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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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Laudadio I, Carissimi C, Scafa N, Bastianelli A, Fulci V, Renzini A, Russo G, Oliva S, Vitali R, Palone F, Cucchiara S, Stronati L. Characterization of patient-derived intestinal organoids for modelling fibrosis in Inflammatory Bowel Disease. Inflamm Res 2024; 73:1359-1370. [PMID: 38842554 PMCID: PMC11282153 DOI: 10.1007/s00011-024-01901-9] [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: 04/05/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND AND AIMS Intestinal fibrosis is a common complication of Inflammatory Bowel Disease (IBD), namely Crohn's disease (CD) and ulcerative colitis (UC), but the precise mechanism by which it occurs is incompletely understood hampering the development of effective therapeutic strategies. Here, we aimed at inducing and characterizing an inflammation-mediated fibrosis in patient-derived organoids (PDOs) issued from crypts isolated from colonic mucosal biopsies of IBD pediatric patients and age matched-control subjects (CTRLs). METHODS Inflammatory-driven fibrosis was induced by exposing CTRL-, CD- and UC-PDOs to the pro-inflammatory cytokine TNF-α for one day, followed by a co-treatment with TNF-α and TGF-β1 for three days. Fibrotic response was proven by analyzing inflammatory and fibrotic markers by RT-qPCR and immunofluorescence. Transcriptomic changes were assessed by RNA-sequencing. RESULTS Co-treatment with TNF-α and TGF-β1 caused in CTRL- and IBD-PDOs morphological changes towards a mesenchymal-like phenotype and up-regulation of inflammatory, mesenchymal, and fibrotic markers. Transcriptomic profiling highlighted that in all intestinal PDOs, regardless of the disease, the co-exposure to TNF-α and TGF-β1 regulated EMT genes and specifically increased genes involved in positive regulation of cell migration. Finally, we demonstrated that CD-PDOs display a specific response to fibrosis compared to both CTRL- and UC-PDOs, mainly characterized by upregulation of nuclear factors controlling transcription. CONCLUSIONS This study demonstrates that intestinal PDOs may develop an inflammatory-derived fibrosis thus representing a promising tool to study fibrogenesis in IBD. Fibrotic PDOs show increased expression of EMT genes. In particular, fibrotic CD-PDOs display a specific gene expression signature compared to UC and CTRL-PDOs.
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Affiliation(s)
- Ilaria Laudadio
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
| | - Claudia Carissimi
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Noemi Scafa
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Alex Bastianelli
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Valerio Fulci
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Alessandra Renzini
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Via. A. Scarpa, 16, 00161, Rome, Italy
| | - Giusy Russo
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Salvatore Oliva
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Roberta Vitali
- Laboratory of Biomedical Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Francesca Palone
- Laboratory of Biomedical Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Salvatore Cucchiara
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Laura Stronati
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
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Yan J, Monlong J, Cougoule C, Lacroix-Lamandé S, Wiedemann A. Mapping the scientific output of organoids for animal and human modeling infectious diseases: a bibliometric assessment. Vet Res 2024; 55:81. [PMID: 38926765 PMCID: PMC11210181 DOI: 10.1186/s13567-024-01333-7] [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: 12/01/2023] [Accepted: 04/11/2024] [Indexed: 06/28/2024] Open
Abstract
The escalation of antibiotic resistance, pandemics, and nosocomial infections underscores the importance of research in both animal and human infectious diseases. Recent advancements in three-dimensional tissue cultures, or "organoids", have revolutionized the development of in vitro models for infectious diseases. Our study conducts a bibliometric analysis on the use of organoids in modeling infectious diseases, offering an in-depth overview of this field's current landscape. We examined scientific contributions from 2009 onward that focused on organoids in host‒pathogen interactions using the Web of Science Core Collection and OpenAlex database. Our analysis included temporal trends, reference aging, author, and institutional productivity, collaborative networks, citation metrics, keyword cluster dynamics, and disruptiveness of organoid models. VOSviewer, CiteSpace, and Python facilitated this analytical assessment. The findings reveal significant growth and advancements in organoid-based infectious disease research. Analysis of keywords and impactful publications identified three distinct developmental phases in this area that were significantly influenced by outbreaks of Zika and SARS-CoV-2 viruses. The research also highlights the synergistic efforts between academia and publishers in tackling global pandemic challenges. Through mostly consolidating research efforts, organoids are proving to be a promising tool in infectious disease research for both human and animal infectious disease. Their integration into the field necessitates methodological refinements for better physiological emulation and the establishment of extensive organoid biobanks. These improvements are crucial for fully harnessing the potential of organoids in understanding infectious diseases and advancing the development of targeted treatments and vaccines.
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Affiliation(s)
- Jin Yan
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, China.
- Research Center of Digestive Disease, Central South University, Changsha, China.
- IRSD - Digestive Health Research Institute, University of Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France.
| | - Jean Monlong
- IRSD - Digestive Health Research Institute, University of Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Céline Cougoule
- Institut de Pharmacologie Et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Agnès Wiedemann
- IRSD - Digestive Health Research Institute, University of Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France.
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4
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Piraino F, Costa M, Meyer M, Cornish G, Ceroni C, Garnier V, Hoehnel-Ka S, Brandenberg N. Organoid models: the future companions of personalized drug development. Biofabrication 2024; 16:032009. [PMID: 38608454 DOI: 10.1088/1758-5090/ad3e30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/12/2024] [Indexed: 04/14/2024]
Abstract
High failure rates of the current drug development process are driving exemplary changes toward methodologies centered on human diseasein-vitromodeling. Organoids are self-organized tissue sub-units resembling their organ of origin and are widely acknowledged for their unique potential in recapitulating human physio-pathological mechanisms. They are transformative for human health by becoming the platform of choice to probe disease mechanisms and advance new therapies. Furthermore, the compounds' validation as therapeutics represents another point of the drug development pipeline where organoids may provide key understandings and help pharma organizations replace or reduce animal research. In this review, we focus on gastrointestinal organoid models, which are currently the most advanced organoid models in drug development. We focus on experimental validations of their value, and we propose avenues to enhance their use in drug discovery and development, as well as precision medicine and diagnostics.
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Affiliation(s)
| | - Mariana Costa
- Doppl SA, EPFL Innovation Park, Lausanne, Switzerland
| | - Marine Meyer
- Doppl SA, EPFL Innovation Park, Lausanne, Switzerland
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Margiotta F, Di Cesare Mannelli L, Morabito A, Ghelardini C, Lucarini E. Investigating epithelial-neuronal signaling contribution in visceral pain through colon organoid-dorsal root ganglion neuron co-cultures. Neural Regen Res 2024; 19:1199-1200. [PMID: 37905863 DOI: 10.4103/1673-5374.386403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/29/2023] [Indexed: 11/02/2023] Open
Affiliation(s)
- Francesco Margiotta
- Department of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA - Pharmacology and Toxicology Section, University of Florence, Florence, Italy (Margiotta F, Di Cesare Mannelli L, Ghelardini C, Lucarini E)
| | - Lorenzo Di Cesare Mannelli
- Department of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA - Pharmacology and Toxicology Section, University of Florence, Florence, Italy (Margiotta F, Di Cesare Mannelli L, Ghelardini C, Lucarini E)
| | - Antonino Morabito
- Department of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA, University of Florence, Florence, Italy (Morabito A)
- Meyer Children's Hospital IRCCS, Florence, Italy (Morabito A)
| | - Carla Ghelardini
- Department of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA - Pharmacology and Toxicology Section, University of Florence, Florence, Italy (Margiotta F, Di Cesare Mannelli L, Ghelardini C, Lucarini E)
| | - Elena Lucarini
- Department of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA - Pharmacology and Toxicology Section, University of Florence, Florence, Italy (Margiotta F, Di Cesare Mannelli L, Ghelardini C, Lucarini E)
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Francis KL, Zheng HB, Suskind DL, Murphree TA, Phan BA, Quah E, Hendrickson AS, Zhou X, Nuding M, Hudson AS, Guttman M, Morton GJ, Schwartz MW, Alonge KM, Scarlett JM. Characterizing the human intestinal chondroitin sulfate glycosaminoglycan sulfation signature in inflammatory bowel disease. Sci Rep 2024; 14:11839. [PMID: 38782973 PMCID: PMC11116513 DOI: 10.1038/s41598-024-60959-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
The intestinal extracellular matrix (ECM) helps maintain appropriate tissue barrier function and regulate host-microbial interactions. Chondroitin sulfate- and dermatan sulfate-glycosaminoglycans (CS/DS-GAGs) are integral components of the intestinal ECM, and alterations in CS/DS-GAGs have been shown to significantly influence biological functions. Although pathologic ECM remodeling is implicated in inflammatory bowel disease (IBD), it is unknown whether changes in the intestinal CS/DS-GAG composition are also linked to IBD in humans. Our aim was to characterize changes in the intestinal ECM CS/DS-GAG composition in intestinal biopsy samples from patients with IBD using mass spectrometry. We characterized intestinal CS/DS-GAGs in 69 pediatric and young adult patients (n = 13 control, n = 32 active IBD, n = 24 IBD in remission) and 6 adult patients. Here, we report that patients with active IBD exhibit a significant decrease in the relative abundance of CS/DS isomers associated with matrix stability (CS-A and DS) compared to controls, while isomers implicated in matrix instability and inflammation (CS-C and CS-E) were significantly increased. This imbalance of intestinal CS/DS isomers was restored among patients in clinical remission. Moreover, the abundance of pro-stabilizing CS/DS isomers negatively correlated with clinical disease activity scores, whereas both pro-inflammatory CS-C and CS-E content positively correlated with disease activity scores. Thus, pediatric patients with active IBD exhibited increased pro-inflammatory and decreased pro-stabilizing CS/DS isomer composition, and future studies are needed to determine whether changes in the CS/DS-GAG composition play a pathogenic role in IBD.
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Affiliation(s)
- Kendra L Francis
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Hengqi B Zheng
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA
| | - David L Suskind
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Bao Anh Phan
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Emily Quah
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Aarun S Hendrickson
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Xisheng Zhou
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Mason Nuding
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA
| | - Alexandra S Hudson
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Gregory J Morton
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Michael W Schwartz
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Kimberly M Alonge
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Jarrad M Scarlett
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA.
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA.
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7
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Wang B, Iglesias-Ledon L, Bishop M, Chadha A, Rudolph SE, Longo BN, Cairns DM, Chen Y, Kaplan DL. Impact of Micro- and Nano-Plastics on Human Intestinal Organoid-Derived Epithelium. Curr Protoc 2024; 4:e1027. [PMID: 38588063 DOI: 10.1002/cpz1.1027] [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: 04/10/2024]
Abstract
The development of patient-derived intestinal organoids represents an invaluable model for simulating the native human intestinal epithelium. These stem cell-rich cultures outperform commonly used cell lines like Caco-2 and HT29-MTX in reflecting the cellular diversity of the native intestinal epithelium after differentiation. In our recent study examining the effects of polystyrene (PS), microplastics (MPs), and nanoplastics (NPs), widespread pollutants in our environment and food chain, on the human intestinal epithelium, these organoids have been instrumental in elucidating the absorption mechanisms and potential biological impacts of plastic particles. Building on previously established protocols in human intestinal organoid culture, we herein detail a streamlined protocol for the cultivation, differentiation, and generation of organoid-derived monolayers. This protocol is tailored to generate monolayers incorporating microfold cells (M cells), key for intestinal particle uptake but often absent in current in vitro models. We provide validated protocols for the characterization of MPs/NPs via scanning electron microscopy (SEM) for detailed imaging and their introduction to intestinal epithelial monolayer cells via confocal immunostaining. Additionally, protocols to test the impacts of MP/NP exposure on the functions of the intestinal barrier using transendothelial electrical resistance (TEER) measurements and assessing inflammatory responses using cytokine profiling are detailed. Overall, our protocols enable the generation of human intestinal organoid monolayers, complete with the option of including or excluding M cells, offering crucial techniques for observing particle uptake and identifying inflammatory responses in intestinal epithelial cells to advance our knowledge of the potential effects of plastic pollution on human gut health. These approaches are also amendable to the study of other gut-related chemical and biological exposures and physiological responses due to the robust nature of the systems. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Human intestinal organoid culture and generation of monolayers with and without M cells Support Protocol 1: Culture of L-WRN and production of WRN-conditioned medium Support Protocol 2: Neuronal cell culture and integration into intestinal epithelium Support Protocol 3: Immune cell culture and integration into intestinal epithelium Basic Protocol 2: Scanning electron microscopy: sample preparation and imaging Basic Protocol 3: Immunostaining and confocal imaging of MP/NP uptake in organoid-derived monolayers Basic Protocol 4: Assessment of intestinal barrier function via TEER measurements Basic Protocol 5: Cytokine profiling using ELISA post-MP/NP exposure.
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Affiliation(s)
- Brooke Wang
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | | | - Matthew Bishop
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Anushka Chadha
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Sara E Rudolph
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Brooke N Longo
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Dana M Cairns
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Ying Chen
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
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8
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Kong L, Chen S, Huang S, Zheng A, Gao S, Ye J, Hua C. Challenges and opportunities in inflammatory bowel disease: from current therapeutic strategies to organoid-based models. Inflamm Res 2024; 73:541-562. [PMID: 38345635 DOI: 10.1007/s00011-024-01854-z] [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: 11/12/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is an increasingly prevalent global health concern that has garnered substantial attention. However, the underlying mechanisms are still unclear and the current treatments have significant limitations. Intestinal organoids provide an in vitro model to explore the pathogenesis, test the therapeutic effects, and develop regenerative treatments as well as offer the potential to transform drug discovery of IBD. METHODS To advance our understanding of the whole story of IBD spanning from the pathogenesis to the current therapeutic strategies and latest advancements, a comprehensive search of major databases including PubMed, Scopus, and Web of Science was conducted to retrieve original articles and reviews related to IBD, organoids, pathogenesis and therapy. RESULTS This review deciphers the etiopathogenesis and the current therapeutic approaches in the treatment of IBD. Notably, critical aspects of intestinal organoids in IBD, such as their potential applications, viability, cell renewal ability, and barrier functionality are highlighted. We also discuss the advances, limitations, and prospects of intestinal organoids for precision medicine. CONCLUSION The latest strides made in research about intestinal organoids help elucidate intricate aspects of IBD pathogenesis, and pave the prospective avenues for novel therapeutic interventions.
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Affiliation(s)
- Lingjie Kong
- School of the 2nd Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Siyan Chen
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Shenghao Huang
- School of the 2nd Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Anzhe Zheng
- School of the 2nd Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Sheng Gao
- Laboratory Animal Center, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| | - Jianzhong Ye
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Chunyan Hua
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
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Ferreira B, Barros AS, Leite-Pereira C, Viegas J, das Neves J, Nunes R, Sarmento B. Trends in 3D models of inflammatory bowel disease. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167042. [PMID: 38296115 DOI: 10.1016/j.bbadis.2024.167042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/11/2023] [Accepted: 01/25/2024] [Indexed: 02/20/2024]
Abstract
Inflammatory bowel disease (IBD) encompasses a set of chronic inflammatory conditions, namely Crohn's disease and ulcerative colitis. Despite all advances in the management of IBD, a definitive cure is not available, largely due to a lack of a holistic understanding of its etiology and pathophysiology. Several in vitro, in vivo, and ex vivo models have been developed over the past few decades in order to abbreviate remaining gaps. The establishment of reliable and predictable in vitro intestinal inflammation models may indeed provide valuable tools to expedite and validate the development of therapies for IBD. Three-dimensional (3D) models provide a more accurate representation of the different layers of the intestine, contributing to a stronger impact on drug screening and research on intestinal inflammation, and bridging the gap between in vitro and in vivo research. This work provides a critical overview on the state-of-the-art on existing 3D models of intestinal inflammation and discusses the remaining challenges, providing insights on possible pathways towards achieving IBD mimetic models. We also address some of the main challenges faced by implementing cell culture models in IBD research while bearing in mind clinical translational aspects.
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Affiliation(s)
- Bárbara Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Andreia S Barros
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Catarina Leite-Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Juliana Viegas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - José das Neves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IUCS-CESPU - Instituto Universitário de Ciências da Saúde, Rua Central de Gandra 1317, 4585-116 Gandra, Portugal
| | - Rute Nunes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IUCS-CESPU - Instituto Universitário de Ciências da Saúde, Rua Central de Gandra 1317, 4585-116 Gandra, Portugal
| | - Bruno Sarmento
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IUCS-CESPU - Instituto Universitário de Ciências da Saúde, Rua Central de Gandra 1317, 4585-116 Gandra, Portugal.
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10
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Inciuraite R, Steponaitiene R, Raudze O, Kulokiene U, Kiudelis V, Lukosevicius R, Ugenskiene R, Adamonis K, Kiudelis G, Jonaitis LV, Kupcinskas J, Skieceviciene J. Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level. Sci Rep 2024; 14:4456. [PMID: 38396014 PMCID: PMC10891043 DOI: 10.1038/s41598-024-55076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/19/2024] [Indexed: 02/25/2024] Open
Abstract
Patient-derived human intestinal organoids are becoming an indispensable tool for the research of digestive system in health and disease. However, very little is still known about the long-term culturing effect on global genomic methylation level in colonic epithelial organoids derived from healthy individuals as well as active and quiescent ulcerative colitis (UC) patients. In this study, we aimed to evaluate the epigenetic stability of these organoids by assessing the methylation level of LINE-1 during prolonged culturing. We found that LINE-1 region of both healthy control and UC patient colon tissues as well as corresponding epithelial organoids is highly methylated (exceeding 60%). We also showed that long-term culturing of colonic epithelial organoids generated from stem cells of healthy and diseased (both active and quiescent UC) individuals results in decrease of LINE-1 (up to 8%) methylation level, when compared to tissue of origin and short-term cultures. Moreover, we revealed that LINE-1 methylation level in sub-cultured organoids decreases at different pace depending on the patient diagnosis (healthy control, active or quiescent UC). Therefore, we propose LINE-1 as a potential and convenient biomarker for reliable assessment of global methylation status of patient-derived intestinal epithelial organoids in routine testing of ex vivo cultures.
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Affiliation(s)
- Ruta Inciuraite
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Ruta Steponaitiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Odeta Raudze
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Ugne Kulokiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Vytautas Kiudelis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Rasa Ugenskiene
- Department of Genetics and Molecular Medicine, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Kestutis Adamonis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Gediminas Kiudelis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Laimas Virginijus Jonaitis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania.
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11
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Malaisé Y, Casale E, Pettes-Duler A, Cartier C, Gaultier E, Martins Breyner N, Houdeau E, Evariste L, Lamas B. Validating Enteroid-Derived Monolayers from Murine Gut Organoids for Toxicological Testing of Inorganic Particles: Proof-of-Concept with Food-Grade Titanium Dioxide. Int J Mol Sci 2024; 25:2635. [PMID: 38473881 DOI: 10.3390/ijms25052635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Human exposure to foodborne inorganic nanoparticles (NPs) is a growing concern. However, identifying potential hazards linked to NP ingestion often requires long-term exposure in animals. Owing these constraints, intestinal organoids are a promising alternative to in vivo experiments; as such, an in vitro approach should enable a rapid and reliable assessment of the effects of ingested chemicals on the gut. However, this remains to be validated for inorganic substances. In our study, a transcriptomic analysis and immunofluorescence staining were performed to compare the effects of food-grade TiO2 (fg-TiO2) on enteroid-derived monolayers (EDMs) from murine intestinal organoids to the known impacts of TiO2 on intestinal epithelium. After their ability to respond to a pro-inflammatory cytokine cocktail was validated, EDMs were exposed to 0, 0.1, 1, or 10 µg fg-TiO2/mL for 24 h. A dose-related increase of the muc2, vilin 1, and chromogranin A gene markers of cell differentiation was observed. In addition, fg-TiO2 induced apoptosis and dose-dependent genotoxicity, while a decreased expression of genes encoding for antimicrobial peptides, and of genes related to tight junction function, was observed. These results validated the use of EDMs as a reliable model for the toxicity testing of foodborne NPs likely to affect the intestinal barrier.
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Affiliation(s)
- Yann Malaisé
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France
| | - Eva Casale
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France
| | - Aurélie Pettes-Duler
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France
| | - Christel Cartier
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France
| | - Eric Gaultier
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France
| | - Natalia Martins Breyner
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France
| | - Eric Houdeau
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France
| | - Lauris Evariste
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France
| | - Bruno Lamas
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France
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12
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Mobbs CL, Darling NJ, Przyborski S. An in vitro model to study immune activation, epithelial disruption and stromal remodelling in inflammatory bowel disease and fistulising Crohn's disease. Front Immunol 2024; 15:1357690. [PMID: 38410518 PMCID: PMC10894943 DOI: 10.3389/fimmu.2024.1357690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
At present, preclinical models of inflammatory bowel disease (IBD) are insufficient, limiting translation between research and new therapeutics. This is especially true for fistulising Crohn's disease (CD), as the severe lack of relevant models hinders research progression. To address this, we present in vitro human IBD mucosal models that recapitulate multiple pathological hallmarks of IBD simultaneously in one model system - immune cell infiltration, stromal remodelling and epithelial disruption. Stimulation of models induces epithelial aberrations common in IBD tissue including altered morphology, microvilli abnormalities, claudin gene expression changes and increased permeability. Inflammatory biomarkers are also significantly increased including cytokines and chemokines integral to IBD pathogenesis. Evidence of extracellular matrix remodelling, including upregulated matrix-metalloproteinases and altered basement membrane components, suggests the models simulate pathological stromal remodelling events that closely resemble fistulising CD. Importantly, MMP-9 is the most abundant MMP and mimics the unique localisation observed in IBD tissue. The inflamed models were subsequently used to elucidate the involvement of TNF-α and IFN- γ in intestinal stromal remodelling, in which TNF-α but not IFN- γ induced MMP upregulation, specifically of MMP-3 and MMP-9. Collectively, our results demonstrate the potential of the IBD models for use in preclinical research in IBD, particularly for fistulising CD.
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Affiliation(s)
- Claire L. Mobbs
- Department of Biosciences, Durham University, Durham, United Kingdom
- Reprocell Europe Ltd, West of Scotland Science Park, Glasgow, United Kingdom
| | - Nicole J. Darling
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Stefan Przyborski
- Department of Biosciences, Durham University, Durham, United Kingdom
- Reprocell Europe Ltd, West of Scotland Science Park, Glasgow, United Kingdom
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13
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Sakib S, Zou S. Attenuation of Chronic Inflammation in Intestinal Organoids with Graphene Oxide-Mediated Tumor Necrosis Factor-α_Small Interfering RNA Delivery. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 38325360 PMCID: PMC10883062 DOI: 10.1021/acs.langmuir.3c02741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract with a complex and multifactorial etiology, making it challenging to treat. While recent advances in immunomodulatory biologics, such as antitumor necrosis factor-α (TNF-α) antibodies, have shown moderate success, systemic administration of antibody therapeutics may lead to several adverse effects, including the risk of autoimmune disorders due to systemic cytokine depletion. Transient RNA interference using exogenous short interfering RNA (siRNA) to regulate target gene expression at the transcript level offers an alternative to systemic immunomodulation. However, siRNAs are susceptible to premature degradation and have poor cellular uptake. Graphene oxide (GO) nanoparticles have been shown to be effective nanocarriers for biologics due to their reduced cytotoxicity and enhanced bioavailability. In this study, we evaluate the therapeutic efficacy of GO mediated TNF-α_siRNA using in vitro models of chronic inflammation generated by treating murine small intestines (enteroids) and large intestines (colonoids) with inflammatory agents IL-1β, TNF-α, and LPS. The organotypic mouse enteroids and colonoids developed an inflammatory phenotype similar to that of IBD, characterized by impaired epithelial homeostasis and an increased production of inflammatory cytokines such as TNF-α, IL-1β, and IL-6. We assessed siRNA delivery to these inflamed organoids using three different GO formulations. Out of the three, small-sized GO with polymer and dendrimer modifications (smGO) demonstrated the highest transfection efficiency, which led to the downregulation of inflammatory cytokines, indicating an attenuation of the inflammatory phenotype. Moreover, the transfection efficiency and inflammation-ameliorating effects could be further enhanced by increasing the TNF-α_siRNA/smGO ratio from 1:1 to 3:1. Overall, the results of this study demonstrate that ex vivo organoids with disease-specific phenotypes are invaluable models for assessing the therapeutic potential of nanocarrier-mediated drug and biologic delivery systems.
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Affiliation(s)
- Sadman Sakib
- Metrology Research Centre, National Research Council of Canada, 100 Sussex Drive, Ottawa, ONK1A 0R6, Canada
| | - Shan Zou
- Metrology Research Centre, National Research Council of Canada, 100 Sussex Drive, Ottawa, ONK1A 0R6, Canada
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14
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Flood P, Hanrahan N, Nally K, Melgar S. Human intestinal organoids: Modeling gastrointestinal physiology and immunopathology - current applications and limitations. Eur J Immunol 2024; 54:e2250248. [PMID: 37957831 DOI: 10.1002/eji.202250248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/15/2023]
Abstract
Human intestinal organoids are an ideal model system for studying gastrointestinal physiology and immunopathology. Altered physiology and mucosal immune response are hallmarks of numerous intestinal functional and inflammatory diseases, including inflammatory bowel disease (IBD), coeliac disease, irritable bowel syndrome (IBS), and obesity. These conditions impact the normal epithelial functions of the intestine, such as absorption, barrier function, secretion, and host-microbiome communication. They are accompanied by characteristic intestinal symptoms and have significant societal, economic, and healthcare burdens. To develop new treatment options, cutting-edge research is required to investigate their etiology and pathology. Human intestinal organoids derived from patient tissue recapitulate the key physiological and immunopathological aspects of these conditions, providing a promising platform for elucidating disease mechanisms. This review will summarize recent reports on patient-derived human small intestinal and colonic organoids and highlight how these models have been used to study intestinal epithelial functions in the context of inflammation, altered physiology, and immune response. Furthermore, it will elaborate on the various organoid systems in use and the techniques/assays currently available to study epithelial functions. Finally, it will conclude by discussing the limitations and future perspectives of organoid technology.
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Affiliation(s)
- Peter Flood
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Naomi Hanrahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, School of Medicine, University College Cork, Cork, Ireland
- Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ken Nally
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Silvia Melgar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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15
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Majumder J, Torr EE, Aisenbrey EA, Lebakken CS, Favreau PF, Richards WD, Yin Y, Chang Q, Murphy WL. Human induced pluripotent stem cell-derived planar neural organoids assembled on synthetic hydrogels. J Tissue Eng 2024; 15:20417314241230633. [PMID: 38361535 PMCID: PMC10868488 DOI: 10.1177/20417314241230633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/20/2024] [Indexed: 02/17/2024] Open
Abstract
The tailorable properties of synthetic polyethylene glycol (PEG) hydrogels make them an attractive substrate for human organoid assembly. Here, we formed human neural organoids from iPSC-derived progenitor cells in two distinct formats: (i) cells seeded on a Matrigel surface; and (ii) cells seeded on a synthetic PEG hydrogel surface. Tissue assembly on synthetic PEG hydrogels resulted in three dimensional (3D) planar neural organoids with greater neuronal diversity, greater expression of neurovascular and neuroinflammatory genes, and reduced variability when compared with tissues assembled upon Matrigel. Further, our 3D human tissue assembly approach occurred in an open cell culture format and created a tissue that was sufficiently translucent to allow for continuous imaging. Planar neural organoids formed on PEG hydrogels also showed higher expression of neural, vascular, and neuroinflammatory genes when compared to traditional brain organoids grown in Matrigel suspensions. Further, planar neural organoids contained functional microglia that responded to pro-inflammatory stimuli, and were responsive to anti-inflammatory drugs. These results demonstrate that the PEG hydrogel neural organoids can be used as a physiologically relevant in vitro model of neuro-inflammation.
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Affiliation(s)
- Joydeb Majumder
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth E Torr
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth A Aisenbrey
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - Yanhong Yin
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Qiang Chang
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
- Departments of Medical Genetics and Neurology, University of Wisconsin-Madison, Madison, WI, USA
| | - William L Murphy
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
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16
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Ding W, Marx OM, Mankarious MM, Koltun WA, Yochum GS. Disease Severity Impairs Generation of Intestinal Organoid Cultures From Inflammatory Bowel Disease Patients. J Surg Res 2024; 293:187-195. [PMID: 37776721 DOI: 10.1016/j.jss.2023.08.027] [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: 04/07/2023] [Revised: 08/02/2023] [Accepted: 08/31/2023] [Indexed: 10/02/2023]
Abstract
INTRODUCTION Chronic inflammation of the intestinal epithelium is an underlying cause of the two main types of inflammatory bowel disease (IBD), ulcerative colitis (UC), and Crohn's disease (CD). Ex vivo organoids derived from the intestinal epithelium are a useful model to study IBD. Whether such cultures can be established from surgically resected diseased IBD intestinal tissues has not been fully explored. In this study, we tested our ability to establish organoids from nondiseased and diseased IBD intestinal tissues. MATERIALS AND METHODS From 12 UC patients (n = 54 tissues) and 20 CD patients (n = 49 tissues), tissues were collected from multiple colonic regions, and for CD, the terminal ileum was also surveyed. Organoids were cultured in Matrigel domes using defined media. In primary tissues, we conducted immunohistochemical analysis for mucin 2 (MUC2) and Alcian blue staining for goblet cells. Organoids were stained for Ki67, E-cadherin, and MUC2. RESULTS For UC, we were highly successful establishing organoids from nondiseased tissue (n = 12 of 13, 92%). This success rates dropped from tissues with mild (n = 6 of 9, 67%), moderate (n = 2 of 9, 22%), or severe disease (n = 1 of 23, 4%). The rates from nondiseased CD tissues were reduced (n = 11 of 23, 48%) in comparison to such tissues from UC patients. In UC, goblet cells and MUC2 were reduced in diseased tissues and these phenotypes were retained in organoids. CONCLUSIONS Organoids can be readily derived from nondiseased surgically resected IBD tissues. While more work is needed to improve their derivation from diseased tissue, our study supports the use of organoids to study IBD pathophysiology.
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Affiliation(s)
- Wei Ding
- Division of Colon & Rectal Surgery, Department of Surgery, Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Olivia M Marx
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Marc M Mankarious
- Division of Colon & Rectal Surgery, Department of Surgery, Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Walter A Koltun
- Division of Colon & Rectal Surgery, Department of Surgery, Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Gregory S Yochum
- Division of Colon & Rectal Surgery, Department of Surgery, Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania; Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania.
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17
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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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18
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Macedo MH, Dias Neto M, Pastrana L, Gonçalves C, Xavier M. Recent Advances in Cell-Based In Vitro Models to Recreate Human Intestinal Inflammation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301391. [PMID: 37736674 PMCID: PMC10625086 DOI: 10.1002/advs.202301391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/03/2023] [Indexed: 09/23/2023]
Abstract
Inflammatory bowel disease causes a major burden to patients and healthcare systems, raising the need to develop effective therapies. Technological advances in cell culture, allied with ethical issues, have propelled in vitro models as essential tools to study disease aetiology, its progression, and possible therapies. Several cell-based in vitro models of intestinal inflammation have been used, varying in their complexity and methodology to induce inflammation. Immortalized cell lines are extensively used due to their long-term survival, in contrast to primary cultures that are short-lived but patient-specific. Recently, organoids and organ-chips have demonstrated great potential by being physiologically more relevant. This review aims to shed light on the intricate nature of intestinal inflammation and cover recent works that report cell-based in vitro models of human intestinal inflammation, encompassing diverse approaches and outcomes.
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Affiliation(s)
- Maria Helena Macedo
- INL – International Iberian Nanotechnology LaboratoryAvenida Mestre José VeigaBraga4715‐330Portugal
| | - Mafalda Dias Neto
- INL – International Iberian Nanotechnology LaboratoryAvenida Mestre José VeigaBraga4715‐330Portugal
| | - Lorenzo Pastrana
- INL – International Iberian Nanotechnology LaboratoryAvenida Mestre José VeigaBraga4715‐330Portugal
| | - Catarina Gonçalves
- INL – International Iberian Nanotechnology LaboratoryAvenida Mestre José VeigaBraga4715‐330Portugal
| | - Miguel Xavier
- INL – International Iberian Nanotechnology LaboratoryAvenida Mestre José VeigaBraga4715‐330Portugal
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19
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Chneiweiss H, Dubart-Kupperschmitt A, Duclos-Vallée JC, Clément B, Flacher V, Galzi JL, Gidrol X, Goureau O, Guasch G, Haiech J, Lemaitre C, Mahé MM, Martin S, Poulain L, Sebastiani C, Vergnolle N, Yates F. [For a good understanding and use of the term "organoids"]. Med Sci (Paris) 2023; 39:876-878. [PMID: 38018932 DOI: 10.1051/medsci/2023155] [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: 11/30/2023] Open
Abstract
Depuis une dizaine d’années, des progrès considérables ont été réalisés concernant les conditions qui permettent à des cellules de s’auto-organiser dans l’espace comme elles le font lors des phases précoces du développement embryonnaire ou dans certains tissus adultes. On nomme ainsi « organoïdes » des structures en trois dimensions complexes, organisées et intégrant plusieurs types cellulaires, qui peuvent reproduire in vitro certaines fonctions d’un organe. Toutefois, ces organoïdes ne peuvent actuellement reproduire à l’identique une architecture anatomique et fonctionnelle complète. Bien qu’utilisé pour des raisons de simplification pour la communication, en particulier dans la presse généraliste, il est donc abusif d’utiliser le terme « mini-organes » pour décrire ces structures.
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Affiliation(s)
| | | | | | - Bruno Clément
- Groupement de recherche CNRS « Organoïdes » (GDR2102)1, France
| | - Vincent Flacher
- Groupement de recherche CNRS « Organoïdes » (GDR2102)1, France
| | - Jean-Luc Galzi
- Groupement de recherche CNRS « Organoïdes » (GDR2102)1, France
| | - Xavier Gidrol
- Groupement de recherche CNRS « Organoïdes » (GDR2102)1, France
| | - Olivier Goureau
- Groupement de recherche CNRS « Organoïdes » (GDR2102)1, France
| | | | - Jacques Haiech
- Groupement de recherche CNRS « Organoïdes » (GDR2102)1, France
| | | | - Maxime M Mahé
- Groupement de recherche CNRS « Organoïdes » (GDR2102)1, France
| | - Sophie Martin
- Groupement de recherche CNRS « Organoïdes » (GDR2102)1, France
| | - Laurent Poulain
- Groupement de recherche CNRS « Organoïdes » (GDR2102)1, France
| | | | | | - Frank Yates
- Groupement de recherche CNRS « Organoïdes » (GDR2102)1, France
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20
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Pasquereau-Kotula E, Nigro G, Dingli F, Loew D, Poullet P, Xu Y, Kopetz S, Davis J, Peduto L, Robbe-Masselot C, Sansonetti P, Trieu-Cuot P, Dramsi S. Global proteomic identifies multiple cancer-related signaling pathways altered by a gut pathobiont associated with colorectal cancer. Sci Rep 2023; 13:14960. [PMID: 37696912 PMCID: PMC10495336 DOI: 10.1038/s41598-023-41951-3] [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: 03/02/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
In this work, we investigated the oncogenic role of Streptococcus gallolyticus subsp. gallolyticus (SGG), a gut bacterium associated with colorectal cancer (CRC). We showed that SGG UCN34 accelerates colon tumor development in a chemically induced CRC murine model. Full proteome and phosphoproteome analysis of murine colons chronically colonized by SGG UCN34 revealed that 164 proteins and 725 phosphorylation sites were differentially regulated. Ingenuity Pathway Analysis (IPA) indicates a pro-tumoral shift specifically induced by SGG UCN34, as ~ 90% of proteins and phosphoproteins identified were associated with digestive cancer. Comprehensive analysis of the altered phosphoproteins using ROMA software revealed up-regulation of several cancer hallmark pathways such as MAPK, mTOR and integrin/ILK/actin, affecting epithelial and stromal colonic cells. Importantly, an independent analysis of protein arrays of human colon tumors colonized with SGG showed up-regulation of PI3K/Akt/mTOR and MAPK pathways, providing clinical relevance to our findings. To test SGG's capacity to induce pre-cancerous transformation of the murine colonic epithelium, we grew ex vivo organoids which revealed unusual structures with compact morphology. Taken together, our results demonstrate the oncogenic role of SGG UCN34 in a murine model of CRC associated with activation of multiple cancer-related signaling pathways.
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Affiliation(s)
- Ewa Pasquereau-Kotula
- Biology of Gram-Positive Pathogens Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, 75015, Paris, France.
| | - Giulia Nigro
- Stroma, Inflammation and Tissue Repair Unit, Institut Pasteur, Université Paris Cité, INSERM U1224, 75015, Paris, France
- Microenvironment and Immunity Unit, Institut Pasteur, Université Paris Cité, INSERM U1224, 75015, Paris, France
| | - Florent Dingli
- Institut Curie, PSL Research University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Patrick Poullet
- Institut Curie, Bioinformatics Core Facility (CUBIC), INSERM U900, PSL Research University, Mines Paris Tech, 75005, Paris, France
| | - Yi Xu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
- Department of Microbial Pathogenesis and Immunology, School of Medicine, Bryan, TX, USA
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Davis
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- University of Kansas, Kansas City, KS, USA
| | - Lucie Peduto
- Stroma, Inflammation and Tissue Repair Unit, Institut Pasteur, Université Paris Cité, INSERM U1224, 75015, Paris, France
| | - Catherine Robbe-Masselot
- Université de Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Philippe Sansonetti
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, and College de France, 75005, Paris, France
| | - Patrick Trieu-Cuot
- Biology of Gram-Positive Pathogens Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, 75015, Paris, France
| | - Shaynoor Dramsi
- Biology of Gram-Positive Pathogens Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, 75015, Paris, France.
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21
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Francis KL, Alonge KM, Pacheco MC, Hu SJ, Krutzsch CA, Morton GJ, Schwartz MW, Scarlett JM. Diabetes exacerbates inflammatory bowel disease in mice with diet-induced obesity. World J Gastroenterol 2023; 29:4991-5004. [PMID: 37731997 PMCID: PMC10507503 DOI: 10.3748/wjg.v29.i33.4991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/22/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND The increased prevalence of inflammatory bowel disease (IBD) among patients with obesity and type 2 diabetes suggests a causal link between these diseases, potentially involving the effect of hyperglycemia to disrupt intestinal barrier integrity. AIM To investigate whether the deleterious impact of diabetes on the intestinal barrier is associated with increased IBD severity in a murine model of colitis in mice with and without diet-induced obesity. METHODS Mice were fed chow or a high-fat diet and subsequently received streptozotocin to induce diabetic-range hyperglycemia. Six weeks later, dextran sodium sulfate was given to induce colitis. In select experiments, a subset of diabetic mice was treated with the antidiabetic drug dapagliflozin prior to colitis onset. Endpoints included both clinical and histological measures of colitis activity as well as histochemical markers of colonic epithelial barrier integrity. RESULTS In mice given a high-fat diet, but not chow-fed animals, diabetes was associated with significantly increased clinical colitis activity and histopathologic markers of disease severity. Diabetes was also associated with a decrease in key components that regulate colonic epithelial barrier integrity (colonic mucin layer content and epithelial tight junction proteins) in diet-induced obese mice. Each of these effects of diabetes in diet-induced obese mice was ameliorated by restoring normoglycemia. CONCLUSION In obese mice, diabetes worsened clinical and pathologic outcomes of colitis via mechanisms that are reversible with treatment of hyperglycemia. Hyperglycemia-induced intestinal barrier dysfunction offers a plausible mechanism linking diabetes to increased colitis severity. These findings suggest that effective diabetes management may decrease the clinical severity of IBD.
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Affiliation(s)
- Kendra L Francis
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children’s Hospital, Seattle, WA 98105, United States
- Diabetes Institute, University of Washington, Seattle, WA 98109, United States
| | - Kimberly M Alonge
- Diabetes Institute, University of Washington, Seattle, WA 98109, United States
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Maria Cristina Pacheco
- Department of Laboratory Medicine and Pathology, Seattle Children's Hospital, Seattle, WA 98105, United States
| | - Shannon J Hu
- Diabetes Institute, University of Washington, Seattle, WA 98109, United States
| | - Cody A Krutzsch
- Diabetes Institute, University of Washington, Seattle, WA 98109, United States
| | - Gregory J Morton
- Diabetes Institute, University of Washington, Seattle, WA 98109, United States
| | - Michael W Schwartz
- Diabetes Institute, University of Washington, Seattle, WA 98109, United States
| | - Jarrad M Scarlett
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children’s Hospital, Seattle, WA 98105, United States
- Diabetes Institute, University of Washington, Seattle, WA 98109, United States
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22
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Kamal S, Parkash N, Beattie W, Christensen B, Segal JP. Are We Ready to Reclassify Crohn's Disease Using Molecular Classification? J Clin Med 2023; 12:5786. [PMID: 37762727 PMCID: PMC10532006 DOI: 10.3390/jcm12185786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/21/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Crohn's disease (CD) is a type of inflammatory bowel disease. The number of IBD cases worldwide was estimated to be 4.9 million in 2019. CD exhibits heterogeneity in clinical presentation, anatomical involvement, disease behaviour, clinical course and response to treatment. The classical description of CD involves transmural inflammation with skip lesions anywhere along the entire gastrointestinal tract. The complexity and heterogeneity of Crohn's disease is not currently reflected in the conventional classification system. Though the knowledge of Crohn's pathophysiology remains far from understood, the established complex interplay of the omics-genomics, transcriptomics, proteomics, epigenomics, metagenomics, metabolomics, lipidomics and immunophenomics-provides numerous targets for potential molecular markers of disease. Advancing technology has enabled identification of small molecules within these omics, which can be extrapolated to differentiate types of Crohn's disease. The multi-omic future of Crohn's disease is promising, with potential for advancements in understanding of its pathogenesis and implementation of personalised medicine.
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Affiliation(s)
- Shahed Kamal
- Department of Gastroenterology, Northern Hospital, Epping, Melbourne VIC 3076, Australia
| | - Nikita Parkash
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - William Beattie
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - Britt Christensen
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
| | - Jonathan P. Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
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23
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Rutherford D, Ho GT. Therapeutic Potential of Human Intestinal Organoids in Tissue Repair Approaches in Inflammatory Bowel Diseases. Inflamm Bowel Dis 2023; 29:1488-1498. [PMID: 37094358 PMCID: PMC10472753 DOI: 10.1093/ibd/izad044] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Indexed: 04/26/2023]
Abstract
Inflammatory bowel diseases (IBDs) are chronic immune-mediated conditions characterized by significant gut tissue damage due to uncontrolled inflammation. Anti-inflammatory treatments have improved, but there are no current prorepair approaches. Organoids have developed into a powerful experimental platform to study mechanisms of human diseases. Here, we specifically focus on its role as a direct tissue repair modality in IBD. We discuss the scientific rationale for this, recent parallel advances in scientific technologies (CRISPR [clustered regularly interspaced short palindromic repeats]/Cas9 and metabolic programming), and in addition, the clinical IBD context in which this therapeutic approach is tractable. Finally, we review the translational roadmap for the application of organoids and the need for this as a novel direction in IBD.
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Affiliation(s)
- Duncan Rutherford
- Gut Research Unit, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Gwo-Tzer Ho
- Gut Research Unit, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
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24
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Crossay E, Jullian V, Trinel M, Sagnat D, Hamel D, Groppi E, Rolland C, Stigliani JL, Mejia K, Cabanillas BJ, Alric L, Buscail E, El Kalamouni C, Mavingui P, Deraison C, Racaud-Sultan C, Fabre N. Daphnanes diterpenes from the latex of Hura crepitans L. and their PKCζ-dependent anti-proliferative activity on colorectal cancer cells. Bioorg Med Chem 2023; 90:117366. [PMID: 37329676 DOI: 10.1016/j.bmc.2023.117366] [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: 02/13/2023] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/19/2023]
Abstract
Hura crepitans L. (Euphorbiaceae) is a thorn-covered tree widespread in South America, Africa and Asia which produces an irritating milky latex containing numerous secondary metabolites, notably daphnane-type diterpenes known as Protein Kinase C activators. Fractionation of a dichloromethane extract of the latex led to the isolation of five new daphnane diterpenes (1-5), along with two known analogs (6-7) including huratoxin. Huratoxin (6) and 4',5'-epoxyhuratoxin (4) were found to exhibit significant and selective cell growth inhibition against colorectal cancer cell line Caco-2 and primary colorectal cancer cells cultured as colonoids. The underlying mechanism of 4 and 6 was further investigated revealing the involvement of PKCζ in the cytostatic activity.
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Affiliation(s)
- Elise Crossay
- UMR 152 PharmaDev, Université de Toulouse, IRD, UPS, France
| | | | - Manon Trinel
- UMR 152 PharmaDev, Université de Toulouse, IRD, UPS, France
| | - David Sagnat
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, France; Toulouse Organoids Platform, Institut de Recherche en Santé Digestive, INSERM, Toulouse, France
| | - Dimitri Hamel
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, France; LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Emie Groppi
- UMR 152 PharmaDev, Université de Toulouse, IRD, UPS, France
| | - Corinne Rolland
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, France
| | | | - Kember Mejia
- Instituto de Investigaciones de la Amazonia Peruana (IIAP), Iquitos, Peru
| | - Billy Joel Cabanillas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Laurent Alric
- Pole Digestif, Centre Hospitalier Universitaire, Toulouse, France
| | - Etienne Buscail
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, France; Département de Chirurgie Digestive, Unité de Chirurgie Colorectale, Centre Hospitalier Universitaire, Toulouse, France
| | - Chaker El Kalamouni
- UMR PIMIT, Université de La Réunion, INSERM U1187, CNRS 9192, IRD 249, La Réunion, France
| | - Patrick Mavingui
- UMR PIMIT, Université de La Réunion, INSERM U1187, CNRS 9192, IRD 249, La Réunion, France
| | - Céline Deraison
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, France
| | | | - Nicolas Fabre
- UMR 152 PharmaDev, Université de Toulouse, IRD, UPS, France.
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25
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Karakasheva TA, Zhou Y, Xie HM, Soto GE, Johnson TD, Stoltz MA, Roach DM, Nema N, Umeweni CN, Naughton K, Dolinsky L, Pippin JA, Wells AD, Grant SF, Ghanem L, Terry N, Muir AB, Hamilton KE. Patient-derived Colonoids From Disease-spared Tissue Retain Inflammatory Bowel Disease-specific Transcriptomic Signatures. GASTRO HEP ADVANCES 2023; 2:830-842. [PMID: 37736163 PMCID: PMC10512767 DOI: 10.1016/j.gastha.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/12/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND AND AIMS A key histopathological feature of inflammatory bowel disease is damage to the mucosa, including breakdown of the epithelial barrier. Human enteroids and colonoids are a critical bench-to-bedside tool for studying the epithelium in inflammatory bowel disease. The goal of the current study was to define transcriptional differences in healthy versus diseased subjects that are sustained in enteroids and colonoids, including from disease-spared tissue. METHODS Biopsies and matching enteroid or colonoid cultures from pediatric patients with ileal Crohn disease (N = 6) and control subjects (N = 17) were subjected to RNA sequencing followed by bioinformatic and machine learning analyses. Late passage enteroids were exposed to cytokines to assess durable transcriptional differences. RESULTS We observed substantial overlap of pathways upregulated in Crohn disease in enteroids and ileal biopsies, as well as colonoids and rectal biopsies. KEGG pathways for cytokine-cytokine receptor interaction, chemokine signaling, protein export, and Toll-like receptor signaling were upregulated in both ileal and rectal biopsies, as well as enteroids and colonoids. In vitro cytokine exposure reactivated genes previously increased in biopsies. Machine learning predicted biopsy location (100% accuracy) and donor disease status (83% accuracy). A random forest classifier generated using ileal enteroids identified rectal colonoids from ileal Crohn disease subjects with 80% accuracy. CONCLUSION We confirmed transcriptional profiles of Crohn disease biopsies are expressed in enteroids and colonoids. Furthermore, transcriptomic data from disease-spared rectal tissue can identify patients with ileal Crohn disease. Our data support the use of patient enteroids and colonoids as critical translational tools for the study of inflammatory bowel disease.
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Affiliation(s)
- Tatiana A. Karakasheva
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Yusen Zhou
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Hongbo M. Xie
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Gloria E. Soto
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Tiana D. Johnson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Madison A. Stoltz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Daana M. Roach
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Noor Nema
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Chizoba N. Umeweni
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kaitlyn Naughton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lauren Dolinsky
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - James A. Pippin
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Struan F.A. Grant
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Division of Diabetes and Endocrinology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Louis Ghanem
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Immunology, Translational Sciences and Medicine, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Natalie Terry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Immunology, Clinical Development, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Amanda B. Muir
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kathryn E. Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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26
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Tindle C, Katkar GD, Fonseca AG, Taheri S, Lee J, Maity P, Sayed IM, Ibeawuchi SR, Vidales E, Pranadinata RF, Fuller M, Stec DL, Anandachar MS, Perry K, Le HN, Ear J, Boland BS, Sandborn WJ, Sahoo D, Das S, Ghosh P. A Living Organoid Biobank of Crohn's Disease Patients Reveals Molecular Subtypes for Personalized Therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.11.532245. [PMID: 36993763 PMCID: PMC10054961 DOI: 10.1101/2023.03.11.532245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Crohn's disease (CD) is a complex, clinically heterogeneous disease of multifactorial origin; there is no perfect pre-clinical model, little insight into the basis for such heterogeneity, and still no cure. To address these unmet needs, we sought to explore the translational potential of adult stem cell-derived organoids that not only retain their tissue identity, but also their genetic and epigenetic disease-driving traits. We prospectively created a biobank of CD patient-derived organoid cultures (PDOs) using biopsied tissues from colons of 34 consecutive subjects representing all clinical subtypes (Montreal Classification B1-B3 and perianal disease). PDOs were generated also from healthy subjects. Comparative gene expression analyses enabled benchmarking of PDOs as tools for modeling the colonic epithelium in active disease and revealed that despite the clinical heterogeneity there are two major molecular subtypes: immune-deficient infectious-CD [IDICD] and stress and senescence-induced fibrostenotic-CD [S2FCD]. The transcriptome, genome and phenome show a surprising degree of internal consistency within each molecular subtype. The spectrum of morphometric, phenotypic, and functional changes within the "living biobank" reveals distinct differences between the molecular subtypes. These insights enabled drug screens that reversed subtype-specific phenotypes, e.g., impaired microbial clearance in IDICD was reversed using agonists for nuclear receptors, and senescence in S2FCD was rectified using senotherapeutics, but not vice versa . Phenotyped-genotyped CD-PDOs may fill the gap between basic biology and patient trials by enabling pre-clinical Phase '0' human trials for personalized therapeutics. GRAPHIC ABSTRACT In Brief This work creates a prospectively biobanked phenotyped-genotyped Crohn's disease patient-derived organoids (CD-PDOs) as platforms for molecular subtyping of disease and for ushering personalized therapeutics. HIGHLIGHTS Prospectively biobanked CD-organoids recapitulate the disease epithelium in patientsThe phenome-transcriptome-genome of CD-organoids converge on two molecular subtypesOne subtype shows impaired microbial clearance, another increased cellular senescencePhenotyped-genotyped PDOs are then used for integrative and personalized therapeutics.
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27
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Morelli M, Kurek D, Ng CP, Queiroz K. Gut-on-a-Chip Models: Current and Future Perspectives for Host-Microbial Interactions Research. Biomedicines 2023; 11:biomedicines11020619. [PMID: 36831155 PMCID: PMC9953162 DOI: 10.3390/biomedicines11020619] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The intestine contains the largest microbial community in the human body, the gut microbiome. Increasing evidence suggests that it plays a crucial role in maintaining overall health. However, while many studies have found a correlation between certain diseases and changes in the microbiome, the impact of different microbial compositions on the gut and the mechanisms by which they contribute to disease are not well understood. Traditional pre-clinical models, such as cell culture or animal models, are limited in their ability to mimic the complexity of human physiology. New mechanistic models, such as organ-on-a-chip, are being developed to address this issue. These models provide a more accurate representation of human physiology and could help bridge the gap between clinical and pre-clinical studies. Gut-on-chip models allow researchers to better understand the underlying mechanisms of disease and the effect of different microbial compositions on the gut. They can help to move the field from correlation to causation and accelerate the development of new treatments for diseases associated with changes in the gut microbiome. This review will discuss current and future perspectives of gut-on-chip models to study host-microbial interactions.
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28
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Lechuga S, Braga-Neto MB, Naydenov NG, Rieder F, Ivanov AI. Understanding disruption of the gut barrier during inflammation: Should we abandon traditional epithelial cell lines and switch to intestinal organoids? Front Immunol 2023; 14:1108289. [PMID: 36875103 PMCID: PMC9983034 DOI: 10.3389/fimmu.2023.1108289] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
Disruption of the intestinal epithelial barrier is a hallmark of mucosal inflammation. It increases exposure of the immune system to luminal microbes, triggering a perpetuating inflammatory response. For several decades, the inflammatory stimuli-induced breakdown of the human gut barrier was studied in vitro by using colon cancer derived epithelial cell lines. While providing a wealth of important data, these cell lines do not completely mimic the morphology and function of normal human intestinal epithelial cells (IEC) due to cancer-related chromosomal abnormalities and oncogenic mutations. The development of human intestinal organoids provided a physiologically-relevant experimental platform to study homeostatic regulation and disease-dependent dysfunctions of the intestinal epithelial barrier. There is need to align and integrate the emerging data obtained with intestinal organoids and classical studies that utilized colon cancer cell lines. This review discusses the utilization of human intestinal organoids to dissect the roles and mechanisms of gut barrier disruption during mucosal inflammation. We summarize available data generated with two major types of organoids derived from either intestinal crypts or induced pluripotent stem cells and compare them to the results of earlier studies with conventional cell lines. We identify research areas where the complementary use of colon cancer-derived cell lines and organoids advance our understanding of epithelial barrier dysfunctions in the inflamed gut and identify unique questions that could be addressed only by using the intestinal organoid platforms.
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Affiliation(s)
- Susana Lechuga
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Manuel B. Braga-Neto
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Nayden G. Naydenov
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Florian Rieder
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Andrei I. Ivanov
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
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29
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Liver Organoids, Novel and Promising Modalities for Exploring and Repairing Liver Injury. Stem Cell Rev Rep 2023; 19:345-357. [PMID: 36199007 PMCID: PMC9534590 DOI: 10.1007/s12015-022-10456-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2022] [Indexed: 02/07/2023]
Abstract
The past decades have witnessed great advances in organoid technology. Liver is the biggest solid organ, performing multifaceted physiological functions. Nowadays, liver organoids have been applied in many fields including pharmaceutical research, precision medicine and disease models. Compared to traditional 2-dimensional cell line cultures and animal models, liver organoids showed the unique advantages. More importantly, liver organoids can well model the features of the liver and tend to be novel and promising modalities for exploring liver injury, thus finding potential treatment targets and repairing liver injury. In this review, we reviewed the history of the development of liver organoids and summarized the application of liver organoids and recent studies using organoids to explore and further repair the liver injury. These novel modalities could provide new insights about the process of liver injury.
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Abstract
Organoids are a new type of 3D model for tumor research, which makes up for the shortcomings of cell lines and xenograft models, and promotes the development of personalized precision medicine. Long-term culture, expansion and storage of organoids provide the necessary conditions for the establishment of biobanks. Biobanks standardize the collection and preservation of normal or pathological specimens, as well as related clinical information. The tumor organoid biobank has a good quality control system, which is conducive to the clinical transformation and large-scale application of tumor organoids, such as disease modeling, new drug development and high-throughput drug screening. This article summarized the common tumor types of patient-derived organoid (PDO) biobanks and the necessary information for biobank construction, such as the number of organoids, morphology, success rate of culture and resuscitation, pathological types. In our results, we found that patient-derived tumor organoid (PDTO) biobanks were being established more and more, with the Netherlands, the United States, and China establishing the most. Biobanks of colorectal, pancreas, breast, glioma, and bladder cancers were established more, which reflected the relative maturity of culture techniques for these tumors. In addition, we provided insights on the precautions and future development direction of PDTO biobank building.
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31
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Park SB, Jung WH, Choi KJ, Koh B, Kim KY. A Comparative Systematic Analysis of The Influence of Microplastics on Colon Cells, Mouse and Colon Organoids. Tissue Eng Regen Med 2023; 20:49-58. [PMID: 36374371 PMCID: PMC9852409 DOI: 10.1007/s13770-022-00496-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Microplastics (MPs) are small fragments from any type of plastic formed from various sources, including plastic waste and microfibers from clothing. MPs degrades slowly, resulting in a high probability of human inhalation, ingestion and accumulation in bodies and tissues. As its impact on humans is a prolonged event, the evaluation of its toxicity and influence on human health are critical. In particular, MPs can enter the human digestive system through food and beverage consumption, and its effect on the human colon needs to be carefully examined. METHODS We monitored the influence of small MPs (50 and 100 nm) on human colon cells, human colon organoids and also examined their toxicity and changes in gene expression in vivo in a mouse model. RESULTS The data suggested that 5 mg/mL concentrations of 50 and 100 nm MPs induced a > 20% decrease in colon organoid viability and an increase in the expression of inflammatory-, apoptosis- and immunity-related genes. In addition, in vivo data suggested that 50 nm MPs accumulate in various mouse organs, including the colon, liver, pancreas and testicles after 7 d of exposure. CONCLUSION Taken together, our data suggest that smaller MPs can induce more toxic effects in the human colon and that human colon organoids have the potential to be used as a predictive tool for colon toxicity.
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Affiliation(s)
- Sung Bum Park
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Won Hoon Jung
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Kyoung Jin Choi
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Byumseok Koh
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea.
| | - Ki Young Kim
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea.
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32
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Lin W, Wang M, Xu L, Tortorella M, Li G. Cartilage organoids for cartilage development and cartilage-associated disease modeling. Front Cell Dev Biol 2023; 11:1125405. [PMID: 36824369 PMCID: PMC9941961 DOI: 10.3389/fcell.2023.1125405] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
Cartilage organoids have emerged as powerful modelling technology for recapitulation of joint embryonic events, and cartilage regeneration, as well as pathophysiology of cartilage-associated diseases. Recent breakthroughs have uncovered "mini-joint" models comprising of multicellular components and extracellular matrices of joint cartilage for development of novel disease-modifying strategies for personalized therapeutics of cartilage-associated diseases. Here, we hypothesized that LGR5-expressing embryonic joint chondroprogenitor cells are ideal stem cells for the generation of cartilage organoids as "mini-joints" ex vivo "in a dish" for embryonic joint development, cartilage repair, and cartilage-associated disease modelling as essential research models of drug screening for further personalized regenerative therapy. The pilot research data suggested that LGR5-GFP-expressing embryonic joint progenitor cells are promising for generation of cartilage organoids through gel embedding method, which may exert various preclinical and clinical applications for realization of personalized regenerative therapy in the future.
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Affiliation(s)
- Weiping Lin
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, Hong Kong SAR, China,The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,*Correspondence: Weiping Lin, ; Liangliang Xu, ; Micky Tortorella, ; Gang Li,
| | - Min Wang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Liangliang Xu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Weiping Lin, ; Liangliang Xu, ; Micky Tortorella, ; Gang Li,
| | - Micky Tortorella
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, Hong Kong SAR, China,Drug Discovery Pipeline at the Guangzhou Institutes for Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China,*Correspondence: Weiping Lin, ; Liangliang Xu, ; Micky Tortorella, ; Gang Li,
| | - Gang Li
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China,Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China,*Correspondence: Weiping Lin, ; Liangliang Xu, ; Micky Tortorella, ; Gang Li,
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33
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Park SB, Kim EA, Kim KY, Koh B. Induction of toxicity in human colon cells and organoids by size- and composition-dependent road dust. RSC Adv 2023; 13:2833-2840. [PMID: 36756445 PMCID: PMC9845984 DOI: 10.1039/d2ra07500h] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Environmental pollution, including the annual resurgence of particulate matter derived from road dust, is a serious issue worldwide. Typically, the size of road dust is less than 10 μm; thus, road dust can penetrate into human organs, including the brain, through inhalation and intake by mouth. Therefore, the toxicity of road dust has been intensively studied in vitro and in vivo. However, in vitro systems, including 2D cell cultures, cannot mimic complex human organs, and there are several discrepancies between in vivo and human systems. Here, we used human colon cells and organoids to evaluate the cytotoxicity of particulate matter derived from road dust. The toxicity of road dust collected in industrialized and high traffic areas and NIST urban particulate matter reference samples were evaluated in 2D and 3D human colon cells as well as colon organoids and their characteristics were carefully examined. Data suggest that the size and elemental compositions of road dust can correlate with colon organoid toxicity, and thus, a more careful assessment of the size and elemental compositions of road dust should be conducted to predict its effect on human health.
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Affiliation(s)
- Sung Bum Park
- Biotechnology and Therapeutics Division, Korea Research Institute of Chemical Technology 141 Gajeong-ro, Yuseong-gu Daejeon 34114 Republic of Korea
| | - Eun-Ah Kim
- National Assembly Futures InstituteMembers Office Bldg, 1 Uisadang-daero, Yeongdeungpo-guSeoul07233Republic of Korea
| | - Ki Young Kim
- Biotechnology and Therapeutics Division, Korea Research Institute of Chemical Technology 141 Gajeong-ro, Yuseong-gu Daejeon 34114 Republic of Korea
| | - Byumseok Koh
- Biotechnology and Therapeutics Division, Korea Research Institute of Chemical Technology 141 Gajeong-ro, Yuseong-gu Daejeon 34114 Republic of Korea
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Establishment of Epithelial Inflammatory Injury Model Using Intestinal Organoid Cultures. Stem Cells Int 2023; 2023:3328655. [PMID: 36926182 PMCID: PMC10014157 DOI: 10.1155/2023/3328655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
Intestinal epithelial dysfunction is critical in the development of inflammatory bowel disease (IBD). However, most cellular experiments related to epithelial barrier studies in IBD have been based on tumor cell line that lack a variety of intestinal epithelial cell types. Thus, intestinal organoids can present the three-dimensional structure and better simulate the physiological structure and function of the intestinal epithelium in vitro. Here, the crypts were isolated from the small intestine of mice; with the participation of major cytokines (EGF, Noggin, and R-Spondin 1 included), the intestinal organoids were established at a density of 100 crypts per well, containing intestinal stem cells (ISC), Paneth cells, goblet cells, and intestinal endocrine cells. We found that tumor necrosis factor-alpha (TNF-α) could induce the inflammatory response of intestinal organoids, and a dose of 10 ng/mL could maintain stable passaging of organoids for dynamic observation. After stimulation with TNF-α, the intestinal organoid cultures showed lower expression of the cell proliferation-related protein identified by monoclonal antibody Ki 67 (Ki67), the ISC marker leucine-rich repeat-containing G protein-coupled receptor 5 (Lgr5), and the intestinal tight junction proteins occludin (Ocln) and claudin-1 (Cldn1) while higher expression of the inflammatory cytokine interleukin- (IL-) 15 and the chemokines C-X-C motif ligand 2 (Cxcl2) and Cxcl10 significantly. In this study, we successfully established an epithelial inflammatory injury model of intestinal organoids, which provides an effective in vitro model for studying the pathogenesis and treatment of IBD.
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35
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Woo CW, Tso P, Yiu JHC. Commensal gut microbiota-based strategies for oral delivery of therapeutic proteins. Trends Pharmacol Sci 2022; 43:1004-1013. [PMID: 36057462 PMCID: PMC9669164 DOI: 10.1016/j.tips.2022.08.002] [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: 05/16/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 01/13/2023]
Abstract
Therapeutic proteins are rarely available in oral dosage form because the hostile environment of the human gastrointestinal (GI) tract and their large size make this delivery method difficult. Commensal bacteria in the gut face the same situation; however, they not only survive but low levels of their structural components such as lipopolysaccharide (LPS), peptidoglycan, and flagellin are also consistently detectable in the circulatory systems of healthy individuals. This opinion article discusses how gut bacteria survive in the gut, how their components penetrate the body from the perspective of the bacteria's and the host's proactivity, and how orally administered therapeutic proteins may be developed that exploit similar mechanisms to enter the body.
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Affiliation(s)
- Connie W Woo
- Department of Pharmacology and Pharmacy, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Patrick Tso
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, OH, USA
| | - Jensen H C Yiu
- Department of Pharmacology and Pharmacy, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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Hammoudi N, Hamoudi S, Bonnereau J, Bottois H, Pérez K, Bezault M, Hassid D, Chardiny V, Grand C, Gergaud B, Bonnet J, Chedouba L, Tran Minh ML, Gornet JM, Baudry C, Corte H, Maggiori L, Toubert A, McBride J, Brochier C, Neighbors M, Le Bourhis L, Allez M. Autologous organoid co-culture model reveals T cell-driven epithelial cell death in Crohn's Disease. Front Immunol 2022; 13:1008456. [PMID: 36439157 PMCID: PMC9685428 DOI: 10.3389/fimmu.2022.1008456] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/24/2022] [Indexed: 09/15/2023] Open
Abstract
Lympho-epithelial interactions between intestinal T resident memory cells (Trm) and the epithelium have been associated with inflammatory bowel disease (IBD) activity. We developed ex vivo autologous organoid-mucosal T cell cocultures to functionally assess lymphoepithelial interactions in Crohn's Disease (CD) patients compared to controls. We demonstrate the direct epithelial cell death induced by autologous mucosal T cells in CD patients but not in controls. These findings were positively correlated with T cell infiltration of the organoids. This potential was inhibited by limiting lympho-epithelial interactions through CD103 and NKG2D blocking antibodies. These data directly demonstrate for the first time the direct deleterious effect of mucosal T cells on the epithelium of CD patients. Such ex-vivo models are promising techniques to unravel the pathophysiology of these diseases and the potential mode of action of current and future therapies.
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Affiliation(s)
- Nassim Hammoudi
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
- Gastroenterology Department, AP-HP, Hôpital Saint-Louis/Lariboisière, Paris, France
| | - Sarah Hamoudi
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Julie Bonnereau
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Hugo Bottois
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Kevin Pérez
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Madeleine Bezault
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Déborah Hassid
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
- Gastroenterology Department, AP-HP, Hôpital Saint-Louis/Lariboisière, Paris, France
| | - Victor Chardiny
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Céline Grand
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Brice Gergaud
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Joëlle Bonnet
- Gastroenterology Department, AP-HP, Hôpital Saint-Louis/Lariboisière, Paris, France
| | - Leila Chedouba
- Gastroenterology Department, AP-HP, Hôpital Saint-Louis/Lariboisière, Paris, France
| | - My-Linh Tran Minh
- Gastroenterology Department, AP-HP, Hôpital Saint-Louis/Lariboisière, Paris, France
| | - Jean-Marc Gornet
- Gastroenterology Department, AP-HP, Hôpital Saint-Louis/Lariboisière, Paris, France
| | - Clotilde Baudry
- Gastroenterology Department, AP-HP, Hôpital Saint-Louis/Lariboisière, Paris, France
| | - Hélène Corte
- Digestive Surgery Department, AP-HP, Hôpital Saint-Louis/Lariboisière, Paris, France
| | - Léon Maggiori
- Digestive Surgery Department, AP-HP, Hôpital Saint-Louis/Lariboisière, Paris, France
| | - Antoine Toubert
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Jacqueline McBride
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | | | - Margaret Neighbors
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - Lionel Le Bourhis
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Matthieu Allez
- Université de Paris, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
- Gastroenterology Department, AP-HP, Hôpital Saint-Louis/Lariboisière, Paris, France
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37
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Dotti I, Mayorgas A, Salas A. Generation of human colon organoids from healthy and inflammatory bowel disease mucosa. PLoS One 2022; 17:e0276195. [PMID: 36301950 PMCID: PMC9612551 DOI: 10.1371/journal.pone.0276195] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/01/2022] [Indexed: 11/05/2022] Open
Abstract
Ulcerative colitis and Crohn's disease are chronic inflammatory bowel diseases (IBD) of unknown cause characterized by a relapsing-remitting behavior. Growing evidence supports the idea that the epithelial barrier plays a central role in the pathogenesis of IBD as well as in its evolution over time, thus representing a potential target for novel therapeutic options. In the last decade, the introduction of 3D epithelial cultures from ex vivo-expanded intestinal adult stem cells (ASCs) has impacted our ability to study the function of the epithelium in several gastrointestinal disorders, including IBD. Here, we describe in detail a reproducible protocol to generate Matrigel-embedded epithelial organoids from ASCs of non-IBD and IBD donors using small colonic biopsies, including steps for its optimization. A slightly modified version of this protocol is also provided in case surgical samples are used. With this method, epithelial organoids can be expanded over several passages, thereby generating a large quantity of viable cells that can be used in multiple downstream analyses including genetic, transcriptional, proteomic and/or functional studies. In addition, 3D cultures generated using our protocol are suitable for the establishment of 2D cultures, which can model relevant cell-to-cell interactions that occur in IBD mucosa.
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Affiliation(s)
- Isabella Dotti
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Aida Mayorgas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Azucena Salas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
- * E-mail:
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Abdul L, Xu J, Sotra A, Chaudary A, Gao J, Rajasekar S, Anvari N, Mahyar H, Zhang B. D-CryptO: deep learning-based analysis of colon organoid morphology from brightfield images. LAB ON A CHIP 2022; 22:4118-4128. [PMID: 36200406 DOI: 10.1039/d2lc00596d] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Stem cell-derived organoids are a promising tool to model native human tissues as they resemble human organs functionally and structurally compared to traditional monolayer cell-based assays. For instance, colon organoids can spontaneously develop crypt-like structures similar to those found in the native colon. While analyzing the structural development of organoids can be a valuable readout, using traditional image analysis tools makes it challenging because of the heterogeneities and the abstract nature of organoid morphologies. To address this limitation, we developed and validated a deep learning-based image analysis tool, named D-CryptO, for the classification of organoid morphology. D-CryptO can automatically assess the crypt formation and opacity of colorectal organoids from brightfield images to determine the extent of organoid structural maturity. To validate this tool, changes in organoid morphology were analyzed during organoid passaging and short-term forskolin stimulation. To further demonstrate the potential of D-CryptO for drug testing, organoid structures were analyzed following treatments with a panel of chemotherapeutic drugs. With D-CryptO, subtle variations in how colon organoids responded to the different chemotherapeutic drugs were detected, which suggest potentially distinct mechanisms of action. This tool could be expanded to other organoid types, like intestinal organoids, to facilitate 3D tissue morphological analysis.
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Affiliation(s)
- Lyan Abdul
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada.
| | - Jocelyn Xu
- Faculty of Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
| | - Alexander Sotra
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada.
| | - Abbas Chaudary
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
| | - Jerry Gao
- Faculty of Science, McGill University, 845 Sherbrooke Street West, Montreal, QC H3A 0G4, Canada
| | - Shravanthi Rajasekar
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
| | - Nicky Anvari
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada.
| | - Hamidreza Mahyar
- W Booth School of Engineering Practice and Technology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
| | - Boyang Zhang
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada.
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
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Iribarren C, Nordlander S, Sundin J, Isaksson S, Savolainen O, Törnblom H, Magnusson MK, Simrén M, Öhman L. Fecal luminal factors from patients with irritable bowel syndrome induce distinct gene expression of colonoids. Neurogastroenterol Motil 2022; 34:e14390. [PMID: 35485994 PMCID: PMC9786662 DOI: 10.1111/nmo.14390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/24/2022] [Accepted: 04/11/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Alteration of the host-microbiota cross talk at the intestinal barrier may participate in the pathophysiology of irritable bowel syndrome (IBS). Therefore, we aimed to determine effects of fecal luminal factors from IBS patients on the colonic epithelium using colonoids. METHODS Colon-derived organoid monolayers, colonoids, generated from a healthy subject, underwent stimulation with fecal supernatants from healthy subjects and IBS patients with predominant diarrhea, phosphate-buffered saline (PBS), or lipopolysaccharide (LPS). Cytokines in cell cultures and fecal LPS were measured by ELISA and mRNA gene expression of monolayers was analyzed using Qiagen RT2 Profiler PCR Arrays. The fecal microbiota profile was determined by the GA-map™ dysbiosis test and the fecal metabolite profile was analyzed by untargeted liquid chromatography/mass spectrometry. KEY RESULTS Colonoid monolayers stimulated with fecal supernatants from healthy subjects (n = 7), PBS (n = 4) or LPS (n = 3) presented distinct gene expression profiles, with some overlap (R2 Y = 0.70, Q2 = 0.43). Addition of fecal supernatants from healthy subjects and IBS patients (n = 9) gave rise to different gene expression profiles of the colonoid monolayers (R2 Y = 0.79, Q2 = 0.64). Genes (n = 22) related to immune response (CD1D, TLR5) and barrier integrity (CLDN15, DSC2) contributed to the separation. Levels of proinflammatory cytokines in colonoid monolayer cultures were comparable when stimulated with fecal supernatants from either donor types. Fecal microbiota and metabolite profiles, but not LPS content, differed between the study groups. CONCLUSIONS Fecal luminal factors from IBS patients induce a distinct colonic epithelial gene expression, potentially reflecting the disease pathophysiology. The culture of colonoids from healthy subjects with fecal supernatants from IBS patients may facilitate the exploration of IBS related intestinal micro-environmental and barrier interactions.
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Affiliation(s)
- Cristina Iribarren
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden,Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Sofia Nordlander
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden,Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Johanna Sundin
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Stefan Isaksson
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry InfrastructureDepartment of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Hans Törnblom
- Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Maria K. Magnusson
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Magnus Simrén
- Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden,Center for Functional GI and Motility DisordersUniversity of North CarolinaChapel HillNorth CarolinaUSA
| | - Lena Öhman
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
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Lee H, Jung KB, Kwon O, Son YS, Choi E, Yu WD, Son N, Jeon JH, Jo H, Yang H, Son YR, Yun CS, Cho HS, Kim SK, Kim DS, Park DS, Son MY. Limosilactobacillus reuteri DS0384 promotes intestinal epithelial maturation via the postbiotic effect in human intestinal organoids and infant mice. Gut Microbes 2022; 14:2121580. [PMID: 36130031 PMCID: PMC9519030 DOI: 10.1080/19490976.2022.2121580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Little is known about the modulatory capacity of the microbiota in early intestinal development. We examined various intestinal models that respond to gut microbial metabolites based on human pluripotent stem cell-derived human intestinal organoids (hIOs): physiologically relevant in vitro fetal-like intestine, intestinal stem cell, and intestinal disease models. We found that a newly isolated Limosilactobacillus reuteri strain DS0384 accelerated maturation of the fetal intestine using 3D hIO with immature fetal characteristics. Comparative metabolomic profiling analysis revealed that the secreted metabolite N-carbamyl glutamic acid (NCG) is involved in the beneficial effect of DS0384 cell-free supernatants on the intestinal maturation of hIOs. Experiments in an intestinal stem cell spheroid model and hIO-based intestinal inflamed model revealed that the cell-free supernatant from DS0384 comprising NCG promoted intestinal stem cell proliferation and was important for intestinal protection against cytokine-induced intestinal epithelial injury. The probiotic properties of DS0384 were also evaluated, including acid and bile tolerance and ability to adhere to human intestinal cells. Seven-day oral administration of DS0384 and cell-free supernatant promoted the intestinal development of newborn mice. Moreover, NCG exerted a protective effect on experimental colitis in mice. These results suggest that DS0384 is a useful agent for probiotic applications and therapeutic treatment for disorders of early gut development and for preventing intestinal barrier dysfunction.
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Affiliation(s)
- Hana Lee
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Kwang Bo Jung
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Ohman Kwon
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Ye Seul Son
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Eunho Choi
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Won Dong Yu
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Naeun Son
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jun Hyoung Jeon
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea
| | - Hana Jo
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea
| | - Haneol Yang
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea
| | - Yeong Rak Son
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea
| | - Chan-Seok Yun
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea
| | - Hyun-Soo Cho
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea,Digital Biotech Innovation Center, KRIBB, Daejeon, Republic of Korea
| | - Sang Kyu Kim
- Laboratory of Efficacy Research, Korea Ginseng Corp., Daejeon, Republic of Korea
| | - Dae-Soo Kim
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea,Digital Biotech Innovation Center, KRIBB, Daejeon, Republic of Korea
| | - Doo-Sang Park
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea,Doo-Sang Park Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, 56212, Republic of Korea
| | - Mi-Young Son
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea,CONTACT Mi-Young Son Stem Cell Research Convergence Center, KRIBB, Daejeon, 34141, Republic of Korea
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Mussard E, Lencina C, Gallo L, Barilly C, Poli M, Feve K, Albin M, Cauquil L, Knudsen C, Achard C, Devailly G, Soler L, Combes S, Beaumont M. The phenotype of the gut region is more stably retained than developmental stage in piglet intestinal organoids. Front Cell Dev Biol 2022; 10:983031. [PMID: 36105361 PMCID: PMC9465596 DOI: 10.3389/fcell.2022.983031] [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: 06/30/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Intestinal organoids are innovative in vitro tools to study the digestive epithelium. The objective of this study was to generate jejunum and colon organoids from suckling and weaned piglets in order to determine the extent to which organoids retain a location-specific and a developmental stage-specific phenotype. Organoids were studied at three time points by gene expression profiling for comparison with the transcriptomic patterns observed in crypts in vivo. In addition, the gut microbiota and the metabolome were analyzed to characterize the luminal environment of epithelial cells at the origin of organoids. The location-specific expression of 60 genes differentially expressed between jejunum and colon crypts from suckling piglets was partially retained (48%) in the derived organoids at all time point. The regional expression of these genes was independent of luminal signals since the major differences in microbiota and metabolome observed in vivo between the jejunum and the colon were not reproduced in vitro. In contrast, the regional expression of other genes was erased in organoids. Moreover, the developmental stage-specific expression of 30 genes differentially expressed between the jejunum crypts of suckling and weaned piglets was not stably retained in the derived organoids. Differentiation of organoids was necessary to observe the regional expression of certain genes while it was not sufficient to reproduce developmental stage-specific expression patterns. In conclusion, piglet intestinal organoids retained a location-specific phenotype while the characteristics of developmental stage were erased in vitro. Reproducing more closely the luminal environment might help to increase the physiological relevance of intestinal organoids.
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Affiliation(s)
- Eloïse Mussard
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
- Lallemand Animal Nutrition, Blagnac Cedex, France
| | - Corinne Lencina
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Lise Gallo
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Céline Barilly
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Maryse Poli
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Katia Feve
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Mikael Albin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Laurent Cauquil
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | | | | | - Laura Soler
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Sylvie Combes
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Martin Beaumont
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
- *Correspondence: Martin Beaumont,
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Sahoo DK, Borcherding DC, Chandra L, Jergens AE, Atherly T, Bourgois-Mochel A, Ellinwood NM, Snella E, Severin AJ, Martin M, Allenspach K, Mochel JP. Differential Transcriptomic Profiles Following Stimulation with Lipopolysaccharide in Intestinal Organoids from Dogs with Inflammatory Bowel Disease and Intestinal Mast Cell Tumor. Cancers (Basel) 2022; 14:3525. [PMID: 35884586 PMCID: PMC9322748 DOI: 10.3390/cancers14143525] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 12/14/2022] Open
Abstract
Lipopolysaccharide (LPS) is associated with chronic intestinal inflammation and promotes intestinal cancer progression in the gut. While the interplay between LPS and intestinal immune cells has been well-characterized, little is known about LPS and the intestinal epithelium interactions. In this study, we explored the differential effects of LPS on proliferation and the transcriptome in 3D enteroids/colonoids obtained from dogs with naturally occurring gastrointestinal (GI) diseases including inflammatory bowel disease (IBD) and intestinal mast cell tumor. The study objective was to analyze the LPS-induced modulation of signaling pathways involving the intestinal epithelia and contributing to colorectal cancer development in the context of an inflammatory (IBD) or a tumor microenvironment. While LPS incubation resulted in a pro-cancer gene expression pattern and stimulated proliferation of IBD enteroids and colonoids, downregulation of several cancer-associated genes such as Gpatch4, SLC7A1, ATP13A2, and TEX45 was also observed in tumor enteroids. Genes participating in porphyrin metabolism (CP), nucleocytoplasmic transport (EEF1A1), arachidonic acid, and glutathione metabolism (GPX1) exhibited a similar pattern of altered expression between IBD enteroids and IBD colonoids following LPS stimulation. In contrast, genes involved in anion transport, transcription and translation, apoptotic processes, and regulation of adaptive immune responses showed the opposite expression patterns between IBD enteroids and colonoids following LPS treatment. In brief, the crosstalk between LPS/TLR4 signal transduction pathway and several metabolic pathways such as primary bile acid biosynthesis and secretion, peroxisome, renin-angiotensin system, glutathione metabolism, and arachidonic acid pathways may be important in driving chronic intestinal inflammation and intestinal carcinogenesis.
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Affiliation(s)
- Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
- SMART Pharmacology, Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Dana C. Borcherding
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Lawrance Chandra
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Albert E. Jergens
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Todd Atherly
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Agnes Bourgois-Mochel
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - N. Matthew Ellinwood
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (N.M.E.); (E.S.)
| | - Elizabeth Snella
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (N.M.E.); (E.S.)
| | - Andrew J. Severin
- Office of Biotechnology’s Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA;
| | | | - Karin Allenspach
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Jonathan P. Mochel
- SMART Pharmacology, Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
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43
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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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44
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Pednekar DD, Liguori MA, Marques CNH, Zhang T, Zhang N, Zhou Z, Amoako K, Gu H. From Static to Dynamic: A Review on the Role of Mucus Heterogeneity in Particle and Microbial Transport. ACS Biomater Sci Eng 2022; 8:2825-2848. [PMID: 35696291 DOI: 10.1021/acsbiomaterials.2c00182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mucus layers (McLs) are on the front line of the human defense system that protect us from foreign abiotic/biotic particles (e.g., airborne virus SARS-CoV-2) and lubricates our organs. Recently, the impact of McLs on human health (e.g., nutrient absorption and drug delivery) and diseases (e.g., infections and cancers) has been studied extensively, yet their mechanisms are still not fully understood due to their high variety among organs and individuals. We characterize these variances as the heterogeneity of McLs, which lies in the thickness, composition, and physiology, making the systematic research on the roles of McLs in human health and diseases very challenging. To advance mucosal organoids and develop effective drug delivery systems, a comprehensive understanding of McLs' heterogeneity and how it impacts mucus physiology is urgently needed. When the role of airway mucus in the penetration and transmission of coronavirus (CoV) is considered, this understanding may also enable a better explanation and prediction of the CoV's behavior. Hence, in this Review, we summarize the variances of McLs among organs, health conditions, and experimental settings as well as recent advances in experimental measurements, data analysis, and model development for simulations.
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Affiliation(s)
- Dipesh Dinanath Pednekar
- Department of Chemistry, Chemical and Biomedical Engineering, University of New Haven, West Haven, Connecticut 06516, United States
| | - Madison A Liguori
- Department of Chemistry, Chemical and Biomedical Engineering, University of New Haven, West Haven, Connecticut 06516, United States
| | | | - Teng Zhang
- Department of Mechanical and Aerospace Engineering, Syracuse University, Syracuse, New York 13244, United States.,BioInspired Syracuse, Syracuse University, Syracuse, New York 13244, United States
| | - Nan Zhang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Zejian Zhou
- Department of Electrical and Computer Engineering and Computer Science, University of New Haven, West Haven, Connecticut 06516, United States
| | - Kagya Amoako
- Department of Chemistry, Chemical and Biomedical Engineering, University of New Haven, West Haven, Connecticut 06516, United States
| | - Huan Gu
- Department of Chemistry, Chemical and Biomedical Engineering, University of New Haven, West Haven, Connecticut 06516, United States
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45
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Weiß F, Holthaus D, Kraft M, Klotz C, Schneemann M, Schulzke JD, Krug SM. Human duodenal organoid-derived monolayers serve as a suitable barrier model for duodenal tissue. Ann N Y Acad Sci 2022; 1515:155-167. [PMID: 35666953 DOI: 10.1111/nyas.14804] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Usually, duodenal barriers are investigated using intestinal cell lines like Caco-2, which in contrast to native tissue are limited in cell-type representation. Organoids can consist of all intestinal cell types and are supposed to better reflect the in vivo situation. Growing three-dimensionally, with the apical side facing the lumen, application of typical physiological techniques to analyze the barrier is difficult. Organoid-derived monolayers (ODMs) were developed to overcome this. After optimizing culturing conditions, ODMs were characterized and compared to Caco-2 and duodenal tissue. Tight junction composition and appearance were analyzed, and electrophysiological barrier properties, like paracellular and transcellular barrier function and macromolecule permeability, were evaluated. Furthermore, transcriptomic data were analyzed. ODMs had tight junction protein expression and paracellular barrier properties much more resembling the originating tissue than Caco-2. Transcellular barrier was similar between ODMs and native tissue but was increased in Caco-2. Transcriptomic data showed that Caco-2 expressed fewer solute carriers than ODMs and native tissue. In conclusion, while Caco-2 cells differ mostly in transcellular properties, ODMs reflect trans- and paracellular properties of the originating tissue. If cultured under optimized conditions, ODMs possess reproducible functionality, and the variety of different cell types makes them a suitable model for human tissue-specific investigations.
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Affiliation(s)
- Franziska Weiß
- Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, CBF, Berlin, Germany
| | - David Holthaus
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Martin Kraft
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Christian Klotz
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Martina Schneemann
- Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, CBF, Berlin, Germany
| | - Jörg D Schulzke
- Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, CBF, Berlin, Germany
| | - Susanne M Krug
- Clinical Physiology/Nutritional Medicine, Charité - Universitätsmedizin Berlin, CBF, Berlin, Germany
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46
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Aguanno D, Metwaly A, Coleman OI, Haller D. Modeling microbiota-associated human diseases: from minimal models to complex systems. MICROBIOME RESEARCH REPORTS 2022; 1:17. [PMID: 38046357 PMCID: PMC10688821 DOI: 10.20517/mrr.2022.01] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/08/2022] [Accepted: 04/24/2022] [Indexed: 12/05/2023]
Abstract
Alterations in the intestinal microbiota are associated with various human diseases of the digestive system, including obesity and its associated metabolic diseases, inflammatory bowel diseases (IBD), and colorectal cancer (CRC). All three diseases are characterized by modifications of the richness, composition, and metabolic functions of the human intestinal microbiota. Despite being multi-factorial diseases, studies in germ-free animal models have unarguably identified the intestinal microbiota as a causal driver of disease pathogenesis. However, for an increased mechanistic understanding of microbial signatures in human diseases, models require detailed refinement to closely mimic the human microbiota and reflect the complexity and range of dysbiosis observed in patients. The transplantation of human fecal microbiota into animal models represents a powerful tool for studying the causal and functional role of the dysbiotic human microbiome in a pathological context. While human microbiota-associated models were initially employed to study obesity, an increasing number of studies have applied this approach in the context of IBD and CRC over the past decade. In this review, we discuss different approaches that allow the functional validation of the bacterial contribution to human diseases, with emphasis on obesity and its associated metabolic diseases, IBD, and CRC. We discuss the utility of simple models, such as in vitro fermentation systems of the human microbiota and ex vivo intestinal organoids, as well as more complex whole organism models. Our focus here lies on human microbiota-associated mouse models in the context of all three diseases, as well as highlighting the advantages and limitations of this approach.
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Affiliation(s)
- Doriane Aguanno
- Chair of Nutrition and Immunology, Technical University of Munich, Freising 85354, Germany
| | - Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising 85354, Germany
| | - Olivia I. Coleman
- Chair of Nutrition and Immunology, Technical University of Munich, Freising 85354, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising 85354, Germany
- ZIEL Institute for Food & Health, Technical University of Munich, Freising 85354, Germany
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47
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Chen Z, Zhang X, Xing Z, Lv S, Huang L, Liu J, Ye S, Li X, Chen M, Zuo S, Tao Y, He Y. OLFM4 deficiency delays the progression of colitis to colorectal cancer by abrogating PMN-MDSCs recruitment. Oncogene 2022; 41:3131-3150. [PMID: 35487976 DOI: 10.1038/s41388-022-02324-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 11/09/2022]
Abstract
Chronic inflammatory bowel disease (IBD) is strongly associated with the development of colitis-associated tumorigenesis (CAT). Despite recent advances in the understanding of polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) responses in cancer, the mechanisms of these cells during this process remain largely uncharacterized. Here, we discovered a glycoprotein, olfactomedin-4 (OLFM4), was highly expressed in PMN-MDSCs from colitis to colorectal cancer (CRC), and its expression level and PMN-MDSC population positively correlated with the progression of IBD to CRC. Moreover, mice lacking OLFM4 in myeloid cells showed poor recruitment of PMN-MDSCs, impaired intestinal homeostasis, and delayed development from IBD to CRC, and increased response to anti-PD1 therapy. The main mechanism of OLFM4-mediated PMN-MDSC activity involved the NF-κB/PTGS2 pathway, through the binding of LGALS3, a galactoside-binding protein expressed on PMN-MDSCs. Our results showed that the OLFM4/NF-κB/PTGS2 pathway promoted PMN-MDSC recruitment, which played an essential role in the maintenance of intestinal homeostasis, but showed resistance to anti-PD1 therapy in CRC.
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Affiliation(s)
- Ziyang Chen
- Department of Neurosurgery, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, China.,Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiaogang Zhang
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhe Xing
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shuaijun Lv
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Linxuan Huang
- Dongguan Institute of Clinical Cancer Research, Department of Medical Oncology, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, China
| | - Jingping Liu
- Department of Clinical Laboratory, the Third Affiliated Hospital of Southern Medical University, Southern Medical University, Guangzhou, China
| | - Shubiao Ye
- Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinyao Li
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Meiqi Chen
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shaowen Zuo
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yingxu Tao
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yumei He
- Department of Neurosurgery, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, China. .,Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China. .,Department of Clinical Laboratory, the Third Affiliated Hospital of Southern Medical University, Southern Medical University, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China.
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48
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Thomas JP, Modos D, Rushbrook SM, Powell N, Korcsmaros T. The Emerging Role of Bile Acids in the Pathogenesis of Inflammatory Bowel Disease. Front Immunol 2022; 13:829525. [PMID: 35185922 PMCID: PMC8850271 DOI: 10.3389/fimmu.2022.829525] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic immune-mediated inflammatory disorder of the gastrointestinal tract that arises due to complex interactions between host genetic risk factors, environmental factors, and a dysbiotic gut microbiota. Although metagenomic approaches have attempted to characterise the dysbiosis occurring in IBD, the precise mechanistic pathways interlinking the gut microbiota and the intestinal mucosa are still yet to be unravelled. To deconvolute these complex interactions, a more reductionist approach involving microbial metabolites has been suggested. Bile acids have emerged as a key class of microbiota-associated metabolites that are perturbed in IBD patients. In recent years, metabolomics studies have revealed a consistent defect in bile acid metabolism with an increase in primary bile acids and a reduction in secondary bile acids in IBD patients. This review explores the evolving evidence that specific bile acid metabolites interact with intestinal epithelial and immune cells to contribute to the inflammatory milieu seen in IBD. Furthermore, we summarise evidence linking bile acids with intracellular pathways that are known to be relevant in IBD including autophagy, apoptosis, and the inflammasome pathway. Finally, we discuss how novel experimental and bioinformatics approaches could further advance our understanding of the role of bile acids and inform novel therapeutic strategies in IBD.
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Affiliation(s)
- John P Thomas
- Gut Microbes and Health Programme, Quadram Bioscience, Norwich, United Kingdom.,Organisms and Ecosystem, Earlham Institute, Norwich, United Kingdom.,Department of Gastroenterology, Norfolk and Norwich University Hospital, Norwich, United Kingdom
| | - Dezso Modos
- Gut Microbes and Health Programme, Quadram Bioscience, Norwich, United Kingdom.,Organisms and Ecosystem, Earlham Institute, Norwich, United Kingdom
| | - Simon M Rushbrook
- Gut Microbes and Health Programme, Quadram Bioscience, Norwich, United Kingdom.,Department of Gastroenterology, Norfolk and Norwich University Hospital, Norwich, United Kingdom.,Department of Hepatology, University of East Anglia Medical School, Norwich, United Kingdom
| | - Nick Powell
- Division of Digestive Diseases, Imperial College London, London, United Kingdom
| | - Tamas Korcsmaros
- Gut Microbes and Health Programme, Quadram Bioscience, Norwich, United Kingdom.,Organisms and Ecosystem, Earlham Institute, Norwich, United Kingdom.,Division of Digestive Diseases, Imperial College London, London, United Kingdom
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49
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Kopper JJ, Iennarella-Servantez C, Jergens AE, Sahoo DK, Guillot E, Bourgois-Mochel A, Martinez MN, Allenspach K, Mochel JP. Harnessing the Biology of Canine Intestinal Organoids to Heighten Understanding of Inflammatory Bowel Disease Pathogenesis and Accelerate Drug Discovery: A One Health Approach. FRONTIERS IN TOXICOLOGY 2022; 3:773953. [PMID: 35295115 PMCID: PMC8915821 DOI: 10.3389/ftox.2021.773953] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
In a recent issue of the Lancet, the prevalence of Inflammatory Bowel Disease (IBD) was estimated at 7 million worldwide. Overall, the burden of IBD is rising globally, with direct and indirect healthcare costs ranging between $14.6 and $31.6 billion in the U.S. alone in 2014. There is currently no cure for IBD, and up to 40% of patients do not respond to medical therapy. Although the exact determinants of the disease pathophysiology remain unknown, the prevailing hypothesis involves complex interplay among host genetics, the intestinal microenvironment (primarily bacteria and dietary constituents), and the mucosal immune system. Importantly, multiple chronic diseases leading to high morbidity and mortality in modern western societies, including type II diabetes, IBD and colorectal cancer, have epidemiologically been linked to the consumption of high-calorie, low-fiber, high monosaccharide, and high-fat diets (HFD). More specifically, data from our laboratory and others have shown that repeated consumption of HFD triggers dysbiotic changes of the gut microbiome concomitant with a state of chronic intestinal inflammation and increased intestinal permeability. However, progress in our understanding of the effect of dietary interventions on IBD pathogenesis has been hampered by a lack of relevant animal models. Additionally, current in vitro cell culture systems are unable to emulate the in vivo interplay between the gut microbiome and the intestinal epithelium in a realistic and translatable way. There remains, therefore, a critical need to develop translatable in vitro and in vivo models that faithfully recapitulate human gut-specific physiological functions to facilitate detailed mechanistic studies on the impact of dietary interventions on gut homeostasis. While the study of murine models has been pivotal in advancing genetic and cellular discoveries, these animal systems often lack key clinical signs and temporal pathological changes representative of IBD. Specifically, some limitations of the mouse model are associated with the use of genetic knockouts to induce immune deficiency and disease. This is vastly different from the natural course of IBD developing in immunologically competent hosts, as is the case in humans and dogs. Noteworthily, abundant literature suggests that canine and human IBD share common clinical and molecular features, such that preclinical studies in dogs with naturally occurring IBD present an opportunity to further our understanding on disease pathogenesis and streamline the development of new therapeutic strategies. Using a stepwise approach, in vitro mechanistic studies investigating the contribution of dietary interventions to chronic intestinal inflammation and "gut leakiness" could be performed in intestinal organoids and organoid derived monolayers. The biologic potential of organoids stems from the method's ability to harness hard-wired cellular programming such that the complexity of the disease background can be reflected more accurately. Likewise, the effect of therapeutic drug candidates could be evaluated in organoids prior to longitudinal studies in dog and human patients with IBD. In this review, we will discuss the value (and limitations) of intestinal organoids derived from a spontaneous animal disease model of IBD (i.e., the dog), and how it can heighten understanding of the interplay between dietary interventions, the gut microbiota and intestinal inflammation. We will also review how intestinal organoids could be used to streamline the preclinical development of therapeutic drug candidates for IBD patients and their best four-legged friends.
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Affiliation(s)
- Jamie J Kopper
- Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,SMART Translational Medicine, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States
| | - Chelsea Iennarella-Servantez
- SMART Pharmacology, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,SMART Translational Medicine, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States
| | - Albert E Jergens
- Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States
| | - Dipak K Sahoo
- Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,SMART Translational Medicine, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States
| | - Emilie Guillot
- 3D Health Solutions, Inc., ISU Research Park, Ames, IA, United States
| | - Agnes Bourgois-Mochel
- Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States
| | - Marilyn N Martinez
- Office of New Animal Drug Evaluation, Center for Veterinary Medicine, Food and Drug Administration, Rockville, MD, United States
| | - Karin Allenspach
- Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,SMART Translational Medicine, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,3D Health Solutions, Inc., ISU Research Park, Ames, IA, United States
| | - Jonathan P Mochel
- SMART Pharmacology, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,SMART Translational Medicine, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,3D Health Solutions, Inc., ISU Research Park, Ames, IA, United States
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50
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Brice DP, Murray GI, Wilson HM, Porter RJ, Berry S, Durum SK, McLean MH. Interleukin-27 Regulates the Function of the Gastrointestinal Epithelial Barrier in a Human Tissue-Derived Organoid Model. BIOLOGY 2022; 11:biology11030427. [PMID: 35336801 PMCID: PMC8945023 DOI: 10.3390/biology11030427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 11/25/2022]
Abstract
A treatment with direct healing effects on the gastrointestinal epithelial barrier is desirable for inflammatory bowel disease (IBD). Interleukin-27 (IL-27) is an immunoregulatory cytokine, and oral delivery is an effective treatment in murine models of IBD. We aimed to define IL-27 effects on the human gastrointestinal epithelial barrier. We characterised gene and protein expression of permeability mediators in a human colon-derived organoid model. Functional permeability was determined in an organoid-derived 2D monolayer by transepithelial electrical resistance. IL-27 effects on epithelial innate immune responses were assessed through expression of cytokines, anti-microbial peptides and MUC genes. IL-27 effects on wound healing and proliferation were determined in human colon epithelial cell lines. IL-27 led to restoration of permeability regulation following inflammatory cytokine insult (p = 0.001), associated with differential expression of tight junction mediators with decrease in claudin 2 (p = 0.024) and increase in claudin 4 (p < 0.001), E-cadherin (p < 0.001) and zona occludens (p = 0.0014). IL-27 evoked differential gene expression of epithelial-derived innate immune responses (reduced IL1B and IL18, and increased IL33, HBD1, MUC1 and MUC2; p < 0.012). IL-27 induced epithelial barrier wound healing through restitution (p < 0.001), and increased proliferation (p < 0.001) following injury. Overall, IL-27 provokes mucosal healing of the human gastrointestinal epithelial barrier.
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Affiliation(s)
- Daniel P. Brice
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (D.P.B.); (G.I.M.); (H.M.W.); (S.B.)
| | - Graeme I. Murray
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (D.P.B.); (G.I.M.); (H.M.W.); (S.B.)
| | - Heather M. Wilson
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (D.P.B.); (G.I.M.); (H.M.W.); (S.B.)
| | - Ross J. Porter
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Susan Berry
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (D.P.B.); (G.I.M.); (H.M.W.); (S.B.)
| | - Scott K. Durum
- Cytokines and Immunity Section, Laboratory of Cancer Immunometabolism, National Cancer Institute (NCI), National Institute of Health (NIH), Frederick, MD 21702, USA;
| | - Mairi H. McLean
- Division of Molecular & Clinical Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
- Correspondence:
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