Extended Data Fig. 10: Targeting CPD may have therapeutic effects in patients with lung cancer.
From: CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities
a, Meta-Z scores of genes in the CPD module across different cancer types, from PRECOG analysis43. Positive Z score predicts that high expression of a given gene is associated with poor prognosis of disease. Pink bars show that high CPD expression predicts poor prognosis of lung adenocarcinoma (ADENO) (Z score = 5.59, PRECOG meta-FDR = 3.23 × 10−6). b, Forest plot showing hazard ratios (HR) of CPD measured from different datasets (authors and PubMed IDs for the datasets are indicated on the y axis). The HR is the increase in risk of death for each unit increase in expression of CPD (see Methods). Blue error bars indicate 95% confidence intervals. Number of patient samples used for each study is listed to the left of the plot. c, Forest plot showing the hazard ratios from an adjusted two-sided Cox proportional-hazard model, using the CPD GSVA score as a continuous variable adjusted by age, TP53, KRAS, stage and gender. d, Kaplan–Meier plots for patients with lung cancer with wild-type (left) or mutant (right) KRAS. Variation of a gene set downregulated by CPD deletion in H23 spheroids was first scored by GSVA (CPD GSVA score) in patients with lung cancer. Differences in survival among patients with lung cancer with high versus low CPD GSVA score are illustrated in Kaplan–Meier plots. High CPD GSVA scores are significantly associated with poor prognosis in both wild-type and mutant KRAS patient groups. However, the separation between high and low CPD GSVA groups is larger among KRAS-mutant patients than wild-type patients, suggesting an interaction between CPD and KRAS mutations in patients with lung cancer. P values calculated using a two-sided log-rank test. e, Hazard plots illustrating the two-sided Cox proportional log relative hazard by expression levels of CPD in KRAS-mutant versus KRAS wild-type samples. Grey shading corresponds to 95% confidence intervals. f, CPD deletion sensitizes H358 cells to ARS-853, a KRAS inhibitor. H358 cells with control safe sgRNA (blue line) or CPD sgRNA (red line) were treated with increasing doses of ARS-853 for 72 h in both 2D (top) and 3D (bottom). Live cells were then quantified using alamar blue assay. Relative growth of treated cells compared with the untreated cells is plotted against ARS-853 concentration. n = 4 wells in a 96-well plate, mean ± s.e.m. g, CPD deletion does not show synergy with ARS-853 in H1792 cells. Similar plots as in f were generated for H1792 cells (n = 4 wells in a 96-well plate, mean ± s.e.m.). h, IGF1R was quantified from immunofluorescence images of IGF1R staining across six lung cancer cell lines. H1792 cells show very low IGF1R expression compared with the other five cell lines. n = 4 for H1437, n = 5 for all other cell lines, mean ± s.e.m.
