Abstract 2115: Multicomponent epigenetic profiling of intermediate epithelial-to-mesenchymal states in triple negative breast cancer identifies distinct regulatory signatures

Abstract

Abstract Epithelial-to-mesenchymal transition (EMT) is an early step in the invasion-metastasis cascade, involving cellular progression through a number of intermediate states through the transition. Due to difficulty in isolating cells with intermediate EMT phenotypes, it has been challenging to investigate their molecular characteristics. Here, we describe multicomponent epigenetic profiles of phenotypes across the EMT spectrum. Six single cell clones on different points of the EMT spectrum were isolated from SUM149 cells, a heterogeneous ER/PR negative inflammatory breast cancer line. Methylation (mC) and hydroxymethylation (hmC) of >860,000 CpGs sites were measured with tandem oxidative bisulfite treatment and Illumina EPIC arrays, global chromatin accessibility was determined using Assay for Transposase Accessible Chromatin (ATAC) seq, and gene expression was measured using RNA-seq. We observed distinct mC and hmC profiles of the EMT intermediate clones compared to clones at either the epithelial or mesenchymal extremes. Intermediate clones demonstrated 17,862 CpGs with significantly higher hmC and 7,903 CpGs with significant hypomethylation, compared to the distal clones (FDR < 0.01). CpGs with higher hmC were enriched in regulatory regions such as promoters (OR = 2.87, p < 0.001), while hypomethylated CpGs were enriched in regions within the gene bodies. High hmC included CpGs located in promoters of key epithelial genes CDH1 and OCLN. In addition, 1,653 differentially accessible chromatin regions from ATAC-seq also were identified in intermediate clones (FDR < 0.1). Differentially accessible regions in the intermediate clones were associated with extracellular matrix organization (q-val = 0.04) in Reactome Pathway analysis. Although a large proportion of differentially accessible regions where differential hmC and mC CpGs were enriched tracked to distal intergenic regions (30.8%) and introns (28.1%), we did not observe significant enrichment of differential cytosine modifications overlapping with the differentially accessible chromatin regions which indicates the importance of multicomponent measures of epigenetic states. In genes with differentially accessible regions and hydroxymethylated CpGs, intermediate clones showed higher gene expression than distal clones. In particular, RUNX3 was observed to harbor all differential chromatin accessibility, hmC and mC CpGs, in intermediate clones. There was a stronger correlation between hmC and gene expression for differentially hydroxymethylated CpGs within accessible regions (R = 0.54, p < 0.01) than within non-accessible regions (R = 0.45, p = 0.02). Our results indicate both shared and distinct epigenetic profiles on the EMT spectrum at the cytosine and chromatin level regulate EMT processes and may be targeted to prevent the progression of EMT. Citation Format: Min Kyung Lee, Meredith S. Brown, Owen M. Wilkins, Diwakar R. Pattabiraman, Brock C. Christensen. Multicomponent epigenetic profiling of intermediate epithelial-to-mesenchymal states in triple negative breast cancer identifies distinct regulatory signatures [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2115.