Patient-Derived Liver on Chips
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE188541 | GEO | 2022/01/24
REPOSITORIES: GEO
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Project description:Human lung organoids (HLOs) were derived from human embryonic stem cell line H9 NIH registry #0062. Sequencing of HLOs was performed by the UM DNA Sequencing Core, using Illumina Hi-Seq platform and single-end 50 bp reads. The UM Bioinformatics Core downloaded the reads files from the Sequencing Core storage, and concatenated those into a single .fastq file for each sample. 3 HLOs were cultured for 65 days and 3 HLOs were cultured in vitro for 110 days. HLO Culture Protocol 4-day Activin A (R&D systems) differentiation protocol was used to derive definitive endoderm from human pluripotent stem cells (hPSCs). Cells were treated with Activin A (100ngml-1) for three consecutive days in RPMI 1640 media (Life Technologies) with increasing concentrations of 0%, 0.2% and 2% HyClone defined fetal bovine serum (dFBS, Thermo Scientific). The fourth day was a repeat of day 3 media (2% HyClone FBS). After differentiation into definitive endoderm, cells were incubated in foregut media (advanced DMEM/F12 plus N-2 and B27 supplement, 10mM Hepes, 1x L-Glutamine (200mM), 1x Penicillin-streptomycin (5,000 U/mL, all from Life Technologies)) with 200ng/mL Noggin (NOG, R&D Systems) and 10uM SB431542 (SB, Stemgent) for 4 days, SB, 500ng/mL FGF4 (R&D Systems), and 2 uM CHIR99021 (Chiron, Stemgent), and 1uM SAG (Enzo Life Sciences) for 4-6 days. After 4 days with treatment of growth factors, three-dimensional floating spheroids were present in the culture. Three-dimensional spheroids were transferred into Matrigel to support 3D growth. Spheroids were embedded in a droplet of Matrigel (BD Bioscience #356237) in one well of a 24 well plate, and incubated at room temperature for 10 minutes. After the Matrigel solidified, foregut media with 1% Fetal bovine serum (FBS, CAT#: 16000-044, Life Technologies) and 500ng/mL FGF10 (R&D Systems) were overlaid and replaced every 4 days. Organoids were transferred into new Matrigel droplets every 10 to 15 days.
2015-03-09 | E-MTAB-3339 | biostudies-arrayexpress
Project description:Hepatic organoids are a recent innovation in in vitro modelling. Initial studies suggest organoids better recapitulate the liver phenotype in vitro compared to pre-existing proliferative cell models. However, their propensity for drug metabolism and detoxification remains poorly characterised. A global proteomic profiling of undifferentiated and differentiated hepatic murine organoids and donor-matched livers was therefore performed to assess both their similarity to liver tissue and DMET expression. iTRAQ analysis revealed 4,405 proteins commonly detected across all sample types. Differentiation of organoids significantly increased the expression of multiple CYP450s, phase II enzymes, liver biomarkers and hepatic transporters. While the final phenotype of differentiated organoids is distinct from liver tissue, they contain multiple DMET proteins necessary for liver function and drug metabolism, such as CYP450 3A, GSTA and MDR1A. Hepatic organoids may therefore represent an attractive novel model for hepatotoxicity testing, although further experimentation, optimisation and characterisation is needed relative to pre-existing models to fully contextualise their use as a putative in vitro model of DILI.
2021-06-03 | PXD017986 | Pride
Project description:Chronic liver injury promotes fibrosis, which can progress to cirrhosis, a major cause of morbidity and mortality worldwide. Resolving the cell-type-specific transcriptional changes orchestrating this transformation remains challenging. Recent advances in differentiation protocols allow the generation of multi-lineage human liver organoids (HLOs) from human pluripotent stem cells (hPSCs), providing a new model system to study evolving liver injury. We differentiated hPSCs into HLOs and defined optimal 3D culture conditions for liver injury induction. We modeled steatohepatitis through treatment with palmitic acid (PA) and fibrotic injury through treatment with transforming growth factor beta 1 (TGF-β1). For each injury type, we evaluated the development of fibrosis and inflammation by monitoring changes in morphology, gene expression, and histology. We then performed single-cell RNA-sequencing (scRNA-seq) to investigate cell-type diversity in healthy organoids at different time-points and to understand how TGF-β1- and PA-mediated injury affects each cell type. We observed transcriptional response signatures in injured HLOs to be both cell-type- and injury-specific. TGF-β1 treatment expanded hepatic stellate cell (HSC)-like populations and remodeled cell-cycle patterning. Gene set scoring revealed increased fibroblast activity with TGF-β1 treatment, while PA treatment was associated with inflammatory activity. Differential gene expression analysis at the subpopulation level showed induced profibrotic and extracellular matrix-remodeling pathways with TGF-β1 and non-alcoholic fatty liver disease (NAFLD) expression signatures with PA treatment. Evaluation of receptor and ligand expression defined hepatocyte-, cholangiocyte-, and HSC-like cell-cell interactions induced upon TGF-β1 treatment, an effect not observed with PA treatment. Tracing the changes at receptor-ligand pair resolution revealed specific COL1A1-Integrin complex interactions with TGF-β1 treatment and inflammation-specific interactions including CXCR7 and HLA-C with PA treatment. Treatment of HLOs with PA and TGF-β1 also demonstrated a sequential increase in expression of gene sets that predict clinical disease progression in non-alcoholic steatohepatitis (NASH). Our results demonstrate the applicability of hPSC-derived HLOs as a dynamic in vitro 3D human liver model system for the study of fibrotic and inflammatory liver injury.
2023-10-02 | GSE207889 | GEO
Project description:Human lung organoids (HLOs) are enabling the study of human lung development and disease by modelling native organ tissue structure, cellular composition, and cellular organization. In this report, we demonstrate that human lung organoids (HLOs) derived from human pluripotent stem cells (hPSCs) cultured in alginate, a fully defined non-animal product substrate, exhibit enhanced cellular differentiation compared to HLOs cultured in the commercially available Matrigel. More specifically, we observed an earlier onset and increase in the number of multi-ciliated cells, along with mucus producing MUC5AC+ goblet-like cells that were not observed in HLOs cultured in Matrigel. The epithelium in alginate-grown HLOs was organized in a pseudostratified epithelium with airway basal cells lining the basal lamina, but with the apical surface of cells on the exterior of the organoid. We further observed that HLOs cultured in Matrigel exhibited mesenchymal overgrowth that was not present in alginate cultures. The containment of the mesenchyme within HLOs in alginate enabled modeling of key features of Idiopathic Pulmonary Fibrosis (IPF) by treatment with TGFb. TGFβ treatment resulted in morphological changes including an increase in mesenchymal growth, increased expression of IPF markers, and decreased numbers of alveolar-like cells. This culture system provides a model to study the interaction of the mesenchyme with the epithelium during lung development and diseased states such as IPF.
2023-01-04 | GSE171331 | GEO
Project description:Drug induced liver injury (DILI) is a leading cause of acute liver failure. Reliable and translational biomarkers are needed for early detection of DILI. microRNAs (miRNAs) have received wide attention as a novel class of potential DILI biomarkers. However, it is unclear how DILI drugs other than acetaminophen may influence miRNA expression or which miRNAs could serve as useful biomarkers in humans. We selected ketoconazole (KCZ), a classic hepatotoxin, to study miRNA biomarkers for DILI as a proof-of-concept for a workflow that integrated in vivo, in vitro, and bioinformatics analyses. We examined hepatic miRNA expression in KCZ-treated rats at multiple doses and durations using miRNA-sequencing and correlated our results with conventional DILI biomarkers such as liver histology. Significant dysregulation of rno-miR-34a-5p, rno-miR-331-3p, rno-miR-15b-3p, and rno-miR-676 was associated with cytoplasmic vacuolization, a phenotype in rat livers with KCZ-induced injury, which preceded the elevation of serum liver transaminases (ALT and AST). Between rats and humans, miR-34a-5p, miR-331-3p, and miR-15b-3p were evolutionarily conserved with identical sequences, whereas miR-676 showed 73% sequence similarity. Using quantitative PCR, we found that the levels of hsa-miR-34a-5p, hsa-miR-331-3p, and hsa-miR-15b-3p were significantly elevated in the culture media of HepaRG cells treated with 100 mM KCZ (a concentration that could induce cytotoxicity). Additionally, we computationally characterized the miRNA candidates for their gene targeting, target functions, and miRNA/target evolutionary conservation. In conclusion, we identified miR-34a-5p, miR-331-3p, and miR-15b-3p as translational biomarker candidates for early detection of KCZ-induced liver injury with a workflow applicable to computational toxicology studies.
2020-10-23 | GSE159200 | GEO
Project description:Symptoms of liver damage are observed in nearly half of patients that succumb to severe SARS-CoV-2 infection. Here we use human induced pluripotent stem cell-derived liver organoids (HLOs) to recapitulate and characterize liver pathology following virus exposure. Utilizing single-cell sequencing technology, we identified robust transcriptomic changes that occur in SARS-CoV-2 infected liver cells as well as uninfected bystander cells. Our results show a significant induction of many inflammatory pathways, including IFN-α, INF-γ and IL-6 signaling. Our results further identify IL-6 signaling as a potential mechanism for liver-mediated activation of circulating macrophages.
2022-10-04 | GSE210059 | GEO
Project description:Symptoms of liver damage are observed in nearly half of patients that succumb to severe SARS-CoV-2 infection. Here we use human induced pluripotent stem cell-derived liver organoids (HLOs) to recapitulate and characterize liver pathology following virus exposure. Utilizing single-cell sequencing technology, we identified robust transcriptomic changes that occur in SARS-CoV-2 infected liver cells as well as uninfected bystander cells. Our results show a significant induction of many inflammatory pathways, including IFN-α, INF-γ and IL-6 signaling. Our results further identify IL-6 signaling as a potential mechanism for liver-mediated activation of circulating macrophages.
2022-10-04 | GSE210058 | GEO
Project description:Drug-Induced-Liver-Injury (DILI) is a leading cause of termination in drug development programs and removal of drugs from the market because of inability to identify potential patients prior to clinical testing. Here, we approached a polygenic risk score (PRS) based strategy by aggregating effects of numerous genome-wide loci identified from previous large-scale genome-wide association studies (GWAS). The PRS predicted the susceptibility to DILI in patients in a clinical trial, and in multi-donor derived primary hepatocytes and stem cell-derived organoids. Pathway analysis highlighted processes previously implicated in DILI, including unfolded protein responses and oxidative stress alleviated by a potent antioxidant. Furthermore, hepatocytic transcriptomic signatures related to polygenic score identified potential drugs with clinical DILI evidence through in silico 941 compound screening. This genetic-, cellular-, organoid- and human-scale evidence underscored the polygenic architectures underlying DILI vulnerability at the level of hepatocytes, thus facilitating future mechanistic studies. Moreover, the proposed “polygenicity-in-a-dish” strategy potentially will contribute to prospective designs of safer, more efficient, and robust clinical trials.
2020-09-07 | GSE152447 | GEO
Project description:Pioneering studies within the last few years have allowed the in vitro expansion of tissue-specific adult stem cells from a variety of endoderm-derived organs, including the stomach, small intestine and colon. Here we derived organoids from mouse gallbladder tissue (gallbladder organoids), from mouse liver (including the extrahepatic biliary ducts and gallbladder; liver organoids) and from mouse small intestine tissue (intestinal organoids). RNA was prepared from these organoids and used to assay expression of 21,258 genes using Affymetrix gene expression arrays. RNA was also prepared from mouse gallbladder, liver and small intestine tissues and used to assay gene expression in these tissues. Finally, gallbladder organoids were induced to differentiate by removing R-spondin 1 and noggin from the culture media and subjected to gene expression array analysis. RNA was extracted from mouse gallbladder organoids, differentiated gallbladder organoids, liver organoids, small intestine organoids, gallbladder tissue, liver tissue and small intestine tissue and then used for hybridization of Affymetrix gene expression microarrays.
2016-04-06 | E-GEOD-77461 | biostudies-arrayexpress
Project description:The key exosomal miRNAs in adaptive response to drug-induced liver (DILI) and liver regeneration were investigated and proved. This study aimed to decipher the mechanism of restorative events in the adaptive response to DILI by investigating circulating exosomal miRNAs. Using toosendanin-induced liver injury model, exosomal miR-106b-5p was identified as a robust driver in the adaptive response of TILI.
2020-11-07 | GSE160961 | GEO