47 Inflamed joints share dominant B-cell clones Figure 1 | Comparing B-cell receptor repertoires within one joint Bar charts of (A) the number of BCR-clones, (B) number of highly expanded BCR-clones (HECs) and (C) impact of HECs on total repertoire per compartment (bars show mean and SD; ** p<0.01 and **** p<0.0001 using a Tukey’s multiple comparison test; ns=not significant). (D) Representative example of overlap-plot in one patient comparing the suprapatellar (SP) to the infrapatellar (IP) synovial tissue (ST) region, showing overlap of dominant BCR-clones in the upper right quadrant. Each dot reflects the frequency of the clone (% of total number of reads) in the ST-IP on the Y-axis and in the ST-SP on the X-axis. Vertical and horizontal dotted lines indicate the 0.5% threshold for HECs. ND=not detected; (E) Representative example of a comparison of ST to peripheral blood (PB), showing little overlap. For explanation of graph see (D) above. Scatter plots of (F) percentage of overlapping top-25 BCR-clones and (G) Chao- modified Sørensen indices of the total BCR-clones repertoire when comparing different compartments (n=12; lines at mean and SD; * p<0.05, ** p<0.01 using a paired t test; ns=not significant). BCR repertoires in different inflamed joints share distinct dominant BCR-clones To test for sharing of clones between different joints in 7 RA patients the BCR repertoire was compared between ST biopsies from inflamed contralateral knee joints in the same patient that were taken on the same day. Again, paired PB samples from the same time-point served as a control. The overall repertoire characteristics from contralateral joints were not significantly different (Figures 2A–C): In the left knee on average 1,269 ± 616.5 BCR-clones, with 30.4 ± 8.6 HECs accounting for 55.8% ± 3
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