Gene expression data from 3D spheroids of human amniotic epithelial stem cell (hAESC) treated with 20 uM Carnosic Acid
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PROVIDER: PRJNA949643 | ENA |
REPOSITORIES: ENA
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Project description:Gene expression profiling reveals multiple tissue-specific functionality of carnosic acid in a stem-based tool. We evaluated the effects of carnosic acid on human amniotic epithelial stem cells. We performed an untargeted whole-genome transcriptome analysis to explore functionality of carnosic acid in a stem cell-based tool.
2023-04-02 | GSE228408 | GEO
Project description:Background: Mesenchymal stem cells (MSC) derived from human embryonic stem cells (hESC), named EMSC here, have been found efficacious in animal models of autoimmune, inflammatory, and degenerative diseases. However, all the EMSC derivation methods reported so far are in two-dimensional (2D) culture systems, which are of low efficiency and high cost, difficult for large-scale production for research and therapeutic applications. Methods: We established a 3D system that allowed differentiation of hESC spheroids into MSC spheroids (EMSCSp) following treatment with BMP4 and A8301 for 5 days and subsequent culture in a MSC medium for about 15 days. All the procedures were conducted in one vessel without intermediate passaging. Results: EMSCsp cells were efficiently derived from hESC spheroids within 20 days in the 3D culture system, which could be scaled up from a small culture vessel to a 100-ml plastic bag. EMSCSp could further differentiate into spheroids of chondrocytes or adipocytes. EMSCSp could also reattach and form a 2D-monolayer culture (EMSCSp-ML). Compared to EMSC differentiated in monolayer, EMSCSp-ML had faster proliferation and higher yield, and developed less apoptosis and slower senescence. EMSCSp-ML also retained immune-modulatory effects in vitro and therapeutic effects on two mouse models of colitis. Conclusions: The 3D method provides a simple and economic system for large-scale production of EMSC as an unlimited source of the therapeutically promising cells.
2018-07-03 | GSE93218 | GEO
Project description:HT-29 and HCT-116 cells were barcoded using the CloneTracker lentiviral barcode library and then dabrafenib and irinotecan resistant derivatives of these cell lines were established, respectively.10 million barcoded HT-29 and HCT-116 cells were seeded equally onto poly-HEMA coated 4xT75 flask (DMSO Control, Replica A, B, C for each drug). After seeding, cells were allowed to form spheroids and barcoded 3D-HT-29 spheroids were treated with dabrafenib at increasing doses starting from IC50/10 dose until IC50/2 dose with monthly doubling of the dosing (16 weeks), and barcoded 3D-HCT-116 cells were treated with irinotecan at increasing doses starting from IC50/4 dose until IC50 dose with weekly doubling of the dosing (4 weeks). Following the end points of treatment for each cell line, DNA was isolated from harvested cell lines and barcode sequencing and whole exome sequencing were carried out.
2023-09-01 | E-MTAB-13216 | biostudies-arrayexpress
Project description:Liver-derived cells from the surface and cave-adapted morphs of Astyanax mexicanus are valuable in vitro resources to explore the metabolism of these unique fish. However, 2D cultures have not yet fully mimicked the metabolic profile of the fish liver. Also, 3D culturing can modulate the transcriptomic profile of cells when compared to its 2D counterpart. Hence, to widen the range of metabolic pathways that can be depicted in vitro, we cultured the liver-derived SFL and CFL into 3D spheroids. We 3D cultured the cells at various cell seeding densities for 4 weeks and characterized the resultant transcriptome. The 3D cultured SFL and CFL cells indeed depicted a wider range of metabolic pathways as compared to the 2D culture. Further, the 3D spheroids also showed surface and cave-specific responses, making the spheroids an exciting system to study cave adaptation. Taken together, SFL and CFL spheroids prove to be a promising model for overall understanding of altered metabolism in Astyanax mexicanus.
2023-06-13 | GSE234212 | GEO
Project description:Gene expression data from 3D spheroids of human amniotic epithelial stem cell (hAESC) treated with Tsuruazuki Extract (Tsuru)
| PRJNA1165280 | ENA
Project description:3D spheroids of primary human hepatocytes (3D PHH) keep a differentiated phenotype with retained metabolic function and proteome fingerprint for weeks in culture. As a result, 3D PHH are gaining ground as a model for mechanistic studies on liver homeostasis and in vitro to in vivo (IVIV)predictions in drug discovery. However, the function of drug-transporting proteins has not yet been studied in the 3D PHH. Here we used the organic cation transporter 1 (OCT1/SLC22A1) as a model to explore both transporter kinetics and long-term regulation of transporter activity via different pathways. The 3D PHH were cultured for one week and then used for short- and long-term studies. The OCT1 transporter kinetics was assessed using the fluorescent model substrate 4-(4-(dimethylamino)styryl)-N-methylpyridinium (ASP+) and known OCT1 inhibitors in individual 3D PHH. For long-term studies, the 3D PHH were exposed to xenobiotics for seven days, after which protein expression and OCT1 function were assessed. Global proteomics analysis was used to track prototypical changes of other regulated proteins. ASP+ kinetics indicated a fully functional OCT1 transporter with a Km value of 14.14±3.97 using three donors. Established OCT1 inhibitors reduced the uptake of ASP+ in the 3D PHH spheroids, resulting in 40-60% of the maximal uptake rate of ASP+. The long-term exposure studies showed that OCT1 is relatively stable to the activation of a broad range of pathways known to regulate ADME proteins. Importantly, while expression levels of other ADME proteins, such as CYP3A4 and MDR1 were regulated as expected, OCT1 levels remained stable. In conclusion, our results show for the first time that 3D PHH spheroids express fully active OCT1 and that transporter kinetics can be studied in 3D PHH. We also confirm that OCT1 remains stable and functional during activation of various pathways that alter the expression and function of other ADME proteins.
2024-08-10 | PXD045733 | Pride
Project description:Human bone marrow mesenchymal stromal cells (MSCs) are conventionally cultured as adherent monolayers on tissue culture plastic. MSCs can also be cultured as 3D cell aggregates (spheroids). Optimised 3D conditions (60,000 MSCs cultured as a spheroid for 5 days) inhibited MSC proliferation and induced cell shrinkage in the absence of cell death. Primary human MSCs isolated from 2 donors were cultured under both monolayer (2D MSCs) and optimised 3D (3D MSCs) conditions. High quality RNA was isolated from all samples, and global gene expression analysis was performed in duplicate (using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays) to identify gene expression changes in 3D compared to 2D MSC cultures.
2015-09-30 | E-MTAB-3795 | biostudies-arrayexpress
Project description:Spheroids are 3D multi-cell aggregates formed in non-addherent culture conditions. In ovarian cancer (OC), they serve as a vehicle for cancer cell dissemination in the peritoneal cavity. We investigated genes and networks upregulated in three dimensional (3D) versus two-dimensional (2D) culture conditions by Affymetrix gene expression profiling and identified ALDH1A1, a cancer stem cell marker as being upregulated in OC spheroids. Network analysis confirmed ALDH1A1 upregulation in spheroids in direct connection with elements of the beta-catenin pathway. A parallel increase in the expression levels of beta-catenin and ALDH1A1 was demonstrated in spheroids vs. monolayers an in successive spheroid generations by using OC cell liness and primary OC cells. The percentage of Aldefluor positive cells was significantly higher in spheroids vs. monolayers in IGROV1, A2780, SKOV3, and primary OC cells. B-catenin knock-down decreased ALDH1A1 expression and chromatin immunoprecipitation demonstrated that beta-catenin directly binds to the ALDH1A1 promoter. Both siRNA mediated beta-catenin knock-down and a novel ALDH1A1 small molecule enzymatic inhibitor described here for the first time, decreased the number of OC spheroids (p<0.001) and cell viability. These data strongly support the role of beta-catenin regulated ALDH1A1 in the maintenance of OC spheroids and of a stem cell phenotype and propose new ALDH1A1 inhibitors targeting this cell population. Different gene profiles were observed in ovarian cancer spheroids versus ovarian cancer monolayers. Nine samples were analyzed in triplicate. Each group is a reference.
2014-01-03 | E-GEOD-53759 | biostudies-arrayexpress
Project description:Organoids or spheroids have emerged as a physiologically relevant in vitro preclinical model to study patient-specific diseases. A recent study used spheroids of MCF10 cells to model breast cancer progression and identified targetable alterations more similar to those in vivo. Thus, it is practical and essential to explore and characterize the spheroids of the commonly used human breast cancer (BC) cells. This study conducted Hi-C analyses in three-dimensional (3D) spheroids of MCF10A, MCF7 and MCF7TR cells and compared TADs and looping genes with those in 2D monolayers. We found that chromatin domains and looping genes’ strength have drastically changed during the 3D culture growth, although we identified very similar numbers of TADs and looping genes. We further identified novel 3D growth-specific looping genes within Hippo relevant pathways, of which two genes showed potential prognostic values in measuring the outcome of the endocrine treatment. We finally confirmed a few selected Hippo relevant pathways genes with enhanced looping in breast cancer patient tissues’ organoid. Hence, our work has provided significant insights into our understanding of 3D-growth-specific chromatin architecture in tamoxifen-resistant breast cancer.
2021-09-29 | GSE165571 | GEO
Project description:Organoids or spheroids have emerged as a physiologically relevant in vitro preclinical model to study patient-specific diseases. A recent study used spheroids of MCF10 cells to model breast cancer progression and identified targetable alterations more similar to those in vivo. Thus, it is practical and essential to explore and characterize the spheroids of the commonly used human breast cancer (BC) cells. This study conducted Hi-C analyses in three-dimensional (3D) spheroids of MCF10A, MCF7 and MCF7TR cells and compared TADs and looping genes with those in 2D monolayers. We found that chromatin domains and looping genes’ strength have drastically changed during the 3D culture growth, although we identified very similar numbers of TADs and looping genes. We further identified novel 3D growth-specific looping genes within Hippo relevant pathways, of which two genes showed potential prognostic values in measuring the outcome of the endocrine treatment. We finally confirmed a few selected Hippo relevant pathways genes with enhanced looping in breast cancer patient tissues’ organoid. Hence, our work has provided significant insights into our understanding of 3D-growth-specific chromatin architecture in tamoxifen-resistant breast cancer.
2021-09-29 | GSE165570 | GEO