Figure 3

RNA-seq analyses of the responses to total knee arthroplasty in total RNA isolated from PAXgene blood RNA tubes. (A) Principal component analysis (PCA, using top 1,000 genes) of RNA-seq data from POD1 (24 h after surgery) and DOS (day of surgery). RNA-seq analysis is based on 36 samples obtained from 18 patients at DOS and POD1. (B) Volcano plot representing the differentially expressed genes comparing POD1 to DOS samples. Red dots correspond to genes with significant changes greater than 1 log2-fold expression change (FDR < 0.05, LogFC > 1). Selected genes with increased or decreased expression that were also identified by NanoString analyses are highlighted in blue. (C) NanoString normalized counts of selected DEGs, confirming changes identified by RNA-seq. Dotted lines indicate background signal. **p < 0.01, ***p < 0.001, by t-test, calculated using ratio data and the nSolver analysis software. NanoString data are represented as means ± S.D. (error bars) normalized counts. (D) Representation of the QuSAGE pathway analyses in POD1 relative to DOS, showing functional pathways differentially expressed at POD1 (FDR < 0.01). Representative genes associated with the (E) IL1, (F) IFNG signaling, (G) IL6 signaling, and (H) DNA repair pathways are shown, representing changes in gene expression (logFC) in POD1 vs. DOS samples. Graphs were created with GraphPad Prism 8 (GraphPad Software, San Diego, CA).