Hepatocellular carcinoma (HCC) is the fifth most common cancer and is the third leading cause of cancer death. HCC is the most common type occurring in adults and induces greater rate of death in people with cirrhosis. Although surgical resection of HCC provides the best chance for cure, the prognosis following surgery varies considerably among different patients, and recurrence is the major drawback of potentially curative treatment. Because of this clinical heterogeneity, predicting the recurrence of HCC patients after surgical resection remains challenging. Although these clinical staging systems are useful, their predictive accuracy is still limited, and they fail to identify biological characteristics of HCC that might account for the clinical heterogeneity. Increasing studies have suggested that the limited gene expression signatures were associated with the prognosis of HCC patients. With the recent advent of gene expression profiling technology, improvement in prediction models for risk assessment in HCC has been also reported. While these gene expression signatures might better reflect the biological characteristics of HCC tumors, the complexity of prediction models based on gene expression signatures hampered their use in clinics. Therefore, there is an urgent need to develop a curative molecular targeted therapy. To overcome the current limitations of prediction models, we developed a simple risk scoring system that can predict the likelihood of recurrence after surgical resection of HCC and validated it in an independent cohort. According to gene expression profiling analyses, we found that hematopoietic- and neurologic-expressed sequence 1 (HN1) gene was upregulated in HCC. Beyond that, HN1 gene is also detected a high expression level in various cancers, and is identified that associates with metastatic carcinoma progression, neural development, nerve and retina regeneration. Nevertheless, its functional significance in HCC still remains unclear. In addition, sirtuin 6 (SIRT6) is a member of sirtuin family of NAD+-dependent enzymes and plays a key role in DNA repair, telomere maintenance, and cellular metabolic processes. Several recent studies reported that SIRT6 functioned as a tumor suppressor. However, the precise molecular mechanism of SIRT6 in HCC has not been clearly understood. Therefore, the purpose of our study is to investigate the biological role of HN1 and SIRT6 in HCC using HCC cell lines. Our results suggested that HN1 was significantly overexpressed in HCC tumors compared to normal liver tissues. Silencing of HN1 significantly diminished the viability of HCC cells whereas overexpression of HN1 stimulated the viability of HCC cells. Silencing of HN1 increased apoptotic proteins and increased the number and size of colonies. In addition, silencing of HN1 inhibited the invasion and metastasis of HCC cells whereas overexpression of HN1 promoted the invasion and metastasis of HCC cells. In gene expression profiling, we identified 130 upregulated genes and 379 downregulated genes after HN1 silencing in HCC cells. Putative gene networks revealed suppressed expression of proteins associated with lipogenic signaling pathway. Silencing of HN1 significantly inhibited the expression levels of SREBP1 and SREBP2 of HCC cells whereas overexpression of HN1 increased the expression levels of SREBP1 and SREBP2 of HCC cells. In addition, silencing of SREBP1 also diminished the expression levels of HN1 and suppressed the survival and metastasis of HCC cells. In cholesterol assay and triglyceride assay, silencing of HN1 inhibited the lipid formation of HCC cells whereas overexpression of HN1 promoted the lipid formation of HCC cells. In brief, HN1 encourages the proliferation, invasion and metastasis of HCC cells in part through the activation of AKT-SREBP signaling pathway. Regarding to SIRT6 investigation, we found that SIRT6 was highly expressed in human HCC cells. Overexpression of SIRT6 significantly diminished the viability of HCC cells whereas silencing of SIRT6 stimulated the viability of HCC cells. Overexpression of SIRT6 increased expression of Cleaved-PARP and Cleaved-Caspase-9 and decreased the PARP, Caspase-9, and Caspase-3. On the other hand, knockdown of SIRT6 decreased expression of Cleaved-PARP and Cleaved-Caspase-9 and increased the PARP, Caspase-9, and Caspase-3. Knockdown of SIRT6 increased the number and size of colonies. In addition, overexpression of SIRT6 significantly inhibited the invasion and metastasis of HCC cells whereas silencing of SIRT6 increased the invasion and metastasis abilities of HCC cells in a time dependent manner. Moreover, overexpression of SIRT6 inhibited vimentin, uPA, and MMP9 protein levels while silencing of SIRT6 in HCC cells increased the protein levels of vimentin, uPA, and MMP9. P-β-catenin levels was increased by overexpression of SIRT6 and was decreased by silencing of SIRT6. In vitro, knockdown of SIRT6 significantly promoted the tumor growth. Although further studies need to be performed to investigate the underlying molecular mechanism of SIRT6, these data suggest that SIRT6 inhibits the proliferation, invasion and metastasis of HCC cells and may play as a tumor suppressor in HCC cells. Taken together, our present studies indicated that targeting these two specific genes HN1 and SIRT6 might provide a potential therapeutic strategy for the treatment of HCC.