To study the spatial organization in RA, we profiled 27 tissue sections and a total of 17,117 tissue spots by ST (“Methods”) collected from seropositive (RF+ACPA+, n = 3) and seronegative (RF−ACPA−, n = 3) RA patients at the time of joint replacement (Fig. 1, Supplementary Table 1). This evidence concerns the gene PRTN3 and rheumatoid arthritis.