Loss of MCL-1 in TEC precipitates thymic hypoplasia. (A) Heat map of BCL-2 family member expression in the indicated TEC subsets from 1- or 4-week-old wild-type (WT) or Aire^−/− mice as assessed by RNA sequencing (n = 2). TEC subsets and genes are hierarchically clustered by Pearson correlation and Euclidean distance, respectively. Genes encoding prosurvival proteins are highlighted in blue. (B) Histograms of flow cytometric analysis of BCL-2 (top), BCL-XL (middle), and MCL-1 levels (bottom) in TEC subsets from 2-month-old WT mice. (C) Histograms of flow cytometric analysis of BCL-2 (top), BCL-XL (middle), and MCL-1 (bottom) expression in CD45⁻EpCAM⁺MHC II⁺ TECs isolated from day 9, 1 month, and E15.5 embryos, respectively, of the indicated genotypes. (D) Pictures of thymi from 2-month-old female mice of the indicated genotypes. (E) Thymic cellularity of 2-month-old mice of the indicated genotypes. (F) Thymic cellularity of controls (blue circles) and Mcl1^ΔFoxn1 (red squares) mice at various ages. The numbers in parentheses indicate the mean fold change in thymic cellularity (controls/Mcl1^ΔFoxn1 mice). Data representative of at least 2 independent experiments are shown. Graph bars indicate mean ± standard error of the mean (SEM), and groups were compared with a Student t test (2 sided, unpaired). *P < .05; **P < .01; ***P < .001; ****P < .0001. The control group includes various combinations of genotypes (Foxn1^Cre/+Mcl1^+/+, Foxn1^+/+Mcl1^lox/+, Foxn1^+/+Mcl1^lox/lox, Foxn1^Cre/+Mcl1^lox/+) that showed no differences from each other in separate experiments (n ≥ 3/group). FMO, fluorescence minus one.