Convergence of YAP/TAZ, TEAD and P63 activity directs premalignant lung gene expression [RNA-seq]

Bronchial premalignant lesions (PMLs) are composed of expanding bronchial basal cells that can progress to lung squamous cell carcinoma (LUSC) by evading immune responses. Despite ongoing efforts that have mapped gene expression and cell diversity across bronchial PML pathologies, signaling and transcriptional events driving malignancy are poorly understood. Evidence has suggested key roles for the Hippo pathway effectors YAP and TAZ and associated TEAD and TP63 transcription factor families in bronchial basal cell biology and LUSC. In this study we mapped target genes regulated by these factors by combined RNA-seq and ChIP-seq in primary human bronchial epithelial cells, revealing a converged transcriptional network that is strongly associated with bronchial PML progression. Our observations suggest that YAP/TAZ-TEAD-TP63 associate to cooperatively promote basal cell proliferation and repress signals associated with interferon responses and immune cell communication. Directly repressed targets include MHC Class II factors expressed in bronchial epithelium that correlate with adaptive immune Th1 cell activities known to contribute to the immunosuppressive microenvironment in lung cancers. Our findings provide a molecular mechanism for gene regulation in progressive PMLs that contributes to immune evasion, offering potential new avenues for lung cancer interception. Overall design: For generating the YAP/TAZ, TEAD and TP63 regulated gene expression signature in human airway cells, HBECs were cultured in Pneumacult EX plus and transfected with control, pan-TEAD targeting, TP63 targeting and LATS1/2 targeting siRNAs and RNA was extracted for quality assessment and library prep for RNA-sequencing. 3 unique siRNA control sequences were used, and all siRNA transfected samples were collected in triplicate, 48hours after transfection. RNA quality for all samples was assessed by BioAnalyzer before proceeding with library preparation for sequencing. Sequencing libraries were prepared from total RNA samples using Illumina TruSeq RNA Sample Preparation Kit v2. The libraries from individual samples were pooled sequencing. HBEC samples were sequenced on the Illumina HiSeq 2500 platform to generate single end 50bp reads.