Browse
Submit Data
Databases
API
Help

Dataset Information

185 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Shift of EMT gradient in 3D spheroid MSCs for activation of mesenchymal niche function

ABSTRACT: This project is described about the detailed characterization of 3D spheroid mesenchymal stem cells (MSCs). Specifically, authors showed the dynamic action towards EMT in 3D MSCs and the potential of EMT-enhanced “naïve” mesenchymal phenotype.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Stem Cell, Cell Culture

SUBMITTER: Jihye Shin

LAB HEAD: Cheolju Lee

PROVIDER: PXD006653 | Pride | 2018-06-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	160122_iho_A4_2D_cell.RAW	Raw
	160122_iho_A4_2D_cell.msf	Msf
	160122_iho_A4_3D_cell.RAW	Raw
	160122_iho_A4_3D_cell.msf	Msf
	160122_iho_N5_2D_cell.RAW	Raw

Items per page:

1 - 5 of 8

Publications

Shift of EMT gradient in 3D spheroid MSCs for activation of mesenchymal niche function.

Jeon Sohee S Lee Ho-Sun HS Lee Ga-Young GY Park Gyeongsin G Kim Tae-Min TM Shin Jihye J Lee Cheolju C Oh Il-Hoan IH

Scientific reports 20170731 1

Despite the wide use of mesenchymal stromal cells (MSCs) for paracrine support in clinical trials, their variable and heterogeneous supporting activity pose major challenges. While three-dimensional (3D) MSC cultures are emerging as alternative approaches, key changes in cellular characteristics during 3D-spheroid formation remain unclear. Here, we show that MSCs in 3D spheroids undergo further progression towards the epithelial-mesenchymal transition (EMT), driven by upregulation of EMT-promoti ...[more]

PMID: 28761088

Similar Datasets

Gene expression analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

Project description:TGFbeta/TNFalpha treated spheroid A549 cultures are a model of the epithelial-mesenchymal transition (EMT). These experiments capture the changes in global gene expression that result from cells being induced to undergo EMT (3D control vs 3D treated), but also the differences in gene expression when A549 is grown in spheroid cultures (2D control vs 3D untreated). EMT is efficiently induced only in the spheroid culture model. A total of 8 samples are analyzed, corresponding to 4 conditions (2D control, 2D treated, 3D control, 3D treated) and 2 biological replicates.

2013-09-12 | E-GEOD-42373 | biostudies-arrayexpress

3D spheroid human placenta-derived mesenchymal stem cells enhances anti-inflammatory response and trophic-factors secretion

Project description:We found significant difference between the 3D-spheroid cultured- and conventionally cultured mesenchymal stem cells (3D MSCs and 2D MSCs) in terms of anti-inflammatory response and ability to secrete trophic factors, implying that 3D MSCs may better improve the tissue repair and promote functional recovery. Next-generation sequencing has revolutionized system-based analysis of cellular pathways. The aims of this study are to compare the transcriptome profile between the 3D-spheroid cultured- and conventionally cultured mesenchymal stem cells (3D MSCs and 2D MSCs).

2021-09-01 | GSE174619 | GEO

Gene expression profiling of primary human bone marrow mesenchymal stromal cells (MSCs) cultured as 2D monolayers and 3D cellular aggregates (spheroids)

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

Gene expression analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

2013-09-12 | GSE42373 | GEO

Histone modification analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

2013-09-12 | GSE42374 | GEO

Histone modification analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

Project description:We studied the extent of chromatin remodeling in an in-vitro model of the epithelial-mesenchymal transition (EMT). EMT is induced in spheroid cultures (3D) using simultaneously two cytokines: TGFbeta and TNFalpha. The epithelial-mesenchymal transition (EMT) is a cellular de-differentiation process that has been implicated in cancer progression and metastasis. Increasing evidence suggests that EMT is regulated and established by epigenetic reprogramming, however a systems-level mechanism describing how chromatin remodeling contributes to the phenotypic switch is not known. We have generated genome-wide maps of 18 histone modifications/variants and variants in both the epithelial and mesenchymal states and quantified patterns of epigenetic changes at gene and enhancer loci. Clusters of these patterns reveal that EMT-related genes and their proximal enhancers are regulated through coordinated patterns of chromatin activation and repression at both gene and enhancer loci. At the cellular level, the remodeling of gene loci translates into a modular protein interaction network that recapitulates EMT-related signaling. Moreover, differentially activated or repressed enhancers are associated with two non-overlapping sets of transcription factors. We propose a chromatin-mediated regulatory feedback loop model where the NFkappaB and AP-1 transcription factors (TFs) bind activated enhancers, that regulate EMT-related genes, which in turn activate signaling pathways upstream of these TFs.

2013-09-12 | E-GEOD-42374 | biostudies-arrayexpress

Regan2022 - Mechanosensitive EMT model with autocrine TGFbeta signaling

Project description:This model is an expansion of the Regan2022 - Mechanosensitive EMT model (MODEL2208050001); it includes a TGFβ signaling module and autocrine signaling in mesenchymal cells. The expanded 150-node (630 link) modular model undergoes EMT triggered by biomechanical and growth signaling crosstalk, or by TGFβ. As its predecessor, this model also reproduces the ability of the core EMT transcriptional network to maintain distinct epithelial, hybrid E/M and mesenchymal states, as well as EMT driven by mitogens such as EGF on stiff ECM. We also reproduce the observed lack of stepwise MET, in that our model's dynamics does not pass through the hybrid E/M state during MET. We show that in the absence of strong autocrine signals such as TGFβ (not included in this version), cells cannot maintain their mesenchymal state in the absence of mitogens, on softer matrices, or at high cell density. In contrast, potent autocrine signaling can stabilize the mesenchymal state in all but very dense monolayers on soft ECM. This expanded model also reproduces the inhibitory effects of TGFβ on proliferation and anoikis resistance in mesenchymal cells, as well as its ability to trigger apoptosis on soft ECM vs. EMT on stiff matrices. The model offers several experimentally testable predictions related to the effect of neighbors on partial vs. full EMT, the tug of war between mitosis and the maintenance of migratory hybrid E/M states, as well as cell cycle defects in dynamic, heterogeneous populations of epithelial, hybrid E/M and mesenchymal cells.

2023-12-13 | MODEL2208050002 | BioModels

Regan2022 - Mechanosensitive EMT model

Project description:This file contains a 136-node modular Boolean network model of EMT triggered by biomechanical and growth signaling crosstalk, linked to a published network of epithelial contact inhibition, proliferation, and apoptosis (MODEL2006170001). This model reproduces the ability of the core EMT transcriptional network to maintain distinct epithelial, hybrid E/M and mesenchymal states, as well as EMT driven by mitogens such as EGF on stiff ECM. We also reproduce the observed lack of stepwise MET, in that our model's dynamics does not pass through the hybrid E/M state during MET. We show that in the absence of strong autocrine signals such as TGFβ (not included in this version), cells cannot maintain their mesenchymal state in the absence of mitogens, on softer matrices, or at high cell density.

2023-12-13 | MODEL2208050001 | BioModels

"High Levels of EMT-TFs for the Diagnosis of Colorectal Cancer (CRC)"

Project description:The present study is aimed at detecting and measuring mRNA levels of genes involved in epithelial to mesenchymal transition (EMT) in biological samples, i.e. in peripheral blood samples of colorectal cancer (CRC) patients and healthy controls, to determine the presence of disease, its progression and risk of recurrence.

| 2334276 | ecrin-mdr-crc

Homo sapiens MSCs: Normoxia vs. Hypoxia

Project description:Transcriptional profiling of human mesenchymal stem cells comparing normoxic MSCs cells with hypoxic MSCs cells. Hypoxia may inhibit senescence of MSCs during expansion. Goal was to determine the effects of hypoxia on global MSCs gene expression. Two-condition experiment, Normoxic MSCs vs. Hypoxic MSCs.

2011-02-19 | E-GEOD-20463 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data