ABSTRACT: This study aims to to compare the gene transcription profiles of endothelial cells and stem cells, when they are cultured alone or when they are cultured together. Thus there are two major questions - how do the cells differ, and how do the cells influence each other's gene expression. Thus there are 4 types of sample: endothelial cell monoculture, endothelial cell coculture, stem cells monoculture, stem cell coculture. There are also 4 biological replicates (independent experiments) leading to 16 array data files.
Project description:Human bone marrow mesenchymal stem cells (MSCs) were co-cultured for 7 days with endothelial cells, where they participated in the formation of microcapillaries. MSCs that were exposed to the microcapillaries or kept as monocultures were isolated by FACS and analyzed by RNAseq.
Project description:Four human mesenchymal stem cells (hMSC) clones (MSC-1, MSC-2, MSC-3, MSC-4) and three different glioblastoma multiformae (GBM) cell lines (U87-MG, U251, U373) were used to study their mutual paracrine interactions in the indirect co-cultures compared to their monocultures, which were grown under the same experimental conditions. The effects on cell growth, proliferation and invasion in matrigel were quantified. Further on, bioinformatic tools were used to relate these results to the data obtained from cytokine macroarrays and DNA microarrays that revealed proteins and genes significantly involved in the interaction. We showed that hMSC are responsible for the impairment of GBM cell invasion and growth, possibly via induction of their senescence. On the other hand, U87-MG cells even more strongly inversely affected some of these characteristics in hMSCs. We found several chemokines that may account for changed co-cultured cells’ phenotype, affecting genes associated with proliferation and senescence. CCL2/MCP-1 was collectively identified as the most significantly regulated chemokine during hMSC and U87-MG paracrine signalling. Its role in U87-MG cell invasion was also functionally confirmed. Microarray data deposited here contain gene expression data from three biological replicates of monocultures and indirect co-cultures of MSC-4 and U87-MG cells, representing 12 microarrays. Three biological replicates of four cell set-ups were performed: MSC-4 monoculture, U87-MG monoculture, MSC-4 co-cultured with U87-MG (in Boyden chambers) and U87-MG co-cultured with MSC-4 (in Boyden chambers).
Project description:Bone marrow (BM) mesenchymal stromal cells (BM-MSC) upregulate their NF-κB signaling to protect leukemia cells from chemotherapy-induced apoptosis. To elucidate molecular mechanisms by which leukemia-stroma interactions within the BM microenvironment could confer chemoresistance to leukemia cells, we used genome-wide gene expression profiling (GEP) to examine human normal BM-MSC that had been co-cultured with the pre-B ALL REH cells and then separated by flow cytometry (FACS). GEP results for co-cultured cells of each type were compared to GEP results for cells of the corresponding type cultured alone, and taken through the same FACS purification procedure, to identify changes in gene expression profiles caused by co-culture.
Project description:Pyruvate fermentation pathway and energetics of Desulfovibrio alaskensis strain G20 under syntrophic coculture and fermentative monoculture conditions Expression data for Desulfovibrio alaskensis strain G20 grown in chemostats on pyruvate under respiratory conditions (sulfate-limited and pyruvate-limited monoculture, dilution rate 0.047 and 0.027 h-1), fermentative conditions (monoculture, dilution rate 0.036 h-1), and syntrophic conditions (coculture with Methanococcus maripaludis or Methanospirillum hungatei, dilution rate of 0.047 and 0.027 h-1) 2 replicates each for syntrophic coculture (M. maripaludis or M. hungatei pairing) and respiratory (sulfate- or pyruvate-limited) monoculture for both growth rates (0.027 and 0.047 h-1), and 4 replicates fermentative monoculture (gas flow rate through head space of bioreactor 10 ml/min (chemostats C91 and C93) or 1 ml/min (chemostats C92 and C94)
Project description:Expression data for Desulfovibrio alaskensis strain G20 grown on lactate in sulfate-limited monoculture and syntrophic coculture with Methanococcus maripaludis in chemostats at a high growth rate of 0.047h-1 5 replicates of coculture and 3 replicates of sulfate-limited monoculture
Project description:Successful implantation and long-term survival of engineered tissue grafts hinges on adequate vascularization of the implant. Endothelial cells are essential for patterning vascular structures, but they require supportive mural cells such as pericytes/mesenchymal stem cells (MSCs) to generate stable, functional blood vessels.1-5 While there is evidence that the angiogenic effect of MSCs is mediated via the secretion of paracrine signals,6,7 the identity of these signals is unknown. Here, by utilizing two functionally distinct human MSC clones, we found that so-called “pericytic” MSCs secrete the pro-angiogenic neurovascular guidance molecule SLIT3,8 which guides vascular development by directing ROBO4-positive endothelial cells to form networks in engineered tissue. In contrast, “non-pericytic” MSCs exhibit reduced activation of the SLIT3/ROBO4 pathway and do not support vascular networks. Using live cell imaging of organizing 3D vascular networks, we show that knockdown of SLIT3 in MSCs leads to disorganized clustering of ECs, and knockdown of its receptor ROBO4 in ECs abolishes the generation of functional human blood vessels in an in vivo xenogenic implant. These data suggest that the SLIT3/ROBO4 pathway regulates MSC-guided vascularization in engineered tissues. Heterogeneity of SLIT3 expression may underlie the variable clinical success of MSCs for tissue repair applications. 4 samples with 2 replicates each
Project description:There is a current interest in reducing the in vivo toxicity testing of nanomaterials in animals by increasing toxicity testing using in vitro cellular assays; however, toxicological results are seldom concordant between in vivo and in vitro models. This study compared global multi-walled carbon nanotube (MWCNT)-induced gene expression from human lung epithelial and microvascular endothelial cells in monoculture and coculture with gene expression from mouse lungs exposed to MWCNT. Using a cutoff of 10% false discovery rate and 1.5 fold change, we determined that there were more concordant genes (gene expression both up- or downregulated in vivo and in vitro) expressed in both cell types in coculture than in monoculture. When reduced to only those genes involved in inflammation and fibrosis, known outcomes of in vivo MWCNT exposure, there were more disease-related concordant genes expressed in coculture than monoculture. Additionally, different cellular signaling pathways are activated in response to MWCNT dependent upon culturing conditions. As coculture gene expression better correlated with in vivo gene expression, we suggest that cellular cocultures may offer enhanced in vitro models for nanoparticle risk assessment and the reduction of in vivo toxicological testing.
Project description:Pyruvate fermentation pathway and energetics of Desulfovibrio alaskensis strain G20 under syntrophic coculture and fermentative monoculture conditions Expression data for Desulfovibrio alaskensis strain G20 grown in chemostats on pyruvate under respiratory conditions (sulfate-limited and pyruvate-limited monoculture, dilution rate 0.047 and 0.027 h-1), fermentative conditions (monoculture, dilution rate 0.036 h-1), and syntrophic conditions (coculture with Methanococcus maripaludis or Methanospirillum hungatei, dilution rate of 0.047 and 0.027 h-1)
Project description:Comparative RNA-Seq profiling of Sideroxydans sp. CL21, a microaerophilic, Fe(II)-oxidizer, and the facultative anaerobe Shewanella oneidensis, an Fe(III) reducer. The microorganisms were grown in co-culture and monoculture batch incubations under microaerobic growth conditions. RNA-Seq profiling was used to compare the transcriptomes of both Sideroxydans sp. CL21 and S. oneidensis when grown in co-culture compared to growth in monoculture
Project description:Mesenchymal stem/stromal cells (MSCs) are multipotent cells that can differentiate into a variety of cell types forming connective tissue and skeleton, and are essential participants in the development of all organs. However, MSC precursors remain largely unknown. In human embryonic stem cells (hESCs) directed to mesendodermal differentiation through coculture with OP9 stromal cells, we identified a population of mesodermal cells by surface expression of apelin receptor (APLNR1). APLNR+ cells were enriched with precursors generating compact spheroid colonies in semisolid suspension culture. Being formed by single cells, these colonies consisted of a uniform population of mesenchymal cells with a transcriptional profile representative of embryonic mesenchyme originating from lateral plate/extraembryonic mesoderm. Mesenchymal colony formation required serum-free medium and FGF2 as a colony-forming factor, could be significantly enhanced by PDGF-BB, but suppressed by VEGF. When transferred to the adherent cultures in serum-free medium with FGF2, individual colonies gave rise to multipotential mesenchymal cell lines with typical phenotype (CD146+CD105+CD73+CD31-CD43-CD45-), differentiation (chondro-, osteo-, and adipogenesis) and proliferation (>80 doublings) potentials. Consistent with lineage-restricted differentiation pattern, neither endothelial nor hematopoietic cells could be produced from adherent mesenchymal cultures, however endothelial cells could be derived from mesenchymal colonies in the early days of colony-forming culture suggesting that mesenchymal cells arose from cells with primary angiogenic potential (mesangioblasts). Together these studies identified mesangioblasts as the earliest clonogenic mesenchymal precursors at this stage of their specification from mesoderm. This set (8 samples) of expression data is a time-course experiment of hESC (H1) differentiated in OP9 coculture for 1-7 days.