Investigating the Genetic and Epigenetic Control of Basal Cell Identity

Project Summary/Abstract How do cells isolated in a dish maintain their transcriptional profile and tissue-specific differentiation patterns throughout multiple generations in the absence of their surrounding tissue? This phenomenon is seen in progenitor cells from different organs that have distinct differentiation and proliferative capacity. Progenitor cells from the same organism contain the same genomic DNA, but in the absence of extracellular signaling from adjacent tissues, still maintain their fate through an intrinsic mechanism inherited by generations of daughter cells. Basal Cells (BCs) carry the ability to maintain the organ-specific programs of differentiation and self- renewal that are responsible for the great diversity of epithelial tissue subtypes5,6. Here, I aim to study these programs within BCs of the respiratory tract (airway BCs), where these progenitors largely give rise to secretory and multiciliated cells in the pseudostratified epithelium, and how they contrast with BCs of the esophagus (esoBCs), where BCs differentiate into a squamous stratified epithelium1,2,3,8. Environmental perturbations both in vitro (disruption of retinoic acid signaling) or in vivo (cigarette smoke, COPD) result in an aberrant pattern of self-renewal and differentiation of airway BCs, causing them to adopt a program characteristic of esoBCs9,12. These changes are hallmark features of squamous metaplasia, a reversible, preneoplastic lesion reported in airways in chronic respiratory conditions15. My proposal is focused on identifying the genetic and epigenetic components of the programs regulating the transition from pseudostratified epithelium to that characteristic of the esophagus. I propose two approaches to address this problem; a) to perform gain or loss of function assays using transcription factors (TFs) differentially expressed in airway BCs or esoBCs to investigate the relevance of these factors in driving their tissue-specific program; b) to conduct a focused CRISPR/Cas9 screen in mouse airway BCs using a library of guide RNAs targeting chromatin modifying genes. Collectively, this data has the potential to identify intrinsic genetic and epigenetic mechanisms maintaining BC identity and shed light on genetic targets for the prevention of preneoplastic lesions in progenitor cell populations.