Extended Data Fig. 6: Receptor sequencing in atypical B cells.

(A) Expression of IgD and IgA in CD11c⁺ B cells from adults with DS (n = 3) and age-matched HCs (n = 3). Significance assessed by unpaired t-tests, ns denotes p > 0.05. Error bars denote SD. (B-F) BCR sequencing from gDNA isolated from sorted naïve, CD11c⁺ and memory B cells from controls (n = 6) and individuals with DS (n = 6). (B) Sorting scheme for naïve, CD11c⁺ and memory B cells (left) and number of cells sorted and number of productive BCRs obtained by sequencing for each cell type (right). (C) Fraction of in-frame BCRs containing no stop codons (“productive BCRs”) in naïve, CD11c⁺ and memory B cells from controls (n = 6) and individuals with DS (n = 6). (D) Simpson clonality in productive BCRs from CD11c⁺ B cells from controls (n = 6) and individuals with DS (n = 6). In (C-D), significance assessed by two-tailed unpaired t-test (ns denotes p > 0.05) and whiskers denote min and max values, bounds of box denote Q1–Q3, and centre bar denotes mean. (E-F) Representative heatmaps of Morisita index indicating overlap between B cell subsets in HC and DS at the (E) nucleotide and (F) amino acid levels. (G) Heatmap of IGHV gene frequency in HC and DS. Only genes that occurred at higher than 0.1% frequency in more than 10 samples are shown. (H) 9G4 IgG antibodies in supernatant after 4-day culture of sorted HC naïve, CD11c⁺ or memory B cells in the presence of BAFF, IL-2, IL-10, IL-21, the TLR7/8 ligand R848 with or without IFN-ɣ. Results representative of 2 independent experiments.