Single-cell RNA-seq of 4SC-202-treated and control ATRT spheroids

4SC-202 is an emerging small molecule epigenetic modulator that is a Class I histone deacetylase inhibitor (HDACi)/lysine-specific histone demethylase (LSD1) inhibitor. Preliminary evidence suggests that 4SC-202 may influence the stem cell population in melanoma and anterior mediastinal mixed germ cell tumor cell lines, but the effect of 4SC-202 on ATRT and stem-like cells in ATRT are not well characterized. Here, we performed single-cell RNA sequencing on 4SC-202-treated and control spheroids from human patient-derived CHLA-06-ATRT cell lines and found higher heterogeneity in the control spheroids than in the treated spheroids. In the integrated data, graph-based clustering identified a population of cells that overexpressed stem cell markers SOX2, SOX4, CD44, GPC3, ID1, ID2, and ID3 as well as cell cycle processes. This cluster was principally composed of cells from control spheroids and was one of two clusters of low mtRNA control cells. In contrast, there was only one cluster of low mtRNA drug-treated cells. Results also indicate that drug-treated populations had a higher percentage of genes mapped to mtRNA than control populations.