Fig. 3: SKIc is lost in cancer and drives PELO dependency.
From: Synthetic lethality of mRNA quality control complexes in cancer
a, Pearson correlation between PELO Chronos CRISPR score and whole-proteome data from cell lines (n = 375) available in the 23Q4 DepMap release. Top 1,000 correlated proteins shown, SKIc proteins are labelled in purple. Two-tailed Student’s t-test. b, FOCAD and SKIV2L protein levels across cell lines analysed in the 23Q4 DepMap release. Pearson’s r = 0.553; n = 375. c, Immunoblot of SKIc proteins in FOCAD homozygous deletion (FOCAD KO) and FOCAD-expressing cell lines. d, Correlation of SKIV2L and TTC37 protein expression in tumours. Data from the PanCancer Clinical Proteomic Tumor Analysis Consortium (CPTAC) cohort (n = 1,022). Models with FOCAD homozygous deletion are highlighted in blue. Pearson’s coefficient of determination (R2) = 0.75. e, Relative SKIV2L and TTC37 protein expression in tumours with (KO, n = 36) and without (WT, n = 986) FOCAD homozygous deletion. Two-tailed Student’s t-test between two groups; SKIV2L, P = 4.5 × 10−4; TTC37, P = 1.8 × 10−7. In box plots, the centre line is the median, box edges delineate 25th and 75th percentiles and whiskers extend to 10th and 90th percentiles; data outside whiskers are shown as individual points. f, Immunoblot of SKIc isogenic clonal knockout (cKO) NCI-H1299 cell lines. Asterisk denotes TTC37-specific bands. g, Validation of PELO and SKIc synthetic lethality. Relative viability of parental or PELO cKO NCI-H1299 cells following acute knockout of indicated SKIc gene or B2M negative control. FOCAD, P = 1.1 × 10−4; SKIV2L, P = 2.5 × 10−5; TTC37, P = 3.6 × 10−5; AVEN, P = 4.0 × 10−5. h, Reconstitution of SKIc. Immunoblot in MIAPACA2 cells with exogenous expression of indicated SKIc proteins. i, Functional rescue of PELO dependency by overexpression (OE) of indicated proteins. Relative viability was assessed on day seven and normalized to B2M sgRNA control. j, FOCAD-driven SKIc stability. Time course of SKIV2L, TTC37, FOCAD and AVEN protein expression following treatment with 500 nM dTAG-v1 (inducible degron tag). Data are mean ± s.e.m. Two-tailed Student’s t-test. Representative data shown as n = 3 independent biological replicates (g,i) or representative data shown from one of two independent replicates (c,f,j).
