenesis of inflammatory bowel diseases (IBD) and the treatment of intestinal epithelial dysfunction will be highlighted. Besides, we review the current knowledge on using intestinal organoids as models to study the pathogenesis of IBD caused by epithelial dysfunction and to develop new therapeutic approaches. Finally, we shed light on the current challenges of using intestinal organoids as in vitro models.
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Affiliation(s)
- Wenxiu Liu
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, 730030, Gansu, China
- Lanzhou Huazhitiancheng Biotechnologies Co., Ltd, Lanzhou, 730000, Gansu, China
| | - Qian Wang
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, 730030, Gansu, China
| | - Yanrui Bai
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, 730030, Gansu, China
| | - Han Xiao
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, 730030, Gansu, China
| | - Zhunduo Li
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, 730030, Gansu, China
| | - Yan Wang
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, 730030, Gansu, China
| | - Qi Wang
- Lanzhou Huazhitiancheng Biotechnologies Co., Ltd, Lanzhou, 730000, Gansu, China.
| | - Jing Yang
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, 730030, Gansu, China.
| | - Hui Sun
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, 730030, Gansu, China.
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12
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Bouges E, Segers C, Leys N, Lebeer S, Zhang J, Mastroleo F. Human Intestinal Organoids and Microphysiological Systems for Modeling Radiotoxicity and Assessing Radioprotective Agents. Cancers (Basel) 2023; 15:5859. [PMID: 38136404 PMCID: PMC10741417 DOI: 10.3390/cancers15245859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Radiotherapy is a commonly employed treatment for colorectal cancer, yet its radiotoxicity-related impact on healthy tissues raises significant health concerns. This highlights the need to use radioprotective agents to mitigate these side effects. This review presents the current landscape of human translational radiobiology, outlining the limitations of existing models and proposing engineering solutions. We delve into radiotherapy principles, encompassing mechanisms of radiation-induced cell death and its influence on normal and cancerous colorectal cells. Furthermore, we explore the engineering aspects of microphysiological systems to represent radiotherapy-induced gastrointestinal toxicity and how to include the gut microbiota to study its role in treatment failure and success. This review ultimately highlights the main challenges and future pathways in translational research for pelvic radiotherapy-induced toxicity. This is achieved by developing a humanized in vitro model that mimics radiotherapy treatment conditions. An in vitro model should provide in-depth analyses of host-gut microbiota interactions and a deeper understanding of the underlying biological mechanisms of radioprotective food supplements. Additionally, it would be of great value if these models could produce high-throughput data using patient-derived samples to address the lack of human representability to complete clinical trials and improve patients' quality of life.
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Affiliation(s)
- Eloïse Bouges
- RadioPharma Research, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium; (E.B.); (C.S.); (N.L.)
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium;
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
| | - Charlotte Segers
- RadioPharma Research, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium; (E.B.); (C.S.); (N.L.)
| | - Natalie Leys
- RadioPharma Research, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium; (E.B.); (C.S.); (N.L.)
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium;
| | - Jianbo Zhang
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, 1105 BK Amsterdam, The Netherlands
| | - Felice Mastroleo
- RadioPharma Research, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium; (E.B.); (C.S.); (N.L.)
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13
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Obreque J, Vergara-Gómez L, Venegas N, Weber H, Owen GI, Pérez-Moreno P, Leal P, Roa JC, Bizama C. Advances towards the use of gastrointestinal tumor patient-derived organoids as a therapeutic decision-making tool. Biol Res 2023; 56:63. [PMID: 38041132 PMCID: PMC10693174 DOI: 10.1186/s40659-023-00476-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023] Open
Abstract
In December 2022 the US Food and Drug Administration (FDA) removed the requirement that drugs in development must undergo animal testing before clinical evaluation, a declaration that now demands the establishment and verification of ex vivo preclinical models that closely represent tumor complexity and that can predict therapeutic response. Fortunately, the emergence of patient-derived organoid (PDOs) culture has enabled the ex vivo mimicking of the pathophysiology of human tumors with the reassembly of tissue-specific features. These features include histopathological variability, molecular expression profiles, genetic and cellular heterogeneity of parental tissue, and furthermore growing evidence suggests the ability to predict patient therapeutic response. Concentrating on the highly lethal and heterogeneous gastrointestinal (GI) tumors, herein we present the state-of-the-art and the current methodology of PDOs. We highlight the potential additions, improvements and testing required to allow the ex vivo of study the tumor microenvironment, as well as offering commentary on the predictive value of clinical response to treatments such as chemotherapy and immunotherapy.
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Affiliation(s)
- Javiera Obreque
- Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, Office 526, 8330024, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Centro de Prevención y Control de Cáncer (CECAN), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis Vergara-Gómez
- Centre of Excellence in Translational Medicine (CEMT) and Scientific and Technological Bioresource Nucleus (BIOREN), Biomedicine and Translational Research Lab, Universidad de La Frontera, 4810296, Temuco, Chile
| | - Nicolás Venegas
- Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, Office 526, 8330024, Santiago, Chile
| | - Helga Weber
- Centre of Excellence in Translational Medicine (CEMT) and Scientific and Technological Bioresource Nucleus (BIOREN), Biomedicine and Translational Research Lab, Universidad de La Frontera, 4810296, Temuco, Chile
| | - Gareth I Owen
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Advanced Center for Chronic Diseases, Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro de Prevención y Control de Cáncer (CECAN), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo Pérez-Moreno
- Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, Office 526, 8330024, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
| | - Pamela Leal
- Centre of Excellence in Translational Medicine (CEMT) and Scientific and Technological Bioresource Nucleus (BIOREN), Biomedicine and Translational Research Lab, Universidad de La Frontera, 4810296, Temuco, Chile
| | - Juan Carlos Roa
- Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, Office 526, 8330024, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Centro de Prevención y Control de Cáncer (CECAN), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carolina Bizama
- Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362, Office 526, 8330024, Santiago, Chile.
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile.
- Advanced Center for Chronic Diseases, Pontificia Universidad Católica de Chile, Santiago, Chile.
- Centro de Prevención y Control de Cáncer (CECAN), Pontificia Universidad Católica de Chile, Santiago, Chile.
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14
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Bornholdt J, Müller CV, Nielsen MJ, Strickertsson J, Rago D, Chen Y, Maciag G, Skov J, Wellejus A, Schweiger PJ, Hansen SL, Broholm C, Gögenur I, Maimets M, Sloth S, Hendel J, Baker A, Sandelin A, Jensen KB. Detecting host responses to microbial stimulation using primary epithelial organoids. Gut Microbes 2023; 15:2281012. [PMID: 37992398 PMCID: PMC10730191 DOI: 10.1080/19490976.2023.2281012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/05/2023] [Indexed: 11/24/2023] Open
Abstract
The intestinal epithelium is constantly exposed to microbes residing in the lumen. Traditionally, the response to microbial interactions has been studied in cell lines derived from cancerous tissues, e.g. Caco-2. It is, however, unclear how the responses in these cancer cell lines reflect the responses of a normal epithelium and whether there might be microbial strain-specific effects. To address these questions, we derived organoids from the small intestine from a cohort of healthy individuals. Culturing intestinal epithelium on a flat laminin matrix induced their differentiation, facilitating analysis of microbial responses via the apical membrane normally exposed to the luminal content. Here, it was evident that the healthy epithelium across multiple individuals (n = 9) demonstrates robust acute both common and strain-specific responses to a range of probiotic bacterial strains (BB-12Ⓡ, LGGⓇ, DSM33361, and Bif195). Importantly, parallel experiments using the Caco-2 cell line provide no acute response. Collectively, we demonstrate that primary epithelial cells maintained as organoids represent a valuable resource for assessing interactions between the epithelium and luminal microbes across individuals, and that these models are likely to contribute to a better understanding of host microbe interactions.
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Affiliation(s)
- Jette Bornholdt
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Human Health Research, Chr. Hansen AS, Hørsholm, Denmark
| | - Christina V. Müller
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Maria Juul Nielsen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Daria Rago
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yun Chen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Human Health Research, Chr. Hansen AS, Hørsholm, Denmark
| | - Grzegorz Maciag
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Skov
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Anja Wellejus
- Human Health Research, Chr. Hansen AS, Hørsholm, Denmark
| | - Pawel J. Schweiger
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Stine L. Hansen
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | | | - Ismail Gögenur
- Center for Surgical Science, Department of Surgery, Zealand University Hospital, Koge, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Martti Maimets
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Stine Sloth
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Hendel
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Adam Baker
- Human Health Research, Chr. Hansen AS, Hørsholm, Denmark
| | - Albin Sandelin
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kim B. Jensen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
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15
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Tan H, Chen X, Wang C, Song J, Xu J, Zhang Y, Suo H. Intestinal organoid technology and applications in probiotics. Crit Rev Food Sci Nutr 2023:1-15. [PMID: 38032232 DOI: 10.1080/10408398.2023.2288887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The impacts of probiotics on maintaining the host's intestinal health have been extensively confirmed. Organoid technology revolutionizes intestinal health research by providing a unique platform to study the effects of probiotics. It overcomes challenges posed by animal models and 2D cell models in accurately simulating the in vivo environment. This review summarizes the development of intestinal organoid technology and its potential applications in intestinal health research as well as highlights the regulatory mechanisms of probiotics on intestinal health, which have been revealed using intestinal organoid technology. Furthermore, an overview of its potential applications in probiotic research has also been provided. This review aims to improve the understanding of intestinal organoid technology's applications in this field as well as to contribute to its further development.
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Affiliation(s)
- Han Tan
- College of Food Science, Southwest University, Chongqing, China
| | - Xiaoyong Chen
- College of Food Science, Southwest University, Chongqing, China
- Chongqing Agricultural Product Processing Technology Innovation Platform, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing, China
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing, China
| | - Chen Wang
- College of Food Science, Southwest University, Chongqing, China
- Chongqing Agricultural Product Processing Technology Innovation Platform, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing, China
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing, China
| | - Jiajia Song
- College of Food Science, Southwest University, Chongqing, China
- Chongqing Agricultural Product Processing Technology Innovation Platform, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing, China
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing, China
| | - Jiahui Xu
- College of Food Science, Southwest University, Chongqing, China
| | - Yuhong Zhang
- Institute of Food Sciences and Technology, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Huayi Suo
- College of Food Science, Southwest University, Chongqing, China
- Chongqing Agricultural Product Processing Technology Innovation Platform, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing, China
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing, China
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16
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Zhang D, Zhou X, Zhou W, Cui SW, Nie S. Intestinal organoids: A thriving and powerful tool for investigating dietary nutrients-intestinal homeostasis axis. Food Res Int 2023; 172:113109. [PMID: 37689878 DOI: 10.1016/j.foodres.2023.113109] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/03/2023] [Accepted: 06/09/2023] [Indexed: 09/11/2023]
Abstract
Dietary nutrients regulate intestinal homeostasis through a variety of complex mechanisms, to affect the host health. Nowadays, various models have been used to investigate the dietary nutrients-intestinal homeostasis axis. Different from the limited flux in animal experiments, limited intestinal cell types and distorted simulation of intestinal environment of 2D cells, intestinal organoid (IO) is a 3D culture system of mini-gut with various intestinal epithelial cells (IECs) and producibility of intestinal biology. Therefore, IOs is a powerful tool to evaluate dietary nutrients-intestinal homeostasis interaction. This review summarized the application of IOs in the investigation of mechanisms for macronutrients (carbohydrates, proteins and fats) and micronutrients (vitamins and minerals) affecting intestinal homeostasis directly or indirectly (polysaccharides-intestinal bacteria, proteins-amino acids). In addition, new perspectives of IOs in combination with advanced biological techniques and their applications in precise nutrition were proposed.
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Affiliation(s)
- Duoduo Zhang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, China
| | - Xingtao Zhou
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, China.
| | - Wengan Zhou
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, China
| | - Steve W Cui
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, China; Agriculture and Agri-Food Canada, Guelph Research and Development Centre, 93 Stone Road West, Guelph, Ontario NIG 5C9, Canada
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, China.
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17
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Motta LCB, Pereira VM, Pinto PAF, Mançanares CAF, Pieri NCG, de Oliveira VC, Fantinato-Neto P, Ambrósio CE. 3D culture of mesenchymal stem cells from the yolk sac to generate intestinal organoid. Theriogenology 2023; 209:98-106. [PMID: 37379588 DOI: 10.1016/j.theriogenology.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 06/30/2023]
Abstract
Organoids are in vitro models that originated from the three-dimensional culture of stem cells with the ability to reproduce part of the in vivo structural and functional specificities of body organs. Intestinal organoids have great relevance in cell therapy, as they provide more accurate information about tissue composition and architecture in relation to two-dimensional culture, in addition to serving as a study model for host interaction and drug testing. The yolk sac (YS) is a promising source of mesenchymal stem cells (MSCs), which are multipotent stem cells with self-renewal ability and potential to differentiated into mesenchymal lineages. Besides this, the YS is responsible for the formation of intestinal epithelium during embryonic development. Thus, the aim of this study was to verify if the three-dimensional in vitro culture of stem cells derived from the canine YS is capable of developing intestinal organoids. MSCs from the canine YS and gut cells were isolated and characterized, then three-dimensionally cultured in Matrigel. In both cells lineages, spherical organoids were observed and after 10 days the gut cells formed crypt-like buds and villus-like structures. Despite having the same induction of differentiation process and having the expression of intestinal markers, the MSC from the YS morphology was not in the form of crypt budding. The hypothesis is that these cells could generate structures equivalent to the intestinal organoids of the colon that other studies showed formed only spherical structures. The culture of MSC from the YS, as well as the establishment of protocols for 3D cultivation of this tissue, is relevant, as it will serve as a tool in various applications in basic and scientific biology.
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Affiliation(s)
- Lina Castelo Branco Motta
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, São Paulo, Brazil; Department of Surgery, Faculty of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo, São Paulo, Brazil; Graduate Program in Translational Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará (UFC), Fortaleza, Ceará, Brazil
| | - Vitória Mattos Pereira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, São Paulo, Brazil; School of Pharmacy, University of Wyoming, Laramie, WY, USA
| | - Priscilla Avelino Ferreira Pinto
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, São Paulo, Brazil; Department of Surgery, Faculty of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo, São Paulo, Brazil
| | - Celina Almeida Furlanetto Mançanares
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, São Paulo, Brazil
| | - Naira Caroline Godoi Pieri
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, São Paulo, Brazil
| | - Vanessa Cristina de Oliveira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, São Paulo, Brazil
| | - Paulo Fantinato-Neto
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, São Paulo, Brazil
| | - Carlos Eduardo Ambrósio
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, São Paulo, Brazil.
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18
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Adeniyi-Ipadeola G, Nwanosike H, Ramani S. Human intestinal organoids as models to study enteric bacteria and viruses. Curr Opin Microbiol 2023; 75:102362. [PMID: 37536261 PMCID: PMC10529792 DOI: 10.1016/j.mib.2023.102362] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023]
Abstract
Laboratory studies of host-microbe interactions have historically been carried out using transformed cell lines and animal models. Although much has been learned from these models, recent advances in the development of multicellular, physiologically active, human intestinal organoid (HIO) cultures are allowing unprecedented discoveries of host-microbe interactions. Here, we review recent literature using HIOs as models to investigate the pathogenesis of clinically important enteric bacteria and viruses and study commensal intestinal microbes. We also discuss limitations of current HIO culture systems and how technical advances and innovative engineering approaches are providing new directions to improve the model. The studies discussed here highlight the potential of HIOs for studying microbial pathogenesis, host-microbe interactions, and for preclinical development of therapeutics and vaccines.
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Affiliation(s)
- Grace Adeniyi-Ipadeola
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Hephzibah Nwanosike
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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19
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Jess AT, Eskander GH, Vu MH, Michail S. Short-Chain Fatty Acid Levels after Fecal Microbiota Transplantation in a Pediatric Cohort with Recurrent Clostridioides difficile Infection. Metabolites 2023; 13:1039. [PMID: 37887364 PMCID: PMC10608736 DOI: 10.3390/metabo13101039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023] Open
Abstract
Though antibiotics are the mainstay treatment for Clostridioides difficile, a large population of individuals infected will experience recurrence. In turn, fecal microbiota transplantation (FMT) has emerged as a promising treatment for recurrent C. difficile infection (rCDI). Mechanistically, by providing a healthy, diverse flora to the infected individual, FMT "resets" the underlying gut microbiome dysbiosis associated with rCDI. A proposed mechanism through which this occurs is via microbiome metabolites such as short-chain fatty acids (SCFAs); however, this has not been previously studied in pediatric patients. Using mass spectroscopy, we quantified pre- and post-transplant levels of acetate, isovalerate, butyrate, formate, and propionate in pediatric patients diagnosed with rCDI (n = 9). We compared pre- and post-transplant levels within the rCDI cohort at 1, 3, 6, and 12 months post-transplant and correlated these levels with healthy controls (n = 19). We witnessed a significant difference in the combined SCFA levels and the individual levels of acetate, butyrate, isovalerate, and propionate in the pre-treatment rCDI cohort compared to the healthy controls. In addition, there was a significant increase in combined SCFA levels at 12 months post-transplant within the rCDI group compared to that of their pre-transplant levels, and, more specifically, acetate, propionate, and isovalerate increased from pre-transplant to 12 months post-transplant. The longitudinal aspect of this study allowed us to identify mechanisms that contribute to the durability of responses to FMT, as well as characterize the unique patterns of short-chain fatty acid level recovery in rCDI pediatric patients.
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Affiliation(s)
- Alison T. Jess
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA;
| | - George Hany Eskander
- School of Medicine & Health Sciences, George Washington University, Washington, DC 20052, USA;
| | - My H. Vu
- Biostatistics Core, The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA;
| | - Sonia Michail
- Division of Gastroenterology, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA
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20
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Kaya YA, de Zoete MR, Steba GS. Advanced Technologies for Studying Microbiome-Female Reproductive Tract Interactions: Organoids, Organoids-on-a-Chip, and Beyond. Semin Reprod Med 2023; 41:160-171. [PMID: 38262440 DOI: 10.1055/s-0043-1778067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The female reproductive tract (FRT) is home to diverse microbial communities that play a pivotal role in reproductive health and disorders such as infertility, endometriosis, and cervical cancer. To understand the complex host-microbiota interactions within the FRT, models that authentically replicate the FRT's environment, including the interplay between the microbiota, mucus layer, immune system, and hormonal cycle, are key. Recent strides in organoid and microfluidic technologies are propelling research in this domain, offering insights into FRT-microbiota interactions and potential therapeutic avenues. This review delves into the current state of FRT organoid models and microbe integration techniques, evaluating their merits and challenges for specific research objectives. Emphasis is placed on innovative approaches and applications, including integrating organoids with microfluidics, and using patient-derived biobanks, as this offers potential for deeper mechanistic insights and personalized therapeutic strategies. Modeling various FRT properties in organoids is explored, from encompassing age-related epithelial features, oxygen levels, and hormonal effects to mucus layers, immune responses, and microbial interactions, highlighting their potential to transform reproductive health research and predict possible outcomes.
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Affiliation(s)
| | - Marcel R de Zoete
- Department of Medical Microbiology, University Medical Centre, Utrecht, The Netherlands
| | - Gaby S Steba
- Division of Female and Baby, Department of Reproductive Medicine and Gynaecology, University Medical Centre Utrecht, Utrecht, The Netherlands
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21
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Jensen KB, Little MH. Organoids are not organs: Sources of variation and misinformation in organoid biology. Stem Cell Reports 2023; 18:1255-1270. [PMID: 37315519 DOI: 10.1016/j.stemcr.2023.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023] Open
Abstract
In the past decade, the term organoid has moved from obscurity to common use to describe a 3D in vitro cellular model of a tissue that recapitulates structural and functional elements of the in vivo organ it models. The term organoid is now applied to structures formed as a result of two distinct processes: the capacity for adult epithelial stem cells to re-create a tissue niche in vitro and the ability to direct the differentiation of pluripotent stem cells to a 3D self-organizing multicellular model of organogenesis. While these two organoid fields rely upon different stem cell types and recapitulate different processes, both share common challenges around robustness, accuracy, and reproducibility. Critically, organoids are not organs. This commentary serves to discuss these challenges, how they impact genuine utility, and shine a light on the need to improve the standards applied to all organoid approaches.
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Affiliation(s)
- Kim Bak Jensen
- Novo Nordisk Foundation Centre for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Melissa Helen Little
- Novo Nordisk Foundation Centre for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Centre for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, Melbourne, VIC 3052, Australia.
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22
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Dang Y, Ma C, Chen K, Chen Y, Jiang M, Hu K, Li L, Zeng Z, Zhang H. The Effects of a High-Fat Diet on Inflammatory Bowel Disease. Biomolecules 2023; 13:905. [PMID: 37371485 DOI: 10.3390/biom13060905] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 05/26/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
The interactions among diet, intestinal immunity, and microbiota are complex and play contradictory roles in inflammatory bowel disease (IBD). An increasing number of studies has shed light on this field. The intestinal immune balance is disrupted by a high-fat diet (HFD) in several ways, such as impairing the intestinal barrier, influencing immune cells, and altering the gut microbiota. In contrast, a rational diet is thought to maintain intestinal immunity by regulating gut microbiota. In this review, we emphasize the crucial contributions made by an HFD to the gut immune system and microbiota.
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Affiliation(s)
- Yuan Dang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Inflammatory Bowel Disease, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chunxiang Ma
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Inflammatory Bowel Disease, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Kexin Chen
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Inflammatory Bowel Disease, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yiding Chen
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mingshan Jiang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Inflammatory Bowel Disease, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Kehan Hu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Inflammatory Bowel Disease, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lili Li
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Inflammatory Bowel Disease, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhen Zeng
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Inflammatory Bowel Disease, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hu Zhang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Inflammatory Bowel Disease, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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23
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Huo C, Zhang X, Gu Y, Wang D, Zhang S, Liu T, Li Y, He W. Organoids: Construction and Application in Gastric Cancer. Biomolecules 2023; 13:biom13050875. [PMID: 37238742 DOI: 10.3390/biom13050875] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Gastric organoids are biological models constructed in vitro using stem cell culture and 3D cell culture techniques, which are the latest research hotspots. The proliferation of stem cells in vitro is the key to gastric organoid models, making the cell subsets within the models more similar to in vivo tissues. Meanwhile, the 3D culture technology also provides a more suitable microenvironment for the cells. Therefore, the gastric organoid models can largely restore the growth condition of cells in terms of morphology and function in vivo. As the most classic organoid models, patient-derived organoids use the patient's own tissues for in vitro culture. This kind of model is responsive to the 'disease information' of a specific patient and has great effect on evaluating the strategies of individualized treatment. Herein, we review the current literature on the establishment of organoid cultures, and also explore organoid translational applications.
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Affiliation(s)
- Chengdong Huo
- Department of the Second Clinical Medical College, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, China
- Department of Ophthalmology, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - Xiaoxia Zhang
- Department of the Second Clinical Medical College, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, China
- Department of Ophthalmology, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - Yanmei Gu
- Department of the Second Clinical Medical College, Lanzhou University, Lanzhou 730030, China
| | - Daijun Wang
- Department of the Second Clinical Medical College, Lanzhou University, Lanzhou 730030, China
| | - Shining Zhang
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, China
| | - Tao Liu
- Department of the Second Clinical Medical College, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, China
| | - Yumin Li
- Department of the Second Clinical Medical College, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, China
| | - Wenting He
- Department of the Second Clinical Medical College, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, China
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24
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Ghorbaninejad M, Asadzadeh-Aghdaei H, Baharvand H, Meyfour A. Intestinal organoids: A versatile platform for modeling gastrointestinal diseases and monitoring epigenetic alterations. Life Sci 2023; 319:121506. [PMID: 36858311 DOI: 10.1016/j.lfs.2023.121506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 03/03/2023]
Abstract
Considering the significant limitations of conventional 2D cell cultures and tissue in vitro models, creating intestinal organoids has burgeoned as an ideal option to recapitulate the heterogeneity of the native intestinal epithelium. Intestinal organoids can be developed from either tissue-resident adult stem cells (ADSs) or pluripotent stem cells (PSCs) in both forms induced PSCs and embryonic stem cells. Here, we review current advances in the development of intestinal organoids that have led to a better recapitulation of the complexity, physiology, morphology, function, and microenvironment of the intestine. We discuss current applications of intestinal organoids with an emphasis on disease modeling. In particular, we point out recent studies on SARS-CoV-2 infection in human intestinal organoids. We also discuss the less explored application of intestinal organoids in epigenetics by highlighting the role of epigenetic modifications in intestinal development, homeostasis, and diseases, and subsequently the power of organoids in mirroring the regulatory role of epigenetic mechanisms in these conditions and introducing novel predictive/diagnostic biomarkers. Finally, we propose 3D organoid models to evaluate the effects of novel epigenetic drugs (epi-drugs) on the treatment of GI diseases where epigenetic mechanisms play a key role in disease development and progression, particularly in colorectal cancer treatment and epigenetically acquired drug resistance.
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Affiliation(s)
- Mahsa Ghorbaninejad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh-Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Baharvand
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran; Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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25
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Rogers AP, Mileto SJ, Lyras D. Impact of enteric bacterial infections at and beyond the epithelial barrier. Nat Rev Microbiol 2023; 21:260-274. [PMID: 36175770 DOI: 10.1038/s41579-022-00794-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2022] [Indexed: 11/09/2022]
Abstract
The mucosal lining of the gut has co-evolved with a diverse microbiota over millions of years, leading to the development of specialized mechanisms to actively limit the invasion of pathogens. However, some enteric microorganisms have adapted against these measures, developing ways to hijack or overcome epithelial micro-integrity mechanisms. This breach of the gut barrier not only enables the leakage of host factors out of circulation but can also initiate a cascade of detrimental systemic events as microbiota, pathogens and their affiliated secretions passively leak into extra-intestinal sites. Under normal circumstances, gut damage is rapidly repaired by intestinal stem cells. However, with substantial and deep perturbation to the gut lining and the systemic dissemination of gut contents, we now know that some enteric infections can cause the impairment of host regenerative processes. Although these local and systemic aspects of enteric disease are often studied in isolation, they heavily impact one another. In this Review, by examining the journey of enteric infections from initial establishment to systemic sequelae and how, or if, the host can successfully repair damage, we will tie together these complex interactions to provide a holistic overview of the impact of enteric infections at and beyond the epithelial barrier.
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Affiliation(s)
- Ashleigh P Rogers
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.,Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Steven J Mileto
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.,Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia. .,Department of Microbiology, Monash University, Melbourne, Victoria, Australia.
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26
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Ok MT, Liu J, Bliton RJ, Hinesley CM, San Pedro EET, Breau KA, Gomez-Martinez I, Burclaff J, Magness ST. A leaky human colon model reveals uncoupled apical/basal cytotoxicity in early Clostridioides difficile toxin exposure. Am J Physiol Gastrointest Liver Physiol 2023; 324:G262-G280. [PMID: 36749911 PMCID: PMC10010926 DOI: 10.1152/ajpgi.00251.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 02/09/2023]
Abstract
Clostridioides difficile (C. difficile) toxins A (TcdA) and B (TcdB) cause antibiotic-associated colitis in part by disrupting epithelial barrier function. Accurate in vitro models are necessary to detect early toxicity kinetics, investigate disease etiology, and develop preclinical models for new therapies. Properties of cancer cell lines and organoids inherently limit these efforts. We developed adult stem cell-derived monolayers of differentiated human colonic epithelium (hCE) with barrier function, investigated the impact of toxins on apical/basal aspects of monolayers, and evaluated whether a leaky epithelial barrier enhances toxicity. Single-cell RNA-sequencing (scRNAseq) mapped C. difficile-relevant genes to human lineages. Transcriptomics compared hCE to Caco-2, informed timing of in vitro stem cell differentiation, and revealed transcriptional responses to TcdA. Transepithelial electrical resistance (TEER) and fluorescent permeability assays measured cytotoxicity. Contribution of TcdB toxicity was evaluated in a diclofenac-induced leaky gut model. scRNAseq demonstrated broad and variable toxin receptor expression. Absorptive colonocytes in vivo displayed increased toxin receptor, Rho GTPase, and cell junction gene expression. Advanced TcdA toxicity generally decreased cytokine/chemokine and increased tight junction and death receptor genes. Differentiated Caco-2 cells remained immature whereas hCE monolayers were similar to mature colonocytes in vivo. Basal exposure of TcdA/B caused greater toxicity and apoptosis than apical exposure. Apical exposure to toxins was enhanced by diclofenac. Apical/basal toxicities are uncoupled with more rapid onset and increased magnitude postbasal toxin exposure. Leaky junctions enhance toxicity of apical TcdB exposure. hCE monolayers represent a physiologically relevant and sensitive system to evaluate the impact of microbial toxins on gut epithelium.NEW & NOTEWORTHY Novel human colonocyte monolayer cultures, benchmarked by transcriptomics for physiological relevance, detect early cytopathic impacts of Clostridioides difficile toxins TcdA and TcdB. A fluorescent ZO-1 reporter in primary human colonocytes is used to track epithelial barrier disruption in response to TcdA. Basal TcdA/B exposure generally caused more rapid onset and cytotoxicity than apical exposure. Transcriptomics demonstrate changes in tight junction, chemokine, and cytokine receptor gene expression post-TcdA exposure. Diclofenac-induced leaky epithelium enhanced apical exposure toxicity.
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Affiliation(s)
- Meryem T Ok
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - Jintong Liu
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - R Jarrett Bliton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - Caroline M Hinesley
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - Ekaterina Ellyce T San Pedro
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Ismael Gomez-Martinez
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
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Intestinal organoids as advanced modeling platforms to study the role of host-microbiome interaction in homeostasis and disease. BMB Rep 2023; 56:15-23. [PMID: 36379514 PMCID: PMC9887104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Indexed: 01/28/2023] Open
Abstract
After birth, animals are colonized by a diverse community of microorganisms. The digestive tract is known to contain the largest number of microbiome in the body. With emergence of the gut-brain axis, the importance of gut microbiome and its metabolites in host health has been extensively studied in recent years. The establishment of organoid culture systems has contributed to studying intestinal pathophysiology by replacing current limited models. Owing to their architectural and functional complexity similar to a real organ, co-culture of intestinal organoids with gut microbiome can provide mechanistic insights into the detrimental role of pathobiont and the homeostatic function of commensal symbiont. Here organoid-based bacterial co-culture techniques for modeling host-microbe interactions are reviewed. This review also summarizes representative studies that explore impact of enteric microorganisms on intestinal organoids to provide a better understanding of host-microbe interaction in the context of homeostasis and disease. [BMB Reports 2023; 56(1): 15-23].
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28
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Busch M, Brouwer H, Aalderink G, Bredeck G, Kämpfer AAM, Schins RPF, Bouwmeester H. Investigating nanoplastics toxicity using advanced stem cell-based intestinal and lung in vitro models. FRONTIERS IN TOXICOLOGY 2023; 5:1112212. [PMID: 36777263 PMCID: PMC9911716 DOI: 10.3389/ftox.2023.1112212] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
Plastic particles in the nanometer range-called nanoplastics-are environmental contaminants with growing public health concern. As plastic particles are present in water, soil, air and food, human exposure via intestine and lung is unavoidable, but possible health effects are still to be elucidated. To better understand the Mode of Action of plastic particles, it is key to use experimental models that best reflect human physiology. Novel assessment methods like advanced cell models and several alternative approaches are currently used and developed in the scientific community. So far, the use of cancer cell line-based models is the standard approach regarding in vitro nanotoxicology. However, among the many advantages of the use of cancer cell lines, there are also disadvantages that might favor other approaches. In this review, we compare cell line-based models with stem cell-based in vitro models of the human intestine and lung. In the context of nanoplastics research, we highlight the advantages that come with the use of stem cells. Further, the specific challenges of testing nanoplastics in vitro are discussed. Although the use of stem cell-based models can be demanding, we conclude that, depending on the research question, stem cells in combination with advanced exposure strategies might be a more suitable approach than cancer cell lines when it comes to toxicological investigation of nanoplastics.
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Affiliation(s)
- Mathias Busch
- Division of Toxicology, Wageningen University and Research, Wageningen, Netherlands
| | - Hugo Brouwer
- Division of Toxicology, Wageningen University and Research, Wageningen, Netherlands
| | - Germaine Aalderink
- Division of Toxicology, Wageningen University and Research, Wageningen, Netherlands
| | - Gerrit Bredeck
- IUF—Leibniz-Research Institute for Environmental Medicine, Duesseldorf, Germany
| | | | - Roel P. F. Schins
- IUF—Leibniz-Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Hans Bouwmeester
- Division of Toxicology, Wageningen University and Research, Wageningen, Netherlands,*Correspondence: Hans Bouwmeester,
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Redistribution of the Novel Clostridioides difficile Spore Adherence Receptor E-Cadherin by TcdA and TcdB Increases Spore Binding to Adherens Junctions. Infect Immun 2023; 91:e0047622. [PMID: 36448839 PMCID: PMC9872679 DOI: 10.1128/iai.00476-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Clostridioides difficile causes antibiotic-associated diseases in humans, ranging from mild diarrhea to severe pseudomembranous colitis and death. A major clinical challenge is the prevention of disease recurrence, which affects nearly ~20 to 30% of the patients with a primary C. difficile infection (CDI). During CDI, C. difficile forms metabolically dormant spores that are essential for recurrence of CDI (R-CDI). In prior studies, we have shown that C. difficile spores interact with intestinal epithelial cells (IECs), which contribute to R-CDI. However, this interaction remains poorly understood. Here, we provide evidence that C. difficile spores interact with E-cadherin, contributing to spore adherence and internalization into IECs. C. difficile toxins TcdA and TcdB lead to adherens junctions opening and increase spore adherence to IECs. Confocal micrographs demonstrate that C. difficile spores associate with accessible E-cadherin; spore-E-cadherin association increases upon TcdA and TcdB intoxication. The presence of anti-E-cadherin antibodies decreased spore adherence and entry into IECs. By enzyme-linked immunosorbent assay (ELISA), immunofluorescence, and immunogold labeling, we observed that E-cadherin binds to C. difficile spores, specifically to the hairlike projections of the spore, reducing spore adherence to IECs. Overall, these results expand our knowledge of how C. difficile spores bind to IECs by providing evidence that E-cadherin acts as a spore adherence receptor to IECs and by revealing how toxin-mediated damage affects spore interactions with IECs.
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30
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Kakni P, Jutten B, Teixeira Oliveira Carvalho D, Penders J, Truckenmüller R, Habibovic P, Giselbrecht S. Hypoxia-tolerant apical-out intestinal organoids to model host-microbiome interactions. J Tissue Eng 2023; 14:20417314221149208. [PMID: 36699634 PMCID: PMC9869231 DOI: 10.1177/20417314221149208] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/16/2022] [Indexed: 01/20/2023] Open
Abstract
Microbiome is an integral part of the gut and is essential for its proper function. Imbalances of the microbiota can be devastating and have been linked with several gastrointestinal conditions. Current gastrointestinal models do not fully reflect the in vivo situation. Thus, it is important to establish more advanced in vitro models to study host-microbiome/pathogen interactions. Here, we developed for the first time an apical-out human small intestinal organoid model in hypoxia, where the apical surface is directly accessible and exposed to a hypoxic environment. These organoids mimic the intestinal cell composition, structure and functions and provide easy access to the apical surface. Co-cultures with the anaerobic strains Lactobacillus casei and Bifidobacterium longum showed successful colonization and probiotic benefits on the organoids. These novel hypoxia-tolerant apical-out small intestinal organoids will pave the way for unraveling unknown mechanisms related to host-microbiome interactions and serve as a tool to develop microbiome-related probiotics and therapeutics.
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Affiliation(s)
- Panagiota Kakni
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, The Netherlands
| | - Barry Jutten
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, The Netherlands
| | - Daniel Teixeira Oliveira Carvalho
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, The Netherlands
| | - John Penders
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, NUTRIM School of Nutrition and Translational Research in Metabolism, CAPHRI Care and Public Health Research Institute, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Roman Truckenmüller
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, The Netherlands
| | - Pamela Habibovic
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, The Netherlands
| | - Stefan Giselbrecht
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, The Netherlands,Stefan Giselbrecht, Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, Maastricht 6229 ER, The Netherlands.
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31
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Sayed IM, Chakraborty A, Das S. Assays with Patient-Derived Organoids to Evaluate the Impact of Microbial Infection on Base Excision Repair (BER) Enzymes. Methods Mol Biol 2023; 2701:157-172. [PMID: 37574481 DOI: 10.1007/978-1-0716-3373-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Microbes play an important role in regulating cellular responses and the induction of chronic diseases. Infection and chronic inflammation can cause DNA damage, and the accumulation of mutations leads to cancer development. The well-known examples of cancer-associated microbes are Helicobacter pylori in gastric cancer and Fusobacterium nucleatum (Fn), Bacteroides fragilis, and E.coli NC101 in colorectal cancer (CRC). These carcinopathogens modify the expressions of the base excision repair enzymes and cause DNA damage. This chapter will show how Fn can initiate CRC through the downregulation of a critical enzyme of the base excision repair (BER) pathway that subsequently causes accumulation of DNA damage. We used the stem cell-based organoid model and enteroid-derived monolayer (EDM) from the murine and human colon to assess the impact of infection on the expression of BER enzymes on the transcriptional and translational levels and to develop other functional assays. For example, we used this EDM model to assess the inflammatory response, DNA damage response, and physiological responses, where we correlated the level of these parameters to BER enzyme levels.
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Affiliation(s)
- Ibrahim M Sayed
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Asyut, Egypt
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Anirban Chakraborty
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Soumita Das
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA.
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Rosselot AE, Park M, Kim M, Matsu‐Ura T, Wu G, Flores DE, Subramanian KR, Lee S, Sundaram N, Broda TR, McCauley HA, Hawkins JA, Chetal K, Salomonis N, Shroyer NF, Helmrath MA, Wells JM, Hogenesch JB, Moore SR, Hong CI. Ontogeny and function of the circadian clock in intestinal organoids. EMBO J 2022; 41:e106973. [PMID: 34704277 PMCID: PMC8762567 DOI: 10.15252/embj.2020106973] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 09/30/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022] Open
Abstract
Circadian rhythms regulate diverse aspects of gastrointestinal physiology ranging from the composition of microbiota to motility. However, development of the intestinal circadian clock and detailed mechanisms regulating circadian physiology of the intestine remain largely unknown. In this report, we show that both pluripotent stem cell-derived human intestinal organoids engrafted into mice and patient-derived human intestinal enteroids possess circadian rhythms and demonstrate circadian phase-dependent necrotic cell death responses to Clostridium difficile toxin B (TcdB). Intriguingly, mouse and human enteroids demonstrate anti-phasic necrotic cell death responses to TcdB. RNA-Seq analysis shows that ~3-10% of the detectable transcripts are rhythmically expressed in mouse and human enteroids. Remarkably, we observe anti-phasic gene expression of Rac1, a small GTPase directly inactivated by TcdB, between mouse and human enteroids, and disruption of Rac1 abolishes clock-dependent necrotic cell death responses. Our findings uncover robust functions of circadian rhythms regulating clock-controlled genes in both mouse and human enteroids governing organism-specific, circadian phase-dependent necrotic cell death responses, and lay a foundation for human organ- and disease-specific investigation of clock functions using human organoids for translational applications.
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Affiliation(s)
- Andrew E Rosselot
- Department of Pharmacology & Systems PhysiologyUniversity of CincinnatiCincinnatiOHUSA
| | - Miri Park
- Department of Pharmacology & Systems PhysiologyUniversity of CincinnatiCincinnatiOHUSA
| | - Mari Kim
- Department of Pharmacology & Systems PhysiologyUniversity of CincinnatiCincinnatiOHUSA
| | - Toru Matsu‐Ura
- Department of Pharmacology & Systems PhysiologyUniversity of CincinnatiCincinnatiOHUSA
| | - Gang Wu
- Division of Human Genetics and ImmunobiologyCenter for ChronobiologyDepartment of PediatricsCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
| | - Danilo E Flores
- Division of Human Genetics and ImmunobiologyCenter for ChronobiologyDepartment of PediatricsCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
| | | | - Suengwon Lee
- Department of Pharmacology & Systems PhysiologyUniversity of CincinnatiCincinnatiOHUSA
| | - Nambirajan Sundaram
- Department of Pediatric SurgeryCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
| | - Taylor R Broda
- Center for Stem Cell and Organoid MedicineDivision of Developmental BiologyCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
| | - Heather A McCauley
- Center for Stem Cell and Organoid MedicineDivision of Developmental BiologyCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
| | - Jennifer A Hawkins
- Department of Pediatric SurgeryCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
| | - Kashish Chetal
- Division of Biomedical InformaticsCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
| | - Nathan Salomonis
- Division of Biomedical InformaticsCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
| | - Noah F Shroyer
- Gastroenterology and HepatologyBaylor College of MedicineHoustonTXUSA
| | - Michael A Helmrath
- Department of Pediatric SurgeryCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
- Center for Stem Cell and Organoid MedicineDivision of Developmental BiologyCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
| | - James M Wells
- Center for Stem Cell and Organoid MedicineDivision of Developmental BiologyCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
- Division of EndocrinologyCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
| | - John B Hogenesch
- Division of Human Genetics and ImmunobiologyCenter for ChronobiologyDepartment of PediatricsCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
- Center for ChronobiologyCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
| | - Sean R Moore
- Division of Pediatric Gastroenterology, Hepatology, and NutritionDepartment of PediatricsUniversity of Virginia School of MedicineCharlottesvilleVAUSA
| | - Christian I Hong
- Department of Pharmacology & Systems PhysiologyUniversity of CincinnatiCincinnatiOHUSA
- Center for Stem Cell and Organoid MedicineDivision of Developmental BiologyCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
- Center for ChronobiologyCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
- Division of Developmental BiologyCincinnati Children’s Hospital Medical CenterCincinnatiOHUSA
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33
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Biagini F, Daddi C, Calvigioni M, De Maria C, Zhang YS, Ghelardi E, Vozzi G. Designs and methodologies to recreate in vitro human gut microbiota models. Biodes Manuf 2022. [DOI: 10.1007/s42242-022-00210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractThe human gut microbiota is widely considered to be a metabolic organ hidden within our bodies, playing a crucial role in the host’s physiology. Several factors affect its composition, so a wide variety of microbes residing in the gut are present in the world population. Individual excessive imbalances in microbial composition are often associated with human disorders and pathologies, and new investigative strategies to gain insight into these pathologies and define pharmaceutical therapies for their treatment are needed. In vitro models of the human gut microbiota are commonly used to study microbial fermentation patterns, community composition, and host-microbe interactions. Bioreactors and microfluidic devices have been designed to culture microorganisms from the human gut microbiota in a dynamic environment in the presence or absence of eukaryotic cells to interact with. In this review, we will describe the overall elements required to create a functioning, reproducible, and accurate in vitro culture of the human gut microbiota. In addition, we will analyze some of the devices currently used to study fermentation processes and relationships between the human gut microbiota and host eukaryotic cells.
Graphic abstract
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Kessler C, Hou J, Neo O, Buckner MMC. In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome. FEMS Microbiol Rev 2022; 47:6807411. [PMID: 36341518 PMCID: PMC9841969 DOI: 10.1093/femsre/fuac044] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.
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Affiliation(s)
- Celia Kessler
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Jingping Hou
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Onalenna Neo
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Michelle M C Buckner
- Corresponding author: Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, United Kingdom. Tel: +44 (0)121 415 8758; E-mail:
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Nie J, Liao W, Zhang Z, Zhang M, Wen Y, Capanoglu E, Sarker MMR, Zhu R, Zhao C. A 3D co-culture intestinal organoid system for exploring glucose metabolism. Curr Res Food Sci 2022; 6:100402. [DOI: 10.1016/j.crfs.2022.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/02/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
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Wang Q, Guo F, Jin Y, Ma Y. Applications of human organoids in the personalized treatment for digestive diseases. Signal Transduct Target Ther 2022; 7:336. [PMID: 36167824 PMCID: PMC9513303 DOI: 10.1038/s41392-022-01194-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/09/2022] [Accepted: 09/13/2022] [Indexed: 11/15/2022] Open
Abstract
Digestive system diseases arise primarily through the interplay of genetic and environmental influences; there is an urgent need in elucidating the pathogenic mechanisms of these diseases and deploy personalized treatments. Traditional and long-established model systems rarely reproduce either tissue complexity or human physiology faithfully; these shortcomings underscore the need for better models. Organoids represent a promising research model, helping us gain a more profound understanding of the digestive organs; this model can also be used to provide patients with precise and individualized treatment and to build rapid in vitro test models for drug screening or gene/cell therapy, linking basic research with clinical treatment. Over the past few decades, the use of organoids has led to an advanced understanding of the composition of each digestive organ and has facilitated disease modeling, chemotherapy dose prediction, CRISPR-Cas9 genetic intervention, high-throughput drug screening, and identification of SARS-CoV-2 targets, pathogenic infection. However, the existing organoids of the digestive system mainly include the epithelial system. In order to reveal the pathogenic mechanism of digestive diseases, it is necessary to establish a completer and more physiological organoid model. Combining organoids and advanced techniques to test individualized treatments of different formulations is a promising approach that requires further exploration. This review highlights the advancements in the field of organoid technology from the perspectives of disease modeling and personalized therapy.
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Affiliation(s)
- Qinying Wang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fanying Guo
- School of Clinical Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yutao Jin
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Kwon JE, Jo SH, Song WS, Lee JS, Jeon HJ, Park JH, Kim YR, Baek JH, Kim MG, Kwon SY, Kim JS, Yang YH, Kim YG. Investigation of metabolic crosstalk between host and pathogenic Clostridioides difficile via multiomics approaches. Front Bioeng Biotechnol 2022; 10:971739. [PMID: 36118584 PMCID: PMC9478559 DOI: 10.3389/fbioe.2022.971739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/11/2022] [Indexed: 11/23/2022] Open
Abstract
Clostridioides difficile is a gram-positive anaerobic bacterium that causes antibiotic-associated infections in the gut. C. difficile infection develops in the intestine of a host with an imbalance of the intestinal microbiota and, in severe cases, can lead to toxic megacolon, intestinal perforation, and even death. Despite its severity and importance, however, the lack of a model to understand host-pathogen interactions and the lack of research results on host cell effects and response mechanisms under C. difficile infection remain limited. Here, we developed an in vitro anaerobic-aerobic C. difficile infection model that enables direct interaction between human gut epithelial cells and C. difficile through the Mimetic Intestinal Host–Microbe Interaction Coculture System. Additionally, an integrative multiomics approach was applied to investigate the biological changes and response mechanisms of host cells caused by C. difficile in the early stage of infection. The C. difficile infection model was validated through the induction of disaggregation of the actin filaments and disruption of the intestinal epithelial barrier as the toxin-mediated phenotypes following infection progression. In addition, an upregulation of stress-induced chaperones and an increase in the ubiquitin proteasomal pathway were identified in response to protein stress that occurred in the early stage of infection, and downregulation of proteins contained in the electron transfer chain and ATP synthase was observed. It has been demonstrated that host cell energy metabolism is inhibited through the glycolysis of Caco-2 cells and the reduction of metabolites belonging to the TCA cycle. Taken together, our C. difficile infection model suggests a new biological response pathway in the host cell induced by C. difficile during the early stage of infection at the molecular level under anaerobic-aerobic conditions. Therefore, this study has the potential to be applied to the development of future therapeutics through basic metabolic studies of C. difficile infection.
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Affiliation(s)
- Ji-Eun Kwon
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Sung-Hyun Jo
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Won-Suk Song
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Jae-Seung Lee
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Hyo-Jin Jeon
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Ji-Hyeon Park
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Ye-Rim Kim
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Ji-Hyun Baek
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Min-Gyu Kim
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Seo-Young Kwon
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, Konkuk University, Seoul, South Korea
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
- *Correspondence: Yun-Gon Kim,
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Plakoglobin and High-Mobility Group Box 1 Mediate Intestinal Epithelial Cell Apoptosis Induced by Clostridioides difficile TcdB. mBio 2022; 13:e0184922. [PMID: 36043787 DOI: 10.1128/mbio.01849-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated intestinal disease, resulting in severe diarrhea and fatal pseudomembranous colitis. TcdB, one of the essential virulence factors secreted by this bacterium, induces host cell apoptosis through a poorly understood mechanism. Here, we performed an RNA interference (RNAi) screen customized to Caco-2 cells, a cell line model of the intestinal epithelium, to discover host factors involved in TcdB-induced apoptosis. We identified plakoglobin, also known as junction plakoglobin (JUP) or γ-catenin, a member of the catenin family, as a novel host factor and a previously known cell death-related chromatin factor, high-mobility group box 1 (HMGB1). Disruption of those host factors by RNAi and CRISPR resulted in resistance of cells to TcdB-mediated and mitochondrion-dependent apoptosis. JUP was redistributed from adherens junctions to the mitochondria and colocalized with the antiapoptotic factor Bcl-XL. JUP proteins could permeabilize the mitochondrial membrane, resulting in the release of cytochrome c. Our results reveal a novel role of JUP in targeting the mitochondria to promote the mitochondrial apoptotic pathway. Treatment with glycyrrhizin, an HMGB1 inhibitor, resulted in significantly increased resistance to TcdB-induced epithelial damage in cultured cells and a mouse ligated colon loop model. These findings demonstrate the critical roles of JUP and HMGB1 in TcdB-induced epithelial cell apoptosis. IMPORTANCE Clostridioides difficile infection (CDI) is the leading cause of hospital-acquired diarrhea. Toxins, especially TcdB, cause epithelial cell apoptosis, but the underlying cell death mechanism is less clear. Through an apoptosis-focused RNAi screen using a bacterium-made small interfering (siRNA) library customized to a human colonic epithelial cell model, we found a novel host factor, plakoglobin (γ-catenin), as a key factor required for cell apoptosis induced by TcdB. Plakoglobin targets and permeabilizes mitochondria after stimulation by TcdB, demonstrating a hitherto underappreciated role of this catenin family member in the apoptosis of intestinal epithelial cells. We also found a previously known cell death-related chromatin factor, HMGB1, and explored the inhibition of HMGB1 for CDI therapy in vivo.
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Yang L, Hung LY, Zhu Y, Ding S, Margolis KG, Leong KW. Material Engineering in Gut Microbiome and Human Health. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9804014. [PMID: 35958108 PMCID: PMC9343081 DOI: 10.34133/2022/9804014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/10/2022] [Indexed: 12/11/2022]
Abstract
Tremendous progress has been made in the past decade regarding our understanding of the gut microbiome's role in human health. Currently, however, a comprehensive and focused review marrying the two distinct fields of gut microbiome and material research is lacking. To bridge the gap, the current paper discusses critical aspects of the rapidly emerging research topic of "material engineering in the gut microbiome and human health." By engaging scientists with diverse backgrounds in biomaterials, gut-microbiome axis, neuroscience, synthetic biology, tissue engineering, and biosensing in a dialogue, our goal is to accelerate the development of research tools for gut microbiome research and the development of therapeutics that target the gut microbiome. For this purpose, state-of-the-art knowledge is presented here on biomaterial technologies that facilitate the study, analysis, and manipulation of the gut microbiome, including intestinal organoids, gut-on-chip models, hydrogels for spatial mapping of gut microbiome compositions, microbiome biosensors, and oral bacteria delivery systems. In addition, a discussion is provided regarding the microbiome-gut-brain axis and the critical roles that biomaterials can play to investigate and regulate the axis. Lastly, perspectives are provided regarding future directions on how to develop and use novel biomaterials in gut microbiome research, as well as essential regulatory rules in clinical translation. In this way, we hope to inspire research into future biomaterial technologies to advance gut microbiome research and gut microbiome-based theragnostics.
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Affiliation(s)
- Letao Yang
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Lin Y. Hung
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Yuefei Zhu
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Suwan Ding
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kara G. Margolis
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
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Aggregation of cryopreserved mid-hindgut endoderm for more reliable and reproducible hPSC-derived small intestinal organoid generation. Stem Cell Reports 2022; 17:1889-1902. [PMID: 35905739 PMCID: PMC9391520 DOI: 10.1016/j.stemcr.2022.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 01/21/2023] Open
Abstract
A major technical limitation hindering the widespread adoption of human pluripotent stem cell (hPSC)-derived gastrointestinal (GI) organoid technologies is the need for de novo hPSC differentiation and dependence on spontaneous morphogenesis to produce detached spheroids. Here, we report a method for simple, reproducible, and scalable production of small intestinal organoids (HIOs) based on the aggregation of cryopreservable hPSC-derived mid-hindgut endoderm (MHE) monolayers. MHE aggregation eliminates variability in spontaneous spheroid production and generates HIOs that are comparable to those arising spontaneously. With a minor modification to the protocol, MHE can be cryopreserved, thawed, and aggregated, facilitating HIO production without de novo hPSC differentiation. Finally, aggregation can also be used to generate antral stomach organoids and colonic organoids. This improved method removes significant barriers to the implementation and successful use of hPSC-derived GI organoid technologies and provides a framework for improved dissemination and increased scalability of GI organoid production. hPSC-derived HIO production requires highly variable spontaneous spheroid formation hPSC-derived MHE can be aggregated to reliably increase HIO production ∼10-fold MHE can be cryopreserved before aggregation and subsequent HIO production Antral stomach and colonic organoids can also be generated by aggregation
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Blake R, Jensen K, Mabbott N, Hope J, Stevens J. The Development of 3D Bovine Intestinal Organoid Derived Models to Investigate Mycobacterium Avium ssp Paratuberculosis Pathogenesis. Front Vet Sci 2022; 9:921160. [PMID: 35859809 PMCID: PMC9290757 DOI: 10.3389/fvets.2022.921160] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the etiological agent of Johne's Disease, a chronic enteritis of ruminants prevalent across the world. It is estimated that approximately 50% of UK dairy herds are infected with MAP, but this is likely an underestimate of the true prevalence. Infection can result in reduced milk yield, infertility and premature culling of the animal, leading to significant losses to the farming economy and negatively affecting animal welfare. Understanding the initial interaction between MAP and the host is critical to develop improved diagnostic tools and novel vaccines. Here we describe the characterisation of three different multicellular in vitro models derived from bovine intestinal tissue, and their use for the study of cellular interactions with MAP. In addition to the previously described basal-out 3D bovine enteroids, we have established viable 2D monolayers and 3D apical-out organoids. The apical-out enteroids differ from previously described bovine enteroids as the apical surface is exposed on the exterior surface of the 3D structure, enabling study of host-pathogen interactions at the epithelial surface without the need for microinjection. We have characterised the cell types present in each model system using RT-qPCR to detect predicted cell type-specific gene expression, and confocal microscopy for cell type-specific protein expression. Each model contained the cells present in the original bovine intestinal tissue, confirming they were representative of the bovine gut. Exposure of the three model systems to the K10 reference strain of MAP K10, and a recent Scottish isolate referred to as C49, led to the observation of intracellular bacteria by confocal microscopy. Enumeration of the bacteria by quantification of genome copy number, indicated that K10 was less invasive than C49 at early time points in infection in all model systems. This study shows that bovine enteroid-based models are permissive to infection with MAP and that these models may be useful in investigating early stages of MAP pathogenesis in a physiologically relevant in vitro system, whilst reducing the use of animals in scientific research. Bos taurus: urn:lsid:zoobank.org:act:4C90C4FA-6296-4972-BE6A-5EF578677D64
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Kim MB, Hwangbo S, Jang S, Jo YK. Bioengineered Co-culture of organoids to recapitulate host-microbe interactions. Mater Today Bio 2022; 16:100345. [PMID: 35847376 PMCID: PMC9283667 DOI: 10.1016/j.mtbio.2022.100345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 11/05/2022] Open
Abstract
The recent spike in the instances of complex physiological host-microbe interactions has raised the demand for developing in vitro models that recapitulate the microbial microenvironment in the human body. Organoids are steadily emerging as an in vitro culture system that closely mimics the structural, functional, and genetic features of complex human organs, particularly for better understanding host-microbe interactions. Recent advances in organoid culture technology have become new avenues for assessing the pathogenesis of symbiotic interactions, pathogen-induced infectious diseases, and various other diseases. The co-cultures of organoids with microbes have shown great promise in simulating host-microbe interactions with a high level of complexity for further advancement in related fields. In this review, we provide an overview of bioengineering approaches for microbe-co-cultured organoids. Latest developments in the applications of microbe-co-cultured organoids to study human physiology and pathophysiology are also highlighted. Further, an outlook on future research on bioengineered organoid co-cultures for various applications is presented.
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Lucafò M, Muzzo A, Marcuzzi M, Giorio L, Decorti G, Stocco G. Patient-derived organoids for therapy personalization in inflammatory bowel diseases. World J Gastroenterol 2022; 28:2636-2653. [PMID: 35979165 PMCID: PMC9260862 DOI: 10.3748/wjg.v28.i24.2636] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/21/2022] [Accepted: 05/17/2022] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders of the intestinal tract that have emerged as a growing problem in industrialized countries. Knowledge of IBD pathogenesis is still incomplete, and the most widely-accepted interpretation considers genetic factors, environmental stimuli, uncontrolled immune responses and altered intestinal microbiota composition as determinants of IBD, leading to dysfunction of the intestinal epithelial functions. In vitro models commonly used to study the intestinal barrier do not fully reflect the proper intestinal architecture. An important innovation is represented by organoids, 3D in vitro cell structures derived from stem cells that can self-organize into functional organ-specific structures. Organoids may be generated from induced pluripotent stem cells or adult intestinal stem cells of IBD patients and therefore retain their genetic and transcriptomic profile. These models are powerful pharmacological tools to better understand IBD pathogenesis, to study the mechanisms of action on the epithelial barrier of drugs already used in the treatment of IBD, and to evaluate novel target-directed molecules which could improve therapeutic strategies. The aim of this review is to illustrate the potential use of organoids for therapy personalization by focusing on the most significant advances in IBD research achieved through the use of adult stem cells-derived intestinal organoids.
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Affiliation(s)
- Marianna Lucafò
- Advanced Translational Diagnostics Laboratory, Institute for Maternal and Child Health-IRCCS “Burlo Garofolo”, Trieste 34137, Italy
| | - Antonella Muzzo
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste 34127, Italy
| | - Martina Marcuzzi
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Lorenzo Giorio
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Giuliana Decorti
- Advanced Translational Diagnostics Laboratory, Institute for Maternal and Child Health-IRCCS “Burlo Garofolo”, Trieste 34137, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste 34127, Italy
| | - Gabriele Stocco
- Advanced Translational Diagnostics Laboratory, Institute for Maternal and Child Health-IRCCS “Burlo Garofolo”, Trieste 34137, Italy
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
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Tang XY, Wu S, Wang D, Chu C, Hong Y, Tao M, Hu H, Xu M, Guo X, Liu Y. Human organoids in basic research and clinical applications. Signal Transduct Target Ther 2022; 7:168. [PMID: 35610212 PMCID: PMC9127490 DOI: 10.1038/s41392-022-01024-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/26/2022] [Accepted: 05/11/2022] [Indexed: 12/12/2022] Open
Abstract
Organoids are three-dimensional (3D) miniature structures cultured in vitro produced from either human pluripotent stem cells (hPSCs) or adult stem cells (AdSCs) derived from healthy individuals or patients that recapitulate the cellular heterogeneity, structure, and functions of human organs. The advent of human 3D organoid systems is now possible to allow remarkably detailed observation of stem cell morphogens, maintenance and differentiation resemble primary tissues, enhancing the potential to study both human physiology and developmental stage. As they are similar to their original organs and carry human genetic information, organoids derived from patient hold great promise for biomedical research and preclinical drug testing and is currently used for personalized, regenerative medicine, gene repair and transplantation therapy. In recent decades, researchers have succeeded in generating various types of organoids mimicking in vivo organs. Herein, we provide an update on current in vitro differentiation technologies of brain, retinal, kidney, liver, lung, gastrointestinal, cardiac, vascularized and multi-lineage organoids, discuss the differences between PSC- and AdSC-derived organoids, summarize the potential applications of stem cell-derived organoids systems in the laboratory and clinic, and outline the current challenges for the application of organoids, which would deepen the understanding of mechanisms of human development and enhance further utility of organoids in basic research and clinical studies.
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Affiliation(s)
- Xiao-Yan Tang
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Shanshan Wu
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Da Wang
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Chu Chu
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Yuan Hong
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Mengdan Tao
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Hao Hu
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Min Xu
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Xing Guo
- Department of Neurobiology, School of Basic Medical Sciences; Nanjing Medical University, Nanjing, China.
| | - Yan Liu
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China.
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de Boer A, van der Harst J, Fehr M, Geurts L, Knipping K, Kramer N, Krul L, Tabernero Urbieta M, van de Water B, Venema K, Schütte K, Triantis V. Animal-free strategies in food safety & nutrition: What are we waiting for? Part II: Nutrition research. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Abstract
PURPOSE OF REVIEW The purpose of this review is to provide an update regarding the gut barrier and its involvement with chronic diseases, as well as to review biomarkers for identification of gut barrier integrity. This review is timely and relevant as our knowledge is increasing regarding the role of the gut microbiome and the gut barrier in health and disease. RECENT FINDINGS This review provides an overview of: the gut barrier, which is complex and comprised of the mucus layer and the intestinal apical junctional protein complex; the gut microbiome in its relation to regulating the integrity of the gut barrier; select acute and chronic conditions that are known to be associated with gut dysbiosis and impaired gut integrity or 'leaky gut'; and current means for identifying loss in gut barrier integrity. SUMMARY Many chronic conditions are associated with gut dysbiosis and systemic inflammation. Identifying whether the gut barrier is compromised in these conditions could help to inform potential therapeutics as a means to correct losses in gut barrier integrity and mitigate associated medical conditions.
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Affiliation(s)
- Anthony Santilli
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
| | - Stavros Stefanopoulos
- Department of General Surgery, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH
| | - Gail A.M. Cresci
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
- Department of Pediatric Gastroenterology, Hepatology & Nutrition, Pediatric Institute, Cleveland Clinic Children’s Hospital, Cleveland, OH
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Abstract
The microbiota-gut-brain-axis (MGBA) is a bidirectional communication network between gut microbes and their host. Many environmental and host-related factors affect the gut microbiota. Dysbiosis is defined as compositional and functional alterations of the gut microbiota that contribute to the pathogenesis, progression and treatment responses to disease. Dysbiosis occurs when perturbations of microbiota composition and function exceed the ability of microbiota and its host to restore a symbiotic state. Dysbiosis leads to dysfunctional signaling of the MGBA, which regulates the development and the function of the host's immune, metabolic, and nervous systems. Dysbiosis-induced dysfunction of the MGBA is seen with aging and stroke, and is linked to the development of common stroke risk factors such as obesity, diabetes, and atherosclerosis. Changes in the gut microbiota are also seen in response to stroke, and may impair recovery after injury. This review will begin with an overview of the tools used to study the MGBA with a discussion on limitations and potential experimental confounders. Relevant MGBA components are introduced and summarized for a better understanding of age-related changes in MGBA signaling and its dysfunction after stroke. We will then focus on the relationship between the MGBA and aging, highlighting that all components of the MGBA undergo age-related alterations that can be influenced by or even driven by the gut microbiota. In the final section, the current clinical and preclinical evidence for the role of MGBA signaling in the development of stroke risk factors such as obesity, diabetes, hypertension, and frailty are summarized, as well as microbiota changes with stroke in experimental and clinical populations. We conclude by describing the current understanding of microbiota-based therapies for stroke including the use of pre-/pro-biotics and supplementations with bacterial metabolites. Ongoing progress in this new frontier of biomedical sciences will lead to an improved understanding of the MGBA's impact on human health and disease.
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Affiliation(s)
- Pedram Honarpisheh
- Department of Neurology, University of Texas McGovern Medical School, Houston (P.H., L.D.M.)
| | - Robert M Bryan
- Department of Anesthesiology, Baylor College of Medicine, Houston, TX (R.M.B.)
| | - Louise D McCullough
- Department of Neurology, University of Texas McGovern Medical School, Houston (P.H., L.D.M.)
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48
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Park NY, Koh A. From the Dish to the Real World: Modeling Interactions between the Gut and Microorganisms in Gut Organoids by Tailoring the Gut Milieu. Int J Stem Cells 2022; 15:70-84. [PMID: 35220293 PMCID: PMC8889331 DOI: 10.15283/ijsc21243] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 11/11/2022] Open
Abstract
The advent of human intestinal organoid systems has revolutionized the way we understand the interactions between the human gut and microorganisms given the host tropism of human microorganisms. The gut microorganisms have regionality (i.e., small versus large intestine) and the expression of various virulence factors in pathogens is influenced by the gut milieu. However, the culture conditions, optimized for human intestinal organoids, often do not fully support the proliferation and functionality of gut microorganisms. In addition, the regional identity of human intestinal organoids has not been considered to study specific microorganisms with regional preference. In this review we provide an overview of current efforts to understand the role of microorganisms in human intestinal organoids. Specifically, we will emphasize the importance of matching the regional preference of microorganisms in the gut and tailoring the appropriate luminal environmental conditions (i.e., oxygen, pH, and biochemical levels) for modeling real interactions between the gut and the microorganisms with human intestinal organoids.
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Affiliation(s)
- Na-Young Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Ara Koh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
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49
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Challenges to, and prospects for, reverse engineering the gastrointestinal tract using organoids. Trends Biotechnol 2022; 40:932-944. [DOI: 10.1016/j.tibtech.2022.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 12/29/2022]
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50
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Youhanna S, Kemas AM, Preiss L, Zhou Y, Shen JX, Cakal SD, Paqualini FS, Goparaju SK, Shafagh RZ, Lind JU, Sellgren CM, Lauschke VM. Organotypic and Microphysiological Human Tissue Models for Drug Discovery and Development-Current State-of-the-Art and Future Perspectives. Pharmacol Rev 2022; 74:141-206. [PMID: 35017176 DOI: 10.1124/pharmrev.120.000238] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
The number of successful drug development projects has been stagnant for decades despite major breakthroughs in chemistry, molecular biology, and genetics. Unreliable target identification and poor translatability of preclinical models have been identified as major causes of failure. To improve predictions of clinical efficacy and safety, interest has shifted to three-dimensional culture methods in which human cells can retain many physiologically and functionally relevant phenotypes for extended periods of time. Here, we review the state of the art of available organotypic culture techniques and critically review emerging models of human tissues with key importance for pharmacokinetics, pharmacodynamics, and toxicity. In addition, developments in bioprinting and microfluidic multiorgan cultures to emulate systemic drug disposition are summarized. We close by highlighting important trends regarding the fabrication of organotypic culture platforms and the choice of platform material to limit drug absorption and polymer leaching while supporting the phenotypic maintenance of cultured cells and allowing for scalable device fabrication. We conclude that organotypic and microphysiological human tissue models constitute promising systems to promote drug discovery and development by facilitating drug target identification and improving the preclinical evaluation of drug toxicity and pharmacokinetics. There is, however, a critical need for further validation, benchmarking, and consolidation efforts ideally conducted in intersectoral multicenter settings to accelerate acceptance of these novel models as reliable tools for translational pharmacology and toxicology. SIGNIFICANCE STATEMENT: Organotypic and microphysiological culture of human cells has emerged as a promising tool for preclinical drug discovery and development that might be able to narrow the translation gap. This review discusses recent technological and methodological advancements and the use of these systems for hit discovery and the evaluation of toxicity, clearance, and absorption of lead compounds.
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Affiliation(s)
- Sonia Youhanna
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Aurino M Kemas
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Lena Preiss
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Joanne X Shen
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Selgin D Cakal
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Francesco S Paqualini
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Sravan K Goparaju
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Reza Zandi Shafagh
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Johan Ulrik Lind
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Carl M Sellgren
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
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