Figure 4.

(A) Expression of FOXJ1 (forkhead box J1) (ciliated-cell marker), MUC5AC (goblet-cell marker), and TP63 (tumor protein p63) (basal-cell marker) from RNA sequencing in COPD HBEC and normal HBEC repopulated on COPD bronchial scaffolds or normal bronchial scaffolds (n = 9 repopulated scaffolds per combination and time point) or grown at the ALI (n = 3 HBEC donors). Day 0 was defined as the day of differentiation induction, which was 4 days after the seeding of cells. FOXJ1 expression was higher in COPD HBEC than in normal HBEC on both COPD scaffolds and normal scaffolds on Day 0. FOXJ1 increased between Day 0 and Day 7 in HBEC repopulated on scaffolds (FDR < 0.001) but was not increased when HBEC were grown at the ALI. MUC5AC increased between Day 0 and Day 7 in HBEC repopulated on scaffolds and grown at the ALI (FDR < 0.001). TP63 decreased between Day 0 and Day 7 in HBEC repopulated on scaffolds and grown at the ALI (FDR < 0.001), except in COPD HBEC on COPD scaffolds. (B) Expression of FOXJ1 protein in COPD HBEC and normal HBEC after 7 days of differentiation on COPD bronchial scaffolds or normal bronchial scaffolds (n = 9 repopulated scaffolds per combination). FOXJ1 concentrations were normalized against GLB1 (β-galactosidase) to account for varying number of cells on the scaffolds. Means and SDs are indicated. *FDR < 0.05, **FDR < 0.01, and ***FDR < 0.001 using DESeq2 (see the data supplement) and the Benjamini-Hochberg method for multiple testing correction in A. *P < 0.05 and **P < 0.01 using the Mann-Whitney test in B.