Abstract P4-04-02: Epigenomic analysis of cancer stem cells (CSCs) from triple-negative breast cancer (TNBC) reveals p63 and p73 as core metastasis drivers

Cancer stem cells (CSCs) are key drivers of cancer metastasis, drug resistance, and disease recurrence. While the transcriptional regulatory circuitry that underlies the generation and propagation of the breast CSC state is not completely understood, defining the core regulators of the CSC state has the potential to reveal how these cells arise and point to potential targetable pathways for therapeutic intervention. We isolated CSCs by selecting for surface expression of integrin β4 (ITGB4). ITGB4-hi cells are highly enriched for CSCs and display cellular and molecular features indicative of their residence in an intermediate EMT state, including the ability to seed metastasis in vivo. Using ITGB4-hi CSCs isolated from the SUM159 breast cancer cell line, we deployed epigenome mapping by H3K27ac ChIP-seq, nucleosome occupancy by ATAC-seq, and transcriptome analysis by RNA-seq. Using comparative analysis of enhancer usage and DNA accessibility, we identified the transcriptional regulatory circuitry of breast cancer CSCs and pinpointed the master transcription factors that control the CSC state. We find that p63/p73 proteins function as master transcriptional regulators in breast CSCs and establish super-enhancers at critical CSC state genes. Loss of p63 and p73 disrupts the transcriptional circuitry of CSCs and leads to a highly mesenchymal state that is incompatible with metastatic colonization. Re-introduction of p63/p73 expression into non-CSCs leads to reactivation of the CSC transcriptional program and enables metastasis. These findings reveal the unique transcriptional circuitry of CSCs and suggest potential dependencies and pathways for therapeutic targeting of cells in the CSC state. Citation Format: Arthur Lambert, Christopher Fiore, Yogesh Chutake, Elisha Verhaar, Mei Wei Chen, Joana Donaher, Ferenc Reinhardt, Ian Engstrom, Bingbing Yuan, Brian Bierie, Daneyal Farouq, John Carulli, Eric Olson, Matthew Guenther, Robert Weinberg. Epigenomic analysis of cancer stem cells (CSCs) from triple-negative breast cancer (TNBC) reveals p63 and p73 as core metastasis drivers [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-04-02.