RNA-seq of chondrogenesis following siRNA depletion of SERPINA3
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE247491 | GEO | 2024/08/05
REPOSITORIES: GEO
Similar Datasets
Project description:SERPINA3 knockdown was observed to reduce cartilage pellet size following differentiation of mesenchymal stem cells (MSCs) to chondrocytes. To additionally understand any effects on the osteogenesis transcriptome, RNA-sequencing was conducted on primary MSCs depleted of SERPINA3 with siRNA and compared to cells transfected with a siRNA control over a 7 day period.
2024-08-05 | GSE247528 | GEO
Project description:RNA-seq of chondrogenesis following siRNA depletion of SERPINA3
| PRJNA1038778 | ENA
Project description:The recruitment of mesenchymal stem cells in order to reconstruct damaged cartilage of osteoarthritis joints is a challenging tissue engineering task. Vision towards this goal is blurred by a lack of knowledge about the underlying differences between chondrocytes and MSC during the chondrogenic cultivation process. The aim of this study was to shed light on the differences between chondrocytes and MSC occurring during chondral differentiation through tissue engineering. As a model we used the pellet culture system under chondrogenic conditions for the comparison of chondrocyte and MSC differentiation. Immunohistology was followed by microarray analysis, which was filtered through already published datasets describing different developmental processes. Validation was performed with quantitative RT-PCR. Results describe inferior chondrogenic ECM-production by MSCs and underline their closer link to the osteogenic lineage. Chondrocytes have an upregulated fatty acid/cholesterol metabolism which might give hints for future modifications of culture conditions. To shed light on the differences between chondrocytes and MSC occurring during chondral differentiation through tissue engineering, a pellet culture system under chondrogenic conditions for the comparison of chondrocyte and MSC differentiation was used after 0, 3, 7 and 14 days
2010-05-14 | E-GEOD-19664 | biostudies-arrayexpress
Project description:Regulation of transcription occurs in a cell type specific manner orchestrated by epigenetic mechanisms including DNA methylation. Methylation changes may also play a key role in lineage specification during stem cell differentiation. To further our understanding of epigenetic regulation in chondrocytes we characterised DNA methylation changes during chondrogenesis of mesenchymal stem cells (MSCs) by Infinium 450K methylation array. Significant DNA hypomethylation was identified during chondrogenesic differentiation including changes at many key cartilage gene loci. Integration with chondrogenesis gene expression data revealed an enrichment of significant CpGs in upregulated genes, while characterisation of significant CpG loci indicated their predominant localisation to enhancer regions. Comparison with methylation profiles of other tissues, including healthy and diseased adult cartilage, identified chondrocyte-specific regions of hypomethylation and the overlap with differentially methylated CpGs in osteoarthritis. Taken together we have associated DNA methylation levels with the chondrocyte phenotype. The consequences of which has potential to improve cartilage generation for tissue engineering purposes and also to provide context for observed methylation changes in cartilage diseases such as osteoarthritis
2019-05-24 | GSE129266 | GEO
Project description:Objective: Cartilage formation is stimulated in mixtures of chondrocytes and human adipose-derived mesenchymal stem cells (MSCs) both in vitro and in vivo. During co-culture, human MSCs perish through an unknown process. The goal of this study is to elucidate the mechanism by which adipose tissue-derived MSC cell death occurs in the presence of chondrocytes. Methods: Human primary chondrocytes were co-cultured with human MSCs derived from three donors. The cells were cultured in mono-culture or co-culture (20% chondrocytes and 80% MSCs) in pellets (200.000 cell/pellet) for 7 days in chondrocyte proliferation media in hypoxia (2% O2). RNA sequencing was performed to assess for differences in gene expression between monocultures or co-culture. Western blot and immune fluorescence assays were performed to quantify the level of Caspase-3, LC3B and P62. Results: RNA sequencing revealed significant up-regulation of >90 genes in the three co-cultures when compared to monocultures. STRING analysis showed interconnections between >50 of these genes. Remarkably, 75% of these genes play a role in cell death pathways such as apoptosis and autophagy. Western blotting shows a clear up-regulation of the autophagic machinery with no substantial activation of the apoptotic pathway. Conclusion: In co-cultures of human MSCs with primary chondrocytes, MSCs perish through autophagy. We propose that this sacrificial cell death may perhaps contribute to the trophic effects of MSCs on cartilage formation.
2020-06-30 | GSE142831 | GEO
Project description:RNA-seq of osteogenesis following siRNA depletion of SERPINA3
| PRJNA1039295 | ENA
Project description:Joint injury and osteoarthritis affect millions of people worldwide, but attempts to generate articular cartilage using adult stem/progenitor cells have been unsuccessful. We hypothesized that recapitulation of the human developmental chondrogenic program using pluripotent stem cells (PSCs) may represent a superior approach for cartilage restoration. Using laser capture microdissection followed by microarray analysis, we first defined a surface phenotype (CD146low/negCD166low/negCD73+CD44lowBMPR1B+) distinguishing the earliest cartilage committed cells (pre-chondrocytes) at 5-6 weeks of development; pellet assays confirmed these cells as functional, chondrocyte-restricted progenitors. Flow cytometry, qPCR and immunohistochemistry at 17 weeks revealed that the superficial layer of peri-articular chondrocytes was enriched in cells with this surface phenotype. Isolation of cells with a similar immunophenotype from differentiating human PSCs revealed a population of CD166negBMPR1B+ putative pre-chondrocytes. Functional characterization confirmed these cells as cartilage-committed, chondrocyte progenitors. The identification of a specific molecular signature for primary cartilagecommitted progenitors may provide essential knowledge for the generation of purified, clinically relevant cartilage cells from PSCs. A total of 15 samples were analyzed. In the first comparison, there were 6 biological replicates for both the chondrogenic condensations and total limb cells. In the second comparison, three biological replicates of chondrocytes from the articular region were compared to the 6 replicates of the condensations.
2013-12-16 | E-GEOD-51812 | biostudies-arrayexpress
Project description:Cartilage is characterized by mature chondrocyte metabolic heterogeneity in a zone-dependent manner. In this study, we used single cell mRNA sequencing (scRNA-seq) to evaluate the corresponding functional and metabolic phenotypic heterogeneity of in vitro cultured primary juvenile murine chondrocytes
2022-12-18 | GSE192668 | GEO
Project description:Joint injury and osteoarthritis affect millions of people worldwide, but attempts to generate articular cartilage using adult stem/progenitor cells have been unsuccessful. We hypothesized that recapitulation of the human developmental chondrogenic program using pluripotent stem cells (PSCs) may represent a superior approach for cartilage restoration. Using laser capture microdissection followed by microarray analysis, we first defined a surface phenotype (CD146low/negCD166low/negCD73+CD44lowBMPR1B+) distinguishing the earliest cartilage committed cells (pre-chondrocytes) at 5-6 weeks of development; pellet assays confirmed these cells as functional, chondrocyte-restricted progenitors. Flow cytometry, qPCR and immunohistochemistry at 17 weeks revealed that the superficial layer of peri-articular chondrocytes was enriched in cells with this surface phenotype. Isolation of cells with a similar immunophenotype from differentiating human PSCs revealed a population of CD166negBMPR1B+ putative pre-chondrocytes. Functional characterization confirmed these cells as cartilage-committed, chondrocyte progenitors. The identification of a specific molecular signature for primary cartilagecommitted progenitors may provide essential knowledge for the generation of purified, clinically relevant cartilage cells from PSCs.
2013-12-16 | GSE51812 | GEO
Project description:Cartilage pellets generated from ectomesenchymal progeny of human pluripotent stem cells (hPSCs) in vitro eventually show signs of commitment of chondrocytes to hypertrophic differentiation. When transplanted subcutaneously, most of the surviving pellets were fully mineralized by 8 weeks. In contrast, treatment with the adenylyl cyclase activator, forskolin, in vitro resulted in slightly enlarged cartilage pellets containing an increased proportion of proliferating immature chondrocytes that expressed very low levels of hypertrophic/terminally matured chondrocyte-specific genes. Forskolin treatment also enhanced hyaline cartilage formation by reducing type I collagen gene expression and increasing sulfated glycosaminoglycan accumulation in the developed cartilage. Furthermore, forskolin treatment in vitro increased the frequency at which the cartilage pellets maintained unmineralized chondrocytes after subcutaneous transplantation. To elucidate the type of cartilage that forskolin preferentially promotes and potential molecular mechanisms involved in the forskolin-suppression of chondrocyte hypertrophic differentiation in vitro, we performed genome-wide, comparative transcriptomic analyses on the cartilage pellets formed from 3 to 4 independent pellet cultures of ectomesenchymal cells with or without forskolin treatment. RNAs were isolated on day 26-28 and mRNA-sequencing (RNA-seq) analyses were performed.
2020-06-01 | GSE116173 | GEO