Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Physical Crowding in 3D Niche Regulates NSCs of Cell Junction and Differentiation

ABSTRACT: Neural stem cells (NSCs) maintain central nervous system (CNS) homeostasis through self-renewal and differentiation into neurons and glia. While physical crowding dynamically regulates NSCs niches during CNS development, yet its role in regulating NSCs fate remains unclear. Herein, we systematically investigated how NSCs crowding influences intercellular junction formation and differentiation in 2D and 3D niches. Using RNA sequencing, RT-qPCR, Western blotting, and immunofluorescence, we found that cell crowding promotes neuron differentiation in both systems. Notably, in 3D cultures, crowding robustly upregulated cell-cell junction genes and enhanced junction-mediated communication. These findings reveal that the 3D environment provides essential biophysical contexts for NSCs, in which cell crowding synergistically enhances differentiation through coordinated cell-cell and cell-ECM signaling. This study offers new insights into the role of physical niche cues in NSCs biology and provides valuable guidance for the design of biomimetic 3D culture platforms and regenerative strategies for neural tissue engineering.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE294177 | GEO | 2026/02/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Physical Crowding in 3D Niche Regulates NSCs of Cell Junction and Differentiation

Project description:Physical Crowding in 3D Niche Regulates NSCs of Cell Junction and Differentiation

| PRJNA1248518 | ENA

Cell Density Regulates Neural Stem Cells of Cellular Contact and Differentiation in 3D Hydrogel Culture System

Project description:Neural Stem Cells (NSCs) of biological behaviors are frequently regulated by the three-dimensional (3D) niches that they located in. The impact of cell density cue inside niche on cellular outcomes are usually underestimated and understudied. In this study, a facile NSCs of 3D culture system was developed using collagen self-assembled fibril hydrogel. We used RNA sequencing and molecular biology technologies to investigate the NSCs of cell contacts and differentiations in developed 3D hydrogel culture system with low (0.75 million/mL), medium (1.5 million/mL), and high (3 million/mL) cell packing density. Compared with low cell density system, cytoskeletal spreading, gap junction, and tight junction mediated cell contacts were significantly improved in high cell density culture. Moreover, high cell density increased NSCs differentiation into immature (Tuj1) neuron, while there is no discrepancy of NSCs differentiation into astrocytes in different cell densities of 3D culturing system. This study provides new understanding in the regulation of 3D cultured NSCs behaviors through niche of cell density cue.

2025-07-15 | GSE239619 | GEO

Prolonged Crowding Drives Cancer Cell Invasiveness

Project description:Our study found that prolonged crowding drives cancer cell invasiveness with memory retention. To further characterize gene expression regulated by prolonged crowding, RNA sequencing was performed in crowding-primed cells (20 days) followed by sparse culture for different times (0, 1, 3, or 10 days).

2024-12-01 | GSE281770 | GEO

Spatiotemporal lineage derepression by cell crowding-induced ETV4 inactivation

Project description:All extant amniotes employ a single-layered epithelium of epiblasts as a starting material for gastrulation, suggesting the necessity of the epithelial structure for three germ layer derivation. Using a human embryonic stem cell (hESC) epithelium as a model system, we found that local epithelial crowding derepresses the neuroectoderm fate by spatiotemporal inactivation of ETV4. ETV4 serves as a genetic toggle switch that links cell density to lineage fates. Mechanistically, cell crowding blocks FGF receptor endocytosis by reduced cell-extracellular matrix (ECM) interaction. Disrupted endocytosis decreases ETV4 protein stability by ERK inactivation. Mathematical modeling of epithelial crowding demonstrates that the cooperativity of integrin-ECM interaction transforms the gradient of crowdedness into bistable ETV4 transition, which ensures the switch-like function of ETV4 in lineage determination. Our results propose local cell crowding in a stem cell epithelium as a key cellular mechanism for spatiotemporal regulation of lineage fates.

2024-03-12 | GSE183702 | GEO

Myelin-allied gene expression profile of adult neural progenitors shortly after onset of differentiation

Project description:Spontaneous neural repair from endogenous neural stem cells (NSCs) occurs in response to central nervous system (CNS) injuries or diseases to only a limited extent from endogenous NSCs niches. Uncovering the mechanisms that control neural repair and can be further manipulated to promote towards oligodendrocyte progenitors cells (OPCs) and myelinating oligodendrocytes is a major objective. Our aim was to identify myelin specific transcriptional regulators amongst large transcriptional changes shortly after differentiation of neural stem cells from the subventricular zone (SVZ) of adult mice SVZ-NSCs from adult mice were differentiated for 12 and 24 h in absence of growth factor (bFGF, EGF) and subjected for gene array as compared with undifferentiated NSCs cultured in presence of growth factors (n=5 samples per condition).

2016-06-01 | E-GEOD-76968 | biostudies-arrayexpress

Myelin-allied gene expression profile of adult neural progenitors shortly after onset of differentiation

2016-06-01 | GSE76968 | GEO

Expression analysis of Antirrhinum majus inflorescence meristems grown under control and crowding conditions

Project description:Investigation of gene expression level changes as a result of crowding growth conditions.

2015-09-10 | GSE72818 | GEO

Investigating the effect of molecular crowding agents on protein stability in a bacterial proteome

Project description:Molecular crowding refers to the restriction of space available for molecular mobility in solution due to the presence of other macromolecules. Crowding can influence biological phenomena such as protein stability and folding, diffusion, enzyme kinetics, molecular interactions, and phase separation. In contrast to many biochemical studies that employ dilute solutions comprising a small number of reactants, the cellular environment is considered to be highly crowded, with up to 40% of cell volume occupied by many thousands of proteins and other large biomolecules. We examined the protein stability effects of widely used cosolvents that are considered to act as molecular crowders for experimental purposes in a bacterial proteome (Cupriavidus necator) using the Thermal Proteome Profiling (TPP) method. While all six tested compounds (Ficoll 70, Ficoll 400, dextran 40, dextran 86, PEG 1, PEG 8) reduced the global mean melting temperature, significantly increased or decreased conformational stability was observed among distinct subsets of the proteome, with some individual proteins showing sensitivity to multiple crowding agents. Proteins displaying enhanced stability in the presence of crowding agents tended to be more hydrophobic, were more likely to show classic enzyme-like properties, and propensity for protein interactions. Our data support a direct binding/preferential exclusion model of enhanced stability, rather than alternative models based on viscosity or crowding.

2026-02-23 | PXD067043 | Pride

Spatiotemporal lineage derepression by cell crowding-induced ETV4 inactivation

Project description:Spatiotemporal lineage derepression by cell crowding-induced ETV4 inactivation

| PRJNA761710 | ENA

Expression analysis of Antirrhinum majus inflorescence meristems grown under control and crowding conditions

Project description:Investigation of gene expression level changes as a result of crowding growth conditions. A five-chip study using total RNA recovered from samples of inflorescence meristems of Antirrhinum majus cv.165E, grown as single plant per pot (control) and 10 plants per pot (crowded conditions). Each chip measures the expression level of 11,959 ESTs with up to six 60-mer probes per target.

2015-09-10 | E-GEOD-72818 | 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