Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA253948 | ENA |
REPOSITORIES: ENA
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Project description:Expression data from hiPS lines after commitment towards mesenchymal lineage (hiPS-MSC) and expression data of mesenchymal lines (MSC), used as positive control of commitment. Following this, hiPS-MSC and MSC are seeded on scaffold to differentiate in a ligamentous (middle) and osseous (edges) part (post 21 days 3D differentiation) We used microarrays to validate efficient commitment of hiPS to generate hiPS-MSC and do whole transcriptome comparison of hiPS-MSC vs isolated MSC (positive control) and then compare the enhanced biological functions after differentiation of these cells on a scaffold
2016-12-20 | GSE58919 | GEO
Project description:Herein we compare mouse (C57B6/J background, 16 week old) adherent bone marrow stromal cell gene expression after 4 weeks of adipogenic differentiation in 3D versus 2D culture. Adipogenic differentiation was compared on a 3D silk scaffold versus a 2D (tissue culture plastic) surface using an microarray mRNA analysis.
2018-12-19 | GSE108374 | GEO
Project description:Development of systems allowing the maintenance of native properties of mesenchymal stromal cells (MSC) is a critical challenge for studying physiological functions of skeletal progenitors, as well as towards cellular therapy and regenerative medicine applications. Conventional stem cell culture in monolayer on plastic dishes (2D) is associated with progressive loss of functionality, likely due to the absence of a biomimetic microenvironment and the selection of adherent populations. Here we demonstrate that 2D MSC expansion can be entirely bypassed by culturing freshly isolated bone marrow cells within the pores of 3D scaffolds in a perfusion-based bioreactor system, followed by enzymatic digestion for cell retrieval. The 3D-perfusion system supported MSC growth while maintaining cells of the hematopoietic lineage, and thus generated a cellular environment mimicking some features of the bone marrow stroma. As compared to 2D-expansion, sorted CD45- cells derived from 3D-perfusion culture after the same time (3 weeks) or a similar extent of proliferation (7-8 doublings) maintained a 4.3-fold higher clonogenicity and exhibited a superior differentiation capacity towards all typical mesenchymal lineages, with similar immunomodulatory function in vitro. Transcriptomic analysis performed on MSC from 5 donors validated the robustness of the process and indicated a reduced inter-donor variability as well as a significant upregulation of multipotency-related gene clusters following 3D-perfusion as compared to 2D expansion. The described system offers a model to study how factors of a 3D engineered niche may regulate MSC function and, by streamlining conventional labor-intensive processes, is prone to automation and scalability within closed bioreactor systems. Nucleated cells were isolated from 5 fresh human bone marrow aspirates by means of red blood cells lyses buffer and then were seeded into a 3D perfusion bioreactor system using a pure hydroxyapatite 3D scaffold and in conventional Petri dishes (2D). After culture for 19 days, cells from both systems were enzymatically retrieved and sorted using anti-CD45-coated magnetic beads. Total RNA was extracted from CD45- cells, QCed and hybridized to Affymetrix microarrays.
2014-08-01 | E-GEOD-52896 | biostudies-arrayexpress
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:The development of more complex but reliable systems for compound testing in a pharmaceutical context is a challenging task to date. Three-dimensional (3D), organ mimetic cell culture is aiming to become an alternative to common two-dimensional (2D) cell culture or animal testing in that field. We developed a biocompatible 3D cell culture environment for a hepatocellular carcinoma (HCC) model that enables cellular maintenance in a polycarbonate scaffold structure. Albumin, regarded as a differentiation marker, was elevated in statically 3D cultivated HepG2 cells. Expression of HCC tumor marker alpha-fetoprotein (AFP) was reduced compared to immunofluorescence stainings of 2D cultivated cells. Remarkably, expression of cytokeratin and pathophysiologically relevant beta-1 integrin (ITGB1) was found enhanced in nonperfused 3D cell culture. Changes in gene expression induced by the 3D cultivation environment were investigated using Ingenuity Pathway Analysis (IPA). Our findings revealed involvement of the insulin growth factor (IGF) signaling pathway in upregulation of matrix metalloproteinases (MMP) and ITGB1. The experimental data indicate a more differentiated state in 3D cultivated HepG2 cells than in the respective 2D experiments. Hence, scaffold-supported 3D cultivation of HepG2 cells may lead to a gain of information valuable for both drug testing and cancer research. HepG2 cells were cultivated for five days under 2D and 3D statical and perfused conditions. Cultivation was started with 0.25x10^6 cells in 2D and with 1x10^6 vital cells for the 3D experiments. The day of seeding was defined as d0. The groups were classified as follows: 2D, i.e., monolayer cultures, 3D, i.e., statical 3D cultures and BR, which denotes perfused 3D culture of HepG2 cells. The perfusable bioreactor system was operated using a peristaltic pump. It houses the MatriGrid, a polycarbonate-based microporous cellular support. For 3D static cultivation, cell-inoculated MatriGrids were placed in wells of a 24-well plate. Microarray experiments of three 2D (i.e., control), three 3D statically and three actively perfused 3D cultivations were performed at SIRS-Lab GmbH (SIRS-Lab GmbH, Jena, Germany) according to the manufacturer's instructions (Illumina, San Diego, CA). Altogether, 9 RNA samples of hepatocyte cultures and an internal control RNA were hybridized on two HumanHT-12 v4 Expression BeadChips.
2012-11-01 | E-GEOD-41962 | biostudies-arrayexpress
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:The objectives of this study were to assess differences in Bone Marrow Derived Menenchymal Stromal Cells (MSCs) during co-culture with myeloma cells, and to assess differences in myeloma patient MSCs compared to normal donor MSCs. In the study presented here, a Bone Marrow Derived Menenchymal Stromal Cells (MSCs) were analyzed after FACS sorting from 2 week culture in osteogenic media lacking dexamethasone in 3D silk scaffold matrices either in co-culture with the multiple myeloma cell line GFP+Luc+MM1.S or Alone, as controls. Also, monocultures of MSCs grown in 2D, in MSC expansion media, from Normal Donor Controls (ND) or Multiple myeloma patients (MM) were analyzed. Analysis was done looking at microRNA expression in samples with the nanoString microRNA platform for 800 microRNAs.
2014-11-01 | E-GEOD-60423 | biostudies-arrayexpress
Project description:The development of more complex but reliable systems for compound testing in a pharmaceutical context is a challenging task to date. Three dimensional (3D), organ mimetic cell culture is aiming to become an alternative to common two dimensional (2D) cell culture or animal testing in that field. We developed a biocompatible 3D cell culture environment for a 3D hepatocyte cell culture that enables cellular maintenance in a polycarbonate scaffold structure. Our data indicate that an actively perfused three dimensional cell culture displays a more pronounced metabolic genotype than statically cultivated hepatocytes. Human hepatocytes of three donors were cultivated for five days under 2D and 3D statical and perfused conditions. Cultivation was started with 0.25 x106 in 2D and with 1x 106 vital cells for the 3D experiments. The day of seeding was defined as d0. The groups were classified as follows: 2D i.e.monolayer cultures, 3D i.e. statical 3D culture and BR denotes perfused 3D culture of hepatocytes. The perfusable bioreactor system was operated using a peristaltic pump. It houses the MatriGrid, a polycarbonate based microporous cellular support. For 3Dstatic cultivation, cell- inoculated MatriGrids were placed in wells of a 24 wells plate. Microarray experiments of three 2D (i.e. control), three 3D statically and three actively perfused 3D cultivations, respectively, were performed at SIRS-Lab GmbH (SIRS-Lab GmbH, Jena, Germany) according to the manufacturerM-bM-^@M-^Ys instructions (Illumina, San Diego, CA). Altogether, 8 RNA samples of hepatocyte cultures and an internal control RNA were hybridized on two HumanHT-12 v4 Expression BeadChips.
2013-03-31 | E-GEOD-44580 | biostudies-arrayexpress
Project description:The development of more complex but reliable systems for compound testing in a pharmaceutical context is a challenging task to date. Three-dimensional (3D), organ mimetic cell culture is aiming to become an alternative to common two-dimensional (2D) cell culture or animal testing in that field. We developed a biocompatible 3D cell culture environment for a hepatocellular carcinoma (HCC) model that enables cellular maintenance in a polycarbonate scaffold structure. Albumin, regarded as a differentiation marker, was elevated in statically 3D cultivated HepG2 cells. Expression of HCC tumor marker alpha-fetoprotein (AFP) was reduced compared to immunofluorescence stainings of 2D cultivated cells. Remarkably, expression of cytokeratin and pathophysiologically relevant beta-1 integrin (ITGB1) was found enhanced in nonperfused 3D cell culture. Changes in gene expression induced by the 3D cultivation environment were investigated using Ingenuity Pathway Analysis (IPA). Our findings revealed involvement of the insulin growth factor (IGF) signaling pathway in upregulation of matrix metalloproteinases (MMP) and ITGB1. The experimental data indicate a more differentiated state in 3D cultivated HepG2 cells than in the respective 2D experiments. Hence, scaffold-supported 3D cultivation of HepG2 cells may lead to a gain of information valuable for both drug testing and cancer research.
2012-11-01 | GSE41962 | GEO
Project description:Development of systems allowing the maintenance of native properties of mesenchymal stromal cells (MSC) is a critical challenge for studying physiological functions of skeletal progenitors, as well as towards cellular therapy and regenerative medicine applications. Conventional stem cell culture in monolayer on plastic dishes (2D) is associated with progressive loss of functionality, likely due to the absence of a biomimetic microenvironment and the selection of adherent populations. Here we demonstrate that 2D MSC expansion can be entirely bypassed by culturing freshly isolated bone marrow cells within the pores of 3D scaffolds in a perfusion-based bioreactor system, followed by enzymatic digestion for cell retrieval. The 3D-perfusion system supported MSC growth while maintaining cells of the hematopoietic lineage, and thus generated a cellular environment mimicking some features of the bone marrow stroma. As compared to 2D-expansion, sorted CD45- cells derived from 3D-perfusion culture after the same time (3 weeks) or a similar extent of proliferation (7-8 doublings) maintained a 4.3-fold higher clonogenicity and exhibited a superior differentiation capacity towards all typical mesenchymal lineages, with similar immunomodulatory function in vitro. Transcriptomic analysis performed on MSC from 5 donors validated the robustness of the process and indicated a reduced inter-donor variability as well as a significant upregulation of multipotency-related gene clusters following 3D-perfusion as compared to 2D expansion. The described system offers a model to study how factors of a 3D engineered niche may regulate MSC function and, by streamlining conventional labor-intensive processes, is prone to automation and scalability within closed bioreactor systems.
2014-08-01 | GSE52896 | GEO