Pluto Bioinformatics

GSE150411: Transcriptional response of fibronectin fragment treatment in human articular chondrocytes

Bulk RNA sequencing

Objective: Fibronectin is a matrix protein that is fragmented during cartilage degradation in osteoarthritis (OA). Treatment of chondrocytes with fibronectin fragments (FN-f) has been used to model OA in vitro, but the system has not yet been fully characterized. This study sought to define the transcriptional response of chondrocytes to FN-f, and directly compare this response to differentially expressed genes traditionally found in OA. Design: Normal primary human femoral chondrocytes isolated from tissue donors were treated with either FN-f or PBS (control) for 3, 6, or 18 hours. RNA-seq libraries were compared between time-matched FN-f and control samples, in order to identify changes in gene expression across time. Differentially expressed genes were compared to a published OA gene set and used for pathway, transcription factor motif, and kinome analysis. Results: FN-f treatment resulted in 1,224 differentially expressed genes over the time course. Significant overlap was noted with genes upregulated (p< 0.0001) or downregulated (p=0.0004) in the OA gene set. Early response genes were involved in inflammatory response pathways and gene promoters were enriched for NFkB-related motifs, whereas many late response genes were involved in ferroptosis and gene promoters were enriched for Jun-related motifs. Highly upregulated kinases included CaMK1, IRAK2, and novel kinase DYRK3, while growth factor receptors TGFR2 and FGFR2 were downregulated. Conclusions: FN-f treatment of normal human chondrocytes recapitulated many key aspects of the OA chondrocyte phenotype. This in vitro model is promising for future OA studies, especially considering its compatibility with genomics and genome-editing techniques. SOURCE: Kathleen,Shaindel Metz,Reed (ksmetz@email.unc.edu) - Douglas Phanstiel University of North Carolina, Chapel Hill