Extended Data Fig. 1: The repressive ETS transcription factor, ETV6, is a selective dependency in Ewing sarcoma cells.
a. Volcano plot of genes in the DepMap screen in Ewing sarcoma cell lines (n = 14) compared to all other cell lines (n = 782). Effect size (x-axis) indicates the impact of gene deletion on growth. Log10(q-value) (y-axis) indicates specificity of dependency in Ewing sarcoma. Blue marks known selective TF dependencies. b. Venn diagram of Ewing sarcoma selective TF dependencies in the DepMap, GeCKO, and Sanger CRISPR/Cas9 screens. c. Scaled rank plot depicting all cell lines in DepMap. Gene effect (x-axis) measures ETV6 deletion impact in each cell line. Ewing lines are enlarged and color-coded by specific EWS/ETS fusion (EWS/FLI n = 11, EWS/ERG n = 2, EWS/FEV n = 1). d and e. Expression (log2(TPM + 1); TPM, transcripts per million) of ETV6 (d) and BCL11B, ZEB2 (e) in primary tumors (Treehouse Childhood Cancer Initiative37, Ewing sarcoma n = 85; other n = 12,571). Points show the full range between maxima and minima. Boxes show values for the 25th and 75th percentiles; middle line shows median (50th percentile). Whiskers extend no further than 1.5 times the inter-quartile range. Gene expression in Ewing sarcoma was different from other tumor types (Welch 2−sample T-test, ETV6 p = 2.067 × 10−15, ZEB2 p = 4.995 × 10−31, BCL11B p = 1.515 × 10−37). f. Line graphs depicting mean cell viability ±SEM in Ewing sarcoma cell lines (n = 8 biological replicates). ETV6 knock-out cells exhibited lower viability than control (2−way ANOVA, Dunnett multiple comparisons EW8 p-adj<0.0001; TC32 p-adj<0.0001). Represents two independent experiments. Westerns show ETV6 and GAPDH loading control (kDa, kiloDaltons). g. Bar plots showing mean ±SEM number of methylcellulose cell colonies. ETV6 knock-out samples formed fewer colonies (EW8 two-tailed t-test, n = 4 biological replicates, p = 0.0001; TC32 two-tailed t-test, n = 4 biological replicates, p = 0.0052). h. (Left) Bar plot showing mean ±SEM number of EW8 ETV6-dTAG cell colonies. dTAGV-1-treated cells formed fewer colonies than control (n = 3 biological replicates, two-tailed t-test, p < 0.0001). (Right) Western blot of dTAG cells shown here and in Fig. 1f.
