4.6 Review

Gastrointestinal organoids in the study of viral infections

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Tissue geometry drives deterministic organoid patterning

N. Gjorevski et al.

Summary: This study describes a method for controlling the formation of epithelial organoids, making the stochastic process more deterministic by spatial and temporal control. By using bioengineering techniques, researchers successfully controlled the formation and patterning of intestinal organoids, and identified the underlying mechanisms of epithelial patterning.

SCIENCE (2022)

Review Immunology

Crosstalk Between the Gut Microbiota and Epithelial Cells Under Physiological and Infectious Conditions

An Zhou et al.

Summary: The gastrointestinal tract (GIT) is the largest immunological organ with a diverse gut microbiota, and the interaction between gut microbiota and intestinal epithelial cells (IECs) plays a crucial role in maintaining GIT homeostasis. This review focuses on the crosstalk between gut microbiota and IECs during infection, and discusses potential therapeutic methods and strategies for prevention and treatment of infectious diseases.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2022)

Review Oncology

Gut microbiota influence immunotherapy responses: mechanisms and therapeutic strategies

Yuting Lu et al.

Summary: The gut microbiota play a crucial role in modulating antitumor immunity and enhancing the efficacy of cancer immunotherapies, particularly immune checkpoint inhibitors. Metabolites are a key mechanism through which the gut microbiota impact antitumor immune responses.

JOURNAL OF HEMATOLOGY & ONCOLOGY (2022)

Article Biochemical Research Methods

Generation of CRISPR-Cas9-mediated genetic knockout human intestinal tissue-derived enteroid lines by lentivirus transduction and single-cell cloning

Shih-Ching Lin et al.

Summary: The authors present a protocol for using the CRISPR-Cas9 genome editing system to knock out a gene of interest in human intestinal tissue-derived enteroids. This protocol provides detailed technical pipeline and step-by-step guidelines for efficient knockout cell line generation. The protocol also highlights the potential applications of this system in assessing host restriction factors for viral replication and investigating the function of essential genes.

NATURE PROTOCOLS (2022)

Article Biochemistry & Molecular Biology

Variable susceptibility of intestinal organoid-derived monolayers to SARS-CoV-2 infection

Kyung Ku Jang et al.

Summary: In this study, researchers used intestinal organoid-derived cultures to investigate the variability in gastrointestinal effects associated with COVID-19. They found that the replication of SARS-CoV-2 in small intestinal and colonic organoids varied significantly between different donors. The susceptibility to infection was correlated with ACE2 expression levels and independent of demographic or clinical features. The study also revealed a delayed but robust interferon response in organoid-derived cultures, with the magnitude of the response corresponding to the degree of SARS-CoV-2 infection. Interestingly, the Omicron variant spike protein showed increased infectivity in the organoids, suggesting a higher tropism for intestinal tissue.

PLOS BIOLOGY (2022)

Article Cell & Tissue Engineering

Optimized human intestinal organoid model reveals interleukin-22-dependency of paneth cell formation

Gui-Wei He et al.

Summary: IL-22 has opposing roles in intestinal pathophysiology, slowing the growth of small intestinal organoids while promoting the formation of Paneth cells and the expression of host defense genes.

CELL STEM CELL (2022)

Article Public, Environmental & Occupational Health

Aetiology and incidence of diarrhoea requiring hospitalisation in children under 5 years of age in 28 low-income and middle-income countries: findings from the Global Pediatric Diarrhea Surveillance network

Adam L. Cohen et al.

Summary: Rotavirus is the leading cause of hospitalised diarrhoea in children, but the introduction of rotavirus vaccine has significantly reduced hospitalisation rates. Shigella, norovirus, and adenovirus are also important pathogens for diarrhoea, and interventions should be prioritised to reduce morbidity and mortality.

BMJ GLOBAL HEALTH (2022)

Review Microbiology

The gut microbiota-brain axis in behaviour and brain disorders

Livia H. Morais et al.

Summary: This Review discusses the intricate and potentially important connections between the gut microbiota and the brain, involving bidirectional communication along the gut-brain axis. Emerging evidence suggests that disruptions in microbial communities may be implicated in neurological disorders, with animal models providing valuable insights into the pathways linking the gut and the brain which could have tangible impacts on human health.

NATURE REVIEWS MICROBIOLOGY (2021)

Review Gastroenterology & Hepatology

Intestinal organoids in coculture: redefining the boundaries of gut mucosa ex vivo modeling

Viktoria Hentschel et al.

Summary: Maintaining the integrity of the mucosal barrier is crucial for intestinal homeostasis and overall health, depending on a balanced signaling system between the intestinal epithelium and other cell populations. Disruptions to this communication may lead to sustained weakening of the intestinal barrier function, causing inflammation, tissue damage, and dysbiosis. Organoid-derived intestinal coculture models provide a convenient tool for studying these pathophysiological events and exploring interactions between cell populations to focus on intestinal barrier recovery and stabilization.

AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY (2021)

Review Biochemistry & Molecular Biology

Strategies for genetic manipulation of adult stem cell-derived organoids

Constantin Menche et al.

Summary: Organoid technology allows the expansion of primary epithelial cells from normal and diseased tissues, providing a unique model for studying human (patho)biology. Through genetic manipulation, researchers can investigate molecular mechanisms underlying cell fate regulation, differentiation, and interactions. Challenges exist in genetic experimentation with organoids due to their multicellularity and dynamic nature, despite the powerful methodologies developed in recent years.

EXPERIMENTAL AND MOLECULAR MEDICINE (2021)

Article Microbiology

New Insights and Enhanced Human Norovirus Cultivation in Human Intestinal Enteroids

Khalil Ettayebi et al.

Summary: The study demonstrates that optimization of cultivation conditions in human intestinal enteroid cultures can effectively replicate multiple strains of human noroviruses (HuNoVs), which is crucial for research on HuNoV biology and the development of treatment methods.

MSPHERE (2021)

Article Biochemistry & Molecular Biology

Development of Three-Dimensional Human Intestinal Organoids as a Physiologically Relevant Model for Characterizing the Viral Replication Kinetics and Antiviral Susceptibility of Enteroviruses

Jessica Oi-Ling Tsang et al.

Summary: The human small intestinal organoids have been established as a novel platform for characterizing viral replication kinetics and evaluating candidate antivirals for enteroviruses, showing promising results for studying pathogenesis and antiviral drug development.

BIOMEDICINES (2021)

Article Cell Biology

Drivers of transcriptional variance in human intestinal epithelial organoids

Zachary K. Criss et al.

Summary: The study investigated the impact of common variations in culture methods on the transcriptome of human intestinal epithelial organoids, finding that substrate and format had the largest effects on transcriptomic variation, while patient heterogeneity and specific experimental manipulations had smaller effects. Results show that variations in culture conditions can significantly influence intestinal organoids and should be considered when designing experiments and comparing results between laboratories.

PHYSIOLOGICAL GENOMICS (2021)

Article Multidisciplinary Sciences

Single-cell sequencing of rotavirus-infected intestinal epithelium reveals cell-type specific epithelial repair and tuft cell infection

Carolyn Bomidi et al.

Summary: Intestinal epithelial damage is associated with most digestive diseases, impacting nutrient absorption, hormone production, and antimicrobial defense. Understanding epithelial repair and regeneration is crucial for developing therapeutics. Research shows that stem cells drive a repair program, involving tuft cells and immature enterocytes in the repair of damaged epithelium.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Cell & Tissue Engineering

Human Intestinal Organoids Recapitulate Enteric Infections of Enterovirus and Coronavirus

Xiaoyu Zhao et al.

Summary: Optimized human intestinal organoids can better simulate enterovirus and coronavirus infections, with significantly more susceptibility to EV-A71 than CVA16. The dynamics of virus-host interaction differ between SARS-CoV and SARS-CoV-2, with SARS-CoV triggering minimal cellular response and SARS-CoV-2 eliciting a moderate cellular response, shedding light on the distinct pathogenicity of these viral pathogens.

STEM CELL REPORTS (2021)

Article Biochemical Research Methods

A low-cost 3D printed microfluidic bioreactor and imaging chamber for live-organoid imaging

Ikram Khan et al.

Summary: Organoids are biological systems grown in vitro that self-organize into 3D cellular tissues of specific organs, with brain organoids being valuable models for studying human brain development. Researchers are developing improved tools, such as microfluidic chips and bioreactors, to track and image brain organoids in real-time on a chip, enabling long-term live-imaging of the growing organoids with high resolution.

BIOMICROFLUIDICS (2021)

Article Biochemistry & Molecular Biology

Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection

Sergio Triana et al.

Summary: The study revealed that interferon controls human astrovirus infection and the virus can infect all major cell types and lineages in human intestinal organoids. Each intestinal epithelial cell lineage undergoes an antiviral transcriptional reprogramming by upregulating distinct sets of interferon-stimulated genes upon infection, indicating a unique role in resolving virus infection.

MOLECULAR SYSTEMS BIOLOGY (2021)

Article Virology

Comparative Analysis of Public RNA-Sequencing Data from Human Intestinal Enteroid (HIEs) Infected with Enteric RNA Viruses Identifies Universal and Virus-Specific Epithelial Responses

Roberto J. Cieza et al.

Summary: Recent studies utilizing novel biomimetic human models of enteric disease have identified conserved and specific epithelial responses to viral infections in acute gastroenteritis (AGE), shedding light on host-microbe interactions at the intestinal epithelial interface.

VIRUSES-BASEL (2021)

Review Medicine, Research & Experimental

Designing and generating a mouse model: frequently asked questions

Channabasavaiah B. Gurumurthy et al.

Summary: Genetically engineered mouse (GEM) models are commonly used in biomedical research, requiring complex experimental procedures and skilled technical staff. Research institutes establish centralized core facilities to create custom GEM for research groups. Careful planning and consideration of various factors are essential for success in generating GEM models.

JOURNAL OF BIOMEDICAL RESEARCH (2021)

Article Multidisciplinary Sciences

Identification of SARS-CoV-2 inhibitors using lung and colonic organoids

Yuling Han et al.

Summary: Researchers have developed lung and colonic organoid models using human pluripotent stem cells, which demonstrate susceptibility to SARS-CoV-2 infection. These models are valuable for studying the infection of the virus and screening drugs, with potential therapeutic implications for COVID-19.

NATURE (2021)

Editorial Material Gastroenterology & Hepatology

Evidence for Gastrointestinal Infection of SARS-CoV-2

Fei Xiao et al.

GASTROENTEROLOGY (2020)

Article Multidisciplinary Sciences

Bile acids and ceramide overcome the entry restriction for GII.3 human norovirus replication in human intestinal enteroids

Kosuke Murakami et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Gastroenterology & Hepatology

Retinoic Acid and Lymphotoxin Signaling Promote Differentiation of Human Intestinal M Cells

Siyuan Ding et al.

GASTROENTEROLOGY (2020)

Letter Medicine, General & Internal

Detection of SARS-CoV-2 in Different Types of Clinical Specimens

Wenling Wang et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2020)

Article Multidisciplinary Sciences

SARS-CoV-2 productively infects human gut enterocytes

Mart M. Lamers et al.

SCIENCE (2020)

Article Multidisciplinary Sciences

Human norovirus targets enteroendocrine epithelial cells in the small intestine

Kim Y. Green et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

Infection of bat and human intestinal organoids by SARS-CoV-2

Zhou Jie et al.

NATURE MEDICINE (2020)

Article Immunology

A Human 2D Primary Organoid-Derived Epithelial Monolayer Model to Study Host-Pathogen Interaction in the Small Intestine

Thomas Roodsant et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2020)

Review Cell Biology

Human organoids: model systems for human biology and medicine

Jihoon Kim et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2020)

Article Multidisciplinary Sciences

A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures

Kenneth H. Dinnon et al.

NATURE (2020)

Article Multidisciplinary Sciences

Human norovirus exhibits strain-specific sensitivity to host interferon pathways in human intestinal enteroids

Shih-Ching Lin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Rotavirus induces intercellular calcium waves through ADP signaling

Alexandra L. Chang-Graham et al.

SCIENCE (2020)

Review Biochemistry & Molecular Biology

Cell Cultures for Virology: Usability, Advantages, and Prospects

Alexander A. Dolskiy et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Gastroenterology & Hepatology

Human Intestinal Enteroids With Inducible Neurogenin-3 Expression as a Novel Model of Gut Hormone Secretion

Alexandra L. Chang-Graham et al.

CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY (2019)

Article Multidisciplinary Sciences

Attempts to grow human noroviruses, a sapovirus, and a bovine norovirus in vitro

Tomoichiro Oka et al.

PLOS ONE (2018)

Review Virology

Distinct Effects of Type I and III Interferons on Enteric Viruses

Harshad Ingle et al.

VIRUSES-BASEL (2018)

Review Infectious Diseases

Human noroviruses: recent advances in a 50-year history

Robert L. Atmar et al.

CURRENT OPINION IN INFECTIOUS DISEASES (2018)

Review Immunology

The Dual Nature of Type I and Type II Interferons

Amanda J. Lee et al.

FRONTIERS IN IMMUNOLOGY (2018)

Review Gastroenterology & Hepatology

The Brain-Gut-Microbiome Axis

Clair R. Martin et al.

CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY (2018)

Article Virology

Propagation of Astrovirus VA1, a Neurotropic Human Astrovirus, in Cell Culture

Andrew B. Janowski et al.

JOURNAL OF VIROLOGY (2017)

Article Multidisciplinary Sciences

Enteroviruses infect human enteroids and induce antiviral signaling in a cell lineage-specific manner

Coyne G. Drummond et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Multidisciplinary Sciences

Forskolin-induced Swelling in Intestinal Organoids: An In Vitro Assay for Assessing Drug Response in Cystic Fibrosis Patients

Sylvia F. Boj et al.

JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (2017)

Article Medicine, General & Internal

Rotavirus infection

Sue E. Crawford et al.

NATURE REVIEWS DISEASE PRIMERS (2017)

Review Biochemistry & Molecular Biology

Human Enteroids/Colonoids and Intestinal Organoids Functionally Recapitulate Normal Intestinal Physiology and Pathophysiology

Nicholas C. Zachos et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2016)

Article Multidisciplinary Sciences

Replication of human noroviruses in stem cell-derived human enteroids

Khalil Ettayebi et al.

SCIENCE (2016)

Review Critical Care Medicine

Enterovirus D68 and Human Respiratory Infections

Zichun Xiang et al.

SEMINARS IN RESPIRATORY AND CRITICAL CARE MEDICINE (2016)

Article Immunology

Astrovirus VA1/HMO-C: An Increasingly Recognized Neurotropic Pathogen in Immunocompromised Patients

Julianne R. Brown et al.

CLINICAL INFECTIOUS DISEASES (2015)

Review Food Science & Technology

Human Norovirus as a Foodborne Pathogen: Challenges and Developments

Matthew D. Moore et al.

ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 6 (2015)

Review Immunology

Type I interferons in infectious disease

Finlay McNab et al.

NATURE REVIEWS IMMUNOLOGY (2015)

Review Biochemistry & Molecular Biology

Hormonal Signaling in the Gut

Clemence D. Cote et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2014)

Article Multidisciplinary Sciences

Enteric bacteria promote human and mouse norovirus infection of B cells

Melissa K. Jones et al.

SCIENCE (2014)

Article Microbiology

Correction: MDA-5 Recognition of a Murine Norovirus

Stephen A. McCartney et al.

PLoS Pathogens (2014)

Review Immunology

Intestinal epithelial cells: regulators of barrier function and immune homeostasis

Lance W. Peterson et al.

NATURE REVIEWS IMMUNOLOGY (2014)

Article Biochemistry & Molecular Biology

A functional CFTR assay using primary cystic fibrosis intestinal organoids

Johanna F. Dekkers et al.

NATURE MEDICINE (2013)

Review Gastroenterology & Hepatology

A nomenclature for intestinal in vitro cultures

Matthias Stelzner et al.

AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY (2012)

Article Multidisciplinary Sciences

Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro

Jason R. Spence et al.

NATURE (2011)

Article Immunology

Detection of Newly Described Astrovirus MLB1 in Stool Samples from Children

Stacy R. Finkbeiner et al.

EMERGING INFECTIOUS DISEASES (2009)

Article Microbiology

Metagenomic analysis of human diarrhea: Viral detection and discovery

Stacy R. Finkbeiner et al.

PLOS PATHOGENS (2008)

Article Virology

Norwalk virus RNA is infectious in mammalian cells

Susana Guix et al.

JOURNAL OF VIROLOGY (2007)

Article Virology

Adenovirus E4 ORF3 protein inhibits the interferon-mediated antiviral response

Amanda. J. Ullman et al.

JOURNAL OF VIROLOGY (2007)

Article Biochemistry & Molecular Biology

Constitutive IFN-α/β signal for efficient IFN-α/β gene induction by virus

N Hata et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2001)