In our HCC cohort, BCL9 was located in the amplification peak at 1q21.1,

which is highly amplified in 8.7% of HCCs (Table 2 and Supporting Table 3). There was a significant correlation between its somatic copy number and gene expression in primary HCCs (Fig. 2A), and protein expression measured by immunohistochemical (IHC) staining (Supporting Materials; Supporting Fig. 5A) correlated well with mRNA expression (Fig. 2B; Supporting Table 7). Transient transfection of siRNA SMARTpool for BCL9 significantly selleck chemicals reduced gene expression of BCL9 in all four cell lines tested (Fig. 2C,D) and significantly decreased cell growth and survival in both proliferation assays (Fig. 2E) and colony formation assays (CFAs) (Fig. 2F) in MHCC97H and MHCC97L, the two

cell lines with BCL9 gene amplification (Supporting Fig. 6). By contrast, siRNA-mediated inhibition of BCL9 gene expression had minimal effect on the SK-HEP-1 cell line, which is copy number neutral for BCL9, although the other BCL9 copy-number–neutral cell line (HUH6) showed significant growth inhibition GSK-3 inhibitor review upon BCL9 knockdown, suggesting that mechanisms other than BCL9 amplification may confer dependence on BCL9 expression. Our analysis also identified a peak at 8q22.1 containing a single gene (MTDH), which encodes metadherin. MTDH has been implicated as an oncogene in a number of cancer types, including HCC.[19] However, previous work in HCC has not yet established the dependency of MTDH-driven tumorigenesis on MTDH focal amplification, especially in relevant preclinical models that harbor the MTDH amplification. In our study, MTDH was highly amplified in 12.9% of HCCs (Table 2 and Supporting Table 3). There was a significant cis-correlation between somatic

copy number and mRNA expression of MTDH in primary HCCs (Fig. 3A), and protein expression by IHC (Supporting Fig. 5B) correlated well with mRNA expression (Fig. 3B; and Supporting Table 8). We further identified Thiamine-diphosphate kinase two HCC models (MHCC97H and SNU-398) with amplification of the MTDH locus (Supporting Fig. 6). Transient transfection of siRNA SMARTpool for MTDH significantly reduced the gene expression levels of MTDH in all four cell lines tested (Fig. 3C,D). In the two MTDH amplified HCC models, siRNA-mediated inhibition of MTDH gene expression significantly decreased cell growth and survival in both proliferation assays (Fig. 3E) and CFAs (Fig. 3F), whereas knockdown had a less-prominent effect on the two MTDH copy-number–neutral lines (L-02 and SMMC-7721). Our study represents one of the most comprehensive characterizations of the genomic landscape in a large primary HCC cohort and models.