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RNA sequencing of three dimensional endothelial spheroids seeded in an artificial collagen matrix with or without VEGF stimulation

ABSTRACT: This study investigates the influence of VEGF on the transcriptome of Human umbilical vein endothelial cells (HUVECs) formed to a spheroid and seeded in a 3D collagen matrix in a standard spheroid sprouting assay as one of the most commen angiogenesis assay.

ORGANISM(S): Homo sapiens

PROVIDER: GSE227549 | GEO | 2024/01/21

REPOSITORIES: GEO

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RNA sequencing of three dimensional endothelial spheroids seeded in an artificial collagen matrix with or without VEGF stimulation

Project description:RNA sequencing of three dimensional endothelial spheroids seeded in an artificial collagen matrix with or without VEGF stimulation

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Chromosome Conformation of Human Fibroblasts Grown in 3-Dimensional Spheroids

Project description:In the study of interphase chromosome organization, genome-wide chromosome conformation capture (Hi-C) maps are often generated using 2-dimensional (2D) monolayer cultures. These 2D cells have morphological deviations from cells that exist in 3-dimensional (3D) tissues in vivo, and may not maintain the same chromosome conformation. We used Hi-C maps to test the extent of differences in chromosome conformation between human fibroblasts grown in 2D cultures and those grown in 3D spheroids. Significant differences in chromosome conformation were found between 2D cells and those grown in spheroids. Intra-chromosomal interactions were generally increased in spheroid cells, with a few exceptions, while inter-chromosomal interactions were generally decreased. Overall, chromosomes located closer to the nuclear periphery had increased intra-chromosomal contacts in spheroid cells, while those located more centrally had decreased interactions. This study highlights the necessity to conduct studies on the topography of the interphase nucleus under conditions that mimic an in vivo environment.

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Gene expression profiles in colon cancer spheroids treated with a ROCK inhibitor

Project description:Spheroid cells derived from colon cancer patients was treated with Y-27632, a ROCK inhibitor, and we have performed whole genome microarray expression assay.

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Transcription profiling time series of the growth of human IMR-90 cells seeded on a collagen/chondroitin sulfate tissue engineering scaffold

Project description:A series of chips with some repeated measurments. Each chip represents a pool of 4 collagen/chondroitin sulfate tissue engineering scaffold meshes seeded with 1 x 10^6 IMR-90 Human Fibroblasts. mRNA was isolated at 30 minutes, 1, 2, 4, 8, 12, 24, 48, and 72 hours after seeding.

2007-12-13 | E-GEOD-409 | biostudies-arrayexpress

Evaluation of comprehensive gene expression and NK cell-mediated killing in glioblastoma cell line-derived spheroids [spheroids]

Project description:GBM is the most common and aggressive primary brain tumor with dismal prognosis. NK cells are large granular lymphocytes with natural cytotoxicity against tumor cells, and they should be established for the novel treatment against patients with GBM. We have previously reported highly activated and ex vivo-expanded NK cells derived from human peripheral blood, which is designated as Genuine-induced natural killer cell (GiNK), induced by our specific culture conditions exerted the cytotoxic effect on GBM cells via apoptosis. First, we comprehensively summarized the molecular characteristics, especially focusing on the expression of stem cell markers, extracellular matrix markers, chemokine, chemokine receptors, and the NK receptors’ ligands, of GBM spheroids compared with 2D adherent GBM cells by using microarray. In the spheroid derived from GBM cell lines, gene expression of stem cell markers, extracellular matrix markers, chemokine, chemokine receptor, NK cell inhibitory receptor’ ligand were up-regulated compared with 2D adherent GBM cells. A preclinical evaluation of the NK cells was performed by ex vivo 3D spheroid model derived from GBM cell lines. In 3D spheroid model, the NK cells accumulated and infiltrated around the spheroids and induced the GBM cell death. Flow cytometry-based apoptosis detection assay clearly showed that the NK cells induced the GBM cell death via apoptosis. Our findings could provide pivotal information for the NK cell based-immunotherapy to patients with GBM.

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Array CGH analysis of single spheroids from glioblastoma spheroid cultures

Project description:The goal of this study was to investigate genomic aberrations of glioblastoma spheroid cultures. Keywords: Comparative genomic hybridization We performed array comparative genomic hybridization of spheroid cultures derived from 2 glioblastoma spheroid cultures using as a reference DNA from healthy donors.

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Particle-based artificial three-dimensional stem cell spheroids for revascularization of ischemic diseases.

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Three-Dimensional Matrix Stiffness Modulates Mechanosensitive and Phenotypic Alterations in Oral Squamous Cell Carcinoma Spheroids

Project description:Extracellular biophysical cues such as matrix stiffness are key stimuli tuning cell fate and affecting tumor progression in vivo. However, it remains unclear how spheroids in a 3D microenvironment perceive matrix mechanical stiffness stimuli and translate them into intracellular signals driving cancer. Mechanosensitive Piezo1 and TRPV4 ion channels, upregulated in many malignancies, are major transducers of such physical stimuli into biochemical responses. Most mechanotransduction studies probing the reception of changing stiffness cues by cells are, however, still limited to 2D culture systems or cell-extracellular matrix models which lack the major cell-cell interactions prevalent in 3D cancer tumors. Here, we engineered a 3D spheroid culture environment with varying mechanobiological properties to study the effect of static matrix stiffness stimuli on mechanosensitive and malignant phenotypes in oral squamous cell carcinoma spheroids. We find that spheroid growth is enhanced when cultured in stiff extracellular matrix. Using flow cytometry, we show that the expression of mechanoreceptor Piezo1 and stemness marker CD44 is upregulated in stiff matrix. We also report the upregulation of a selection of genes with associations to mechanoreception, ion channel transport, extracellular matrix organization, and tumorigenic phenotypes in stiff matrix spheroids. Together, our results indicate that cancer cells in 3D spheroids utilize mechanosensitive ion channels Piezo1 and TRPV4 to sense changes in static extracellular matrix stiffness and that stiffness drives pro-tumorigenic phenotypes in oral squamous cell carcinoma.

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Mechanical cues guide the formation and patterning of 3D spheroids in fibrous environments

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