For example, a frequent amplification target is COL4A1 on 13q34, and a frequent deletion p38 MAPK inhibitors clinical trials target is SERPINA5 on 14q32.13. Moreover, the differential expressions of eight DEGs in several of these new CNAs were also validated by q-PCR
(Supporting Fig. 2B). Additionally, SERPINA5 was also observed to inhibit the migration ability of HCC cells in this study (Supporting Fig. 7). To the best of our knowledge, this is the first study to use high-resolution copy number analysis of a relatively large numbers of paired specimens to create a comprehensive catalog of CNAs in HCC genomes. Several findings have emerged from our studies, mainly based on the opportunity provided by integrated analysis of genomic and transcriptional profiles. One finding is that several regulatory modules were identified as functioning in a concerted manner, including involved in cell adhesion,
cell cycle, regulation of the actin cytoskeleton, and WNT signaling pathways, which have all been implicated in HCC.33, 34 Another finding is the identification of three novel cancer genes related to HCC, including one tumor suppressor candidate TRIM35 and two possible oncogenes Wnt inhibitor HEY1 and SNRPE. TRIM35 is a member of the Ring finger, B box, coiled-coil (RBCC), or Tripartite motif (TRIM) family.35 It was originally isolated as a gene up-regulated during an erythroid-to-myeloid lineage switch, and independently as a proapoptotic gene activated during macrophage maturation.31, 35 It is notable that enforced expression of TRIM35 in HeLa cells could inhibit cell proliferation and tumorigenicity.31 However, the functions of this gene in HCC are largely unknown. In this study we found that TRIM35 was located in a frequently deleted region of 8p21.2-21.1. Consistently, the mRNA and protein levels of TRIM35 were also significantly down-regulated in HCC
specimens. However, it is worth noting that additional regulatory mechanisms other than its genomic loss for TRIM35 down-regulation in HCC exist. Therefore, we examined the methylation status of CpG click here islands within TRIM35 promoter using quantitative real-time methylation-specific PCR on 31 out of 58 paired HCC and nontumor tissues. We found that the frequency of hypermethylation was approximately 45.2% (14/31) in HCC tissues compared with the nontumor tissues, which might account for the down-regulation of TRIM35 mRNA and protein level in HCC tissues in addition to that caused by genomic loss of 14q32.13 loci (17.2%). Furthermore, we found that TRIM35 could significantly suppress the in vitro cell proliferation and in vivo tumorigenicity of HCC cells. Most important, the expression level of TRIM35 was negatively correlated with the tumor grade, tumor size, and serum AFP level of HCC patients.