Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids
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PROVIDER: PRJNA431159 | ENA |
REPOSITORIES: ENA
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Project description:Here we describe a method for fabricating a primary human Small Intestine-on-a-Chip (Intestine Chip) containing epithelial cells isolated from healthy regions of intestinal biopsies. The primary epithelial cells are expanded as 3D organoids, dissociated, and cultured on a porous membrane within a microfluidic device with human intestinal microvascular endothelium cultured in a parallel microchannel under flow and cyclic deformation. In the Intestine Chip, the epithelium forms villi-like projections lined by polarized epithelial cells that undergo multi-lineage differentiation similar to that of intestinal organoids, however, these cells expose their apical surfaces to an open lumen and interface with endothelium. Transcriptomic analysis also indicates that the Intestine Chip more closely mimics whole human duodenum in vivo when compared to the duodenal organoids used to create the chips. Because fluids flowing through the lumen of the Intestine Chip can be collected continuously, sequential analysis of fluid samples can be used to quantify nutrient digestion, mucus secretion and establishment of intestinal barrier function over a period of multiple days in vitro. The Intestine Chip therefore may be useful as a research tool for applications where normal intestinal function is crucial, including studies of metabolism, nutrition, infection, and drug pharmacokinetics, as well as personalized medicine.
2018-02-15 | GSE109471 | GEO
Project description:Here we describe a method for fabricating a primary human Small Intestine-on-a-Chip (Intestine Chip) containing epithelial cells isolated from healthy regions of intestinal biopsies. The primary epithelial cells are expanded as 3D organoids, dissociated, and cultured on a porous membrane within a microfluidic device with human intestinal microvascular endothelium cultured in a parallel microchannel under flow and cyclic deformation. In the Intestine Chip, the epithelium forms villi-like projections lined by polarized epithelial cells that undergo multi-lineage differentiation similar to that of intestinal organoids, however, these cells expose their apical surfaces to an open lumen and interface with endothelium. Transcriptomic analysis also indicates that the Intestine Chip more closely mimics whole human duodenum in vivo when compared to the duodenal organoids used to create the chips. Because fluids flowing through the lumen of the Intestine Chip can be collected continuously, sequential analysis of fluid samples can be used to quantify nutrient digestion, mucus secretion and establishment of intestinal barrier function over a period of multiple days in vitro. The Intestine Chip therefore may be useful as a research tool for applications where normal intestinal function is crucial, including studies of metabolism, nutrition, infection, and drug pharmacokinetics, as well as personalized medicine.
| S-EPMC5811607 | biostudies-literature
Project description:The entire small intestine was obseved by balloon endoscopy. Biopsy specimens were taken from jejunum, ileum and colon, respectively.
2015-06-11 | GSE69762 | GEO
Project description:Patient-derived gastrointestinal epithelium-only organoids from the small and large intestine, also referred to as colonoids and enteroids, were generated as part of the development of an on-going organoid biobank at the Michigan Medicine Translational Tissue Modeling Laboratory (TTML) (www.UmichTTML.org). Gene expression in organoids was characterized using RNA-sequencing
2020-07-24 | E-MTAB-9339 | biostudies-arrayexpress
Project description:Intestinal failure (IF), following extensive anatomical or functional loss of small intestine (SI), hasdebilitating long-term consequences on children1. Priority of care is to increase the child’s length of functional intestine, jejunum in particular, to promote nutritional independence2. Here we construct autologous jejunal mucosal grafts using primary patient biomaterials. We show that organoids derived from patients can be expanded efficiently in vitro. In parallel, we generate decellularized human intestinal matrix with intact nanotopography, which form optimal biological scaffolds. Remarkably, proteomic and Raman spectroscopy analyses reveal highly analogous biochemical profiles of human SI and colon scaffolds, indicating that both can be used interchangeably as platforms for intestinal engineering. Indeed, seeding jejunal organoids onto either scaffold type reliably reconstructs grafts that exhibit several aspects of physiological jejunal function with potential to survive after transplantation. Our findings provide proof-of-concept data for engineering IF patient-specific jejunal grafts, ultimately aiding in restoration of nutritional autonomy.
2020-09-16 | PXD019816 | Pride
Project description:The goal of this study was to compare RNA expression of the A) CEA gene obtained from i) colon intestine organoids cultured in conventional plastic-adherent Matrigel drop overlaid with growth medium; ii) Colon Intestine-Chips derived from organoids in the presence of constant flow and stretch; iii) human colon intestine tissue and to verify whether Colon Intestine-Chip faithfully recapitulates human duodenum tissue and to better understand how much it differs from the organoids from which it’s derived, and B) FLOR1 gene obtained from i) human alveolar epithelial cells in T-25 Flasks, ii) human Alveolus Lung-Chip on day 5 and day 10 of the culture.
2021-08-24 | GSE175821 | GEO
Project description:The goal of this study was to compare global RNA expression data obtained from: i) duodenal organoids cultured in conventional plastic-adherent Matrigel drop overlaid with growth medium; ii) Duodenum Intestine-Chips derived from organoids in the presence of constant flow and stretch; iii) human adult duodenum tissue and to verify whether Duodenum Intestine-Chip faithfully recapitulates human adult duodenum tissue and to better understand how much it differs from the organoids from which it’s derived.
2020-01-06 | GSE135196 | GEO
Project description:Small intestine organoids generated from young adult mice were passaged once on day 3. Medium was changed again on day 7 and, one day later, organoids were stimulated for 20 hours with either 25ng/ml IFN-β (R&D Systems), or 25ng/ml IFN-γ (BioLegend) or with 200ng/ml IFN-λ2 (PeproTech) or were left untreated (unstimulated group).
2023-07-01 | E-MTAB-12662 | biostudies-arrayexpress
Project description:Human intestinal epithelial organoids (IEO) culture models are rapidly emerging as novel experimental tools to investigate fundamental aspects of intestinal epithelial (patho)physiology. Cellular source and culture protocols vary between different IEO models and reliable markers for their characterization/validation are currently limited. DNA methylation has been demonstrated to play a key role in regulating gene expression and cellular function. This epigenetic mark is comparably stable and has been shown to reflect cellular identity such as tissue origin, developmental stage and age. Our genome wide DNA methylation datasets of purified human epithelium represent a unique resource, which can be used by other researchers to validate their model systems We provide the following datasets of genome-wide DNA methylation profiling by Infinium HumanMethylation450 BeadChip: Purified intestinal epithelial cells (EpCAM+) from paediatric ileum and colon, Non-epithelial mucosal cells (EpCAM-), Whole colonic mucosal biopsies, Intestinal organoid cultures from paediatric ileum and colon, Purified intestinal epithelial cells (EpCAM+) from foetal small intestine and foetal large intestine, Intestinal organoid cultures from foetal small intestine and foetal large intestine, Intestinal organoid cultures derived from induced pluripotent stem cells.<br>Note:</br><br>Some samples in this data set were previously submitted to ArrayExpress under accession number E-MTAB-3709. They're clearly marked in the âDescriptionâ field in sample annotations. </br><br>Information about batch effect during sample handling is included in the experimental variable âblockâ. Batch effect is not massive but present, so it is recommended that batch correction is carried out in data analysis.</br><br>Complementary RNA-seq data on the purified cells and organoids can be found in ArrayExpress at E-MTAB-5015 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5015/ ). </br>
2017-10-31 | E-MTAB-4957 | biostudies-arrayexpress
Project description:To begin to identify genes involved in the transdifferentiation process we analyzed Barrett’s esophagus (with no dysplasia), normal esophagus and small intestine biopsy samples by Affymetrix microarray. Keywords: microarray expression analysis
2008-10-08 | GSE13083 | GEO