Extended Data Fig. 9: RA serum protein analysis.

a, Line plots showing pre- and post-treatment serum protein quantification of selected fibrogenic and immune markers reported as NPX values. A difference of 1 NPX signifies a doubling of protein. Statistics by two-sided Wilcoxon test, FDR corrected. b, Volcano plot showing the R-values and nominal p-values of baseline serum proteins correlated with baseline patient-level fibrogenic signature score (left) and posttreatment serum proteins with change in fibrogenic signature score (right) with the top 10 positively and negatively correlated genes indicated. Statistics by two-sided Pearson correlation coefficient test. c, Violin plot representing the distribution of fibrogenic gene signature score and COMP expression of synovial fibroblasts from each CTAP (EFM: n = 7, F: n = 11, M: n = 18, T + B: n = 14, T + F: n = 8, T + M: n = 12). Statistics by two-sided Wilcoxon test with Bonferroni correction. p < 2.22e-16 in the comparison between E + F + M and other CTAPs. d, Violin plot representing the distribution of disease duration in RA patients classified as CTAP-EFM (n = 7) versus RA patients classified as other CTAPs (n = 63). Statistics by two-sided Wilcoxon test. e, Volcano plot of differentially abundant serum proteins in CTAP-EFM patients compared to patients assigned to other CTAPs with selected genes highlighted. Differential expression was assessed with limma: linear models fitted per gene and empirical Bayes moderation of the standard errors to produce moderated t‑statistics; p‑values shown are unadjusted. f, Bar plot of selected serum proteins that are differentially abundant in RA patients classified as CTAP-EFM compared to RA patients classified as other CTAPs. The height of the bar represents the log-fold change, and the shading of the bar represents adjusted p-values with FDR correction. c,d the box plots show the median and 25th–75th percentiles; the whiskers represent 1.5 times the interquartile range (IQR); outliers are shown beyond the whiskers.