Extended Data Fig. 7: Tlr9^P915H and Tlr9^−/− induce distinct ABC and PB states.

a,b, Costimulatory molecules and PB-associated transcripts from the RNA-seq analysis that were more highly expressed in Tlr9^−/− and Tlr9^WT ABCs compared to Tlr9^P915H ABCs (upper row, n = 4) were investigated at the protein level by flow cytometry (lower row) in a separate cohort of 3-way BM chimera MRL/lpr mice (n = 12) ((a) CD80, Tlr9^−/− versus Tlr9^P915H, p < 0.0001; Tlr9^P915H versus Tlr9^WT,p = 0.0023; CD86, Tlr9^−/− versus Tlr9^P915H, p < 0.0001; Tlr9^P915H versus Tlr9^WT,p = 0.0017; CD200, Tlr9^−/− versus Tlr9^P915H, p = 0.0040; Tlr9^−/− versus Tlr9^WT,p = 0.0073; Itgb7, Tlr9^−/− versus Tlr9^P915H, p = 0.0003; Tlr9^P915H versus Tlr9^WT,p = 0.0057; (b) CD44, Tlr9^−/− versus Tlr9^P915H, p = 0.0003; Tlr9^P915H versus Tlr9^WT,p = 0.0076; CXCR4, Tlr9^−/− versus Tlr9^P915H, p < 0.0001; Tlr9^P915H versus Tlr9^WT,p = 0.0008; CD138, Tlr9^−/− versus Tlr9^P915H, p < 0.0001; Tlr9^P915H versus Tlr9^WT,p = 0.0094). c,d, Flow cytometry analysis shows differential expression (MFI) of selected transcription factors (c) and the inhibitory molecule CD300a (d) among Tlr9 genotypes in ABCs of the 3-way BM chimera MRL/lpr mice ((c) IRF4, Tlr9^−/− versus Tlr9^P915H, p = 0.0002; BCL6, Tlr9^−/− versus Tlr9^P915H, p = 0.0015; Tlr9^P915H versus Tlr9^WT, p = 0.0011; Tlr9^−/− versus Tlr9^WT,p = 0.0025; TBET, Tlr9^−/− versus Tlr9^P915H, p = 0.0002; Tlr9^−/− versus Tlr9^WT,p = 0.0107; (d) CD300a, Tlr9^−/− versus Tlr9^P915H, p < 0.0001; Tlr9^P915H versus Tlr9^WT,p = 0.0188). (a-d) Splenocytes from twelve 3-way BM chimera mice (n = 6 females, and n = 6 males from 2 experiments) were stained for the indicated markers and the CD45.1/CD45.2 congenic markers. (Each line represents a 3-way BM chimera MRL/lpr mouse, * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001, RM one-way ANOVA with Turkey’s multiple comparisons test).

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