Transcriptomic Profiling of Murine Chondrocytes Following APOE Knockout: Insights into Gene Expression Alterations

We have previously demonstrated that cold stress significantly reduces APOE expression in chondrocytes, which correlates with intracellular lipid accumulation and elevated reactive oxygen species (ROS) levels. The objective of this study was to elucidate the downstream regulatory mechanisms of APOE in chondrocyte homeostasis. To achieve this, we compared genome-wide transcriptional profiles of wild-type (WT) and APOE-knockout (Apoe-KO) murine chondrocytes through RNA sequencing (RNA-seq). Primary chondrocytes were isolated from C57BL/6 mice, including wild-type (WT, n=3) and Apoe knockout (Apoe-KO, n=3 ) groups. Cells from each genotype were cultured under standardized conditions, followed by RNA extraction and sequencing. Genome-wide transcriptomic profiling via RNA-seq was performed to compare gene expression patterns between Apoe-KO (Case) and WT (Control) chondrocytes, aiming to identify APOE-dependent downstream targets and regulatory pathways.