Fig. 6: Sequence and array analyses of no bridge and bridge chimeras.

Hypothesized cell interactions for germinal center (GC) entry in no bridge chimeras A and bridge chimeras B. C Global clustering of ~38,000 splenocytes from no bridge (Chimera 1 and 2) and bridge (Chimera 3) chimeras. For the bridge chimera, splenocytes were additionally enriched for GC B cells. D UMAP dimensionality reduction of B and GC B-cell populations from C. E Cluster definitions for D. Highly differentially expressed markers are listed. F Gating for CD3 + , B220+ and dbneg populations based on Abseq. G Stratification of B220+ population into MHC^b/b (b/b), MHC^b/d (b/d) or MHC^d/d (d/d), based on Abseq. As F but split for no bridge chimera 1 H and 2 I, and bridge chimera 3 J. K MHCII haplotype distribution among total and naive (Clusters 0–3 from D) B cells, and among GC B cells (Cluster 7 from D) relative to their representation in the primary repertoire, for each of the three chimeras. L Average isoelectric point for the agglomerated heavy and light chain CDR3s of naive (peach) and GC (purple) B cells. M Average isoelectric point for the agglomerated heavy chain CDR3s of naive (peach) vs. GC (purple) B cells, stratified by whether they are predicted to be included in (I-A^b/b of chimeras 1 + 2 and I-A^d/d of chimera 3) or excluded from (I-A^d/d of chimera 1 + 2) the autoreactive response. N Frequency of arginine, asparagine, lysine, and histidine in the agglomerated CDR3s of naive vs. GC B cells. O Class-switched frequency among naive vs. GC B cells. P CDR3 sequences of the 10 most expanded GC B-cell clones. Q Volcano plot of median IgG signal intensities in no bridge chimeras (n = 14) vs. homozygous 564Igi mice (n = 12). R As Q, but bridge chimeras (n = 16) vs. homozygous 564Igi mice (n = 12). S As Q, but no bridge chimeras (n = 14) vs. bridge chimeras (n = 16). Bars represent mean ± SD. Statistical comparison in L and M by two-way ANOVA with Šidák’s post-test, and in N and O unpaired, two-tailed t-test, for n = 3 mice. ns = p > 0.05.