Abstract P5-08-04: Defining chromatin accessibility profiles of partial and reversible EMT

Abstract

Abstract The epithelial-to-mesenchymal transition (EMT) reversible cellular reprogramming event, used repeatedly throughout development, is hypothesized to be involved in the cell migration and consequently metastasis that ultimately contributes to most breast cancer-related fatalities. In this process, cuboidal epithelial cells, marked by the presence of tight junction proteins and cell-cell adhesions, lose their apicobasal polarity and acquire a spindle-like morphology and migratory traits. EMT was originally regarded to have only two states, with cells exhibiting either epithelial or mesenchymal phenotypes; however, recently, researchers have demonstrated the existence of a dual epithelial/mesenchymal state, termed hybrid- or partial-EMT. Due to its inherent plasticity, it is believed that EMT and its reversal mesenchymal-to-epithelial transition (MET) is, at least, partly regulated by epigenetic means such as alterations in chromatin structure. Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) is a novel technique that employs the use of a mutant Tn5 transposase to cleave nucleosome-free DNA regions in a non-biased manner. In this investigation, we induced MCF10A mammary epithelial cells to undergo a short-term (<4 days) or long-term (>4 days) EMT. Addition and withdrawal of exogenous TGFβ1 produced partial- or full-EMT and MET conditions which were interrogated by ATAC- and RNA-seq. Hierarchical clustering of ATAC cleavage peaks revealed that pre-EMT and short- and long-term MET conditions demonstrate similar chromatin accessibility profiles with cleavage sites enriched for specific binding motifs. Notably, transcription factors typically not associated with EMT displayed dynamic enrichment in the accessible chromatin at various timepoints in our assay. Correlation with RNA-seq data reveals highly dynamic changes in gene expression suggesting dynamic and reversible use of regulatory programs. Importantly, partial-EMT cells were characterized by unique accessibility patterns, motif enrichment, and gene expression supporting the conclusion that this is not merely an intermediate but a unique state. Citation Format: Johnson KS, Hussein S, Lin Y, Taube JH. Defining chromatin accessibility profiles of partial and reversible EMT [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-08-04.