Gene expression of human mesenchymal stem cells in 3D cell culture
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PROVIDER: PRJNA854157 | ENA |
REPOSITORIES: ENA
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Project description:mRNA sequencing of mesenchymal stem cells in 2D culture systems, mesenchymal stem cells spheroids and mesenchymal stem cells/extracellular matrix in 3D culture systems to profile gene expressions
2023-11-28 | GSE247989 | GEO
Project description:Two-dimensional (2D) monolayer cell cultures are inevitable for drug development to identify drug candidate molecules because they are extremely potent for screening procedures. They can be used to predict in vivo drug responses for a variety of targets and pathways but they also face disadvantages like a lack of cell-to-cell and cell-to-matrix interaction as well as the loss of tissue-specific architecture. To overcome the drawbacks of 2D systems, three-dimensional (3D) cell culture was designed to provide cells a more physiological environment. In light of the multiple benefits of 3D cell culture it is important to note that this cultivation system is not automated and thus not ideal for high throughput screening (HTS) so far. An automated technique is critical for reproducible and standardized in vitro cultivation and it can greatly speed up preclinical research and total drug development. This procedure also requires a quality control system to monitor results and ensure that it is suitable for customers´ applications. For this purpose, the physiological condition of 2 D and 3D cell cultures will be assessed analyzing gene expression profiles of human mesenchymal stem cells (hMSCs). This will be accomplished by extracting total ribonucleic acid (RNA) from 2D and 3D cells followed by Affymetrix microarrays to get transcription profiles. The resulting data from both cell systems can be compared, and changes in cell behaviour caused by the 3D system can be observed.
2022-06-30 | GSE207210 | GEO
Project description:Mesenchymal stem cells (MSC) are heterogeneous in morphology and transcriptome, resulting in varying therapeutic outcomes. In this study, we found that 3D spheroid culture of heterogeneous MSC, which have undergone conventional 2D monolayer culture for 5-6 passages, synchronized the cells into a uniform cell population with dramatically reduced cell size, and considerably increased levels of immunosuppressive genes and growth factors. Sc-RNA-Seq analysis of the cells revealed that 3D MSC consisted of 2 major cell subpopulations and both expressed high levels of immunosuppressive factors, compared to 6 subpopulations in 2D MSC. In addition, 3D MSC showed a greater suppressive effect on T cells. Moreover, intravenous infusion of a large dose of 3D MSC prior to Imiquimod (IMQ) treatment significantly improved psoriatic lesion. Thus, our results indicate that 3D spheroid culture reprograms heterogeneous mesenchymal stem cells into a uniform immunosuppressive phenotype and promises a novel therapeutic potential for inflammatory diseases.
2024-09-25 | GSE268973 | GEO
Project description:To investigate the mechanisms underlying chondrocyte differentiation of bone marrow mesenchymal stem cells during 3D culture, we employed whole genome microarray expression profiling as a discovery platform to identify key genes influencing differentiation. By comparing differentially expressed genes at different time points, we identified POU5F1 and several autophagy-related genes as potential key players. By using PCR technology and autophagy-related assays, we confirmed that POU5F1 and autophagy pathways influence the chondrogenic differentiation of bone marrow-derived mesenchymal stem cells.
2026-01-07 | GSE315306 | GEO
Project description:Extracellular vesicles (EVs) contain proteins, enzymes and metabolites that contribute to the therapeutic potential of human mesenchymal stem cells (hMSCs). However, scale-up production of hMSC EVs has become a major challenge. In current study, hMSCs were grown as 3D aggregates under wave motion to promote EV secretion (3D EVs). mRNA sequencing reveals global transcriptome alterations (e.g., upregulated Wnt, TNF, and Hippo signaling and downregulated cellular senescence) for 3D aggregates. Compared to 2D EVs, the quantity of 3D EVs was enhanced significantly with smaller size, higher miR-21 and miR-22 expression, and the altered protein cargo revealed by proteomics. 3D hMSC aggregates promote activation of the endosomal sorting complexes required for transport (ESCRT) pathway and ESCRT-independent pathway. In addition, 3D EVs rejuvenated stem cells expressing cellular senescence and modulated immune response determined by T lymphocyte and macrophage phenotype assays. In summary, this study provides a promising strategy for high-quality EV production from hMSCs with enhanced therapeutic potentials.
2022-08-12 | PXD028975 | Pride
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:Therapeutic benefits of mesenchymal stem/stromal cells (MSCs) are now widely believed to come from their paracrine signalling, i.e. secreted factors such as cytokines, chemokines, and extracellular vesicles (EVs). Cell-free therapy using EVs is an active and emerging field in regenerative medicine. The cellular environment of MSCs is of critical importance when directing paracrine activity. Typical 2D cultivation of stem cells on tissue culture plastic is far removed from the physiological environment of MSCs. The application of 3D cell culture allows MSCs to adapt to their cellular niche environment which, in turn, influences their paracrine signalling activity. In this study we evaluated the impact of 3D MSCs culture on EVs secretion and cargo proteome composition and functional assessment. The outcome highlights critical differences between MSC-EVs obtained from different culture microenvironments, which should be considered when scaling up MSC culture for clinical manufacturing.
2021-11-17 | PXD029766 | Pride
Project description:Distinctive Biological Properties Between Mesenchymal Stem Cells Spheroids and Clumps of Mesenchymal Stem Cells/Extracellular Matrix Complexes in 3D Culture Systems.
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Project description:Human mesenchymal stromal cells (MSCs) hold great regenerative medicine potential due to their pluripotency and paracrine functions. However, MSCs lose stemness and immunomodulatory capabilities in two-dimensional (2D) culture, which differs from the natural MSC niche. We investigated methods to enhance MSC characteristics by employing an in vivo-like culture using functional polymers. Implementing FP003 polymer-based 3D culture, we observed increased expression of stemness markers (Oct4, Nanog), in hMSCs compared to 2D culture on regular plastic. This 3D environment also enhanced expression COX2 and HO1, known for their immunomodulatory functions. MSCs cultured in 3D exhibited higher secretion of PGE2 and effectively suppressed TNF- release from LPS-stimulated splenocytes, surpassing 2D-cultured MSCs. To explore therapeutic potential in vivo, we administered 3D-cultured MSCs via intravenous injection in a mouse model of neuroinflammation. Remarkably, this approach significantly reduced the expression of Iba1 and GFAP compared to 2D-cultured MSC injection. RNA-seq analysis revealed upregulated adhesion-related genes, including ITGA2, in MSCs cultured in 3D. Ectopic ITGA2 expression notably enhanced immunomodulatory function. In summary, our findings demonstrate that an in vivo mimetic 3D culture provides a beneficial microenvironment for MSCs, enhancing their immunomodulatory function through ITGA2 expression. Engineered MSCs can thus be utilized as an effective cell therapy source.
2025-05-21 | GSE236113 | GEO
Project description:Development of gene expression signatures for bone marrow mesenchymal stem cells with 3D culture in collagen hydrogel
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