Fig. 6.

Interactions with the microbiota contribute to the apoptosis of Atg7-deficient Lgr5⁺ISC. (A) Representative TUNEL staining on tissue sections of Atg7^−/− mice treated with water or broad-spectrum antibiotics (ATB). Quantification of the mean number of TUNEL-positive cells per crypt over 50 consecutive whole crypts in 6 control WT mice, 11 control Atg7^−/− mice, 8 WT, and 7 Atg7^−/− ATB-treated mice. The data shown are means ± SD. (Scale bars: 50 µm.) (B) Percentage survival from day 1 of WT or Atg7^fl/fl organoids in the presence or absence of 4OHT in the culture medium (n = 6 mice per condition). (C) Percentage survival from day 1 of WT organoids in the presence or absence of chloroquine (CQ) in the culture medium (n = 6 mice per condition). (D) Western blotting for ATG7 and LC3 on protein extracts from day 4 WT or Atg7^fl/fl organoids in the presence or absence of 4OHT and/or CQ in the culture medium. γ-Tubulin was used as a loading control. (Scale bars: 50 µm.) (E) Fold change in survival relative to untreated controls of WT or Atg7^fl/fl organoids in the presence of 4OHT (control [Ctrl], n = 8 WT and n = 9 Atg7^fl/fl mice) and in the presence or absence of MDP, lipopolysaccharide (LPS), flagellin, polyinosinic:polycytidylic acid (PolyIC), or lipoteichoic acid (LTA) in the culture medium (n = 3 mice per condition). Significant differences are shown with asterisks. *P < 0.05; ***P < 0.005.