RA patients can be divided into two main subgroups based on the presence or absence of autoantibodies [1, 29], therefore we stratified the RA patients into seropositive (RA+) vs. seronegative patients (RA−) (Supplementary Fig. 2A), based on the presence of RF and/or ACPA. Here, PRTN3 is linked to rheumatoid arthritis.