Extended Data Fig. 3: Characterizing the molecular alterations underlying PELO dependency.
From: SKI complex loss renders 9p21.3-deleted or MSI-H cancers dependent on PELO
(a) Pearson correlation of relative copy number for genes on cytoband 9p21.3 with PELO dependency scores in 9p21.3−/− cell lines. Genes included in the Cas12a library targeting 9p21.3 in red. (b) Left figure: immunoblot of FOCAD, PELO, Vinculin levels in KP4. Right figure: relative viability with indicated DOX-inducible gRNAs treated with DMSO or DOX. (c) Frequency of select alterations in TCGA dataset (n = 10,715 profiled tumors for HOMDEL and n = 10,443 for MUT_DRIVER). (d) TTC37 mRNA transcript expression versus number of TTC37 microsatellite repeats in cell lines (n = 1407). (e) TTC37 protein levels versus number of TTC37 microsatellite repeats in cell lines (n = 372). (f) PELO dependency versus FOCAD relative copy number in cell lines (n = 1100), with cell lines harboring TTC37 indels (≤ 9 microsatellite repeats, n = 32) highlighted. (g) Left figure: immunoblot of TTC37, PELO and β-actin. Right figure: relative viability of KM12 stably expressing indicated cDNA ± DOX-induced PELO KD. (h) Immunoblot of TTC37, PELO and β-actin. Relative viability of DLD1 stably expressing indicated cDNA ± DOX-induced PELO KD. (i) PELO, KRAS, BRAF dependency in cell lines with or without their corresponding biomarker and in 4 immortalized non-cancerous cell lines. Data are mean ± s.e.m. of biological replicates: n = 3 in (b); n = 3 except for TTC37 cDNA DOX- where n = 2 in (g) and n = 3 in (h). For box plots in (i), the center line marks the median, the edges of the box represent the 25th–75th percentiles, and the whiskers span minimum-maximum values. Significance was calculated as follows: (b) left-tailed Student’s t-test, (g,h) right-tailed Student’s t-test, (i) left-tailed Student’s t-test. Representative data from one experiment are shown. All experiments were performed twice. For immunoblots, Vinculin and β-actin were used as loading controls.
