27 Synovitis is dominated by shared T-cell clones Table 1 | Patient characteristics (n=13) Age (mean (SD)), years 52 (13) Male (n (%)) 3 (23%) IgM-RF positive (n (%)) 12 (92%) IgM RF level (median (IQR)), kU/L 68 (26-276) ACPA positive (n (%)) 7 (54%) ACPA level (median (IQR)), kAU/L 84 (8-644) IgM-RF and ACPA both pos. (n (%)) 7 (54%) Disease duration (median (IQR)), months 7 (3-159) DAS28 (mean (SD)) 5.2 (1.1) Patients without therapy (n (%)) 7 (54%) Patients treated with csDMARD (n (%)) 4 (31%) Patients treated with bDMARD (n(%)) 2 (15%) IgM-RF, IgM rheumatoid factor; ACPA, anti-citrullinated peptide antibodies; csDMARD, conventional synthetic disease-modifying antirheumatic drugs; bDMARD, biological disease-modifying antirheumatic drugs. Linear amplification and next-generation sequencing The protocol used for linear amplification and next-generation sequencing has been described before [9,28,29]. Sequencing was performed on the MiSeq Gene and Small Genome Sequencer (Illumina). Based on earlier studies, TCRβ clones with a frequency ≥0.5% were considered dominant and therefore called HECs [9,30]. Statistics Values are either expressed as mean or median depending on the presence of a normal or nonnormal distribution of the data. To test for similarity between different sites, the Chao-modified Sørensen index was used. This index, originating from the field of biodiversity, measures dispersion and gives a value between 0 and 1. Values near 0 indicate no overlap between two locations, whereas values close to 1 indicate that the two locations are identical [31–34]. Differences between groups were analyzed using the unpaired Mann–Whitney U test, paired t test, one-way ANOVA, or Tukey multiple comparison test if appropriate. The p values <0.05 (two-sided) were considered statistically significant. R (version 3.1.0), package SpadeR (version 0.1.1), and GraphPad Prism (version 6.0) were used to perform the analyses. 2
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