Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human and rat liver microtissue

ABSTRACT: Cross species comparison of liver enzyme induction caused by phenobarbital treatment of human and rat liver microtissues.

INSTRUMENT(S):

ORGANISM(S): Rattus Norvegicus (rat) Homo Sapiens (human)

TISSUE(S): Hepatocyte, Liver

SUBMITTER: Matthew Elcombe

LAB HEAD: Simon Plummer

PROVIDER: PXD056101 | Pride | 2024-09-27

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	HumanLiMT__DCB4006.xlsx	Xlsx
	HumanLiMT__DCB4006_Fraction_1.raw	Raw
	HumanLiMT__DCB4006_Fraction_2.raw	Raw
	HumanLiMT__DCB4006_Fraction_3.raw	Raw
	HumanLiMT__DCB4006_Fraction_4.raw	Raw

Items per page:

1 - 5 of 12

Similar Datasets

Single-Cell Transcriptomics of Acetaminophen-Induced Responses in Human 2D and 3D Liver Microtissues

Project description:This study aimed to investigate how liver cell culture architecture influences acetaminophen (APAP)-induced transcriptional responses at single-cell resolution. We used human liver microtissues composed of primary human hepatocytes (PHHs), Kupffer cells (KCs), and hepatic sinusoidal endothelial cells (HSECs), cultured as 2D monolayers or 3D spheroids. Microtissues were exposed to vehicle, low-dose (350 µM), or high-dose (2687 µM) APAP for 24 hours. Single-cell suspensions were generated, and RNA libraries were prepared using the 10x Genomics Chromium platform, followed by Illumina sequencing. The resulting data were analyzed using Cell Ranger and Seurat to identify differentially expressed genes, assess pathway enrichment, and characterize cell-type–specific transcriptional responses to APAP exposure.

2025-09-01 | E-MTAB-15516 | biostudies-arrayexpress

Multicellular spheroids treated with the compound VLX600

Project description:Microarray based mRNA profiling was used to charactarize the response to the compound VLX600 in cells grown as spheroids. Cells used was colon cancer cells HCT116 and HCT116HIF1a knock-out. We identify the small molecule VLX600 as a drug that is preferentially active against quiescent cells in colon cancer 3-D microtissues. The anticancer activity is associated with reduced mitochondrial respiration, leading to a bioenergetic catastrophe and tumor cell death. VLX600 shows enhanced cytotoxic activity under conditions of nutrient starvation. Microarray based mRNA profiling was used to charactarize the response to the compound VLX600 in cells grown as spheroids. Cells used was colon cancer cells HCT116 and HCT116HIF1a knock-out cells.

2014-02-17 | E-GEOD-53777 | biostudies-arrayexpress

Brain tumor model phenotype study

Project description:This experiment aims at assessing the molecular difference at the transcriptome level of invasive and angiogenic phenotype samples from a rat brain tumor model.

2012-07-31 | E-MTAB-1185 | biostudies-arrayexpress

Proteomic workflows for deep phenotypic profiling of 3D organotypic liver models

Project description:Organotypic human tissue models constitute promising systems to facilitate drug discovery and development. They allow to maintain native cellular phenotypes and functions, which enables long-term pharmacokinetic and toxicity studies, as well as phenotypic screening. To trace relevant phenotypic changes back to specific targets or signaling pathways, comprehensive proteomic profiling is the gold-standard. A multitude of proteomic workflows have been applied on 3D tissue models to quantify their molecular phenotypes; however, their impact on analytical results and biological conclusions has not been evaluated. Here, we compared the performance of twelve mass spectrometry-based global proteomic workflows that differed in the amount of cellular input, lysis protocols and quantification methods for the analysis of primary human liver spheroids. We find that the different protocols differ majorly in the total number and subcellular compartment bias of identified proteins, which is particularly relevant for the reliable quantification of transporters and drug metabolizing enzymes. However, using a model of non-alcoholic fatty liver disease, we show that critical disease pathways are robustly identified using a standardized high throughput-compatible workflow based on thermal lysis, even using only individual spheroids (1,500 cells) as input. The results increase the applicability of proteomic profiling to phenotypic screens in organotypic microtissues and provides a scalable platform for deep phenotyping from limited biological material.

2024-04-29 | PXD047462 | Pride

The angiogenic switch leads to a metabolic shift in human glioblastoma

Project description:The gene expression profiles of two groups of triplicate human glioblastoma (GBM) xenografts grown in immunodeficient rats were compared. The first group of xenografts was derived from a patient biopsy with Epidermal Growth Factor Receptor (EGFR) amplification which grows highly invasive and is independent of angiogenesis. The second group was obtained by introducing a dominant-negative EGFR mutant into the tumor cells, leading to a progression of the tumors to an angiogenic phenotype associated with a transition from a proneural to a mesenchymal GBM molecular subtype.

2017-07-05 | E-MTAB-4898 | biostudies-arrayexpress

Gene expression profiles for genetically engineered human hepatoma hi-Hep cells with or without heat treatment, cultured as monolayer or spheroids using serum-containing or serum-free functional media

Project description:We developed a heat-inducible hepatic cell line (hi-Hep) in which BRCA1-associated protein-1 (BAP1) was introduced under the control of a TRE/PCMVmin promoter, in addition to the existing eight liver-enriched transcription factor (LETF) genes (HNF-1α, HNF-1β, HNF-3β, HNF-4α, HNF-6, C/EBP-α, C/EBP-β and C/EBP-γ). The synthetic heat-inducible promoter system utilizes a tetracycline-responsive transactivator (tTA) with a transcriptional positive-feedback loop and EGFP reporter, enabling stringent induction of transgenes upon transient heat treatment (43 °C, 30 min). Following induction, hi-Hep cells exhibit enhanced hepatic functions including ammonia detoxification, albumin secretion, and cytochrome P450 activity compared to parental HepG2 and HepG2/8F_HS cells. Transcriptome profiling was performed using Agilent SurePrint G3 Human GE 8×60K v3 arrays to compare hi-Hep cells with or without heat treatment, in monolayer and spheroid culture formats, under both serum-containing and optimized serum-free conditions, alongside parental HepG2/8F_HS controls.

2026-01-01 | E-MTAB-15803 | biostudies-arrayexpress

Cooperative blockade of CK2 and ATM kinases drives apoptosis in VHL-deficient renal carcinoma cells / RNA-seq (BRB-seq) of treated 786-O spheroids

Project description:Multicellular Tumor Spheroids (MCTS) were pre-formed for 3 days with 786-O cell line to better mimic the tumor microenviroenment. These spheroids were treated with either vehicle (DMSO), drugs alone (KU-60019 10 μM; CX-4945 5 μM) or in combination (KU + CX) for 48h before RNA extraction.

2021-02-04 | E-MTAB-9977 | biostudies-arrayexpress

Mass Spectrometry Methods and Mathematical PK/PD Model for Decision Tree-Guided Covalent Drug Development

Project description:Covalent drug discovery efforts are growing rapidly but have major unaddressed limitations. These include high false positive rates during hit-to-lead identification; the inherent uncoupling of covalent drug concentration and effect [i.e., uncoupling of pharmacokinetics (PK) and pharmacodynamics (PD)]; and a lack of bioanalytical and modeling methods for determining PK and PD parameters. We present a covalent drug discovery workflow that addresses these limitations. Our bioanalytical methods are based upon a mass spectrometry (MS) assay that can measure the percentage of drug-target protein conjugation (% target engagement) in biological matrices. Further we develop an intact protein PK/PD model (iPK/PD) that outputs PK parameters (absorption and distribution) as well as PD parameters (mechanism of action, protein metabolic half-lives, dose, regimen, effect) based on time-dependent target engagement data. Notably, the iPK/PD model is applicable to any measurement (e.g., bottom-up MS and other drug binding studies) that yields % of target engaged. A Decision Tree is presented to guide researchers through the covalent drug development process. Our bioanalytical methods and the Decision Tree are applied to two approved drugs (ibrutinib and sotorasib); the most common plasma off-target, human serum albumin; three protein targets (KRAS, BTK, SOD1), and to a promising SOD1-targeting ALS drug candidates.

2025-01-23 | PXD046903 | Pride

Gene microarray data for HT-29 monolayer and spheroids

Project description:Colorectal cancers have a rare population of cells that express specific cell surface markers, and are referred to as cancer stem cells (CSC). Targeting CSCs, implicated in tumor relapse, is a paradigm shifting approach for colorectal cancer. We used gene microarray to analyze gene expression in HT-29, a colon cancer cell line, grown as monolayer and spheroid and identify metabolic pathways that are upregulated. HT-29 monolayer cells were grown in DMEM/F12 media supplemented with 10% FBS, and 1X Antibiotic-Antimycotic liquid (AA); and spheroids were grown in stem cell media [DMEM:F12, 1X AA, 1X B27, epidermal growth factors, and fibroblast growth factor for five days. Total RNA was isolated using the mirVana™ miRNA Isolation Kit according to the manufacturer's protocol. RNA intergrity was confirmed on the Nanodrop ND-1000 and analyzed with Agilent 2100 bioanalyzer. The arrays were scanned with the Affymetrix 3000 7G plus scanner.

2015-04-01 | E-GEOD-65433 | biostudies-arrayexpress

RNA-seq of transplanted pluripotent stem cells-derived human intestinal organoids upon mechanical lengthening and human jejunum tissues

Project description:Human Intestinal Organoids (HIOs) generated from embryonic and/or induced pluripotent stem cell lines offer an avenue to study both developmental and human specific disease states. Recently, progress has been made in scaling and maturing these inherently immature tissues through transplanting them in vivo. However, these resultant grafts best approximate fetal intestinal tissue thus limiting their utility. To induce growth and maturation of HIOs we used a nitinol spring device to mechanically induce enterogenesis of HIO in vivo. HIOs are cultured prior to implantation within the mesentery of immunodeficient mice. They are allowed to grow, vascularize, and mature before a second procedure is performed wherein a compressed nitinol spring is implanted within the lumen of the transplanted HIO (tHIO). Next Generation RNA sequencing was performed across transplanted samples as well as on human surgical samples to highlight the transcriptional similarities and differences between groups. Transcriptionally, the tHIO+S samples were more similar to human tissues than the tHIO. With these initial experiments, we concluded that the application of an intraluminal uniaxial force is a practical method to induce maturation of tHIOs in vivo without concomitant architectural disruptions. While our current system does lack certain complexities, we have demonstrated enterogenesis by means of mechanical manipulation.

2018-03-30 | E-MTAB-6017 | biostudies-arrayexpress