Figure 4. Functional gene set analysis of iOA and cOA.

RNA sequencing of synovial macrophages and data analyses were conducted following description in methods. (A) UpSet plot visualizing the sets of differentially expressed genes from different contrasts, including the quantitative analysis of aggregate intersections between comparisons. Sets ordered by frequency. DEGs (>1.5-fold change; P < 0.05, multiple test corrected) identified in OA vs. IA, iOA vs. IA, and cOA vs. iOA. (B) Percentage of macrophages in CD45⁺ cell fraction of synovial tissue of RNA-sequenced samples. n = 8. (C) Cell subsets measured as a percentage of CD45⁺ cell fraction isolated from synovial tissue. cOA and iOA subgroups from additional samples identified initially by enumeration of synovial macrophages. cOA ≤ 30% macrophages; iOA ≥ 30% macrophages. n = 6. (D) KI67⁺ macrophages in iOA group identified in C. Data are representative of 6 individual experiments. (E) Enumeration of Ki67⁺ macrophages in cOA and iOA groups identified in C. n = 6. *P ≤ 0.05, **P ≤ 0.01 by 2-tailed unpaired t test.