Figure 6 from Passenger Gene Coamplifications Create Collateral Therapeutic Vulnerabilities in Cancer

High DDX1 expression is sufficient to increase sensitivity to pharmacologic mTORC1 inhibition in vitro and in vivo. A, Relative cell viability of different neuroblastoma cell lines with DDX1-MYCN coamplification (red, N = 3) or with MYCN amplifications (blue, N = 2) treated with rapamycin (2.5 μmol/L for 72 hours) compared with cell viability after DMSO (vehicle control) treatment (Welch t test, P = 2.291e−05 DDX1-MYCN vs. MYCN; each data point represents a technical replicate). B, Relative cell viability of KELLY cells inducibly expressing DDX1, DDX1-Δ269-295aa, or an empty vector and treated with rapamycin (2.5 μmol/L for 72 hours) compared with cell viability after DMSO (vehicle control) treatment (Welch t test, P = 3.943e−05; data are shown as mean ± SE; N = 3 technical replicates). C, Relative cell viability of IMR5/75 cells expressing shRNAs directed against DDX1 (blue) or GFP (red) and treated with rapamycin (2.5 μmol/L for 72 hours) compared with cell viability after DMSO (vehicle control) treatment (Pairwise t test adjusted by Benjamini–Hochberg correction, P = 1.3e−05, 4.1e−05, and 2.2e−05 for each independent shRNA directed against DDX1 vs. shGFP, respectively; data are shown as mean ± SE; N = 3 technical replicates). D, Correlation between the DDX1 copy number and the IC₅₀ value of rapamycin in different neuroblastoma cell lines derived from the GDSC2 database (Pearson correlation, R = −0.05043, P = 0.0394, N = 13 independent cancer cell lines). E, Relative cell viability of neuroblastic tumor cells derived from transgenic zebrafish expressing MYCN or MYCN and DDX1 and treated with rapamycin (2.5 μmol/L for 72 hours) compared with cell viability after DMSO (vehicle control) treatment (Welch t test, P = 0.02707; data are shown as mean ± SE; N = 3 independent replicates from cells derived from different zebrafish). F, Nanopore sequencing read coverage over the MYCN amplicon region in MYCN-amplified neuroblastoma PDX with or without DDX1 coamplification (log-scaled). G, Relative change in tumor volume of MYCN-amplified NB PDX with or without DDX1 coamplification treated with rapamycin compared with mice treated with vehicle controls (N = 4 mice per group; *, P < 0.05).H, Tumor volumes after treatment with rapamycin compared with vehicle treatment in MYCN-amplified PDX (N = 4 independent mice per treatment group; P = 0.7918, 0.01286, respectively). I, Representative photomicrographs of PDX after IHC staining for cleaved caspase-3 or Ki-67 (scale bar, 50 μm). J, Quantification of cleaved caspase-3 or Ki-67-positive cells in PDX shown in I (N = 10 sections of 200 μm × 200 μm; P = 0.7454, 1.717e−08, 0.886, and 1.218e−11 independently).