Extended Data Fig. 7: Features of the top plasma cell clones in PSC patients.

a, Volcano plot of the negative log base 10 adjusted p-value versus log base 2 fold change of the genes differentially expressed in the whole tissue biopsies of I2 versus U patients (n = 34 I2, 133 U). Closed circles denote genes coding for immunoglobulin constant region; heavy chain V, D, or J segments; or light chain V or J segments. b, Mean forward scatter (FSC) of right colon plasma cells across clusters as determined by flow cytometry. c, Proportion of IgA-secreting plasma cells amongst total right colon plasma cells as determined by ELISpot. d, Proportion of IgM-secreting plasma cells amongst total right colon plasma cells as determined by ELISpot. e, Proportion of the total repertoire made up by the top clone within each subject. f, Proportion of plasma cells of each isotype by clone. g, Mean amino acid divergence from inferred germline across entire heavy chain sequence of largest clones identified in each patient. h, Mean pairwise amino acid divergence across entire heavy chain sequence of largest clones identified in each patient. (b–e, g–h) Each symbol represents an individual patient (open circles denote patients without dysplasia at the time of sampling, ‘x’ denote patients with dysplasia at the time of sampling, open squares denote patients indefinite for dysplasia at the time of sampling). Center line represents the median value; hinges indicate the 1st and 3rd quartiles; upper and lower whiskers extend to the largest and smallest values that are within 1.5 times the interquartile range from 1st and 3rd quartiles, respectively. Significance determined by two-sided, unpaired Wilcoxon test without adjustment for multiple comparisons. b–h, n = 4 PSC I2, 3 PSC I1, 7 PSC U.