Fig. 2: CDS1 and CDS2 are synthetic lethal across cancer types.
a, Plot depicting synthetic lethality upon CRISPR perturbation of CDS2 (ΔCDS2 lethality) and CDS1 RNA expression for cancer cell lines (DepMap). Cancer cell lines were categorized by CDS1 RNA levels and cell lines used for validation are marked. The data distribution is depicted by a ΔCDS2 lethality histogram (top) and a CDS1 expression histogram (right). n = 913 cancer cell lines. b, Plot depicting CDS1 RNA expression as measured by RNA sequencing (RNA-seq; DepMap) or qPCR analysis. The correlation (Pearson’s r) and associated P value were added. There was an average of two independent experiments with each n = 4 replicates for 8 cancer cell lines. c, Diagram depicting the method for quantifying lethality on CRISPR perturbation using fluorescent tracker cells. The mCherry-positive percentage was quantified by flow cytometry. d, Graph depicting cumulative lethality 14 d after CRISPR perturbation of CDS2 using tracker cells (c). CDS2 sgRNAs, positive control sgRNA (RPL19) and negative control sgRNA (sgControl) were included. Two-way ANOVA followed up by Dunnett’s test was used. n = 3 replicates for 7 cancer cell lines with 2 CDS2 sgRNAs; see the 8-d measurement in Extended Data Fig. 2b. There is an independent experiment repeat in e (three cancer cell lines) and Fig. 3b (four cancer cell lines); the latter also includes an additional CDS1-high cancer cell line. e, For two CDS1-negative cell lines (NCI-H2030 and SK-MEL-2), CDS1 or GFP (control) was ectopically expressed and the 14-d ΔCDS2 lethality was determined using tracker cells (c). For one CDS1-high cell line CDS1 (sgCDS1 versus sgControl) was perturbed by CRISPR and the 8-d ΔCDS2 lethality was determined using tracker cells (c). Two-way ANOVA followed by Tukey’s test was used. n = 3 replicates for 3 cancer cell lines. A431 and NCI-H2030/SK-MEL-2 are separate experiments. f, Left: diagram depicting method for quantifying synthetic lethality using ectopic CDS1 or GFP expression. The GFP-positive percentage was quantified by flow cytometry. Right: graph depicting quantification of the 14-d synthetic lethality in melanoma. Two-way ANOVA followed by Šidák’s test was used. n = 3 replicates for 4 cancer cell lines; see the 7-d measurement in Extended Data Fig. 2d. g, Graph depicting snapshot of the total protein-normalized level of cleaved caspase-3 in ΔCDS2 or control samples of BLM and SK-MEL-2 cell lines, as determined by quantitative western blotting. Two-way ANOVA followed by Šidák’s test was used. n = 3 replicates from independent lentiviral transductions for 2 cancer cell lines. h, Left: diagram depicting the in vivo variant of the method for quantifying synthetic lethality. Right: graph depicting quantification of the in vivo synthetic lethality in two melanoma cell-line models 17 d after subcutaneous melanoma tumor inoculation. Tumors were analyzed by flow cytometry. Two-way ANOVA followed by Šidák’s test was used. n = 6 NOD-scid Il2rγ-null mice per group each for 2 cancer cell lines. In b and d–h: ***P < 0.001.
