Figure 6 from Passenger Gene Coamplifications Create Collateral Therapeutic Vulnerabilities in Cancer
Authors: Bei Yi , Bramé Luca , Kirchner Marieluise , Fritsche-Guenther Raphaela , Kunz Severine , Bhattacharya Animesh , Rusu Mara-Camelia , Gürgen Dennis , Dubios Frank P.B. , Köppke Julia K.C. , Proba Jutta , Wittstruck Nadine , Sidorova Olga Alexandra , Chamorro González Rocío , Dorado Garcia Heathcliff , Brückner Lotte , Xu Robin , Giurgiu Mădălina , Rodriguez-Fos Elias , Yu Qinghao , Spanjaard Bastiaan , Koche Richard P. , Schmitt Clemens A. , Schulte Johannes H. , Eggert Angelika , Haase Kerstin , Kirwan Jennifer , Hagemann Anja I.H. , Mertins Philipp , Dörr Jan R. , Henssen Anton G. 
Published: March 2024

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