Extended Data Fig. 5: MHCII expression on CX3CR1+ cells is required for the thymic expansion of bacteria-specific T cells.
a–g, Wild-type and CX3-DTR mice were colonized with SFB or E. coli at weaning or left untreated and tissues were compared one week (qPCR) or two weeks (flow cytometry analysis) later. a, Flow cytometry of thymic SFB-tetramer+ cells (CTRL: n = 5; SFB: WT n = 6; CX3-DTR n = 8). b, c, 16S qPCR in the thymus (b; n = 8 (WT); n = 9 (CX3-DTR)); and MLNs (c; n = 13 (WT); n = 12 (CX3-DTR)). d, e, SFB-specific qPCR in the thymus (d; n = 5 per group) and faecal pellets (e; n = 10 (WT); n = 5 (CX3-DTR)). f, g, E. coli-specific qPCR in the thymus (f; WT n = 7; CX3-DTR n = 12) and faecal pellets (g; n = 10). h, Diphtheria-toxin-treated littermate wild-type mice and mice depleted of CD103+ DCs (CD103-DTR CD11c-Cre) were analysed two weeks after weaning. Flow cytometry of CD103+ and CX3CR1+ DC subsets in colon lamina propria (n = 5). i, j, Diphtheria-toxin-treated littermate wild-type, CX3-DTR CD11c-Cre and CD103-DTR CD11c-Cre mice were colonized with E. coli at weaning and thymi were compared one week later. i, E. coli-specific qPCR (n = 8 (WT); n = 10 (CX3-DTR); n = 8 (CD103-DTR)). j, 16S qPCR (n = 24 (WT); n = 10 (CX3-DTR); n = 8 (CD103-DTR)). k–m, 4-OHT-treated MHCIIfl/+ (WT) and MHCIIfl/− (KO) CX3-Cre mice were colonized with SFB at weaning and thymi were compared two weeks later. k, Frequencies and counts of SFB-tetramer+ cells (n = 10 per group). l, SFB-specific qPCR (n = 5 per group). m, Frequencies of CD103+ and CX3CR1+ DC subsets (n = 10 per group). Each replicate is a biologically independent sample. Data are shown as individual values and mean P values by two-tailed unpaired t-test (b–g, k, l) or one-way ANOVA with Tukey’s (i, j) or Sidak’s (m) post hoc test.
