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High-throughput RNA-seq analysis of mocetinostat- and DMSO-treated TC28a2 cells

ABSTRACT: We performed global gene expression analysis in mocetinostat- and DMSO-treated TC28a2 human chondrocyte cells, to study genes regulated by mocesinostat comprehensively.

ORGANISM(S): Homo sapiens

PROVIDER: GSE220755 | GEO | 2023/07/21

REPOSITORIES: GEO

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Project description:Background: Glucocorticoids (GCs) are widely used anti-inflammatory drugs. While useful in clinical practice, patients taking GCs often suffer from skeletal side effects including growth retardation and decreased bone quality in adults. On a physiological level, GCs have been implicated in the regulation of chondrogenesis and osteoblast differentiation, as well as maintaining homeostasis in cartilage and bone. We identified the glucocorticoid receptor (GR) as a potential regulator of chondrocyte hypertrophy in a microarray screen of primary limb bud mesenchyme micromass cultures. Some targets of GC regulation in chondrogenesis are known, but the global effects of pharmacological GC doses on chondrocyte gene expression have not been comprehensively evaluated. Results: This study systematically identifies a spectrum of GC target genes in embryonic growth plate chondrocytes treated with synthetic GR agonist, dexamethasone (DEX), at 6 and 24 hrs. Conventional analysis of this data set and gene set enrichment analysis (GSEA) was performed. Transcripts associated with metabolism were enriched in the DEX condition along with extracellular matrix genes. In contrast, a subset of growth factors and cytokines were negatively correlated with DEX treatment. Comparing DEX-induced gene expression data to developmental changes in gene expression in micromass cultures revealed an additional layer of complexity in which DEX maintains the expression of certain chondrocyte marker genes while inhibiting factors that promote vascularization and ultimately ossification of the cartilaginous template. Conclusions: Together, these results provide insight into the mechanisms and major molecular classes functioning downstream of DEX in primary chondrocytes monolayers. In addition, comparison of our data with microarray studies of DEX treatment in other cell types demonstrated that the majority of DEX effects are tissue-specific. This study provides novel insights into the effects of pharmacological GC on chondrocyte gene transcription and establishes the basis for subsequent functional studies. Experiment Overall Design: Primary chondrocytes isolated from the tibiae, humeri and femurs of 15.5 day old mice are treated with 10EXP-7M DEX or an equal volume of the DMSO vehicle for 24 hrs. Total RNA is isolated after 6 hrs and 24 hrs of treatment. Samples from three independent experiments independent time courses were hybridized to Affymetrix MOE 430 2.0 mouse chips. Experiment Overall Design: Number of time points: 2 (6hr and 24 hr) Experiment Overall Design: Number of treatments: 2 (DEX and the vehicle control) Experiment Overall Design: Number of Samples: 3 replicates per time point per treatment Experiment Overall Design: Affymetrix chip: MOE 430 2.0 Experiment Overall Design: Cell type: Primary chondrocyte Experiment Overall Design: Tissue or origin: Tibiae, humerus, femur Experiment Overall Design: Species E15.5 mice Experiment Overall Design: Samples: Total RNA

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High-throughput RNA-seq analysis of mocetinostat- and DMSO-treated TC28a2 cells

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