Extended Data Fig. 1: Upregulation of CDC7 mRNA correlates with poor prognosis of patients with HCC, and TP53 knockdown sensitizes liver cancer cells with wild-type TP53 to the CDC7 inhibitor.

a, Thirty-eight common hits (among the top-50 most-strongly depleted hits in each cell line) were identified by CRISPR screen in Hep3B and Huh7 cells. Hits in red represent factors that are targetable with small-molecule compounds. Blue represents non-targetable hits. b, Western blot analysis of levels of CDC7, MCM2 and phosphorylated MCM2 in non-transformed cell lines and liver cancer cell lines. HSP90 served as a loading control. c, Immunohistochemical analysis showing increased expression of CDC7 in HCC tissues, compared to paired adjacent non-tumour tissues. d, According to the level of CDC7 mRNA obtained from the TCGA database (n = 365 patients), patients with HCC were classified into 3 groups: the top 33.3% were considered as high-expression, the medium 33.3% were considered as intermediate-expression and the lowest 33.3% were considered as low-expression. Kaplan–Meier curves depicting that upregulation of CDC7 mRNA correlates with poor prognosis of patients with HCC. Statistical significance was calculated using a two-sided log-rank test. e, Liver cancer cell lines with wild-type TP53 (SK-Hep1 and Huh6) were stably transduced with control pLKO vector or with one of three independent shRNAs that target TP53 (labelled here as shp53 #1, #2 and #3). On the basis of knockdown efficiency, TP53 shRNA no. 1 and TP53 shRNA no. 3 were selected for further experiments. f, SK-Hep1 and Huh6 cells that express a control shRNA (pLKO) or knockdown of TP53 (shp53) were exposed to the indicated concentrations of XL413 in colony-formation assays. Cells were fixed, stained and photographed after 10–14 days of culture. g, SK-Hep1 and Huh6 cells expressing control shRNA or shRNA against TP53 were exposed to the indicated concentrations of XL413 for five days. CellTiter-Blue viability assays revealed that TP53 knockdown synergizes with treatment with XL413 in SK-Hep1 and Huh6 cells. Graphs represent mean ± s.d. from six technical replicates. For gel source images, see Supplementary Fig. 1. Data in a, b, e–g are representative of three independent biological experiments. Data in c are representative images from immunohistochemical analyses using a tissue microarray containing 80 specimens of HCC.