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RNA-sequencing of human intestinal enteroids infected with or without human rotavirus (strain Ito)

ABSTRACT: We report the human intestinal epithelial host transcriptional response to human enteric virus infection using primary human intestinal enteroids cultures as a model system.

ORGANISM(S): Homo sapiens

PROVIDER: GSE90796 | GEO | 2016/12/03

SECONDARY ACCESSION(S): PRJNA355975

REPOSITORIES: GEO

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Expression data from human intestinal enteroids altered for Tgfbeta signaling

Project description:We treated intestinal enteroids continuously for 6 days with or without TgfbR1/2 inhibitor (LY2109761) or Tgfb1 ligand

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Development of in vitro enteroids derived from bovine small intestinal crypts

Project description:In vitro 2D cultures of intestinal epithelial cells or epithelial cell lines have been widely used to study cell function and host-pathogen interactions in the bovine intestine. However, these cultures lack the cellular diversity encountered in the intestinal epithelium, and the physiological relevance of monocultures of transformed cell lines is uncertain. Little is also known of the factors that influence cell differentiation and homeostasis in the bovine intestinal epithelium, and few cell-specific markers that can distinguish the different intestinal epithelial cell lineages have been reported. Here we describe a simple and reliable procedure to establish in vitro 3D enteroid, or “mini gut”, cultures from bovine small intestinal (ileal) crypts. These enteroids contained a continuous central lumen lined with a single layer of polarized enterocytes, bound by tight junctions with abundant microvilli on their apical surfaces. Histological and transcriptional analyses suggested that the enteroids comprised a mixed population of intestinal epithelial cell lineages including intestinal stem cells, enterocytes, Paneth cells, goblet cells and enteroendocrine cells. We show that bovine enteroids can be successfully maintained long-term through multiple serial passages without observable changes to their growth characteristics, morphology or transcriptome. Furthermore, the bovine enteroids can be cryopreserved and viable cultures recovered from frozen stocks. Our data suggest that these 3D bovine enteroid cultures represent a novel, physiologically-relevant and tractable in vitro system in which epithelial cell differentiation and function, and host-pathogen interactions in the bovine small intestine can be studied.

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single-cell RNA sequencing for enteroids treated with IL-17

Project description:To evaluate the intestinal epithelial responses induced by IL-17, single-cell RNA-sequencing (scRNA-seq) was performed on the human small intestinal organoids (enteroids) sample of treated with and without 100 mg/ml IL-17

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Ontogeny and function of the circadian clock in intestinal organoids [human]

Project description:Circadian rhythms regulate diverse aspects of gastrointestinal physiology ranging from the composition of microbiota to motility. However, development of the intestinal circadian clock and detailed molecular mechanisms regulating circadian physiology of the intestine remain largely unknown. The lack of appropriate human model systems that enable organ- and/or diseasespecific interrogation of clock functions is a major obstacle hindering advancements of translational applications using chronotherapy. In this report, we show that both pluripotent stem cell-derived human intestinal organoids engrafted into mice and patient-derived human intestinal enteroids (HIEs) possess robust circadian rhythms, and demonstrate circadian phase-dependent necrotic cell death responses to Clostridium difficile toxin B (TcdB). Intriguingly, mouse and human enteroids demonstrate anti-phasic necrotic cell death responses. RNA-Seq data show ~4% of genes are rhythmically expressed in HIEs. Remarkably, we observe anti-phasic gene expression of Rac1, a small GTPase directly inactivated by TcdB, between mouse and human enteroids. Importantly, the observed circadian time-dependent necrotic cell death response is abolished in both mouse enteroids and human intestinal organoids (HIOs) lacking robust circadian rhythms. Our findings uncover robust functions of circadian rhythms regulating critical clock-controlled genes (CCGs) in human enteroids governing organism-specific, circadian phasedependent necrotic cell death responses. Our data highlight unique differences between mouse and human enteroids, and lay a foundation for human organ- and disease-specific investigation of clock functions using human organoids for translational applications.

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Project description:Transcriptional responses of GII.4 human norovirus infection in jejunal human intestinal enteroids

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Ontogeny and function of the circadian clock in intestinal organoids [mouse]

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