Abstract 500: Discovering epigenetic regulators of cells states in triple negative breast cancers

The implementation of targeted therapies have been instrumental in achieving clinical responses for ER, PR, and HER2 receptor expressing breast cancers. However, triple negative breast cancers in themselves do not respond to such therapies and are highly heterogeneous diseases with significantly worse progression and survival. Our preliminary data and literature have also shown that in TNBC different cancer cell subpopulations are present in any given tumor, each with its own unique chemo-response and resistance. To discover novel targets regulating cancer cell states in TNBCs, we have created a reporter cell line using CRISPR/Cas9 mediated knock-in of fluorescent reporter proteins after the endogenous loci of major cell type markers in SUM149. Using this reporter line allows for the direct visualization of ALDH1A3+/- and CD24+/- cells, facilities tracking of distinct cell state transitions in a given cell, and allows for lineage tracing following cell divisions. These reporter cells were subjected to HTS-FACS analysis after exposure to a siRNA library of known epigenetic regulators. Following secondary screening, three siRNA targets are able to uniquely inhibit distinct subpopulations of cells within the cell line DCAF1 (ALDH-/CD24- cells), MLL2 (ALDH-/CD24+ cells), and TRIM24 (ALDH+ cells). In combination, these siRNA9s proportionally eliminated all cell types. Due to the inherent heterogeneity of TNBCs we then sought to determine if efficacy was consistent or unique across different cell lines with varying percentages of CD44, CD24, and Aldefluor+ cell populations. Most notably, in MDA-MB-468 which contains similar cell population percentages to SUM149 each siRNA was capable of reducing cell proliferation. Similarly, TRIM24 was also capable of reducing cellular proliferation in BT20, MLL2 in MDA-MB-231, and DCAF1 in HCC1937. Knockdown of TRIM24 consistently reduced Aldefluor+ cells in MDA-MB-468 and BT20 cells. Finally, coupled with sc-Omics technologies we utilized this efficacy data identify a subset of TNBC patients likely to respond to therapies which will target these genes in the future. Citation Format: Joseph Patrick Burnett, Garrett Johnson, Nathan Truchan, Michael Brooks, Max S. Wicha, Duxin Sun. Discovering epigenetic regulators of cells states in triple negative breast cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 500.