Expression profiling of mitochondria-associated microRNAs during osteogenic differentiation of human MSCs
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PROVIDER: PRJNA556862 | ENA |
REPOSITORIES: ENA
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Project description:The goal of this study was to determine expression profiles of mitochondria-associated microRNAs (mitomiR) in human bone marrow-derived mesenchymal stem/stromal cells (MSCs) as well as in MSCs during osteogenic differentiation. MicroRNAs are epigenetic regulators that commonly function by targeting specific mRNAs resulting in suppression of protein expression. In addition to their location in the cytosol, microRNAs have also been found in other sub-cellular compartments including the mitochondria. While some studies suggest that mitomiRs may affect mitochondrial function, research on mitomiRs is still in its infancy. To date, there is no information on mitomiR expression in MSCs or osteoblasts. A standard in vitro osteogenesis assay system was used to differentiate MSCs toward the osteoblast lineage. Purified mitochondrial extracts were obtained from MSCs or from MSCs at specific time points of osteogenic induction. RNA was isolated from mitochondrial extracts and then biotin-labeled in preparation for microRNA array (Affymetrix miRNA array 4.0). Array data was analyzed to generate information on most abundantly-expressed mitomiRs in non-induced MSCs as well as in MSCs at set time points (day 3, 7, or 14) of osteogenic induction. Information on significantly differentially-expressed mitomiRs during osteogenesis (comparing day 0 with either day 3, 7 or 14) was also obtained.
2020-01-01 | GSE134946 | GEO
Project description:The goal of this study was to determine expression profiles of microRNAs (miRNAs) in whole cell extracts of human bone marrow-derived mesenchymal stem/stromal cells (MSCs) as well as in MSCs during osteogenic differentiation. MicroRNAs are epigenetic regulators that commonly function by targeting specific mRNAs resulting in suppression of protein expression and modulation of a number of cellular pathways. This experiment is part of a larger study analyzing the expression of mitochondria-associated miRNAs in MSCs during osteogenesis that we recently submitted to GEO (Series GSE134946). Here, the same three human MSC lines were used in this study, under the same osteogenic induction conditions, to generate expression profiles of miRNAs present in whole cell extracts. A standard in vitro osteogenesis assay system was used to differentiate MSCs toward the osteoblast lineage.Purified whole cell extracts were obtained from MSCs or from MSCs at specific time points of osteogenic induction. RNA was isolated from whole cell extracts and then biotin-labeled in preparation for microRNA array (Affymetrix miRNA array 4.0). Array data was analyzed to generate information on most abundantly-expressed miRNAs in non-induced MSCs as well as in MSCs at set time points (day 3, 7, or 14) of osteogenic induction. Information on significantly differentially-expressed miRNAs during osteogenesis (comparing day 0 with either day 3, 7 or 14) was also obtained.
2021-01-01 | GSE148049 | GEO
Project description:Expression profiling of microRNAs during osteogenic differentiation of human MSCs
| PRJNA622951 | ENA
Project description:The intriThe intricate balance between MSCs differentiation to osteoblasts or adipocytes is finely regulated. To explore novel participating molecules, we screened for early-stage osteogenesis- or adipogenesis-based MSCs protein expression profile using TMT-based quantitative proteomic analysis. Protein annotation, hierarchical clustering, functional stratification, and protein-protein association assessments were performed. Moreover, two upregulated proteins, namely, FBLN2 and NPR3, were validated to participate in the osteogenic differentiation process of MSCs. Subsequently, we independently downregulated FBLN2 and NPR3 during 7 days of osteogenic differentiation, and conducted quantitative proteomics analysis to assess the differential protein regulation between knockdown and control cells. Based on gene ontology (GO) and network analyses, FBLN2 deficiency induced functional alterations associated with biological regulation and stimulus response, whereas, NPR3 deficiency induced functional alterations related to cellular and metabolic processes, and so on. These results demonstrated that proteomics is still an effective tool for the comprehensive exploration of the MSCs differentiation process. cate balance between MSCs differentiation to osteoblasts or adipocytes is finely regulated. To explore novel participating molecules, we screened for early-stage osteogenesis- or adipogenesis-based MSCs protein expression profile using TMT-based quantitative proteomic analysis. Protein annotation, hierarchical clustering, functional stratification, and protein-protein association assessments were performed. Moreover, two upregulated proteins, namely, FBLN2 and NPR3, were validated to participate in the osteogenic differentiation process of MSCs. Subsequently, we independently downregulated FBLN2 and NPR3 during 7 days of osteogenic differentiation, and conducted quantitative proteomics analysis to assess the differential protein regulation between knockdown and control cells. Based on gene ontology (GO) and network analyses, FBLN2 deficiency induced functional alterations associated with biological regulation and stimulus response, whereas, NPR3 deficiency induced functional alterations related to cellular and metabolic processes, and so on. These results demonstrated that proteomics is still an effective tool for the comprehensive exploration of the MSCs differentiation process.
2023-10-24 | PXD041404 | Pride
Project description:LncRNA transcriptional profiling of human bone marrow-derived mesenchymal stem cells comparing control undifferentiated MSCs with Day 0 and Day 10 osteogenic differentiation stages
2018-04-19 | GSE113359 | GEO
Project description:Ability to perform osteogenic differentiation is one of the minimal criteria of mesenchymal stem cells (MSCs). Still, it is generally unknown whether osteogenic differentiation is universal cell fate or various phenotypically similar cell states. Besides this, MSCs and their secretomes are actively using for cell/cell-free therapy development, but systemic inter-source variation in MSCs secretomes, proteomes and differentiation mechanisms are still poorly understood. Therefore, here we compared proteomic and secretomic profiles of human mesenchymal cells from six sources: osteoblasts (bone), WJ-MSCs (Warton’s jelly), AD-MSCs (adipose), PDLSCs (tooth: Periodontal Ligament Stem Cells), DPSCs (tooth: Dental Pulp Stem Cells) and GFs (tooth: Gingival Fibroblasts). For experiments we used cells in early passages (3-5) isolated from 3-6 individuals. All cells were compared in standard cultivation and in the 10th day after induction of osteogenic differentiation.
2023-11-05 | PXD037320 | Pride
Project description:Mesenchymal stem cells (MSCs) are the multipotent stem cells of adult human tissues that have the ability to replicate with high proliferative rates and are responsible for the tissue renewal and regeneration. Effective osteogenic differentiation of adipose-derived stem cells (ADSCs) encourages clinical application of the cells in bone regeneration. Regeneration of damaged joints is highly dependent on the presence of MSC in synovia. Synovial membrane-derived MSCs (SM-MSCs) show good multi-lineage differentiation potential, low degree of invasiveness, and are considered as an alternative treatment strategy for arthritis-damaged tissues. Studies in MSCs from different sources identified several miRNAs important for osteogenesis. Less is known about the participation of particular miRNAs in osteogenic differentiation of SM-MSCs, the potential source of MSCs for authologous cell therapy in arthritis. In the present study, the changes in miRNA expression profile occurring during osteogenic differentiation were analyzed in human ADSCs and SM-MSCs by microarray-based and quantitative PCR approaches. We aimed at the identification of miRNAs involved in the maintenance of these MSCs and regulation of osteogenic differentiation of ADSCs and SM-MSCs.
2016-02-01 | GSE72429 | GEO
Project description:To investigate how histone demethylases KDM4B and KDM6B may be involved in osteogenic commitment of mesenchymal stem cells (MSCs), we performed gene expression profiling and comparison on control, KDM4B- and KDM6B-knockdown MSCs at different stages of osteogenic differentiation. Human MSCs infected with scramble shRNAs, shRNAs against KDM4B or KDM6B are treated with BMP4/7 for 0, 4 and 24hrs. Total RNA were extracted from these 9 samples.
2012-07-31 | E-GEOD-36970 | biostudies-arrayexpress
Project description:Although various sources of cMSCs show similar characteristics, they are different in osteogenic potential due to their original cellular sources. Thus, this study was designed to globally explore and analyze the in vitro differentiation potential and behavior of canine bone-marrow derived mesenchymal stem cells (cBM-MSCs) and canine dental pulp stem cells (cDPSCs) toward osteogenic lineage. Global study of an in vitro osteogenic differentiation potential of the isolated cells was performed using proteomic-based analysis through mass spectrometry with dimethyl labelling method at day 7 and 14 post-induction, comparing with undifferentiated cells. The obtained results could be used as a comprehensive data and principal knowledge of the osteogenic differentiation potential of cBM-MSCs and cDPSCs in vitro and the trend of MSC-based tissue engineering for osteogenic regenerative therapy, concentrating on cMSCs application.
2021-09-08 | PXD015512 | Pride
Project description:To investigate how histone demethylases KDM4B and KDM6B may be involved in osteogenic commitment of mesenchymal stem cells (MSCs), we performed gene expression profiling and comparison on control, KDM4B- and KDM6B-knockdown MSCs at different stages of osteogenic differentiation.
2012-08-01 | GSE36970 | GEO