Some critical genes are located in these modules, including GNAO1, GNAZ, PLCB1, CDC25B, LAMC1, FOS, ETS1, and SHC1 (Fig. 2B), suggesting that these genes may have important roles in the pathogenesis of HCC. To further determine which genes among these 362 DEGs represent novel cancer genes, we next examined the potential driver roles of the candidates in hepatic carcinogenesis. By combining the results of interaction network analysis with functional suggestions obtained from PubMed data mining, a set of 20 potential genes in frequently aberrant regions (amplification ≥12 samples and deletion ≥4 samples, respectively) were chosen

for further functional assessments (Supporting Table 3). Specifically, Selleck ITF2357 eight genes (DDEF1, SHC1, HAX1, RAD21, MPZL1, YWHAZ, SERPINA5, and GNAO1) were selected according to the results of network analysis (Fig. 2B). Four genes selected (PEA15, MK-2206 cost ILF2, MT1G, and PER1) have been identified previously in HCC.20-23 Eight genes selected (SNRPE, C1ORF2, BOP1, HEY1, DUSP12, C8ORF4, SLC25A4, and TRIM35) have been reported in other tumors.24-31 First, the mRNA expression levels of these 20 genes were confirmed by

quantitative real-time polymerase chain reaction (q-PCR) analysis in 47 of the 49 paired HCC samples (Supporting Fig. 2A). The results indicated that there was greater than two-fold up-regulation of HEY1 in 42.6% of HCC tumors (20/47), whereas there was greater than two-fold down-regulation of TRIM35 in 60% of HCC tumors (27/47) compared with matched noncancerous tissues. Additionally, in order to choose suitable cell line tools for the following functional assessments, the expression levels of these 20 genes in eight liver cancer cell lines were determined by q-PCR PJ34 HCl (Supporting Fig. 3). To investigate whether these genes are involved in liver tumorigenesis,

they were overexpressed using a lentivirus vector in SMMC-7721 and Huh-7 cells, which was confirmed by q-PCR (Supporting Fig. 4). The results showed that of the seven deleted genes, TRIM35 was capable of significantly inhibiting the in vitro cell proliferation and in vivo tumor growth of both SMMC-7721 and Huh-7 cells, whereas of the 13 amplified genes, HEY1 and SNRPE were capable of significantly promoting the proliferation of both SMMC-7721 and Huh-7 cells in vitro and in vivo (Fig. 3A-D). Consistent with the above results, knockdown of TRIM35 was observed to markedly promote HCC cell proliferation, whereas knockdown of HEY1 and SNRPE significantly suppress HCC cell proliferation, based on small interfering RNA (siRNA) analyses in HepG2 cells (Fig. 3E). Taken together, wededuced that TRIM35 may be a new tumor suppressor candidate and that HEY1 and SNRPE may be novel putative oncogenes in HCC.