Extended Data Fig. 6: Related to Figs. 4 and 5: Additional in-vivo and in-vitro data on the IDO1-Kyn-AhR pathway.

a-c, The thymi of the mice from Fig. 4g–e were immunostained for IDO1 (red) and Mac2 (green) and quantified for IDO1 MFI in Mac2⁺ areas (arrows). Also shown are thymus weight, thymus cellularity, and F4/80⁺ macrophages/thymus (n = 8 mice/group). d, Control and Ido1^−/− BMDMs (top 2 graphs), or Scr- and siSlc364-transfected BMDMs (bottom graph), were pre-treated for 1 h ± Kyn and incubated ± ACs. After a 6-h chase, the cells were assayed for Cyp1a1 and Cyp1b1 (n = 3 biological replicates/group). e, BMDMs were incubated ± apoptotic macrophages and assayed for Cyp1a1. f, Scr- or siSLC36A4-transfected HMDMs were incubated ± ACs, chased for 3 h, and assayed for CYP1A1 and CYP1B1 (n = 3 biological replicates/group). g, Scr- or siAhr-transfected BMDMs were incubated with DiD-labelled ACs and quantified for percent DiD⁺ macrophages (arrows). Scale bar, 50 μm (n = 4 biological replicates/group). h, BMDMs pre-treated ± CH223191 were assayed for continuing efferocytosis as in Fig. 2a. Arrows, PKH26⁺PKH67⁺ macrophages. Scale bar, 50 μm (n = 3 biological replicates/group). i, As in panel h, but one of the cohorts was also treated with cytochalasin D before the second round of efferocytosis. Arrows, PKH26⁺PKH67⁺ macrophages. Scale bar, 50 μm (n = 3 biological replicates/group). j, Scr- or siAhr-transfected BMDMs were assayed for Ahr (n = 3 biological replicates/group) and immunoblotted for AhR protein (n = 3 samples/group). k, Scr- or siAHR-transfected HMDMs were assayed for AHR (n = 3 biological replicates/group). l, Scr- or siArnt-transfected BMDMs were assayed for Arnt (n = 3 biological replicates/group). All mRNA data are expressed relative to the indicated control groups. Data are mean ± SEM, and significance was determined by two-tailed Student’s t-test or one-way ANOVA with Fisher’s LSD post-hoc analysis.

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