Figure 1. Differences in isotype, IGHV gene usages and clonality between IMDs.
a) Heatmap of the normalized isotype usages per disease. b) The percentages of normalized IgA1/2 and IgE BCR percentage usages per disease. c) IgA titre in healthy individuals (n=4) and CD (n=20) and SLE (n=8) patients. d) Heatmap of IGHV gene frequency and BCR subtypes in health and disease: IgM+D+SHM- BCR sequences, (>78% derived from naive B cells); IgM+D+SHM+ BCR sequences - SHM is evidence of antigenic stimulation; and IgM-D- BCR sequences, all isotype-switched and therefore post-antigenic. Light and dark orange squares indicate significantly higher, and light and dark blue squares lower, gene frequency in disease than health. Only genes >0.1% in frequency are shown. Relative mean gene frequencies in healthy individuals are indicated at the top (full heatmap in Supplemental data file 3). IGHV genes are ordered according to amino acid similarity, indicated by the IGHV gene amino acid similarity tree (see methods). e) Explanations of clonality measures and network representations of BCR repertoires. f) Heatmap showing the (left) Clonal Expansion Index and (right) Clonal Diversification Index of each isotype per disease from total PBMC B cells. g) The (left) Clonal Expansion Index and (right) Clonal Diversification Index for PBMC BCR repertoires per disease. For (a),(b),(d),(f),(g): n=32, 18, 32, 12, 10, 23, 10 and 13 for healthy, AAV MP0+, AAV PR3+, EGPA, SLE, CD IgAV and Behçet’s patients respectively. P-values calculated by two-sided ANOVA for (a)-(c) and * denotes false discovery rate (FDR) <0.05, ** <0.005, *** <0.0005, where FDR determined by Šidák method. For (d),(f): Light and dark orange squares indicate significantly higher, and light and dark blue squares significantly lower, isotype use in disease compared to health. Boxplots show the 25th, 50th and 75th percentiles; whiskers show upper and lower quartiles.