Fig. 5

CIITA associates with bronchial PML progressive pathology and tracks with MHC Class II gene expression and the presence of Th1 T cells. a TEAD and TP63 ChIP-seq tracks showing the co-binding peaks associated with CIITA. Overlapped peak regions are shown with red strips below. The grey rectangles indicate the fragment regions in pcHi-C and the black arc depicts the interactions between distal elements and CIITA promoter. b Proliferating HBECs were lysed and ChIP-qPCR was performed using TEAD, TP63, YAP or IGG control antibodies examining the peak region identified by ChIP-seq as overlapping for TEAD and TP63 binding upstream of CIITA. The average % input from three experiments is shown -/ + standard error of mean. Unpaired t-test, *p < 0.01, **p < 0.001, ***p < 0.0001. c. Heatmap of significantly repressed MHC Class II gene expression (FDR < 0.01) in siYAP/TAZ, siTEAD and siTP63 treatment in HBECs. d Heatmap of communication significance levels between MHC Class II genes in basal cell and binding partners in immune cells in the human lung scRNA-seq data from Travaglini et al. The ligand-receptor pairs that involve MHC Class II gene expression in the basal cells are plotted as the row, and the immune cell types that the basal cells are communicating to are plotted as the columns. The color of heatmap reflects the significance levels of the cell–cell communication based on CellChat. e Expression levels of CIITA in progressive/persistent and regressive PML samples of the Proliferative subtype in the Beane et al. Discovery cohort. f Scatter plots show the Pearson correlation between the expression level of CIITA and Th1 scores (calculated using GSVA based on genes from Bindea et al.) in the Beane et al. Discovery cohort. g Immune cell-type ranked by their Pearson correlation coefficients with CIITA expression level in the Beane et al. Discovery cohort. The dashed line indicates the Pearson correlation coefficient that reaches p-value = 0.05. h Th1 cell scores in progressive/persistent and regressive PML samples of the Proliferative subtype in the Beane et al. Discovery cohort